diff --git a/.gitignore b/.gitignore
index f53d807f..f93d5842 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,5 +25,5 @@ node_modules
**/gen/**
# Ignore merged file and one downloaded for processor-controller
-/openapi/v1/odmApi.yaml
+/openapi/v1/openapi.yaml
/openapi/v1/processorsController.yaml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 83c8ba3c..0587954c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,3 +10,19 @@ repos:
- id: check-toml
- id: check-merge-conflict
- id: end-of-file-fixer
+- repo: local
+ hooks:
+ - id: spectral-lint
+ name: spectral-lint
+ entry: npx @stoplight/spectral-cli lint
+ language: node
+ files: openapi/v1/odm.yaml
+ additional_dependencies: ['@stoplight/spectral-cli@6.15.0']
+- repo: local
+ hooks:
+ - id: redocly-lint
+ name: redocly-lint
+ entry: npx @redocly/cli lint
+ language: node
+ files: openapi/v1/odm.yaml
+ additional_dependencies: ['@redocly/cli@2.0.7']
diff --git a/.spectral.yml b/.spectral.yml
new file mode 100644
index 00000000..d47c47d3
--- /dev/null
+++ b/.spectral.yml
@@ -0,0 +1 @@
+extends: ["spectral:oas"]
diff --git a/Earthfile b/Earthfile
index 203d8ae1..31fd6f63 100644
--- a/Earthfile
+++ b/Earthfile
@@ -151,12 +151,12 @@ swagger:
COPY +build/v1 /usr/share/nginx/html/yaml/
COPY openapi/swagger/fs /
- RUN rm -f /usr/share/nginx/html/yaml/odmApi.yaml
+ RUN rm -f /usr/share/nginx/html/yaml/odm.yaml && \
+ rm -f /usr/share/nginx/html/yaml/processorsController.yaml
RUN apk add bash --no-cache && \
rewrite_entrypoint.sh && \
apk del bash
- # Remove merged api spec
# IDK why it's required
RUN ln -s /usr/share/nginx/html/yaml /usr/share/nginx/html/helper/yaml
@@ -170,8 +170,7 @@ swagger:
stoplight:
FROM nginxinc/nginx-unprivileged:1.29.1-alpine
- COPY +build/v1/schemas /usr/share/nginx/html/schemas/
- COPY +build/v1/odmApi.yaml /usr/share/nginx/html/
+ COPY +build/v1/openapi.yaml /usr/share/nginx/html/
COPY openapi/stoplight/fs /
ARG --required OPENAPI_VERSION
@@ -182,5 +181,5 @@ main:
BUILD +swagger
BUILD +stoplight
BUILD +docs
- BUILD +r-api-client
+ #BUILD +r-api-client
BUILD +python-api-client
diff --git a/build.gradle.kts b/build.gradle.kts
index 80d225e4..5af49f3b 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -23,14 +23,12 @@ val processorsControllerVersion: String = System.getenv("PROCESSORS_CONTROLLER_V
val processorsControllerFileName = "processorsController.yaml"
val processorsControllerFilePath = "${sourceDirectory}/${processorsControllerFileName}"
-val openApiVersion: String = System.getenv("OPENAPI_VERSION")
-val mergedFileName = "odmApi.yaml"
-val mergedFilePath = "${sourceDirectory}/${mergedFileName}"
+val odmFileName = "odm.yaml"
+val odmFilePath = "${sourceDirectory}/${odmFileName}"
-val sourceFileList = KotlinPath(sourceDirectory)
- .listDirectoryEntries("*.yaml")
- .sorted()
- .map { layout.projectDirectory.file("${sourceDirectory}/${it.name}") }
+val openapiVersion: String = System.getenv("OPENAPI_VERSION")
+val openapiFileName = "openapi.yaml"
+val openapiFilePath = "${sourceDirectory}/${openapiFileName}"
tasks {
val downloadSpec by registering(DownloadSpecification::class) {
@@ -43,20 +41,21 @@ tasks {
}
val mergeSpecifications by registering(MergeSpecifications::class) {
dependsOn(downloadSpec)
- inputFiles = sourceFileList
- outputFile = layout.projectDirectory.file(mergedFilePath)
+ inputFiles = listOf(odmFilePath, processorsControllerFilePath)
+ .sorted().map { layout.projectDirectory.file(it) }
+ outputFile = layout.projectDirectory.file(openapiFilePath)
}
val generateOdmApiPython by registering(GenerateTask::class) {
dependsOn(mergeSpecifications)
generatorName.set("python")
- inputSpec.set(mergedFilePath)
+ inputSpec.set(openapiFilePath)
outputDir.set("$rootDir/generated/python")
packageName.set("odm_api")
gitUserId.set("genestack")
gitRepoId.set("openapi")
nameMappings.set(mapOf("genestack:accession" to "genestackaccession"))
configOptions = mapOf(
- "packageVersion" to openApiVersion,
+ "packageVersion" to openapiVersion,
// Workaround for https://github.com/OpenAPITools/openapi-generator/issues/21619
// The second version asks for license, which we can't provide due to unavailability of
// "licenseName" and "licenseUrl" fields in the specification for python generator.
@@ -67,28 +66,28 @@ tasks {
val generateOdmApiR by registering(GenerateTask::class) {
dependsOn(mergeSpecifications)
generatorName.set("r")
- inputSpec.set(mergedFilePath)
+ inputSpec.set(openapiFilePath)
outputDir.set("$rootDir/generated/r")
packageName.set("odmApi")
gitUserId.set("genestack")
gitRepoId.set("openapi")
nameMappings.set(mapOf("genestack:accession" to "genestackaccession"))
configOptions = mapOf(
- "packageVersion" to openApiVersion
+ "packageVersion" to openapiVersion
// "disallowAdditionalPropertiesIfNotPresent" to "true"
)
}
val generateOdmApiPostmanCollection by registering(GenerateTask::class) {
dependsOn(mergeSpecifications)
generatorName.set("postman-collection")
- inputSpec.set(mergedFilePath)
+ inputSpec.set(openapiFilePath)
outputDir.set("$rootDir/generated/postman-collection")
packageName.set("odm-api")
gitUserId.set("genestack")
gitRepoId.set("openapi")
nameMappings.set(mapOf("genestack:accession" to "genestackaccession"))
configOptions = mapOf(
- "packageVersion" to openApiVersion
+ "packageVersion" to openapiVersion
// "disallowAdditionalPropertiesIfNotPresent" to "true"
)
}
diff --git a/openapi/stoplight/fs/usr/share/nginx/html/index.html b/openapi/stoplight/fs/usr/share/nginx/html/index.html
index b2e28d47..b5c6af4f 100644
--- a/openapi/stoplight/fs/usr/share/nginx/html/index.html
+++ b/openapi/stoplight/fs/usr/share/nginx/html/index.html
@@ -11,7 +11,7 @@
diff --git a/openapi/v1/cellCurator.yaml b/openapi/v1/cellCurator.yaml
deleted file mode 100644
index 127461f5..00000000
--- a/openapi/v1/cellCurator.yaml
+++ /dev/null
@@ -1,120 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the APIs for retrieving cells.
- title: ODM API
- version: default-released
-tags:
- - name: Cells as Curator
-paths:
- /api/v1/as-curator/cells/{id}:
- get:
- operationId: getCellByIdAsCurator
- parameters:
- - description: Unique cell identifier. Consists of a cell group accession and a cell barcode, separated by a hyphen, e.g. `GSF123456-AAACCTGAGCGCTCCA-1`.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Cell"
- description: The request was successful. The returned value is the object.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: Object with provided ID could not be found in ODM.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve a cell by ID
- tags:
- - Cells as Curator
- /api/v1/as-curator/cells/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag.
- To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page.
- If there are no more results you will just retrieve an empty result.
- operationId: getCellsByGroupAsCurator
- parameters:
- - description: Unique identifier (accession) of the cell group.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 10000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: The page tag to resume results from (see Paging above). Cell ID is currently used as a cursor.
- in: query
- name: cursor
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/CellListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: { }
- description: Cell data cannot be retrieved.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: No object exists with the given ID.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve cells from a given group
- tags:
- - Cells as Curator
-components:
- schemas:
- Cell:
- $ref: "./schemas/cell/Cell.yaml"
- CellListResponse:
- $ref: "./schemas/cell/CellListResponse.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/cellUser.yaml b/openapi/v1/cellUser.yaml
deleted file mode 100644
index 9af2eb80..00000000
--- a/openapi/v1/cellUser.yaml
+++ /dev/null
@@ -1,120 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the APIs for retrieving cells.
- title: ODM API
- version: default-released
-tags:
- - name: Cells as User
-paths:
- /api/v1/as-user/cells/{id}:
- get:
- operationId: getCellByIdAsUser
- parameters:
- - description: Unique cell identifier. Consists of a cell group accession and a cell barcode, separated by a hyphen, e.g. `GSF123456-AAACCTGAGCGCTCCA-1`.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Cell"
- description: The request was successful. The returned value is the object.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: Object with provided ID could not be found in ODM.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve a cell by ID
- tags:
- - Cells as User
- /api/v1/as-user/cells/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag.
- To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page.
- If there are no more results you will just retrieve an empty result.
- operationId: getCellsByGroupAsUser
- parameters:
- - description: Unique identifier (accession) of the cell group.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 10000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: The page tag to resume results from (see Paging above). Cell ID is currently used as a cursor.
- in: query
- name: cursor
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/CellListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: { }
- description: Cell data cannot be retrieved.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: No object exists with the given ID.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve cells from a given group
- tags:
- - Cells as User
-components:
- schemas:
- Cell:
- $ref: "./schemas/cell/Cell.yaml"
- CellListResponse:
- $ref: "./schemas/cell/CellListResponse.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/expressionCurator.yaml b/openapi/v1/expressionCurator.yaml
deleted file mode 100644
index 8f24aead..00000000
--- a/openapi/v1/expressionCurator.yaml
+++ /dev/null
@@ -1,740 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the expressionCurator APIs.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
- The server response will be in the section that follows.
- title: ODM API
- version: default-released
-tags:
-- name: Expression SPoT as Curator
-paths:
- /api/v1/as-curator/expressions:
- get:
- description: |+
- Retrieve all expression data and metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
-
- operationId: getExpressionDataAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by expression metadata (key-value metadata pair(s)). E.g.
- `"Normalization Method"=TPM`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for expression objects via a full text query over all
- expression metadata. E.g. `TPM`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Autogenerated numeric ID that corresponds to the column and is used to link data from the same
- run to a sample, library or preparation. Multiple values can be provided as a list.
- in: query
- name: runFilter
- schema:
- $ref: "#/components/schemas/RunFilter"
- style: form
- - description: Column name from the file to which all data for a sample, library or preparation is related. Multiple values can be provided as a list to retrieve data from multiple columns.
- explode: true
- in: query
- name: runSourceFilter
- schema:
- items:
- type: string
- example: Run Source ID
- type: array
- style: form
- - description: Minimum threshold (inclusive) for returned expression values.
- in: query
- name: minExpressionLevel
- schema:
- format: double
- type: number
- - description: "List of features to return. These features must match exactly\
- \ the probe IDs in the GCT file. Example: `1552269_at`"
- explode: true
- in: query
- name: featureList
- schema:
- items:
- type: string
- example: KRAS
- type: array
- style: form
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ExpressionResponse"
- description: Retrieved Expression data.
- "400":
- content: {}
- description: Expression data cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve multiple expression data and metadata objects
- tags:
- - Expression SPoT as Curator
- /api/v1/as-curator/expressions/group:
- get:
- description: |-
- Retrieve all group metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- ## List operation
-
- This endpoint can be called with no `query` parameter. Doing so returns a list of all data objects.
- operationId: searchExpressionGroupsAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by expression metadata (key-value metadata pair(s)). E.g.
- `"Normalization Method"=TPM`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for expression objects via a full text query over all
- expression metadata. E.g. `TPM`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve groups that match a query
- tags:
- - Expression SPoT as Curator
- /api/v1/as-curator/expressions/group/by/run/{id}:
- get:
- operationId: getExpressionGroupByRunAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (runId) of the run.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single group object by run ID (runId)
- tags:
- - Expression SPoT as Curator
- /api/v1/as-curator/expressions/group/{id}:
- get:
- operationId: getExpressionGroupAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Expression group identifier (groupId).
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single expression group by ID (groupId)
- tags:
- - Expression SPoT as Curator
- /api/v1/as-curator/expressions/runs/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To return all results iterate through pages using pageOffset values of `n * pageLimit` until the `resultsExhausted` response field is true.
-
- operationId: searchExpressionRunsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve run objects related to the given group
- tags:
- - Expression SPoT as Curator
- /api/v1/as-curator/expressions/{id}:
- get:
- operationId: getExpressionAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Expression object unique identifier (itemId).
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ExpressionItem"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single expression object by ID (itemId)
- tags:
- - Expression SPoT as Curator
- patch:
- description: |-
- ## Basic operation
- The object metadata is updated using the supplied map of attribute names to attribute values. There are three cases:
- 1. The attribute name does not already exist in the object metadata. In this case, the attribute and value are added to the object metadata.
- 2. The attribute name already exists in the object metadata. In this case, the value is updated.
- 3. The attribute value is `null`.In this case, the attribute is removed from the object metadata.
-
- ## Attribute values
- The attribute values are intelligently parsed as booleans, integers, etc.
- operationId: updateExpressionRunAsCurator
- parameters:
- - description: Expression object run ID (runId).
- in: path
- name: id
- required: true
- schema:
- type: string
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataContent"
- description: "Metadata in the form of `{key: value, key2: value2, ...}`"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SignalRun"
- description: "The objects was successfully created. The returned value is\
- \ the updated object, along with any warnings."
- "400":
- content: {}
- description: The supplied object ID or metadata is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Update metadata object by expression object run ID (runId)
- tags:
- - Expression SPoT as Curator
- x-codegen-request-body-name: body
- /api/v1/as-curator/expressions/{id}/versions:
- get:
- operationId: getExpressionVersionsAsCurator
- parameters:
- - description: Expression object run ID (runId).
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/CommitInfo"
- type: array
- description: The request was successful. The returned value is the list
- of object versions.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a list of expression object versions by run ID (runId)
- tags:
- - Expression SPoT as Curator
- /api/v1/as-curator/expressions/{id}/versions/{version}:
- get:
- operationId: getExpressionByVersionAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Expression object run ID (runId).
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Unique version of the expression object.
- in: path
- name: version
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SignalRun"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single expression object by run ID and its version
- tags:
- - Expression SPoT as Curator
-components:
- schemas:
- CommitInfo:
- $ref: "./schemas/common/CommitInfo.yaml"
- ExpressionItem:
- $ref: "./schemas/expression/ExpressionItem.yaml"
- ExpressionResponse:
- $ref: "./schemas/expression/ExpressionResponse.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- MetadataContent:
- $ref: "./schemas/common/MetadataContent.yaml"
- MetadataWithId:
- $ref: "./schemas/common/MetadataWithId.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- RunFilter:
- $ref: "./schemas/common/RunFilter.yaml"
- RunsResponse:
- $ref: "./schemas/common/RunsResponse.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- SignalRun:
- $ref: "./schemas/common/SignalRun.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/expressionUser.yaml b/openapi/v1/expressionUser.yaml
deleted file mode 100644
index 6477fdeb..00000000
--- a/openapi/v1/expressionUser.yaml
+++ /dev/null
@@ -1,683 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the expressionUser API endpoints for ODM. These are typically used to find and retrieve any tabular data (not only expression data) except Gene Variant or Flow Cytometry.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
-
- The server response will be in the section that follows.
- title: ODM API
- version: default-released
-tags:
-- name: Expression SPoT as User
-paths:
- /api/v1/as-user/expressions:
- get:
- description: |+
- Retrieve all expression data and metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
-
- operationId: getExpressionDataAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by expression metadata (key-value metadata pair(s)). E.g.
- `"Normalization Method"=TPM`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for expression objects via a full text query over all
- expression metadata. E.g. `TPM`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Autogenerated numeric ID that corresponds to the column and is used to link data from the same
- run to a sample, library or preparation. Multiple values can be provided as a list.
- in: query
- name: runFilter
- schema:
- $ref: "#/components/schemas/RunFilter"
- style: form
- - description: Column name from the file to which all data for a sample, library or preparation is related. Multiple values can be provided as a list to retrieve data from multiple columns.
- explode: true
- in: query
- name: runSourceFilter
- schema:
- items:
- type: string
- example: Run Source ID
- type: array
- style: form
- - description: Minimum threshold (inclusive) for returned expression values.
- in: query
- name: minExpressionLevel
- schema:
- format: double
- type: number
- - description: "List of features to return. These features must match exactly\
- \ the probe IDs in the GCT file. Example: `1552269_at`"
- explode: true
- in: query
- name: featureList
- schema:
- items:
- type: string
- example: KRAS
- type: array
- style: form
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ExpressionResponse"
- description: Retrieved Expression data.
- "400":
- content: {}
- description: Expression data cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve multiple expression data and metadata objects
- tags:
- - Expression SPoT as User
- /api/v1/as-user/expressions/group:
- get:
- description: |-
- Retrieve all group metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- ## List operation
-
- This endpoint can be called with no `query` parameter. Doing so returns a list of all data objects.
- operationId: searchExpressionGroupsAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by expression metadata (key-value metadata pair(s)). E.g.
- `"Normalization Method"=TPM`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for expression objects via a full text query over all
- expression metadata. E.g. `TPM`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve groups that match a query
- tags:
- - Expression SPoT as User
- /api/v1/as-user/expressions/group/by/run/{id}:
- get:
- operationId: getExpressionGroupByRunAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (runId) of the run.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single group object by run ID (runId)
- tags:
- - Expression SPoT as User
- /api/v1/as-user/expressions/group/{id}:
- get:
- operationId: getExpressionGroupAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Expression group identifier (groupId).
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single expression group by ID (groupId)
- tags:
- - Expression SPoT as User
- /api/v1/as-user/expressions/runs/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To return all results iterate through pages using pageOffset values of `n * pageLimit` until the `resultsExhausted` response field is true.
-
- operationId: searchExpressionRunsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve run objects related to the given group
- tags:
- - Expression SPoT as User
- /api/v1/as-user/expressions/{id}:
- get:
- operationId: getExpressionAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Expression object unique identifier (itemId).
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ExpressionItem"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single expression object by ID (itemId)
- tags:
- - Expression SPoT as User
- /api/v1/as-user/expressions/{id}/versions:
- get:
- operationId: getExpressionVersionsAsUser
- parameters:
- - description: Expression object run ID (runId).
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/CommitInfo"
- type: array
- description: The request was successful. The returned value is the list
- of object versions.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a list of expression object versions by run ID (runId)
- tags:
- - Expression SPoT as User
- /api/v1/as-user/expressions/{id}/versions/{version}:
- get:
- operationId: getExpressionByVersionAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Expression object run ID (runId).
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Unique version of the object.
- in: path
- name: version
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SignalRun"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single expression object by run ID and its version
- tags:
- - Expression SPoT as User
-components:
- schemas:
- CommitInfo:
- $ref: "./schemas/common/CommitInfo.yaml"
- ExpressionItem:
- $ref: "./schemas/expression/ExpressionItem.yaml"
- ExpressionResponse:
- $ref: "./schemas/expression/ExpressionResponse.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- MetadataContent:
- $ref: "./schemas/common/MetadataContent.yaml"
- MetadataWithId:
- $ref: "./schemas/common/MetadataWithId.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- RunFilter:
- $ref: "./schemas/common/RunFilter.yaml"
- SignalRun:
- $ref: "./schemas/common/SignalRun.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/fileCurator.yaml b/openapi/v1/fileCurator.yaml
deleted file mode 100644
index 591e3860..00000000
--- a/openapi/v1/fileCurator.yaml
+++ /dev/null
@@ -1,245 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the APIs for retrieving files.
- title: ODM API
- version: default-released
-tags:
- - name: Files as Curator
-paths:
- /api/v1/as-curator/files/{id}/download:
- head:
- description: |+
- Check if a file exists by its accession.
-
- This endpoint can be used to check if a file exists and accessible before downloading it.
- operationId: headFileAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- description: File exists. Additional metadata is provided in the response headers.
- "400":
- content: {}
- description: File cannot be downloaded.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "406":
- content: {}
- description: File cannot be downloaded.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to"
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- tags:
- - Files as Curator
- get:
- description: |+
- Download a file by its accession.
- operationId: getFileAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - name: Range
- in: header
- required: false
- schema:
- type: string
- example: bytes=0-
- description: |
- Request a specific range of bytes to support partial downloads.
- Example: `bytes=0-1024` to download the first 1024 bytes. Supplying several
- ranges is not supported.
- responses:
- "200":
- description: File downloaded successfully
- content:
- application/octet-stream:
- schema:
- type: string
- format: binary
- "206":
- description: Partial content downloaded successfully
- content:
- application/octet-stream:
- schema:
- type: string
- format: binary
- "400":
- content: {}
- description: File cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "406":
- content: {}
- description: File cannot be downloaded.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a file by ID (accession)
- tags:
- - Files as Curator
- /api/v1/as-curator/files/{id}:
- get:
- operationId: getFileMetadataByIdAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response.
- in: query
- name: includeContents
- required: false
- schema:
- default: false
- type: boolean
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/AFile"
- description: The request was successful. The returned value is the object.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: Object with provided accession could not be found in ODM.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve file's metadata by ID (accession)
- tags:
- - Files as Curator
- /api/v1/as-curator/files:
- get:
- operationId: getFilesMetadataAsCurator
- description: |-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Paging
- For performance reasons, this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the `pageOffset` query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages by increasing the offset in multiples of limit (e.g., `offset = n * limit`), until all results have been retrieved. The total number of pages can be calculated by dividing the total number of results by the limit.
-
- ## List operation
-
- This endpoint can be called without any query parameters. When called this way, it returns a list of all files metadata objects.
- parameters:
- - in: query
- name: filter
- description: Filter by files metadata (key-value metadata pair(s)).
- schema:
- type: string
- - in: query
- name: query
- description: Search for files via a full-text query over all file metadata.
- schema:
- type: string
- - in: query
- name: includeContents
- description: Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response.
- required: false
- schema:
- default: false
- type: boolean
- - in: query
- name: pageLimit
- description: Maximum number of results to return per page (see Paging above). This value must be
- between 0 and 2000 (inclusive). The default is 2000.
- schema:
- format: int32
- type: integer
- - in: query
- name: pageOffset
- description: Show the page {pageOffset + 1} results from the start of the results. E.g. 100 will show
- a page of results starting from the 101st result. The default value is 0.
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of objects.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve file's metadata by its fields
- tags:
- - Files as Curator
-components:
- schemas:
- AFile:
- $ref: "./schemas/afile/AFile.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/fileUser.yaml b/openapi/v1/fileUser.yaml
deleted file mode 100644
index 6bbf2e5e..00000000
--- a/openapi/v1/fileUser.yaml
+++ /dev/null
@@ -1,246 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the APIs for retrieving files.
- title: ODM API
- version: default-released
-tags:
- - name: Files as User
-paths:
- /api/v1/as-user/files/{id}/download:
- head:
- description: |+
- Check if a file exists by its accession.
-
- This endpoint can be used to check if a file exists and accessible before downloading it.
- operationId: headFileAsUser
- summary: Check if a file exists by ID (accession).
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- description: File exists. Additional metadata is provided in the response headers.
- "400":
- content: {}
- description: File cannot be downloaded.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "406":
- content: {}
- description: File cannot be downloaded.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to"
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- tags:
- - Files as User
- get:
- description: |+
- Download a file by its accession.
- operationId: getFileAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - name: Range
- in: header
- required: false
- schema:
- type: string
- example: bytes=0-
- description: |
- Request a specific range of bytes to support partial downloads.
- Example: `bytes=0-1024` to download the first 1024 bytes. Supplying several
- ranges is not supported.
- responses:
- "200":
- description: File downloaded successfully
- content:
- application/octet-stream:
- schema:
- type: string
- format: binary
- "206":
- description: Partial content downloaded successfully
- content:
- application/octet-stream:
- schema:
- type: string
- format: binary
- "400":
- content: {}
- description: File cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "406":
- content: {}
- description: File cannot be downloaded.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a file by ID (accession)
- tags:
- - Files as User
- /api/v1/as-user/files/{id}:
- get:
- operationId: getFileMetadataByIdAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response.
- in: query
- name: includeContents
- required: false
- schema:
- default: false
- type: boolean
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/AFile"
- description: The request was successful. The returned value is the object.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: Object with provided accession could not be found in ODM.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve file's metadata by ID (accession)
- tags:
- - Files as User
- /api/v1/as-user/files:
- get:
- operationId: getFilesMetadataAsUser
- description: |-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Paging
- For performance reasons, this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the `pageOffset` query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages by increasing the offset in multiples of limit (e.g., `offset = n * limit`), until all results have been retrieved. The total number of pages can be calculated by dividing the total number of results by the limit.
-
- ## List operation
-
- This endpoint can be called without any query parameters. When called this way, it returns a list of all files metadata objects.
- parameters:
- - in: query
- name: filter
- description: Filter by files metadata (key-value metadata pair(s)).
- schema:
- type: string
- - in: query
- name: query
- description: Search for files via a full-text query over all file metadata.
- schema:
- type: string
- - in: query
- name: includeContents
- description: Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response.
- required: false
- schema:
- default: false
- type: boolean
- - in: query
- name: pageLimit
- description: Maximum number of results to return per page (see Paging above). This value must be
- between 0 and 2000 (inclusive). The default is 2000.
- schema:
- format: int32
- type: integer
- - in: query
- name: pageOffset
- description: Show the page {pageOffset + 1} results from the start of the results. E.g. 100 will show
- a page of results starting from the 101st result. The default value is 0.
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of objects.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve file's metadata by its fields
- tags:
- - Files as User
-components:
- schemas:
- AFile:
- $ref: "./schemas/afile/AFile.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/flowCytometryCurator.yaml b/openapi/v1/flowCytometryCurator.yaml
deleted file mode 100644
index 3bc7c13d..00000000
--- a/openapi/v1/flowCytometryCurator.yaml
+++ /dev/null
@@ -1,747 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the flowCytometryCurator API endpoints for ODM. These are typically used to find and retrieve flow cytometry data and metadata as well as update metadata.
- The APIs can be used for gated flow cytometry data in FACS format. For flow cytometry data in FCS format use expression endpoints.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
- The server response will be in the section that follows.
- title: ODM API
- version: default-released
-tags:
-- name: Flow Cytometry SPoT as Curator
-paths:
- /api/v1/as-curator/flow-cytometries:
- get:
- description: |+
- Retrieve all flow cytometry data and metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
-
- operationId: getFlowCytometryDataAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by flow cytometry metadata (key-value metadata pair(s)).
- E.g. `Organ=blood`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for flow cytometry objects via a full text query over
- all flow cytometry metadata. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Autogenerated numeric ID that identifies a set of rows related to one run and is used to link
- data from the run to a sample. Multiple values can be provided as a list.
- in: query
- name: runFilter
- schema:
- $ref: "#/components/schemas/RunFilter"
- style: form
- - description: Sample name from the file which allows retrieval of all the rows related to the sample. Multiple values can be provided as a list.
- explode: true
- in: query
- name: runSourceFilter
- schema:
- items:
- type: string
- example: Run Source ID
- type: array
- style: form
- - description: "Required value of \"Readout type\" column. E.g.: `Count`, `Median`"
- in: query
- name: readoutType
- schema:
- type: string
- - description: |-
- Value of "Cell Population" column. E.g.: `"total cells"`, `CD45+,live/CD45+`, `CD3+`.
-
- Note that if this value contains special characters like `/` which is used as a URI path separator, such characters should be escaped manually before sending request. For example, `/` should be escaped as `%2F`.
- in: query
- name: population
- schema:
- type: string
- - description: "Marker value. E.g.: `PD1`, `BV786`"
- in: query
- name: marker
- schema:
- type: string
- - description: Minimum threshold (inclusive) for returned expression values.
- in: query
- name: minValue
- schema:
- type: number
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/FlowCytometryResponse"
- description: Retrieved Flow Cytometry data.
- "400":
- content: {}
- description: Flow Cytometry data cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve multiple flow cytometry data and metadata objects
- tags:
- - Flow Cytometry SPoT as Curator
- /api/v1/as-curator/flow-cytometries/group:
- get:
- description: |-
- Retrieve all group metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- ## List operation
-
- This endpoint can be called with no `query` parameter. Doing so returns a list of all data objects.
- operationId: searchFlowCytometryGroupsAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by flow cytometry metadata (key-value metadata pair(s)).
- E.g. `Organ=blood`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for flow cytometry objects via a full text query over
- all flow cytometry metadata. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve groups that match a query
- tags:
- - Flow Cytometry SPoT as Curator
- /api/v1/as-curator/flow-cytometries/group/by/run/{id}:
- get:
- operationId: getFlowCytometryGroupByRunAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single group object by run ID (accession)
- tags:
- - Flow Cytometry SPoT as Curator
- /api/v1/as-curator/flow-cytometries/group/{id}:
- get:
- operationId: getFlowCytometryGroupAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single group object by ID (accession)
- tags:
- - Flow Cytometry SPoT as Curator
- /api/v1/as-curator/flow-cytometries/runs/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: searchFlowCytometryRunsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve run objects related to the given group
- tags:
- - Flow Cytometry SPoT as Curator
- /api/v1/as-curator/flow-cytometries/{id}:
- get:
- operationId: getFlowCytometryAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/FlowCytometryItem"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single sample flow cytometry by ID (accession)
- tags:
- - Flow Cytometry SPoT as Curator
- patch:
- description: |-
- ## Basic operation
- The object metadata is updated using the supplied map of attribute names to attribute values. There are three cases:
- 1. The attribute name does not already exist in the object metadata. In this case, the attribute and value are added to the object metadata.
- 2. The attribute name already exists in the object metadata. In this case, the value is updated.
- 3. The attribute value is `null`.In this case, the attribute is removed from the object metadata.
-
- ## Attribute values
- The attribute values are intelligently parsed as booleans, integers, etc.
- operationId: updateFlowCytometryAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataContent"
- description: "Metadata in the form of `{key: value, key2: value2, ...}`"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SignalRun"
- description: "The objects was successfully created. The returned value is\
- \ the updated object, along with any warnings."
- "400":
- content: {}
- description: The supplied object ID or metadata is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Update object metadata
- tags:
- - Flow Cytometry SPoT as Curator
- x-codegen-request-body-name: body
- /api/v1/as-curator/flow-cytometries/{id}/versions:
- get:
- operationId: getFlowCytometryVersionsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/CommitInfo"
- type: array
- description: The request was successful. The returned value is the list
- of object versions.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a list of object versions by ID
- tags:
- - Flow Cytometry SPoT as Curator
- /api/v1/as-curator/flow-cytometries/{id}/versions/{version}:
- get:
- operationId: getFlowCytometryByVersionAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Unique version of the object.
- in: path
- name: version
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SignalRun"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single sample flow cytometry by ID (accession)
- tags:
- - Flow Cytometry SPoT as Curator
-components:
- schemas:
- CommitInfo:
- $ref: "./schemas/common/CommitInfo.yaml"
- FlowCytometryItem:
- $ref: "./schemas/flow-cytometry/FlowCytometryItem.yaml"
- FlowCytometryResponse:
- $ref: "./schemas/flow-cytometry/FlowCytometryResponse.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- MetadataContent:
- $ref: "./schemas/common/MetadataContent.yaml"
- MetadataWithId:
- $ref: "./schemas/common/MetadataWithId.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- RunFilter:
- $ref: "./schemas/common/RunFilter.yaml"
- RunsResponse:
- $ref: "./schemas/common/RunsResponse.yaml"
- SignalRun:
- $ref: "./schemas/common/SignalRun.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/flowCytometryUser.yaml b/openapi/v1/flowCytometryUser.yaml
deleted file mode 100644
index 35ce875c..00000000
--- a/openapi/v1/flowCytometryUser.yaml
+++ /dev/null
@@ -1,689 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the flowCytometryUser API endpoints for ODM. These are typically used to find and retrieve flow cytometry data and metadata.
- The APIs can be used for gated flow cytometry data in FACS format. For flow cytometry data in FCS format use expression endpoints.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
- The server response will be in the section that follows.
- title: ODM API
- version: default-released
-tags:
-- name: Flow Cytometry SPoT as User
-paths:
- /api/v1/as-user/flow-cytometries:
- get:
- description: |+
- Retrieve all flow cytometry data and metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a `cursor` tag. To retrieve the next page of results please supply this `cursor` tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result.
-
- operationId: getFlowCytometryDataAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by flow cytometry metadata (key-value metadata pair(s)).
- E.g. `Organ=blood`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for flow cytometry objects via a full text query over
- all flow cytometry metadata. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Autogenerated numeric ID that identifies a set of rows related to one run and is used to link
- data from the run to a sample. Multiple values can be provided as a list.
- in: query
- name: runFilter
- schema:
- $ref: "#/components/schemas/RunFilter"
- style: form
- - description: Sample name from the file which allows retrieval of all the rows related to the sample. Multiple values can be provided as a list.
- explode: true
- in: query
- name: runSourceFilter
- schema:
- items:
- type: string
- example: Run Source ID
- type: array
- style: form
- - description: "Required value of \"Readout type\" column. E.g.: `Count`, `Median`"
- in: query
- name: readoutType
- schema:
- type: string
- - description: |-
- Value of "Cell Population" column. E.g.: `"total cells"`, `CD45+,live/CD45+`, `CD3+`.
-
- Note that if this value contains special characters like `/` which is used as a URI path separator, such characters should be escaped manually before sending request. For example, `/` should be escaped as `%2F`.
- in: query
- name: population
- schema:
- type: string
- - description: "Marker value. E.g.: `PD1`, `BV786`"
- in: query
- name: marker
- schema:
- type: string
- - description: Minimum threshold (inclusive) for returned expression values.
- in: query
- name: minValue
- schema:
- type: number
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/FlowCytometryResponse"
- description: Retrieved Flow Cytometry data.
- "400":
- content: {}
- description: Flow Cytometry data cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve multiple flow cytometry data and metadata objects
- tags:
- - Flow Cytometry SPoT as User
- /api/v1/as-user/flow-cytometries/group:
- get:
- description: |-
- Retrieve all group metadata objects that match a query.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- ## List operation
-
- This endpoint can be called with no `query` parameter. Doing so returns a list of all data objects.
- operationId: searchFlowCytometryGroupsAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by flow cytometry metadata (key-value metadata pair(s)).
- E.g. `Organ=blood`.
- in: query
- name: filter
- schema:
- type: string
- - description: Search for flow cytometry objects via a full text query over
- all flow cytometry metadata. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve groups that match a query
- tags:
- - Flow Cytometry SPoT as User
- /api/v1/as-user/flow-cytometries/group/by/run/{id}:
- get:
- operationId: getFlowCytometryGroupByRunAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single group object by run ID (accession)
- tags:
- - Flow Cytometry SPoT as User
- /api/v1/as-user/flow-cytometries/group/{id}:
- get:
- operationId: getFlowCytometryGroupAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataWithId"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single group object by ID (accession)
- tags:
- - Flow Cytometry SPoT as User
- /api/v1/as-user/flow-cytometries/runs/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: searchFlowCytometryRunsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve run objects related to the given group
- tags:
- - Flow Cytometry SPoT as User
- /api/v1/as-user/flow-cytometries/{id}:
- get:
- operationId: getFlowCytometryAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/FlowCytometryItem"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single sample flow cytometry by ID (accession)
- tags:
- - Flow Cytometry SPoT as User
- /api/v1/as-user/flow-cytometries/{id}/versions:
- get:
- operationId: getFlowCytometryVersionsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/CommitInfo"
- type: array
- description: The request was successful. The returned value is the list
- of object versions.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a list of object versions by ID
- tags:
- - Flow Cytometry SPoT as User
- /api/v1/as-user/flow-cytometries/{id}/versions/{version}:
- get:
- operationId: getFlowCytometryByVersionAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Unique version of the object.
- in: path
- name: version
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SignalRun"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single sample flow cytometry by ID (accession)
- tags:
- - Flow Cytometry SPoT as User
-components:
- schemas:
- CommitInfo:
- $ref: "./schemas/common/CommitInfo.yaml"
- FlowCytometryItem:
- $ref: "./schemas/flow-cytometry/FlowCytometryItem.yaml"
- FlowCytometryResponse:
- $ref: "./schemas/flow-cytometry/FlowCytometryResponse.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- MetadataContent:
- $ref: "./schemas/common/MetadataContent.yaml"
- MetadataWithId:
- $ref: "./schemas/common/MetadataWithId.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- RunFilter:
- $ref: "./schemas/common/RunFilter.yaml"
- SignalRun:
- $ref: "./schemas/common/SignalRun.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/integrationCurator.yaml b/openapi/v1/integrationCurator.yaml
deleted file mode 100644
index cb1ce90d..00000000
--- a/openapi/v1/integrationCurator.yaml
+++ /dev/null
@@ -1,6837 +0,0 @@
-openapi: 3.1.0
-info:
- description: |
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
- The server response will be in the section that follows.
- title: ODM Integration API
- version: default-released
-tags:
-- name: Cell integration as Curator
-- name: Expression integration as Curator
-- name: Files integration as Curator
-- name: Flow Cytometry (FACS) integration as Curator
-- name: Library integration as Curator
-- name: Linkage as Curator
-- name: Metadata versioning as Curator
-- name: Omics queries as Curator
-- name: Preparation integration as Curator
-- name: Sample integration as Curator
-- name: Study integration as Curator
-- name: Validation summary as Curator
-- name: Variant integration as Curator
-paths:
- /api/v1/as-curator/data-types:
- get:
- description: This endpoint is for instructional uses and can be used to get
- the latest list of Data Types.
- operationId: getDataTypesAsCurator
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- type: string
- type: array
- uniqueItems: true
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Lists all available data types.
- tags:
- - Linkage as Curator
- /api/v1/as-curator/data-types/links:
- get:
- description: "This endpoint should be used for instructional needs, and can\
- \ be used in order to get the links between the Data Types."
- operationId: getDataTypesLinksAsCurator
- parameters:
- - description: Return only links with the specified data type.
- in: query
- name: type
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/SourceTypePair"
- type: array
- uniqueItems: true
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: List all possible links between data types that match the specified
- criteria.
- tags:
- - Linkage as Curator
- /api/v1/as-curator/integration/link/expression/by/library/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionByLibraryAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve expression run-level data by querying related library ID (accession)
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/by/preparation/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionByPreparation
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve expression run-level data by querying related preparation
- ID (accession)
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/by/sample/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionBySampleAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve expression run-level data by querying related sample ID (accession)
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/group/by/study/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- operationId: getExpressionGroupsByStudyAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Expression integration as Curator
- ? /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/library/group/{targetId}
- : delete:
- description: Delete link between a group of expression objects and a group of
- library objects
- operationId: deleteExpressionGroupLibraryGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to a GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the library group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a group of expression objects and a group of library
- objects
- tags:
- - Expression integration as Curator
- post:
- description: |-
- Create a link between a group of expression objects and a group of library objects.
-
- An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Expression objects of the same group can only be linked to objects of the same study.
- operationId: createExpressionGroupLibraryGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to a GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the library group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "200":
- content: {}
- description: Some (not all) sample links created.
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: "Library group, signal group or libraries to link not found"
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a group of expression objects and a group of
- library objects
- tags:
- - Expression integration as Curator
- ? /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/preparation/group/{targetId}
- : delete:
- description: Delete link between a group of expression objects and a group of
- preparation objects
- operationId: deleteExpressionGroupPreparationGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to a GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the preparation group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a group of expression objects and a group of preparation
- objects
- tags:
- - Expression integration as Curator
- post:
- description: |-
- Create a link between a group of expression objects and a group of preparation objects.
-
- An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Expression objects of the same group can only be linked to objects of the same study.
- operationId: createExpressionGroupPreparationGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to a GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the preparation group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "200":
- content: {}
- description: Some (not all) sample links created.
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: "Preparation group, signal group or preparations to link not\
- \ found"
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a group of expression objects and a group of
- preparation objects
- tags:
- - Expression integration as Curator
- ? /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId}
- : delete:
- description: Delete link between a group of expression objects and a group of
- sample objects
- operationId: deleteExpressionGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to a GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a group of expression objects and a group of sample
- objects
- tags:
- - Expression integration as Curator
- post:
- description: |-
- Create a link between a group of expression objects and a group of sample objects.
-
- An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Expression objects of the same group can only be linked to objects of the same study.
-
- Users can specify a custom metadata field for linking omics data to samples via the “linkingAttribute” parameter, if not specified the “Sample Source ID“ sample metadata attribute will be used by default.
- operationId: createExpressionGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to a GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- - description: Metadata field containing sample IDs to link omics data to samples.
- The template applied to the study must contain this field in the sample
- section.
- in: query
- name: linkingAttribute
- schema:
- type: string
- responses:
- "200":
- content: {}
- description: Not all signal data were linked to the samples.
- "204":
- content: {}
- description: All signal data were linked to the samples from the specified
- sample group.
- "400":
- content: {}
- description: "Sample group, signal group or samples to the link were not\
- \ found, or the specified linking attribute was not found."
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a group of expression objects and a group of
- sample objects
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/run-to-libraries/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionRunToLibraryPairsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-library pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/run-to-preparations/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionRunToPreparationPairsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-preparation pairs by group id. Pagination is based on\
- \ unique runs, not unique pairs."
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/run-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionRunToSamplePairsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/{sourceId}/to/library/{targetId}:
- delete:
- description: Delete link between an expression object and a library
- operationId: deleteExpressionLibraryLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the library object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between an expression object and a library
- tags:
- - Expression integration as Curator
- post:
- description: |-
- Create a link between an expression object and a library.
-
- An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Expression objects of the same group can only be linked to objects of the same study.
- operationId: createExpressionLibraryLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the library object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between an expression object and a library
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/{sourceId}/to/preparation/{targetId}:
- delete:
- description: Delete link between an expression object and a preparation
- operationId: deleteExpressionPreparationLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the preparation object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between an expression object and a preparation
- tags:
- - Expression integration as Curator
- post:
- description: |-
- Create a link between an expression object and a preparation.
-
- An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Expression objects of the same group can only be linked to objects of the same study.
- operationId: createExpressionPreparationLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the preparation object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between an expression object and a preparation
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/expression/{sourceId}/to/sample/{targetId}:
- delete:
- description: Delete link between an expression object and a sample
- operationId: deleteExpressionSampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between an expression object and a sample
- tags:
- - Expression integration as Curator
- post:
- description: |-
- Create a link between an expression object and a sample.
-
- An expression object can be linked to one object only. If an expression object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Expression objects of the same group can only be linked to objects of the same study.
- operationId: createExpressionSampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between an expression object and a sample
- tags:
- - Expression integration as Curator
- /api/v1/as-curator/integration/link/flow-cytometry/by/sample/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getFlowCytometryBySampleAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve flow cytometry run-level data by querying related sample ID
- (accession)
- tags:
- - Flow Cytometry (FACS) integration as Curator
- /api/v1/as-curator/integration/link/flow-cytometry/group/by/study/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- operationId: getFlowCytometryGroupsByStudyAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Flow Cytometry (FACS) integration as Curator
- ? /api/v1/as-curator/integration/link/flow-cytometry/group/{sourceId}/to/sample/group/{targetId}
- : delete:
- description: Delete link between a group of flow-cytometry objects and a group
- of sample objects
- operationId: deleteFlowCytometryGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to the column in a FACS file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a group of flow-cytometry objects and a group of
- sample objects
- tags:
- - Flow Cytometry (FACS) integration as Curator
- post:
- description: |-
- Create a link between a group of flow-cytometry objects and a group of sample objects.
-
- A flow-cytometry object can be linked to one object only. If a flow-cytometry object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Flow-cytometry objects of the same group can only be linked to objects of the same study.
-
- Users can specify a custom metadata field for linking omics data to samples via the “linkingAttribute” parameter, if not specified the “Sample Source ID“ sample metadata attribute will be used by default.
- operationId: createFlowCytometryGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to the column in a FACS file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- - description: Metadata field containing sample IDs to link omics data to samples.
- The template applied to the study must contain this field in the sample
- section.
- in: query
- name: linkingAttribute
- schema:
- type: string
- responses:
- "200":
- content: {}
- description: Not all signal data were linked to the samples.
- "204":
- content: {}
- description: All signal data were linked to the samples from the specified
- sample group.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: "Sample group, signal group or samples to the link were not\
- \ found, or the specified linking attribute was not found."
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a group of flow-cytometry objects and a group
- of sample objects
- tags:
- - Flow Cytometry (FACS) integration as Curator
- /api/v1/as-curator/integration/link/flow-cytometry/run-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getFlowCytometryRunToSamplePairsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Flow Cytometry (FACS) integration as Curator
- /api/v1/as-curator/integration/link/flow-cytometry/{sourceId}/to/sample/{targetId}:
- delete:
- description: Delete link between a flow-cytometry object and a sample
- operationId: deleteFlowCytometrySampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level data block
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a flow-cytometry object and a sample
- tags:
- - Flow Cytometry (FACS) integration as Curator
- post:
- description: |-
- Create a link between a flow-cytometry object and a sample.
-
- A flow-cytometry object can be linked to one object only. If a flow-cytometry object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Flow-cytometry objects of the same group can only be linked to objects of the same study.
- operationId: createFlowCytometrySampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level data block
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a flow-cytometry object and a sample
- tags:
- - Flow Cytometry (FACS) integration as Curator
- /api/v1/as-curator/integration/link/libraries/by/samples:
- get:
- description: |+
- Retrieve library metadata objects whose linked sample metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getLibrariesBySamplesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve library metadata by querying related samples
- tags:
- - Library integration as Curator
- /api/v1/as-curator/integration/link/library/by/sample/{id}:
- get:
- operationId: getLibraryBySampleAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/Library"
- type: array
- text/tab-separated-values:
- schema:
- items:
- $ref: "#/components/schemas/Library"
- type: array
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve library metadata by querying related sample ID (accession)
- tags:
- - Library integration as Curator
- /api/v1/as-curator/integration/link/library/group/by/study/{id}:
- get:
- operationId: getLibraryGroupsByStudyAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Library integration as Curator
- /api/v1/as-curator/integration/link/library/group/{sourceId}/to/sample/group/{targetId}:
- delete:
- description: Delete links between samples and libraries related to the specified
- group
- operationId: deleteLibraryGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the library group object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete links between samples and libraries related to the specified
- group
- tags:
- - Library integration as Curator
- post:
- description: |-
- Create links between samples and libraries.
-
- Library objects of the same group can only be linked to objects of the same study.
- operationId: createLibraryGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the library group object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create links between samples and libraries
- tags:
- - Library integration as Curator
- /api/v1/as-curator/integration/link/library/libraries-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getLibraryLinksToSamplesAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve library-samples pairs by group id. Pagination is based on\
- \ unique libraries, not unique pairs."
- tags:
- - Library integration as Curator
- /api/v1/as-curator/integration/link/library/{sourceId}/to/sample/{targetId}:
- delete:
- description: Delete a link between a library and a sample
- operationId: deleteLibrarySampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the library object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete a link between a library and a sample
- tags:
- - Library integration as Curator
- post:
- description: |-
- Create a link between a library and a sample.
-
- Library objects of the same group can only be linked to objects of the same study.
- operationId: createLibrarySampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the library object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a library and a sample
- tags:
- - Library integration as Curator
- /api/v1/as-curator/integration/link/preparation/by/sample/{id}:
- get:
- operationId: getPreparationBySampleAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/Preparation"
- type: array
- text/tab-separated-values:
- schema:
- items:
- $ref: "#/components/schemas/Preparation"
- type: array
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve preparation metadata by querying related sample ID (accession)
- tags:
- - Preparation integration as Curator
- /api/v1/as-curator/integration/link/preparation/group/by/study/{id}:
- get:
- operationId: getPreparationGroupsByStudyAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Preparation integration as Curator
- ? /api/v1/as-curator/integration/link/preparation/group/{sourceId}/to/sample/group/{targetId}
- : delete:
- description: Delete links between samples and preparations related to the specified
- group
- operationId: deletePreparationGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the preparation group object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete links between samples and preparations related to the specified
- group
- tags:
- - Preparation integration as Curator
- post:
- description: |-
- Create links between samples and preparations.
-
- Preparation objects of the same group can only be linked to objects of the same study.
- operationId: createPreparationGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the preparation group object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create links between samples and preparations
- tags:
- - Preparation integration as Curator
- /api/v1/as-curator/integration/link/preparation/preparations-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getPreparationLinksToSamplesAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ preparations, not unique pairs."
- tags:
- - Preparation integration as Curator
- /api/v1/as-curator/integration/link/preparation/{sourceId}/to/sample/{targetId}:
- delete:
- description: Delete a link between a preparation and a sample
- operationId: deletePreparationSampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the preparation object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete a link between a preparation and a sample
- tags:
- - Preparation integration as Curator
- post:
- description: |-
- Create a link between a preparation and a sample.
-
- Preparation objects of the same group can only be linked to objects of the same study.
- operationId: createPreparationSampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the preparation object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a preparation and a sample
- tags:
- - Preparation integration as Curator
- /api/v1/as-curator/integration/link/preparations/by/samples:
- get:
- description: |+
- Retrieve preparation metadata objects whose linked sample metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getPreparationsBySamplesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve preparation metadata by querying related samples
- tags:
- - Preparation integration as Curator
- /api/v1/as-curator/integration/link/sample/group/{sourceId}/to/study/{targetId}:
- delete:
- description: Delete link between a group of sample objects and a study
- operationId: deleteSampleGroupStudyLinkAsCurator
- parameters:
- - description: The ID (accession) of the sample group object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the study object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a group of sample objects and a study
- tags:
- - Sample integration as Curator
- post:
- description: |-
- Create a link between a group of sample objects and a study.
-
- Sample objects of the same group can only be linked to the same study.
- operationId: createSampleGroupStudyLinkAsCurator
- parameters:
- - description: The ID (accession) of the sample group object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the study object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a group of sample objects and a study
- tags:
- - Sample integration as Curator
- /api/v1/as-curator/integration/link/sample/{sourceId}/to/study/{targetId}:
- delete:
- description: Delete link between a sample and a study
- operationId: deleteSampleStudyLinkAsCurator
- parameters:
- - description: The ID (accession) of the sample object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the study object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a sample and a study
- tags:
- - Sample integration as Curator
- post:
- description: |-
- Create a link between a sample and a study.
-
- Sample objects of the same group can only be linked to the same study.
- operationId: createSampleStudyLinkAsCurator
- parameters:
- - description: The ID (accession) of the sample object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the study object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a sample and a study
- tags:
- - Sample integration as Curator
- /api/v1/as-curator/integration/link/samples/by/libraries:
- get:
- description: |+
- Retrieve sample metadata objects whose linked library metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getSamplesByLibrariesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata by querying related libraries
- tags:
- - Sample integration as Curator
- /api/v1/as-curator/integration/link/samples/by/preparations:
- get:
- description: |+
- Retrieve sample metadata objects whose linked preparation metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getSamplesByPreparationsAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata by querying related preparations
- tags:
- - Sample integration as Curator
- /api/v1/as-curator/integration/link/samples/by/study/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getSamplesByStudyAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata by querying related study ID (accession)
- tags:
- - Sample integration as Curator
- /api/v1/as-curator/integration/link/studies/by/libraries:
- get:
- description: |+
- Retrieve study metadata objects whose linked library metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesByLibrariesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related libraries
- tags:
- - Study integration as Curator
- /api/v1/as-curator/integration/link/studies/by/preparations:
- get:
- description: |+
- Retrieve study metadata objects whose linked preparation metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesByPreparationsAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related preparations
- tags:
- - Study integration as Curator
- /api/v1/as-curator/integration/link/studies/by/samples:
- get:
- description: |+
- Retrieve study metadata objects whose linked sample metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesBySamplesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by sample metadata (key-value metadata pair(s)). E.g.
- "Species or strain"="Homo sapiens"
- in: query
- name: filter
- schema:
- type: string
- - description: Search for study metadata objects via a full-text query over
- all sample metadata fields. E.g. "RNA-Seq of human dendritic cells". Queries
- matching dictionary terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related samples
- tags:
- - Study integration as Curator
- /api/v1/as-curator/integration/link/study/by/sample/{id}:
- get:
- operationId: getStudyBySampleAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Study"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata by querying sample ID (accession)
- tags:
- - Study integration as Curator
- /api/v1/as-curator/integration/link/studies/by/files:
- get:
- description: |+
- Retrieve study metadata objects whose linked attached files metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Attachment files (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesByFilesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by attachment file metadata (key-value metadata pair(s)). E.g.
- "Species or strain"="Homo sapiens"
- in: query
- name: filter
- schema:
- type: string
- - description: Search for study metadata objects via a full-text query over
- all attached files metadata fields. E.g. "RNA-Seq of human dendritic cells". Queries
- matching dictionary terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related attachment files
- tags:
- - Study integration as Curator
- /api/v1/as-curator/integration/link/study/by/file/{id}:
- get:
- operationId: getStudyByFileAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Study"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata by querying attachment file ID (accession)
- tags:
- - Study integration as Curator
- /api/v1/as-curator/integration/link/variant/by/sample/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getVariantBySampleAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve variant run-level data by querying related sample ID (accession)
- tags:
- - Variant integration as Curator
- /api/v1/as-curator/integration/link/variant/group/by/study/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- operationId: getVariantGroupsByStudyAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Variant integration as Curator
- /api/v1/as-curator/integration/link/variant/group/{sourceId}/to/sample/group/{targetId}:
- delete:
- description: Delete link between a group of variant objects and a group of sample
- objects
- operationId: deleteVariantGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to the column in a VCF file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a group of variant objects and a group of sample
- objects
- tags:
- - Variant integration as Curator
- post:
- description: |-
- Create a link between a group of variant objects and a group of sample objects.
-
- A variant object can be linked to one object only. If a variant object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Variant objects of the same group can only be linked to objects of the same study.
-
- Users can specify a custom metadata field for linking omics data to samples via the “linkingAttribute” parameter, if not specified the “Sample Source ID“ sample metadata attribute will be used by default.
- operationId: createVariantGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the group of run-level objects (corresponding
- to the column in a VCF file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- - description: Metadata field containing sample IDs to link omics data to samples.
- The template applied to the study must contain this field in the sample
- section.
- in: query
- name: linkingAttribute
- schema:
- type: string
- responses:
- "200":
- content: {}
- description: Not all signal data were linked to the samples.
- "204":
- content: {}
- description: All signal data were linked to the samples from the specified
- sample group.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: "Sample group, signal group or samples to the link were not\
- \ found, or the specified linking attribute was not found."
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a group of variant objects and a group of sample
- objects
- tags:
- - Variant integration as Curator
- /api/v1/as-curator/integration/link/variant/run-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getVariantRunToSamplePairsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Variant integration as Curator
- /api/v1/as-curator/integration/link/variant/{sourceId}/to/sample/{targetId}:
- delete:
- description: Delete link between a variant object and a sample
- operationId: deleteVariantSampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link deleted.
- "400":
- content: {}
- description: Link cannot be deleted.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete link between a variant object and a sample
- tags:
- - Variant integration as Curator
- post:
- description: |-
- Create a link between a variant object and a sample.
-
- A variant object can be linked to one object only. If a variant object is already linked to another object, this link will be deleted and a new link with the specified object will be created.
- Variant objects of the same group can only be linked to objects of the same study.
- operationId: createVariantSampleLinkAsCurator
- parameters:
- - description: The ID (accession) of the run-level object (corresponding to
- the column in a VCG/GCT file)
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link created.
- "400":
- content: {}
- description: Link cannot be created.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Create a link between a variant object and a sample
- tags:
- - Variant integration as Curator
- /api/v1/as-curator/integration/fulltext/search/studies:
- post:
- description: |-
- Find studies and retrieve their data using full-text search or facet search by metadata of study itself or child object (samples, libraries, preparations, signal groups). Only studies available to that users are returned.
-
- The endpoint returns:
- - a list of studies with their metadata summary;
- - a list of filter objects with counts; filter list is the same for all users in an and can be configured in “Study Browser” application via "Configure facets" (by a user with corresponding permission); for each filter object, only the first 5 most popular facets are returned, the facts are sorted by the count value in descending order; only studies available to user are counted.
-
- Filter attributes for fulltext search:
- - `"type": "FULL_TEXT"`
- - `"match"`
- - `"mode"`
-
- For details on two latter ones, see the request body model. Only one filter with `"type=": "FULL_TEXT"` can be passed in the request body.
-
- To filter studies via facets, the filter attributes are necessary: type = SELECT, filterOptionId. For details, use the request body model. filterOptionId can be obtained from the response body when the endpoint is first called without filters. Multiple filters with type = SELECT can be passed in the request body. Filters within the same attribute are automatically used with the OR operator. Filters of different attributes are automatically used with the AND operator. This behaviour can not be changed.
-
- It is possible to call the endpoint without any filters, then all the studies available to the user are returned.
-
- The endpoint searches by staging version of the object metadata.
- operationId: searchStudiesByFilterAsCurator
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SearchStudyRequest"
- required: true
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/FindObjectsResponse"
- description: The request was successful. Retrieved studies and filters.
- "400":
- content: {}
- description: Invalid request body
- "401":
- content: {}
- description: User is not authenticated. Please supply a valid Genestack
- API token in the `Genestack-API-Token` HTTP header (this token may be
- obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Genestack-API-Token: []
- summary: Find and retrieve studies by full-text or facet query
- tags:
- - Study integration as Curator
- x-codegen-request-body-name: request
- /api/v1/as-curator/links:
- delete:
- description: "This method should be used in case you want to delete the links\
- \ of an object. Please, keep in mind that deleting a link between Study and\
- \ Sample will not delete a link between corresponding Sample and it’s signal."
- operationId: deleteLinkAsCurator
- parameters:
- - description: Object ID (accession) (e.g. accession of study)
- in: query
- name: firstId
- required: true
- schema:
- type: string
- - description: Type of the object (e.g. study)
- in: query
- name: firstType
- schema:
- type: string
- - description: Object ID (accession) (e.g. accession of study)
- in: query
- name: secondId
- required: true
- schema:
- type: string
- - description: Type of the object (e.g. study)
- in: query
- name: secondType
- schema:
- type: string
- responses:
- "204":
- content: {}
- description: Link has been successfully deleted.
- "400":
- content: {}
- description: Invalid data in request.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No links were found.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Deletes existing links matching the specified criteria.
- tags:
- - Linkage as Curator
- get:
- description: Please make sure that this endpoint should be used only for getting
- all links to a specific object. In case you specify both firstId and secondId
- an expected answer would be true for existing links and false for no link
- between the objects.
- operationId: getLinksByParamsAsCurator
- parameters:
- - description: Object ID (accession) (e.g. accession of study)
- in: query
- name: firstId
- required: true
- schema:
- type: string
- - description: Type of the object (e.g. study)
- in: query
- name: firstType
- schema:
- type: string
- - description: Object ID (accession) (e.g. accession of study)
- in: query
- name: secondId
- schema:
- type: string
- - description: Type of the object (e.g. study)
- in: query
- name: secondType
- schema:
- type: string
- - description: Param says to skip that many links before beginning to return
- links.
- in: query
- name: offset
- schema:
- default: 0
- format: int32
- type: integer
- - description: Param says to limit the count of returned links.
- in: query
- name: limit
- schema:
- default: 1000
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Finds existing links matching the specified criteria.
- tags:
- - Linkage as Curator
- post:
- description: "This method should be used only in case you need to create links\
- \ between 2 objects. Links are created both ways (e.g. when linking Object\
- \ A to Object B it can be done both ways, by linking firstType to secondType\
- \ and vice versa)."
- operationId: saveLinksAsCurator
- requestBody:
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/Link"
- type: array
- required: false
- responses:
- "200":
- content: {}
- description: Links were updated or not modified.
- "201":
- content: {}
- description: At least one new link has been created.Some other links might
- have been updated or not modified.
- "400":
- content: {}
- description: Invalid data in request.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "409":
- content: {}
- description: Link cannot be created due to conflict with existing link
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Creates new links between objects.
- tags:
- - Linkage as Curator
- x-codegen-request-body-name: links
- /api/v1/as-curator/links/get-batch:
- post:
- description: Please make sure to use that endpoint for batch calls only. You
- are not allowed to pass 'mixed' objects. e.g. Studies and Samples at the same
- time. Please always specify firstType.
- operationId: getLinksByIdsAsCurator
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/BatchOfIds"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Finds existing links by passing many IDs. \nPagination goes through\
- \ all links matched the criteria."
- tags:
- - Linkage as Curator
- x-codegen-request-body-name: request
- /api/v1/as-curator/omics/expression/data:
- get:
- description: "Retrieve any data objects whose linked data matches all supplied\
- \ conditions. \n\nNote: An expression data query must be supplied.\n\n## Conditions\n\
- It is possible to supply conditions for:\n\n1. Samples (full-text or metadata\
- \ key-value pair)\n2. Parent studies (full-text or metadata key-value pair)\n\
- 3. Linked variant objects (list of data key-value pairs)\n4. Linked flow cytometry\
- \ objects (list of data key-value pairs)\n5. Linked any data (except variant\
- \ and flow cytometry) objects (list of data key-value pairs)\n\n## Metadata\
- \ full-text queries\nSingle words can be supplied as is; otherwise, use speech\
- \ marks (`\"`) to quote queries that include whitespace. Speech marks and\
- \ backslash characters in the query need to be escaped with a backslash (`\\\
- `).\n\n## Metadata filters\nMetadata filters are key-value pairs joined by\
- \ an operator. The `=` operator matches literal values/string. The `!=` operator\
- \ matches anything except the literal value/string. The `<` or `>` operators\
- \ match numerical results that are less or greater than the supplied value.\
- \ Strings containing whitespace need to be quoted with (`\"`).\n\n## Data\
- \ queries\nData queries must be a list of key-value pairs, separated by whitespace.\
- \ The set of valid keys depends on the specific query type, and is documented\
- \ in the query parameter summary. The values can be simple non-whitespace\
- \ strings, or strings enclosed by speech marks (`\"`). Depending on the key,\
- \ the value may be be a comma-delimited list of string values. Others require\
- \ numerical values. Ranges can be supplied with `(0:1)` syntax, OR values\
- \ with `|`.\n\n## Combinations\nMetadata queries/filters for the same parameter\
- \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\
- \ to separate out the terms and operators. Parentheses `( )` can be used for\
- \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\
- \ (eg. GCT) can be queried via the useVersions parameter. Different versions\
- \ of an omics data file are associated via their CHAIN_ID metadata value.\
- \ This CHAIN_ID can be supplied to the useVersions parameter along with the\
- \ version number or specific omics data file accessions to include them in\
- \ the query. If nothing is supplied to the useVersions parameter then only\
- \ the active version (which is usually the last one imported) is queried.\
- \ This acts as a filter before the rest of the query is carried out.\n\nExample\
- \ usage:\nuseVersions=* (query all versions, including those without CHAIN_IDs)\n\
- useVersions=v2 (query the second version. If there is no second version then\
- \ the data file is not queried)\nuseVersions=v1,v0 (query the first version\
- \ and any data files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for\
- \ omics data files with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
- \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
- \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
- \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
- \ reasons this endpoint returns results in \"pages\" of limited size together\
- \ with a `cursor` tag. To retrieve the next page of results please supply\
- \ this `cursor` tag to resume the query from your previous result and get\
- \ the next page. To return all results iterate through pages using \
- \ cursor values until the `resultsExhausted` response field is true.\n\n"
- operationId: omicsSearchExpressionDataAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve data objects by searching across multiple data types
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/expression/group:
- get:
- description: |+
- Retrieve group objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchExpressionGroupsAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group objects by searching across multiple data types
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/expression/streamed-data:
- get:
- description: |+
- Stream data from a given group for a tabular file that matches a sample/library/preparations query/filter. If no query/filters are supplied all expression data is returned. If a metadata filter is specified, this endpoint will only return expression data that is associated with a sample via the Sample Source ID attribute.
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Libraries (full-text or metadata key-value pair)
- 3. Preparations (full-text or metadata key-value pair)
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- operationId: omicsSearchStreamedExpressionDataAsCurator
- parameters:
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `features.NAME=1007_s_at`\
- \ or `features.\"Average Mz\"=2.218`. As in the case of sample metadata\
- \ queries, single words can be supplied as is; otherwise, use speech marks\
- \ (`\"`) to quote queries that include whitespace. \n2. It is possible to\
- \ specify a set of possible values, separated by comma: `features.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`features.Name_1 > 3`: Select all rows where the\
- \ feature attribute Name_1 values are greater than 3. \n`features.Name_2\
- \ >= 6`: Select all rows where the feature attribute Name_2 values are greater\
- \ than or equal to 6. \n`-3 < features.Name_3 < 3`: Select all rows where\
- \ the feature attribute Name_3 values lie within the interval between -3\
- \ and 3. \n4. Use substring search to get the records where the attribute\
- \ field contains the provided substring: `features.attribute1 =~ \"some\
- \ text\"`. \n5. The first column for each original data file is identified\
- \ as feature accession (typically, it contains gene or protein names, accession\
- \ IDs, etc.). Searching by such feature accession would significantly outperform\
- \ more complex queries by combining the other feature attributes. To enable\
- \ such a search, use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`values.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < values.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`) logical operators and parentheses: \n\
- * `features.Name_1!=A`: Select all rows where Name_1 is not A. \n* `features.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `features.Name_1=A\
- \ AND features.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `features.Name_1=A && features.Name_2=B`: Equivalent to the example\
- \ above. \n* `features.Name_1=A OR features.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `features.Name_1=A || features.Name_2=B`:\
- \ Equivalent to the example above. \n* `features.Name_1=A AND (features.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Deprecated; use `exQuery` parameter instead. Filters results\
- \ by the feature column (e.g., Gene ID). The feature parameter value must\
- \ match the name of the identifier in the GCT file (under the NAME column).\
- \ Example: `ENSG00000077044`"
- explode: true
- in: query
- name: featureList
- schema:
- items:
- type: string
- example: KRAS
- type: array
- style: form
- - description: Accession of the expression group object (GCT)
- in: query
- name: groupAccession
- required: true
- schema:
- type: string
- - description: The number of digits after the decimal point for floating-point
- values. The final value is rounded up. Must be non-negative. The default
- is 4.
- in: query
- name: roundDigits
- schema:
- default: 4
- format: int32
- type: integer
- responses:
- "200":
- content:
- text/csv:
- schema:
- $ref: "#/components/schemas/StreamingOutput"
- description: Stream of retrieved Expression data.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Stream data from a given tabular file
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/flow-cytometry/data:
- get:
- description: |+
- Retrieve flow cytometry data objects whose linked data matches all supplied conditions.
-
- Note: A flow cytometry data query must be supplied.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchFlowCytometryDataAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve flow cytometry data objects by searching across multiple data
- types
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/flow-cytometry/group:
- get:
- description: |+
- Retrieve group objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchFlowCytometryGroupsAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group objects by searching across multiple data types
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/samples:
- get:
- description: |+
- Retrieve sample metadata objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchSamplesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata objects by searching across multiple data
- types
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/variant/data:
- get:
- description: |+
- Retrieve variant data objects whose linked data matches all supplied conditions.
-
- Note: A variant data query must be supplied.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked expression objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchVariantDataAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve variant data objects by searching across multiple data types
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/variant/group:
- get:
- description: |+
- Retrieve group objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchVariantGroupsAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: "Unique identifier (accession) of Reference Genome object."
- in: query
- name: referenceGenomeId
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group objects by searching across multiple data types
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/omics/variant/streamed-data:
- get:
- description: |+
- Stream data from a given group for a VCF file that matches a sample query/filter. If no query/filters are supplied all variant data is returned. If a metadata filter is specified, this endpoint will only return variant data that is associated with a sample via metadata attribute.
-
- ## Conditions
- It is possible to supply conditions for Samples (full-text or metadata key-value pair)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- operationId: omicsSearchStreamedVariantDataAsCurator
- parameters:
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `features.NAME=1007_s_at`\
- \ or `features.\"Average Mz\"=2.218`. As in the case of sample metadata\
- \ queries, single words can be supplied as is; otherwise, use speech marks\
- \ (`\"`) to quote queries that include whitespace. \n2. It is possible to\
- \ specify a set of possible values, separated by comma: `features.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`features.Name_1 > 3`: Select all rows where the\
- \ feature attribute Name_1 values are greater than 3. \n`features.Name_2\
- \ >= 6`: Select all rows where the feature attribute Name_2 values are greater\
- \ than or equal to 6. \n`-3 < features.Name_3 < 3`: Select all rows where\
- \ the feature attribute Name_3 values lie within the interval between -3\
- \ and 3. \n4. Use substring search to get the records where the attribute\
- \ field contains the provided substring: `features.attribute1 =~ \"some\
- \ text\"`. \n5. The first column for each original data file is identified\
- \ as feature accession (typically, it contains gene or protein names, accession\
- \ IDs, etc.). Searching by such feature accession would significantly outperform\
- \ more complex queries by combining the other feature attributes. To enable\
- \ such a search, use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`values.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < values.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`) logical operators and parentheses: \n\
- * `features.Name_1!=A`: Select all rows where Name_1 is not A. \n* `features.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `features.Name_1=A\
- \ AND features.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `features.Name_1=A && features.Name_2=B`: Equivalent to the example\
- \ above. \n* `features.Name_1=A OR features.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `features.Name_1=A || features.Name_2=B`:\
- \ Equivalent to the example above. \n* `features.Name_1=A AND (features.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: Accession of the variant group object (VCF)
- in: query
- name: groupAccession
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/StreamingOutput"
- description: Stream of retrieved Variant data.
- "400":
- content: { }
- description: Invalid data in request. See error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Stream data from a given VCF file
- tags:
- - Omics queries as Curator
- /api/v1/as-curator/integration/studies/{id}/tasks/publish-versions:
- post:
- description: This endpoint publishes information from staging and creates new
- metadata versions for the specified study and all associated objects. The
- version name is set to “Auto-published by API call”. Only curators with access
- to the specified studies can use this method.
- operationId: publishStudyByAccessionAsCurator
- parameters:
- - description: Supply the accession of the study to be published
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Supply text to name this version. If not supplied the version
- name is set to “Auto-published by API call”
- in: query
- name: versionMessage
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/TaskInfo"
- description: Task information.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "403":
- content: {}
- description: Forbidden
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Asynchronous task that publishes all pending versions for a single
- study.
- tags:
- - Metadata versioning as Curator
- /api/v1/as-curator/integration/studies/{id}/validation-summary:
- get:
- operationId: getStudyValidationSummary
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/StudyValidationSummary"
- description: Study validation result.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve validation summary by querying study ID (accession)
- tags:
- - Validation summary as Curator
- /api/v1/as-curator/integration/link/files/by/study/{id}:
- get:
- operationId: getFilesByStudyAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response.
- in: query
- name: includeContents
- required: false
- schema:
- default: false
- type: boolean
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/AFile"
- type: array
- text/tab-separated-values:
- schema:
- items:
- $ref: "#/components/schemas/AFile"
- type: array
- description: The request was successful. The returned value is a list of objects.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: Object with provided accession could not be found in ODM.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve file's metadata by study ID
- tags:
- - Files integration as Curator
- /api/v1/as-curator/integration/link/cell/group/{sourceId}/to/sample/group/{targetId}:
- post:
- description: |-
- Create links between cells and samples.
-
- Cell objects of the same group can be linked to sample objects from multiple sample groups, but only within the same study.
- operationId: createCellGroupSampleGroupLinkAsCurator
- parameters:
- - description: The ID (accession) of the cell group object
- in: path
- name: sourceId
- required: true
- schema:
- type: string
- - description: The ID (accession) of the sample group object
- in: path
- name: targetId
- required: true
- schema:
- type: string
- responses:
- "200":
- content: { }
- description: Cell objects have been partially linked to samples.
- "204":
- content: { }
- description: Cell objects have been fully linked to samples.
- "400":
- content: { }
- description: Sample group, cell group or samples to the link were not found.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Create links between cells and samples
- tags:
- - Cell integration as Curator
-components:
- schemas:
- AttributeInvalidValue:
- $ref: "./schemas/integration/AttributeInvalidValue.yaml"
- AttributeValidationSummary:
- $ref: "./schemas/integration/AttributeValidationSummary.yaml"
- BatchOfIds:
- $ref: "./schemas/integration/BatchOfIds.yaml"
- DataItem:
- $ref: "./schemas/integration/DataItem.yaml"
- DataPresentation:
- $ref: "./schemas/integration/DataPresentation.yaml"
- GroupValidationSummary:
- $ref: "./schemas/integration/GroupValidationSummary.yaml"
- IMetadata:
- $ref: "./schemas/integration/IMetadata.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- Library:
- $ref: "./schemas/library/Library.yaml"
- Link:
- $ref: "./schemas/integration/Link.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- MetadataContent:
- $ref: "./schemas/common/MetadataContent.yaml"
- MetadataPresentation:
- $ref: "./schemas/integration/MetadataPresentation.yaml"
- MetadataWithId:
- $ref: "./schemas/common/MetadataWithId.yaml"
- OmicsResponse:
- $ref: "./schemas/integration/OmicsResponse.yaml"
- OmicsResponseDataPresentation:
- $ref: "./schemas/integration/OmicsResponseDataPresentation.yaml"
- OmicsResponseMetadataPresentation:
- $ref: "./schemas/integration/OmicsResponseMetadataPresentation.yaml"
- OmicsResponseMetadataWithId:
- $ref: "./schemas/integration/OmicsResponseMetadataWithId.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- Preparation:
- $ref: "./schemas/preparation/Preparation.yaml"
- Relationships:
- $ref: "./schemas/integration/Relationships.yaml"
- SourceTypePair:
- $ref: "./schemas/integration/SourceTypePair.yaml"
- StreamingOutput:
- $ref: "./schemas/integration/StreamingOutput.yaml"
- Study:
- $ref: "./schemas/study/Study.yaml"
- StudyValidationSummary:
- $ref: "./schemas/integration/StudyValidationSummary.yaml"
- TaskInfo:
- $ref: "./schemas/tasks/TaskInfo.yaml"
- ValidationError:
- $ref: "./schemas/integration/ValidationError.yaml"
- SearchStudyRequest:
- $ref: "./schemas/integration/SearchStudyRequest.yaml"
- AppliedFilter:
- $ref: "./schemas/integration/AppliedFilter.yaml"
- PageRequest:
- $ref: "./schemas/integration/PageRequest.yaml"
- FindObjectsResponse:
- $ref: "./schemas/integration/FindObjectsResponse.yaml"
- ObjectsPage:
- $ref: "./schemas/integration/ObjectsPage.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- StudySearchInfo:
- $ref: "./schemas/integration/StudySearchInfo.yaml"
- MetainfoKeyForSummary:
- $ref: "./schemas/integration/MetainfoKeyForSummary.yaml"
- FilterOptionGroup:
- $ref: "./schemas/integration/FilterOptionGroup.yaml"
- FilterOption:
- $ref: "./schemas/integration/FilterOption.yaml"
- AFile:
- $ref: "./schemas/afile/AFile.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/integrationUser.yaml b/openapi/v1/integrationUser.yaml
deleted file mode 100644
index 547c191c..00000000
--- a/openapi/v1/integrationUser.yaml
+++ /dev/null
@@ -1,5194 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the integrationUser APIs for ODM. These are typically used to find and retrieve study, sample and processed (signal) data and metadata for a given query.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
-
- The server response will be in the section that follows.
- title: ODM Integration API
- version: default-released
-tags:
-- name: Expression integration as User
-- name: Files integration as User
-- name: Flow Cytometry (FACS) integration as User
-- name: Library integration as User
-- name: Linkage as User
-- name: Omics queries as User
-- name: Preparation integration as User
-- name: Sample integration as User
-- name: Study integration as User
-- name: Variant integration as User
-paths:
- /api/v1/as-user/data-types:
- get:
- description: This endpoint is for instructional uses and can be used to get
- the latest list of Data Types.
- operationId: getDataTypesAsUser
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- type: string
- type: array
- uniqueItems: true
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Lists all available data types.
- tags:
- - Linkage as User
- /api/v1/as-user/data-types/links:
- get:
- description: "This endpoint should be used for instructional needs, and can\
- \ be used in order to get the links between the Data Types."
- operationId: getDataTypesLinksAsUser
- parameters:
- - description: Return only links with the specified data type.
- in: query
- name: type
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/SourceTypePair"
- type: array
- uniqueItems: true
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: List all possible links between data types that match the specified
- criteria.
- tags:
- - Linkage as User
- /api/v1/as-user/integration/link/expression/by/library/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionByLibraryAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve expression run-level data by querying related library ID (accession)
- tags:
- - Expression integration as User
- /api/v1/as-user/integration/link/expression/by/preparation/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionByPreparationAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve expression run-level data by querying related preparation
- ID (accession)
- tags:
- - Expression integration as User
- /api/v1/as-user/integration/link/expression/by/sample/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionBySampleAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve expression run-level data by querying related sample ID (accession)
- tags:
- - Expression integration as User
- /api/v1/as-user/integration/link/expression/group/by/study/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- operationId: getExpressionGroupsByStudyAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Expression integration as User
- /api/v1/as-user/integration/link/expression/run-to-libraries/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionRunToLibraryPairsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-library pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Expression integration as User
- /api/v1/as-user/integration/link/expression/run-to-preparations/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionRunToPreparationPairsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-preparation pairs by group id. Pagination is based on\
- \ unique runs, not unique pairs."
- tags:
- - Expression integration as User
- /api/v1/as-user/integration/link/expression/run-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getExpressionRunToSamplePairsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Expression integration as User
- /api/v1/as-user/integration/link/flow-cytometry/by/sample/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getFlowCytometryBySampleAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve flow cytometry run-level data by querying related sample ID
- (accession)
- tags:
- - Flow Cytometry (FACS) integration as User
- /api/v1/as-user/integration/link/flow-cytometry/group/by/study/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- operationId: getFlowCytometryGroupsByStudyAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Flow Cytometry (FACS) integration as User
- /api/v1/as-user/integration/link/flow-cytometry/run-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getFlowCytometryRunToSamplePairsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Flow Cytometry (FACS) integration as User
- /api/v1/as-user/integration/link/libraries/by/samples:
- get:
- description: |+
- Retrieve library metadata objects whose linked sample metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getLibrariesBySamplesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve library metadata by querying related samples
- tags:
- - Library integration as User
- /api/v1/as-user/integration/link/library/by/sample/{id}:
- get:
- operationId: getLibraryBySampleAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/Library"
- type: array
- text/tab-separated-values:
- schema:
- items:
- $ref: "#/components/schemas/Library"
- type: array
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve library metadata by querying related sample ID (accession)
- tags:
- - Library integration as User
- /api/v1/as-user/integration/link/library/group/by/study/{id}:
- get:
- operationId: getLibraryGroupsByStudyAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Library integration as User
- /api/v1/as-user/integration/link/library/libraries-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getLibraryLinksToSamplesAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve library-samples pairs by group id. Pagination is based on\
- \ unique libraries, not unique pairs."
- tags:
- - Library integration as User
- /api/v1/as-user/integration/link/preparation/by/sample/{id}:
- get:
- operationId: getPreparationBySampleAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/Preparation"
- type: array
- text/tab-separated-values:
- schema:
- items:
- $ref: "#/components/schemas/Preparation"
- type: array
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve preparation metadata by querying related sample ID (accession)
- tags:
- - Preparation integration as User
- /api/v1/as-user/integration/link/preparation/group/by/study/{id}:
- get:
- operationId: getPreparationGroupsByStudyAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Preparation integration as User
- /api/v1/as-user/integration/link/preparation/preparations-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getPreparationLinksToSamplesAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ preparations, not unique pairs."
- tags:
- - Preparation integration as User
- /api/v1/as-user/integration/link/preparations/by/samples:
- get:
- description: |+
- Retrieve preparation metadata objects whose linked sample metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getPreparationsBySamplesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve preparation metadata by querying related samples
- tags:
- - Preparation integration as User
- /api/v1/as-user/integration/link/samples/by/libraries:
- get:
- description: |+
- Retrieve sample metadata objects whose linked library metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getSamplesByLibrariesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata by querying related libraries
- tags:
- - Sample integration as User
- /api/v1/as-user/integration/link/samples/by/preparations:
- get:
- description: |+
- Retrieve sample metadata objects whose linked preparation metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getSamplesByPreparationsAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata by querying related preparations
- tags:
- - Sample integration as User
- /api/v1/as-user/integration/link/samples/by/study/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getSamplesByStudyAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata by querying related study ID (accession)
- tags:
- - Sample integration as User
- /api/v1/as-user/integration/link/studies/by/libraries:
- get:
- description: |+
- Retrieve study metadata objects whose linked library metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesByLibrariesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related libraries
- tags:
- - Study integration as User
- /api/v1/as-user/integration/link/studies/by/preparations:
- get:
- description: |+
- Retrieve study metadata objects whose linked preparation metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesByPreparationsAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related preparations
- tags:
- - Study integration as User
- /api/v1/as-user/integration/link/studies/by/samples:
- get:
- description: |+
- Retrieve study metadata objects whose linked sample metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesBySamplesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by sample metadata (key-value metadata pair(s)). E.g.
- "Species or strain"="Homo sapiens"
- in: query
- name: filter
- schema:
- type: string
- - description: Search for study metadata objects via a full-text query over
- all sample metadata fields. E.g. "RNA-Seq of human dendritic cells". Queries
- matching dictionary terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related samples
- tags:
- - Study integration as User
- /api/v1/as-user/integration/link/study/by/sample/{id}:
- get:
- operationId: getStudyBySampleAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Study"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata by querying sample ID (accession)
- tags:
- - Study integration as User
- /api/v1/as-user/integration/link/studies/by/files:
- get:
- description: |+
- Retrieve study metadata objects whose linked attached files metadata matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Attachment files (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getStudiesByFilesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by attachment file metadata (key-value metadata pair(s)). E.g.
- "Species or strain"="Homo sapiens"
- in: query
- name: filter
- schema:
- type: string
- - description: Search for study metadata objects via a full-text query over
- all attached files metadata fields. E.g. "RNA-Seq of human dendritic cells". Queries
- matching dictionary terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata objects by querying related attachment files
- tags:
- - Study integration as User
- /api/v1/as-user/integration/link/study/by/file/{id}:
- get:
- operationId: getStudyByFileAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Study"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve study metadata by querying attachment file ID (accession)
- tags:
- - Study integration as User
- /api/v1/as-user/integration/fulltext/search/studies:
- post:
- description: |-
- Find studies and retrieve their data using full-text search or facet search by metadata of study itself or child object (samples, libraries, preparations, signal groups). Only studies available to that users are returned.
-
- The endpoint returns:
- - a list of studies with their metadata summary;
- - a list of filter objects with counts; filter list is the same for all users in an and can be configured in “Study Browser” application via "Configure facets" (by a user with corresponding permission); for each filter object, only the first 5 most popular facets are returned, the facts are sorted by the count value in descending order; only studies available to user are counted.
-
- Filter attributes for fulltext search:
- - `"type": "FULL_TEXT"`
- - `"match"`
- - `"mode"`
-
- For details on two latter ones, see the request body model. Only one filter with `"type=": "FULL_TEXT"` can be passed in the request body.
-
- To filter studies via facets, the filter attributes are necessary: type = SELECT, filterOptionId. For details, use the request body model. filterOptionId can be obtained from the response body when the endpoint is first called without filters. Multiple filters with type = SELECT can be passed in the request body. Filters within the same attribute are automatically used with the OR operator. Filters of different attributes are automatically used with the AND operator. This behaviour can not be changed.
-
- It is possible to call the endpoint without any filters, then all the studies available to the user are returned.
-
- The endpoint searches by staging version of the object metadata.
- operationId: searchStudiesByFilterAsUser
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/SearchStudyRequest"
- required: true
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/FindObjectsResponse"
- description: The request was successful. Retrieved studies and filters.
- "400":
- content: {}
- description: Invalid request body
- "401":
- content: {}
- description: User is not authenticated. Please supply a valid Genestack
- API token in the `Genestack-API-Token` HTTP header (this token may be
- obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Genestack-API-Token: []
- summary: Find and retrieve studies by full-text or facet query
- tags:
- - Study integration as User
- x-codegen-request-body-name: request
- /api/v1/as-user/integration/link/variant/by/sample/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getVariantBySampleAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve variant run-level data by querying related sample ID (accession)
- tags:
- - Variant integration as User
- /api/v1/as-user/integration/link/variant/group/by/study/{id}:
- get:
- description: |+
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- operationId: getVariantGroupsByStudyAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/MetadataWithId"
- type: array
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group metadata by querying study ID (accession)
- tags:
- - Variant integration as User
- /api/v1/as-user/integration/link/variant/run-to-samples/by/group/{id}:
- get:
- description: |+
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- operationId: getVariantRunToSamplePairsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Maximum number of results to return. This value must be between
- 0 and 2000 (inclusive).
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
- \ runs, not unique pairs."
- tags:
- - Variant integration as User
- /api/v1/as-user/links:
- get:
- description: Please make sure that this endpoint should be used only for getting
- all links to a specific object. In case you specify both firstId and secondId
- an expected answer would be true for existing links and false for no link
- between the objects.
- operationId: getLinksByParamsAsUser
- parameters:
- - description: Object ID (accession) (e.g. accession of study)
- in: query
- name: firstId
- required: true
- schema:
- type: string
- - description: Type of the object (e.g. study)
- in: query
- name: firstType
- schema:
- type: string
- - description: Object ID (accession) (e.g. accession of study)
- in: query
- name: secondId
- schema:
- type: string
- - description: Type of the object (e.g. study)
- in: query
- name: secondType
- schema:
- type: string
- - description: Param says to skip that many links before beginning to return
- links.
- in: query
- name: offset
- schema:
- default: 0
- format: int32
- type: integer
- - description: Param says to limit the count of returned links.
- in: query
- name: limit
- schema:
- default: 1000
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Finds existing links matching the specified criteria.
- tags:
- - Linkage as User
- /api/v1/as-user/links/get-batch:
- post:
- description: Please make sure to use that endpoint for batch calls only. You
- are not allowed to pass 'mixed' objects. e.g. Studies and Samples at the same
- time. Please always specify firstType.
- operationId: getLinksByIdsAsUser
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/BatchOfIds"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: Entities cannot be retrieved.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: "Finds existing links by passing many IDs. \nPagination goes through\
- \ all links matched the criteria."
- tags:
- - Linkage as User
- x-codegen-request-body-name: request
- /api/v1/as-user/omics/expression/data:
- get:
- description: "Retrieve any data objects whose linked data matches all supplied\
- \ conditions. \n\nNote: An expression data query must be supplied.\n\n## Conditions\n\
- It is possible to supply conditions for:\n\n1. Samples (full-text or metadata\
- \ key-value pair)\n2. Parent studies (full-text or metadata key-value pair)\n\
- 3. Linked variant objects (list of data key-value pairs)\n4. Linked flow cytometry\
- \ objects (list of data key-value pairs)\n5. Linked any data (except variant\
- \ and flow cytometry) objects (list of data key-value pairs)\n\n## Metadata\
- \ full-text queries\nSingle words can be supplied as is; otherwise, use speech\
- \ marks (`\"`) to quote queries that include whitespace. Speech marks and\
- \ backslash characters in the query need to be escaped with a backslash (`\\\
- `).\n\n## Metadata filters\nMetadata filters are key-value pairs joined by\
- \ an operator. The `=` operator matches literal values/string. The `!=` operator\
- \ matches anything except the literal value/string. The `<` or `>` operators\
- \ match numerical results that are less or greater than the supplied value.\
- \ Strings containing whitespace need to be quoted with (`\"`).\n\n## Data\
- \ queries\nData queries must be a list of key-value pairs, separated by whitespace.\
- \ The set of valid keys depends on the specific query type, and is documented\
- \ in the query parameter summary. The values can be simple non-whitespace\
- \ strings, or strings enclosed by speech marks (`\"`). Depending on the key,\
- \ the value may be be a comma-delimited list of string values. Others require\
- \ numerical values. Ranges can be supplied with `(0:1)` syntax, OR values\
- \ with `|`.\n\n## Combinations\nMetadata queries/filters for the same parameter\
- \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\
- \ to separate out the terms and operators. Parentheses `( )` can be used for\
- \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\
- \ (eg. GCT) can be queried via the useVersions parameter. Different versions\
- \ of an omics data file are associated via their CHAIN_ID metadata value.\
- \ This CHAIN_ID can be supplied to the useVersions parameter along with the\
- \ version number or specific omics data file accessions to include them in\
- \ the query. If nothing is supplied to the useVersions parameter then only\
- \ the active version (which is usually the last one imported) is queried.\
- \ This acts as a filter before the rest of the query is carried out.\n\nExample\
- \ usage:\nuseVersions=* (query all versions, including those without CHAIN_IDs)\n\
- useVersions=v2 (query the second version. If there is no second version then\
- \ the data file is not queried)\nuseVersions=v1,v0 (query the first version\
- \ and any data files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for\
- \ omics data files with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
- \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
- \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
- \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
- \ reasons this endpoint returns results in \"pages\" of limited size together\
- \ with a `cursor` tag. To retrieve the next page of results please supply\
- \ this `cursor` tag to resume the query from your previous result and get\
- \ the next page. To return all results iterate through pages using cursor \
- \ values until the `resultsExhausted` response field is true.\n\n"
- operationId: omicsSearchExpressionDataAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve data objects by searching across multiple data types
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/expression/group:
- get:
- description: |+
- Retrieve group objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchExpressionGroupsAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group objects by searching across multiple data types
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/expression/streamed-data:
- get:
- description: "Stream data from a given group for a tabular file that matches\
- \ a sample/library/preparations query/filter. If no query/filters are supplied\
- \ all expression data is returned. If a metadata filter is specified, this\
- \ endpoint will only return expression data that is associated with a sample\
- \ via the Sample Source ID attribute.\n## Conditions\nIt is possible to supply\
- \ conditions for:\n\n1. Samples (full-text or metadata key-value pair)\n2.\
- \ Libraries (full-text or metadata key-value pair)\n3. Preparations (full-text\
- \ or metadata key-value pair)\n## Metadata full-text queries\nSingle words\
- \ can be supplied as is; otherwise, use speech marks (`\"`) to quote queries\
- \ that include whitespace. Speech marks and backslash characters in the query\
- \ need to be escaped with a backslash (`\\`).\n\n## Metadata filters\nMetadata\
- \ filters are key-value pairs joined by an operator. The `=` operator matches\
- \ literal values/string. The `!=` operator matches anything except the literal\
- \ value/string. The `<` or `>` operators match numerical results that are\
- \ less or greater than the supplied value. Strings containing whitespace need\
- \ to be quoted with (`\"`).\n\n## Combinations\nMetadata queries/filters for\
- \ the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators,\
- \ using white-space to separate out the terms and operators. Parentheses `(\
- \ )` can be used for complex expressions.\n \n\n## Error Handling\n In case\
- \ of unexpected internal error during data retrieval, the last line of the\
- \ body will contain an error message, prefixed by the `#` character \n\n"
- operationId: omicsSearchStreamedExpressionDataAsUser
- parameters:
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g.`"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `features.NAME=1007_s_at`\
- \ or `features.\"Average Mz\"=2.218`. As in the case of sample metadata\
- \ queries, single words can be supplied as is; otherwise, use speech marks\
- \ (`\"`) to quote queries that include whitespace. \n2. It is possible to\
- \ specify a set of possible values, separated by comma: `features.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`features.Name_1 > 3`: Select all rows where the\
- \ feature attribute Name_1 values are greater than 3. \n`features.Name_2\
- \ >= 6`: Select all rows where the feature attribute Name_2 values are greater\
- \ than or equal to 6. \n`-3 < features.Name_3 < 3`: Select all rows where\
- \ the feature attribute Name_3 values lie within the interval between -3\
- \ and 3. \n4. Use substring search to get the records where the attribute\
- \ field contains the provided substring: `features.attribute1 =~ \"some\
- \ text\"`. \n5. The first column for each original data file is identified\
- \ as feature accession (typically, it contains gene or protein names, accession\
- \ IDs, etc.). Searching by such feature accession would significantly outperform\
- \ more complex queries by combining the other feature attributes. To enable\
- \ such a search, use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`values.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < values.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`) logical operators and parentheses: \n\
- * `features.Name_1!=A`: Select all rows where Name_1 is not A. \n* `features.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `features.Name_1=A\
- \ AND features.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `features.Name_1=A && features.Name_2=B`: Equivalent to the example\
- \ above. \n* `features.Name_1=A OR features.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `features.Name_1=A || features.Name_2=B`:\
- \ Equivalent to the example above. \n* `features.Name_1=A AND (features.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Deprecated; use `exQuery` parameter instead. Filters results\
- \ by the feature column (e.g., Gene ID). The feature parameter value must\
- \ match the name of the identifier in the GCT file (under the NAME column).\
- \ Example: `ENSG00000077044`"
- explode: true
- in: query
- name: featureList
- schema:
- items:
- type: string
- example: KRAS
- type: array
- style: form
- - description: Accession of the expression group object (GCT)
- in: query
- name: groupAccession
- required: true
- schema:
- type: string
- - description: The number of digits after the decimal point for floating-point
- values. The final value is rounded up. Must be non-negative. The default
- is 4.
- in: query
- name: roundDigits
- schema:
- default: 4
- format: int32
- type: integer
- responses:
- "200":
- content:
- text/csv:
- schema:
- $ref: "#/components/schemas/StreamingOutput"
- description: Stream of retrieved Expression data.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Stream data from a given tabular file
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/flow-cytometry/data:
- get:
- description: |+
- Retrieve flow cytometry data objects whose linked data matches all supplied conditions.
-
- Note: A flow cytometry data query must be supplied.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchFlowCytometryDataAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve flow cytometry data objects by searching across multiple data
- types
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/flow-cytometry/group:
- get:
- description: |+
- Retrieve group objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchFlowCytometryGroupsAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group objects by searching across multiple data types
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/samples:
- get:
- description: |+
- Retrieve sample metadata objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchSamplesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve sample metadata objects by searching across multiple data
- types
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/variant/data:
- get:
- description: |+
- Retrieve variant data objects whose linked data matches all supplied conditions.
-
- Note: A variant data query must be supplied.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked expression objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchVariantDataAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve variant data objects by searching across multiple data types
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/variant/group:
- get:
- description: |+
- Retrieve group objects whose linked data matches all supplied conditions.
-
- ## Conditions
- It is possible to supply conditions for:
-
- 1. Samples (full-text or metadata key-value pair)
- 2. Parent studies (full-text or metadata key-value pair)
- 3. Linked variant objects (list of data key-value pairs)
- 4. Linked flow cytometry objects (list of data key-value pairs)
- 5. Linked any data (except variant and flow cytometry) objects (list of data key-value pairs)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Data queries
- Data queries must be a list of key-value pairs, separated by whitespace. The set of valid keys depends on the specific query type, and is documented in the query parameter summary. The values can be simple non-whitespace strings, or strings enclosed by speech marks (`"`). Depending on the key, the value may be be a comma-delimited list of string values. Others require numerical values. Ranges can be supplied with `(0:1)` syntax, OR values with `|`.
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Versioning
- Specific versions of omics data files (eg. GCT) can be queried via the useVersions parameter. Different versions of an omics data file are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied to the useVersions parameter along with the version number or specific omics data file accessions to include them in the query. If nothing is supplied to the useVersions parameter then only the active version (which is usually the last one imported) is queried. This acts as a filter before the rest of the query is carried out.
-
- Example usage:
- useVersions=* (query all versions, including those without CHAIN_IDs)
- useVersions=v2 (query the second version. If there is no second version then the data file is not queried)
- useVersions=v1,v0 (query the first version and any data files without CHAIN_IDs(v0) )
- useVersions=GSVC002:v3 (for omics data files with a CHAIN_ID of GSCV002 query the third version)
- useVersions=GSVC002:GSF00494,GSF000496 (for omics data files with a CHAIN_ID of GSCV002 query only the specific accessions GSF00494 and GSF000496)
-
- Rules for multiple CHAIN_IDs can be supplied to the parameter using the ; separator.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size together with a cursor tag. To retrieve the next page of results please supply this cursor tag to resume the query from your previous result and get the next page. If there are no more results you will just retrieve an empty result. To return all results iterate through pages using cursor values until the `resultsExhausted` response field is true.
-
- operationId: omicsSearchVariantGroupsAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: |
- Filter by study metadata (key-value metadata pair(s)). E.g. `"Study Source"=ArrayExpress`
- in: query
- name: studyFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all study metadata
- fields. E.g. `"RNA-Seq of human dendritic cells"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: studyQuery
- schema:
- type: string
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: libraryFilter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: libraryQuery
- schema:
- type: string
- - description: Filter by preparation metadata (key-value metadata pair(s)).
- E.g. `Digestion=Trypsin`
- in: query
- name: preparationFilter
- schema:
- type: string
- - description: Search for preparation objects via a full-text query over all
- preparation metadata fields. E.g. `"reversed-phase liquid chromatography"`.
- Queries matching dictionary terms are automatically expanded to include
- synonyms.
- in: query
- name: preparationQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: "Filter by variant metadata (key-value metadata pair(s)). E.g.\
- \ `\"Variant Source\"=dbSNP`."
- in: query
- name: vxFilter
- schema:
- type: string
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `feature.NAME=1007_s_at`\
- \ or `feature.\"Average Mz\"=2.218`. As in the case of sample metadata queries,\
- \ single words can be supplied as is; otherwise, use speech marks (`\"`)\
- \ to quote queries that include whitespace. \n2. It is possible to specify\
- \ a set of possible values, separated by comma: `feature.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`feature.Name_1 > 3`: Select all rows where the feature\
- \ attribute Name_1 values are greater than 3. \n`feature.Name_2 >= 6`: Select\
- \ all rows where the feature attribute Name_2 values are greater than or\
- \ equal to 6. \n`-3 < feature.Name_3 < 3`: Select all rows where the feature\
- \ attribute Name_3 values lie within the interval between -3 and 3. \n4.\
- \ Use substring search to get the records where the attribute field contains\
- \ the provided substring: `feature.attribute1 =~ \"some text\"`. \n5. The\
- \ first column for each original data file is identified as feature accession\
- \ (typically, it contains gene or protein names, accession IDs, etc.). Searching\
- \ by such feature accession would significantly outperform more complex\
- \ queries by combining the other feature attributes. To enable such a search,\
- \ use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`value.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < value.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`), `NOT` (`!`) logical operators and parentheses: \n\
- * `NOT feature.Name_1=A`: Select all rows where Name_1 is not A. \n* `feature.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `feature.Name_1=A\
- \ AND feature.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `feature.Name_1=A && feature.Name_2=B`: Equivalent to the example\
- \ above. \n* `feature.Name_1=A OR feature.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `feature.Name_1=A || feature.Name_2=B`:\
- \ Equivalent to the example above. \n* `feature.Name_1=A AND (feature.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Filter by expression metadata (key-value metadata pair(s)).\
- \ E.g. `\"Genome Version\"=hg19-BROAD`."
- in: query
- name: exFilter
- schema:
- type: string
- - description: "Search for objects linked to flow cytometry data via data query\
- \ (key-value pair(s)). E.g. `ReadoutType=Median|Count` `CellPopulation=\"\
- CD45+, live\"` `MinValue=3.5`"
- in: query
- name: fxQuery
- schema:
- type: string
- - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
- \ E.g. `Organ=blood`."
- in: query
- name: fxFilter
- schema:
- type: string
- - description: "Unique identifier (accession) of Reference Genome object."
- in: query
- name: referenceGenomeId
- schema:
- type: string
- - description: |-
- Specify which versions of omics data files are used in the query. By default the active version is used. See Versioning above. Syntax:
-
- \* or `v` or ``:`v` or ``:``
- in: query
- name: useVersions
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: The page tag to resume results from (see paging above).
- in: query
- name: cursor
- schema:
- type: string
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/OmicsResponse"
- description: Omics query result.
- "400":
- content: {}
- description: Invalid data in request. See error message for details.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve group objects by searching across multiple data types
- tags:
- - Omics queries as User
- /api/v1/as-user/omics/variant/streamed-data:
- get:
- description: |+
- Stream data from a given group for a VCF file that matches a sample query/filter. If no query/filters are supplied all variant data is returned. If a metadata filter is specified, this endpoint will only return variant data that is associated with a sample via metadata attribute.
-
- ## Conditions
- It is possible to supply conditions for Samples (full-text or metadata key-value pair)
-
- ## Metadata full-text queries
- Single words can be supplied as is; otherwise, use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- operationId: omicsSearchStreamedVariantDataAsUser
- parameters:
- - description: |
- Filter by sample metadata (key-value metadata pair(s)). E.g. `"Species or strain"="Homo sapiens"`
- in: query
- name: sampleFilter
- schema:
- type: string
- - description: Search for objects via a full-text query over all sample metadata
- fields. E.g. `Clozapine`. Queries matching dictionary terms are automatically
- expanded to include synonyms.
- in: query
- name: sampleQuery
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: "Search for objects linked to expression data and originally\
- \ uploaded in TSV or GCT format via data query, e.g., `feature=ENSG00000230368,ENSG00000188976\
- \ value>=1.50`\n For the case when the original data is represented by multiple\
- \ attributes per feature scenarios, extended filtering syntax is as follows:\
- \ \n1. By feature attribute value for numeric and string attributes: `features.NAME=1007_s_at`\
- \ or `features.\"Average Mz\"=2.218`. As in the case of sample metadata\
- \ queries, single words can be supplied as is; otherwise, use speech marks\
- \ (`\"`) to quote queries that include whitespace. \n2. It is possible to\
- \ specify a set of possible values, separated by comma: `features.NAME=1007_s_at,121_at`.\
- \ \n3. Utilize range filters to search numeric attributes. Apply `<` (less\
- \ than), `>` (greater than), and `=` (equal to) symbols to specify the desired\
- \ ranges as follows: \n`features.Name_1 > 3`: Select all rows where the\
- \ feature attribute Name_1 values are greater than 3. \n`features.Name_2\
- \ >= 6`: Select all rows where the feature attribute Name_2 values are greater\
- \ than or equal to 6. \n`-3 < features.Name_3 < 3`: Select all rows where\
- \ the feature attribute Name_3 values lie within the interval between -3\
- \ and 3. \n4. Use substring search to get the records where the attribute\
- \ field contains the provided substring: `features.attribute1 =~ \"some\
- \ text\"`. \n5. The first column for each original data file is identified\
- \ as feature accession (typically, it contains gene or protein names, accession\
- \ IDs, etc.). Searching by such feature accession would significantly outperform\
- \ more complex queries by combining the other feature attributes. To enable\
- \ such a search, use `feature` without any attribute extension, e.g., `feature=ENSG00000230368,ENSG00000188976`.\n\
- \ \nThe `value` keyword can be used to select rows where the sample (library\
- \ or preparation) measurements has values from a certain range. Examples:\
- \ `value = 3`, `value > 3`, `-3 < value < 3`. When the original data contains\
- \ multiple measurements for a single item, such as a sample (library or\
- \ preparation), use the measurement name to specify the exact column type,\
- \ e.g.: \n1. `value.intensity = 3`: Selects all rows where the measurement\
- \ attribute intensity equals 3. \n `value.intensity != 2,null`: Select all\
- \ rows where the measurement attribute intensity is not equal 2 and is not\
- \ an empty value. \n`values.p_value > 3`: Selects all rows where the measurement\
- \ attribute 'p_value' values are greater than 3. \n`-3 < values.FC < 3`:\
- \ Selects all rows where the measurement attribute 'FC' values lie within\
- \ the interval between -3 and 3.\n \n2. Note: The `MinValue` keyword has\
- \ been deprecated and should be replaced with the aforementioned comparisons.\n\
- \ \nCombine multiple filters for different feature attributes and measurements\
- \ using `AND` (`&&`), `OR` (`||`) logical operators and parentheses: \n\
- * `features.Name_1!=A`: Select all rows where Name_1 is not A. \n* `features.Name_1!=A,B,C`:\
- \ Select all rows where Name_1 is not A, B, or C. \n* `features.Name_1=A\
- \ AND features.Name_2=B`: Select all rows where Name_1 is A and Name_2 is\
- \ B. \n* `features.Name_1=A && features.Name_2=B`: Equivalent to the example\
- \ above. \n* `features.Name_1=A OR features.Name_2=B`: Select all rows where\
- \ Name_1 is A or Name_2 is B. \n* `features.Name_1=A || features.Name_2=B`:\
- \ Equivalent to the example above. \n* `features.Name_1=A AND (features.Name_2=B\
- \ OR value>=1.0)`: Select all rows where Name_1 is A and either Name_2 is\
- \ B or minimal possible measurement value is 1.0."
- in: query
- name: exQuery
- schema:
- type: string
- - description: "Search for objects linked to variant data by SNPs properties. Filtering is currently supported by `filter`, `id`, `region` and `info` keywords,
- as well as `exists` keyword for `INFO` field and their logical combinations by means of `not` (`!`), `and` (`&&`), and `or` (`||`) operators with standard boolean precedence. Keyword case is ignored.\n
- * `filter` corresponds to the `FILTER` column in the original vcf file. Could be either equals or not equals to `PASS` : `filter = PASS`
- or `filter != pass`.\n
- * `id` is a string value that corresponds to the `ID` column. Multiple values could be added via a comma. Expression `id = rs3214,rg1234` is equivalent
- to `id = rs3214 or id = rg1234`.\n
- * `region` corresponds to CHROM and POS columns. Supports querying by the whole chromosome `region = chr1` , by interval within a chromosome
- `region = chr1:4567-9876543` by exact position `region = chr1:456789` or by indefinite ranges like `region = x:3456789-*` . Multiple regions could be
- separated via comma, e.g. `region = chr1:34567-98767,chr3` is equivalent to `region = chr1:34567-98767 or region = chr3`.\n
- * `feature` is the name of the reference gene associated with a specific location in the reference genome which corresponds to the VCF file (variant group) from which the variant information is derived.
- By providing the gene name(s), such as `feature=TP53` or `feature=TP53,TGFB`, variants located within the same genomic region as the specified gene(s) will be retrieved.\n
- * Filter by vcf `INFO` fields. E.g. to filter all variants annotated in dbSNP add `exists(INFO.KEY)`. Use `!exists(INFO.KEY)` to exclude variants having the key from the search results.
- Provide `info.key=value` pair to search for an exact match or `info.key!=value` to exclude it from the search. Due to the limits of precision in floating point numbers,
- we use a small range of 0.0000001 to identify close matches. This means any differences smaller than that won't be detected. For more precise results, please use range queries."
- in: query
- name: vxQuery
- schema:
- type: string
- - description: Accession of the variant group object (VCF)
- in: query
- name: groupAccession
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/StreamingOutput"
- description: Stream of retrieved Variant data.
- "400":
- content: { }
- description: Invalid data in request. See error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Stream data from a given VCF file
- tags:
- - Omics queries as User
- /api/v1/as-user/integration/link/files/by/study/{id}:
- get:
- operationId: getFilesByStudyAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Select `true` in order to include file structure (contents) for .h5, .h5ad, .zip, .gz to the response.
- in: query
- name: includeContents
- required: false
- schema:
- default: false
- type: boolean
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/AFile"
- type: array
- text/tab-separated-values:
- schema:
- items:
- $ref: "#/components/schemas/AFile"
- type: array
- description: The request was successful. The returned value is a list of objects.
- "400":
- content: { }
- description: Invalid data in the request. See the error message for details.
- "401":
- content: { }
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: { }
- description: Object with provided accession could not be found in ODM.
- "500":
- content: { }
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Retrieve file's metadata by study ID
- tags:
- - Files integration as User
-components:
- schemas:
- BatchOfIds:
- $ref: "./schemas/integration/BatchOfIds.yaml"
- DataItem:
- $ref: "./schemas/integration/DataItem.yaml"
- DataPresentation:
- $ref: "./schemas/integration/DataPresentation.yaml"
- IMetadata:
- $ref: "./schemas/integration/IMetadata.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- Library:
- $ref: "./schemas/library/Library.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- MetadataContent:
- $ref: "./schemas/common/MetadataContent.yaml"
- MetadataPresentation:
- $ref: "./schemas/integration/MetadataPresentation.yaml"
- MetadataWithId:
- $ref: "./schemas/common/MetadataWithId.yaml"
- OmicsResponse:
- $ref: "./schemas/integration/OmicsResponse.yaml"
- OmicsResponseDataPresentation:
- $ref: "./schemas/integration/OmicsResponseDataPresentation.yaml"
- OmicsResponseMetadataPresentation:
- $ref: "./schemas/integration/OmicsResponseMetadataPresentation.yaml"
- OmicsResponseMetadataWithId:
- $ref: "./schemas/integration/OmicsResponseMetadataWithId.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- Preparation:
- $ref: "./schemas/preparation/Preparation.yaml"
- Relationships:
- $ref: "./schemas/integration/Relationships.yaml"
- SourceTypePair:
- $ref: "./schemas/integration/SourceTypePair.yaml"
- StreamingOutput:
- $ref: "./schemas/integration/StreamingOutput.yaml"
- Study:
- $ref: "./schemas/study/Study.yaml"
- SearchStudyRequest:
- $ref: "./schemas/integration/SearchStudyRequest.yaml"
- AppliedFilter:
- $ref: "./schemas/integration/AppliedFilter.yaml"
- PageRequest:
- $ref: "./schemas/integration/PageRequest.yaml"
- FindObjectsResponse:
- $ref: "./schemas/integration/FindObjectsResponse.yaml"
- ObjectsPage:
- $ref: "./schemas/integration/ObjectsPage.yaml"
- StudySearchInfo:
- $ref: "./schemas/integration/StudySearchInfo.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- MetainfoKeyForSummary:
- $ref: "./schemas/integration/MetainfoKeyForSummary.yaml"
- FilterOptionGroup:
- $ref: "./schemas/integration/FilterOptionGroup.yaml"
- FilterOption:
- $ref: "./schemas/integration/FilterOption.yaml"
- AFile:
- $ref: "./schemas/afile/AFile.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/job.yaml b/openapi/v1/job.yaml
deleted file mode 100644
index f92f5296..00000000
--- a/openapi/v1/job.yaml
+++ /dev/null
@@ -1,827 +0,0 @@
-openapi: 3.1.0
-info:
- description: |
-
- These API endpoints serve to start, control, monitor and retrieve results for a set of available Genestack jobs.
-
- A job is an arbitrary process that, once started, runs asynchronously in the background.
- Upon starting a job the user receives a job execution identifier (`jobExecId`) that they can use to control and monitor the job and to retrieve the job result (output).
-
- #### Basic workflow:
-
- Start a job (POST endpoints) to return a `jobExecId`
- Periodically poll the `GET /{jobExecId}/output` endpoint to get the job status for a given `jobExecId`
- When the status is `COMPLETED` or `FAILED`, queries to the `GET /{jobExecId}/output` endpoint will also contain any output (result/errors)
-
- To retrieve more information about a job, such as start time etc., use the `GET /{jobExecId}/info` endpoint.
-
- #### Available statuses:
-
- - `STARTING`: initial job status
- - `RUNNING`: the job has successfully started and is running
- - `COMPLETED` (terminal): the job has completed and the result is available in the `GET /{jobExecId}/output` response
- - `FAILED` (terminal): the job has failed, you can extract errors from the `GET /{jobExecId}/output` response
- - `STOPPING`: a stop request has been initiated, the job is in the process of stopping
- - `STOPPED` (terminal): the job has been stopped (it may be able to be restarted)
- - `ABANDONED` (terminal): the job has been abandoned for an unknown reason, please contact your system administrator.
- - `UNKNOWN`: the job status is unknown, please contact your system administrator.
- title: Job API
- version: default-released
-tags:
-- name: Data import jobs
-- name: Data import via direct file upload
-- name: Job operations
-paths:
- /api/v1/jobs/import/study:
- post:
- description: |2
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportStudy
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportMetadataRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import study metadata from a TSV file
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/samples:
- post:
- description: |2
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportSamples
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportMetadataRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import a group of sample metadata objects from a TSV file
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/samples/multipart:
- post:
- description: |2
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportSamplesMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportMetadataFromMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import a group of sample metadata objects from a TSV file via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/import/libraries:
- post:
- description: |2
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportLibraries
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportMetadataRequest"
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportMetadataFromMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Import a group of library metadata objects from a TSV file
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/libraries/multipart:
- post:
- description: |2
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportLibrariesMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportMetadataFromMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import a group of library metadata objects from a TSV file via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/import/preparations:
- post:
- description: |2
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportPreparations
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportMetadataRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Import a group of preparation metadata objects from a TSV file
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/preparations/multipart:
- post:
- description: |2
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportPreparationsMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportMetadataFromMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import a group of preparation metadata objects from a TSV file via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/import/cells:
- post:
- description: |2
-
- The endpoint initiates a job to import cell data and creates a Cell Group to manage it.
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportCells
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportCellsRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Import a group of cell data objects from a TSV file
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/cells/multipart:
- post:
- description: |2
-
- The endpoint initiates a job to import cell data and creates a Cell Group to manage it.
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportCellsMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportCellsFromMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import a group of cell data objects from a TSV file via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/import/expression:
- post:
- description: |-
- ## Data
- This operation necessitates the URL of a tabular data file, which must be either in TSV or GCT 1.2 format. Consult the user guide for a comprehensive understanding of the file content requirements. The endpoint is capable of handling uploads of any data type, which can be detailed in the parameters section, not only Gene Expression data.
-
- ## Metadata
- It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file.
- ## Metadata file format
- * Extension: any, `.zip` and `.gz` extensions are treated as archives and get decompressed
- * Format: plain text, Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`)
- * Header: the first line is treated as table header that contains attribute names
- * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice.
- * Skip zeros in original data file: If this option is selected, zeros in the file will be ignored, thus conserving time and space. This option is particularly useful for handling very sparse data such as Single Cell data.
- operationId: startImportExpression
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportExpressionSignalRunRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import any tabular data from TSV or GCT files
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/expression/multipart:
- post:
- description: |-
- ## Data
- This operation necessitates the URL of a tabular data file, which must be either in TSV or GCT 1.2 format. Consult the user guide for a comprehensive understanding of the file content requirements. The endpoint is capable of handling uploads of any data type, which can be detailed in the parameters section, not only Gene Expression data.
-
- ## Metadata
- It is also possible to optionally supply the URL of a metadata file. This metadata will be used as the original metadata for the created objects. The file is expected to contain single record with metadata describing the uploaded signal file.
- ## Metadata file format
- * Extension: any, `.zip` and `.gz` extensions are treated as archives and get decompressed
- * Format: plain text, Tab-separated format (TSV), attribute names and record values are separated with tabs (`U+0009`), lines are separated with `CRLF` sequence (`U+000D U+000A`)
- * Header: the first line is treated as table header that contains attribute names
- * Records: the second line contains the values for each of the attributes described in the header line. Values represent single string or list of strings. List values are separated using the "pipe" `|` (`U+007C`) separator. Values are trimmed of whitespace before parsing, and a literal `|` (`U+007C`) character may be escaped by repeating it twice.
- * Skip zeros in original data file: If this option is selected, zeros in the file will be ignored, thus conserving time and space. This option is particularly useful for handling very sparse data such as Single Cell data.
- operationId: startImportExpressionMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportExpressionSignalRunFromMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import any tabular data from TSV or GCT files via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/import/variant:
- post:
- description: "\nWhen job finishes successfully the following **result** object\
- \ can be obtained using `GET /job/{id}/output` request:\n\n```\n{\n \"\
- groupAccession\": \"GSF1234567\"\n}\n```\n "
- operationId: startImportVariant
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportSignalRunRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Import variation data and metadata from VCF and TSV files
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/variant/multipart:
- post:
- description: "\nWhen job finishes successfully the following **result** object\
- \ can be obtained using `GET /job/{id}/output` request:\n\n```\n{\n \"\
- groupAccession\": \"GSF1234567\"\n}\n```\n "
- operationId: startImportVariantMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportSignalRunFomMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import variation data and metadata from VCF and TSV files via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/import/flow-cytometry:
- post:
- description: |-
- This operation necessitates the URL of a gated flow cytometry data file, which must be in FACS format.
- Consult the user guide for a comprehensive understanding of the file content requirements.
- For flow cytometry data in FCS format use expression endpoint.
-
- When job finishes successfully the following **result** object
- can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportFlowCytometry
- parameters:
- - description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to\
- \ load this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportSignalRunRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import flow-cytometry data and metadata from FACS and TSV files
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/flow-cytometry/multipart:
- post:
- description: |-
- This operation necessitates the URL of a gated flow cytometry data file, which must be in FACS format.
- Consult the user guide for a comprehensive understanding of the file content requirements.
- For flow cytometry data in FCS format use expression endpoint.
-
- When job finishes successfully the following **result** object
- can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "groupAccession": "GSF1234567"
- }
- ```
- operationId: startImportFlowCytometryMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportSignalRunFomMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import flow-cytometry data and metadata from FACS and TSV files via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/import/file:
- post:
- description: |-
- In order to import a file as an attachment to a study, please fill in the following fields:
-
- * `source` - The source parameter is ignored and will be removed in version 1.61. The source is automatically extracted from the link.
- * `dataLink` - a link to a file to import as an attachment.
- The file will be associated with a study and will be searchable by its name and metadata.
- * `metadataLink` - an optional URL of a metadata file to be used as the original metadata
- for the created objects. The file must contain a single record describing the uploaded attachment.
- * `studyAccession` - an accession of a study the file will be associated with.
- * `dataClass` - file data class with the following possible values: `Bulk
- transcriptomics`, `Single-cell transcriptomics`, `Differential abundance (FC,
- pval, etc.)`, `Pathway analysis`, `Proteomics`, `Single-cell proteomics`, `Metabolomics`,
- `Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`, `Imaging features`,
- `Gene panel data`, `Biomarker data`, `Physical measures`, `Blood counts`, `Other body
- fluid counts`, `Nanopore`, `Flow Cytometry (FCS)`, `Document`, `Other`.
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "accession": "GSF1234567"
- }
- ```
- operationId: startImportAFile
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ImportAFileRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Import file as an attachment
- tags:
- - Data import jobs
- x-codegen-request-body-name: body
- /api/v1/jobs/import/file/multipart:
- post:
- description: |-
- In order to import a file as an attachment to a study, please fill in the following fields:
-
- * `data` - a file to import as an attachment.
- The file will be associated with a study and will be searchable by its name and metadata.
- * `metadata` - an optional metadata file to be used as the original metadata
- for the created objects. The file must contain a single record describing the uploaded attachment.
- * `studyAccession` - an accession of a study the file will be associated with.
- * `dataClass` - file data class with the following possible values: `Bulk
- transcriptomics`, `Single-cell transcriptomics`, `Differential abundance (FC,
- pval, etc.)`, `Pathway analysis`, `Proteomics`, `Single-cell proteomics`, `Metabolomics`,
- `Lipidomics`, `Epigenomics`, `DNA methylation`, `Chemoinformatics`, `Imaging features`,
- `Gene panel data`, `Biomarker data`, `Physical measures`, `Blood counts`, `Other body
- fluid counts`, `Nanopore`, `Flow Cytometry (FCS)`, `Document`, `Other`.
-
- When job finishes successfully the following **result** object can be obtained using `GET /job/{id}/output` request:
-
- ```
- {
- "accession": "GSF1234567"
- }
- ```
- operationId: startImportAFileMultipart
- requestBody:
- content:
- multipart/form-data:
- schema:
- $ref: "#/components/schemas/ImportAFileFromMultipartRequest"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: [ ]
- - Genestack-API-Token: [ ]
- summary: Import file as an attachment via multipart/form-data upload
- tags:
- - Data import via direct file upload
- x-codegen-request-body-name: body
- /api/v1/jobs/{jobExecId}/info:
- get:
- operationId: info
- parameters:
- - in: path
- name: jobExecId
- required: true
- schema:
- format: int64
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: get information about one particular job execution
- tags:
- - Job operations
- /api/v1/jobs/{jobExecId}/output:
- get:
- operationId: output
- parameters:
- - in: path
- name: jobExecId
- required: true
- schema:
- format: int64
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Output"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: retrieve job output (result)
- tags:
- - Job operations
- /api/v1/jobs/{jobExecId}/restart:
- put:
- operationId: restart
- parameters:
- - in: path
- name: jobExecId
- required: true
- schema:
- format: int64
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: restart stopped (failed) job
- tags:
- - Job operations
- /api/v1/jobs/{jobExecId}/stop:
- put:
- operationId: stop
- parameters:
- - in: path
- name: jobExecId
- required: true
- schema:
- format: int64
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Info"
- description: successful operation
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: stop running job
- tags:
- - Job operations
-components:
- parameters:
- AllowDuplicates:
- description: "Load duplicate data: the data from the link(s) has already been\
- \ previously loaded into ODM, and for **testing purposes**, you need to load\
- \ this data again."
- in: query
- name: allow_dups
- schema:
- default: false
- type: boolean
- schemas:
- ExceptionTypeAndMessage:
- $ref: "./schemas/job/ExceptionTypeAndMessage.yaml"
- ImportCellsRequest:
- $ref: "./schemas/job/ImportCellsRequest.yaml"
- ImportCellsFromMultipartRequest:
- $ref: "./schemas/job/ImportCellsFromMultipartRequest.yaml"
- ImportMetadataRequest:
- $ref: "./schemas/job/ImportMetadataRequest.yaml"
- ImportMetadataFromMultipartRequest:
- $ref: "./schemas/job/ImportMetadataFromMultipartRequest.yaml"
- ImportSignalRunRequest:
- $ref: "./schemas/job/ImportSignalRunRequest.yaml"
- ImportSignalRunFomMultipartRequest:
- $ref: "./schemas/job/ImportSignalRunFomMultipartRequest.yaml"
- ImportExpressionSignalRunRequest:
- $ref: "./schemas/job/ImportExpressionSignalRunRequest.yaml"
- ImportExpressionSignalRunFromMultipartRequest:
- $ref: "./schemas/job/ImportExpressionSignalRunFromMultipartRequest.yaml"
- ImportAFileRequest:
- $ref: "./schemas/job/ImportAFileRequest.yaml"
- ImportAFileFromMultipartRequest:
- $ref: "./schemas/job/ImportAFileFromMultipartRequest.yaml"
- Info:
- $ref: "./schemas/job/Info.yaml"
- JobRuntimeError:
- $ref: "./schemas/job/JobRuntimeError.yaml"
- Output:
- $ref: "./schemas/job/Output.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/libraryCurator.yaml b/openapi/v1/libraryCurator.yaml
deleted file mode 100644
index 832d2ccd..00000000
--- a/openapi/v1/libraryCurator.yaml
+++ /dev/null
@@ -1,470 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the libraryCurator APIs.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
- The server response will be in the section that follows.
- title: ODM API
- version: default-released
-tags:
-- name: Library SPoT as Curator
-paths:
- /api/v1/as-curator/libraries:
- get:
- description: |-
- Retrieve library metadata objects by searching/listing library metadata.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- ## List operation
-
- This endpoint can be called with no `query` parameter. Doing so returns a list of all variant objects.
- operationId: searchLibrariesAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: |-
- Attribute to sort by, with optional ascending/descending marker, of the form `"[+|-]"`.
-
- No marker or `"+"` indicates ascending sort, and `"-"` indicates descending sort.
-
- *Default:* sort by ID in ascending order.
- in: query
- name: sort
- schema:
- enum:
- - id
- - creation
- - last_update
- - name
- - +id
- - +creation
- - +last_update
- - +name
- - -id
- - -creation
- - -last_update
- - -name
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: List or search for library metadata objects
- tags:
- - Library SPoT as Curator
- /api/v1/as-curator/libraries/by/group/{id}:
- get:
- operationId: getLibrariesByGroupAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve libraries related to the given group
- tags:
- - Library SPoT as Curator
- /api/v1/as-curator/libraries/{id}:
- get:
- operationId: getLibraryAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Library"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single library object by ID (accession)
- tags:
- - Library SPoT as Curator
- patch:
- description: |-
- ## Basic operation
- The object metadata is updated using the supplied map of attribute names to attribute values. There are three cases:
- 1. The attribute name does not already exist in the object metadata. In this case, the attribute and value are added to the object metadata.
- 2. The attribute name already exists in the object metadata. In this case, the value is updated.
- 3. The attribute value is `null`.In this case, the attribute is removed from the object metadata.
-
- ## Attribute values
- The attribute values are intelligently parsed as booleans, integers, etc.
- operationId: updateLibraryAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- requestBody:
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/MetadataContent"
- description: "Metadata in the form of `{key: value, key2: value2, ...}`"
- required: false
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Library"
- description: "The objects was successfully created. The returned value is\
- \ the updated object, along with any warnings."
- "400":
- content: {}
- description: The supplied object ID or metadata is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Update a library object
- tags:
- - Library SPoT as Curator
- x-codegen-request-body-name: body
- /api/v1/as-curator/libraries/{id}/versions:
- get:
- operationId: getLibraryVersionsAsCurator
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/CommitInfo"
- type: array
- description: The request was successful. The returned value is the list
- of object versions.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a list of object versions by ID
- tags:
- - Library SPoT as Curator
- /api/v1/as-curator/libraries/{id}/versions/{version}:
- get:
- operationId: getLibraryByVersionAsCurator
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Unique version of the object.
- in: path
- name: version
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Library"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single library object by ID (accession)
- tags:
- - Library SPoT as Curator
-components:
- schemas:
- CommitInfo:
- $ref: "./schemas/common/CommitInfo.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- Library:
- $ref: "./schemas/library/Library.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- MetadataContent:
- $ref: "./schemas/common/MetadataContent.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/libraryUser.yaml b/openapi/v1/libraryUser.yaml
deleted file mode 100644
index d5ed6482..00000000
--- a/openapi/v1/libraryUser.yaml
+++ /dev/null
@@ -1,413 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the libraryUser API endpoints for ODM. These are typically used to find and retrieve library metadata.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
-
- The server response will be in the section that follows.
- title: ODM API
- version: default-released
-tags:
-- name: Library SPoT as User
-paths:
- /api/v1/as-user/libraries:
- get:
- description: |-
- Retrieve library metadata objects by searching/listing library metadata.
-
- ## Metadata full-text queries
- Single words can be supplied as is, otherwise use speech marks (`"`) to quote queries that include whitespace. Speech marks and backslash characters in the query need to be escaped with a backslash (`\`).
-
- ## Metadata filters
- Metadata filters are key-value pairs joined by an operator. The `=` operator matches literal values/string. The `!=` operator matches anything except the literal value/string. The `<` or `>` operators match numerical results that are less or greater than the supplied value. Strings containing whitespace need to be quoted with (`"`).
-
- ## Combinations
- Metadata queries/filters for the same parameter can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space to separate out the terms and operators. Parentheses `( )` can be used for complex expressions.
-
- ## Paging
- For performance reasons this endpoint returns results in "pages" of limited size. In order to retrieve all matching results the client needs to request multiple pages starting from an offset to the first result. You can do this using the pageOffset query parameter. A value of 0 (the default) instructs the server to return the first page of results, 100 would return a page of results starting from the 101st result and so on. To retrieve all results, iterate through pages using `pageOffset` values of `n * pageLimit` until a page returns fewer results than the page limit, which indicates there are no more results.
-
- ## List operation
-
- This endpoint can be called with no `query` parameter. Doing so returns a list of all variant objects.
- operationId: searchLibrariesAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Filter by library metadata (key-value metadata pair(s)). E.g.
- `"Library Type"=RNA-Seq-1`
- in: query
- name: filter
- schema:
- type: string
- - description: Search for library objects via a full-text query over all library
- metadata fields. E.g. `"illumina HiSeq500"`. Queries matching dictionary
- terms are automatically expanded to include synonyms.
- in: query
- name: query
- schema:
- type: string
- - description: |-
- If the full-text query term is present in an ODM dictionary, enabling this parameter will modify the query to include child terms of the full-text query.
-
- For example, the search query "Body fluid" can be expanded to include the term "Blood" (a child term of "Body fluid") so files containing either "Body fluid" or "Blood" in their metadata will be returned in the search results.
-
- The parent-child relationship is defined by the key "broaders" or "subClassOf" in the dictionary.
-
- If the full query term is not present in a dictionary then this parameter has no effect.
- in: query
- name: searchSpecificTerms
- schema:
- type: boolean
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: |-
- Attribute to sort by, with optional ascending/descending marker, of the form `"[+|-]"`.
-
- No marker or `"+"` indicates ascending sort, and `"-"` indicates descending sort.
-
- *Default:* sort by ID in ascending order.
- in: query
- name: sort
- schema:
- enum:
- - id
- - creation
- - last_update
- - name
- - +id
- - +creation
- - +last_update
- - +name
- - -id
- - -creation
- - -last_update
- - -name
- type: string
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- text/tab-separated-values:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: List or search for library metadata objects
- tags:
- - Library SPoT as User
- /api/v1/as-user/libraries/by/group/{id}:
- get:
- operationId: getLibrariesByGroupAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- - description: "Show the page {pageOffset+1} results from the start of the results.\
- \ E.g. 100 will show a page of results starting from the 101st result.\
- \ The default value is 0."
- in: query
- name: pageOffset
- schema:
- format: int32
- type: integer
- - description: Maximum number of results to return per page (see Paging above).
- This value must be between 0 and 2000 (inclusive). The default is 2000.
- in: query
- name: pageLimit
- schema:
- format: int32
- type: integer
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/ListResponse"
- description: The request was successful. The returned value is a list of
- objects.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve libraries related to the given group
- tags:
- - Library SPoT as User
- /api/v1/as-user/libraries/{id}:
- get:
- operationId: getLibraryAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Library"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single library object by ID (accession)
- tags:
- - Library SPoT as User
- /api/v1/as-user/libraries/{id}/versions:
- get:
- operationId: getLibraryVersionsAsUser
- parameters:
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/CommitInfo"
- type: array
- description: The request was successful. The returned value is the list
- of object versions.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a list of object versions by ID
- tags:
- - Library SPoT as User
- /api/v1/as-user/libraries/{id}/versions/{version}:
- get:
- operationId: getLibraryByVersionAsUser
- parameters:
- - description: Supply this parameter with the value `term_id` as part of the
- query to return extended information including IDs for values and dictionaries.
- in: query
- name: responseFormat
- schema:
- $ref: "#/components/schemas/ResponseFormat"
- - description: Unique identifier (accession) of the object.
- in: path
- name: id
- required: true
- schema:
- type: string
- - description: Unique version of the object.
- in: path
- name: version
- required: true
- schema:
- type: string
- - description: |-
- The parameter defines amount of metadata attributes to return:
-
- 1. `minimal_data` - return metadata attributes according to the default template.
- 2. `extended_data_included` - return metadata attributes according to applied template, if object doesn’t have applied template, default template will be used. This is the default for User endpoints.
- 3. `original_data_included` - return all metadata attributes with values and null attributes, if they are present in the applied template. This is the default for Curator endpoints.
- in: query
- name: returnedMetadataFields
- schema:
- enum:
- - minimal_data
- - extended_data_included
- - original_data_included
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/Library"
- description: The request was successful. The returned value is the object.
- "400":
- content: {}
- description: The supplied object ID is invalid.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "404":
- content: {}
- description: No object exists with the given ID.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a single library object by ID (accession)
- tags:
- - Library SPoT as User
-components:
- schemas:
- CommitInfo:
- $ref: "./schemas/common/CommitInfo.yaml"
- IntegrationHelper:
- $ref: "./schemas/common/IntegrationHelper.yaml"
- Library:
- $ref: "./schemas/library/Library.yaml"
- ListResponse:
- $ref: "./schemas/common/ListResponse.yaml"
- MetaResponse:
- $ref: "./schemas/common/MetaResponse.yaml"
- PaginationInfo:
- $ref: "./schemas/common/PaginationInfo.yaml"
- ResponseFormat:
- $ref: "./schemas/common/ResponseFormat.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/manageData.yaml b/openapi/v1/manageData.yaml
deleted file mode 100644
index ebc052b5..00000000
--- a/openapi/v1/manageData.yaml
+++ /dev/null
@@ -1,184 +0,0 @@
-openapi: 3.1.0
-info:
- description: |-
- This swagger page describes the manageData APIs.
-
- Before carrying out any API calls you will need an API token. API tokens can be obtained under your profile within the Genestack software.
-
- To try out calls in this swagger page:
-
- 1. Click the 'Authorize' button below to enter your API token
- 2. Scroll to the 'Parameters' section for the method you wish to try out and click the 'Try it out' button
- 3. Enter parameter values that you wish to try
- 4. Scroll to the bottom of the Parameters section and click the 'Execute' bar that appears
-
- The server response will be in the section that follows.
- title: ODM API
- version: default-released
-tags:
-- name: Manage Data
-paths:
- /api/v1/manage-data/detached-objects:
- get:
- description: |+
- Retrieve various types of detached data objects. An object is defined as 'detached' if it lacks any direct or indirect link to a root-level object, which in this context is referred to as 'study'.
- Study is considered as detached object itself in case there are no links to objects at a lower level.
- Data with specific `detachedObjectType` can be retrieved by specifying the types in `detachedObjectType` parameter.
- The detached objects are sorted according to their `detachedObjectType` and `genestack:accession`.
- Specific ordering can be observed in the list of supported detached types found below.
- Pagination of the results can be conveniently managed using the `cursor` and `limit` parameters.
- Supported types of detached objects (listed in the order of retrieval) include:
- * `STUDY`
- * `SAMPLE_GROUP`
- * `LIBRARY_GROUP`
- * `PREPARATION_GROUP`
- * `CELL_GROUP`
- * `TABULAR_DATA`
- * `GENE_VARIANT`
- * `FLOW_CYTOMETRY`
-
- operationId: getDetachedObjects
- parameters:
- - description: Filter by detached object type. Multiple values can be used to
- filter the data.
- explode: true
- in: query
- name: detachedObjectType
- schema:
- items:
- type: string
- type: array
- style: form
- - description: "This parameter determines the number of results to retrieve\
- \ per page, with the default set at 2000."
- in: query
- name: limit
- schema:
- format: int32
- type: integer
- - description: |-
- This parameter enables retrieval of objects starting from a specific point.
- Currently, it represents the accession of the last obtained object. However, please note that its functionality might change over time, so it is advisable to consider the cursor's content as a general string.
- in: query
- name: cursor
- schema:
- type: string
- responses:
- "200":
- content:
- application/json:
- schema:
- $ref: "#/components/schemas/DetachedCollection"
- description: Retrieved detached data.
- "400":
- content: {}
- description: Detached data cannot be retrieved due to Bad Request.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "403":
- content: {}
- description: Not enough permissions to call method.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Retrieve a list of detached objects
- tags:
- - Manage Data
- /api/v1/manage-data/data:
- delete:
- description: |-
- The objects will be marked for deletion. In case the selected object has more than one version, the endpoint deletes all of them. The following object types can be deleted by the endpoint:
- * `STUDY`
- * `SAMPLE_GROUP`
- * `LIBRARY_GROUP`
- * `PREPARATION_GROUP`
- * `TABULAR_DATA`
- * `GENE_VARIANT`
- * `FLOW_CYTOMETRY`
- * `REFERENCE_GENOME`
- * `FILE`
-
- Moreover, if the selected object is linked to any other data, the endpoint will also delete the linked data associated with it according to the specified rules:
- * If you delete a `STUDY`, the entire study with all the listed group types and files, will be removed.
- * Deleting a `SAMPLE_GROUP` will result in the removal of all samples associated with this sample group, along with any linked `TABULAR_DATA`/`GENE_VARIANT`/`FLOW_CYTOMETRY`/`LIBRARY_GROUP`/`PREPARATION_GROUP`. The linked `TABULAR_DATA`/`GENE_VARIANT`/`FLOW_CYTOMETRY` will be deleted, even if it is linked to another metadata group.
- * If you delete `TABULAR_DATA`/`GENE_VARIANT`/`FLOW_CYTOMETRY`, all associated data, such as links and runs will be removed from ODM.
- * If you delete `REFERENCE_GENOME`, searching for variant by variantFeature (genes) won't be available for linked VCF groups.
- * If you delete `FILE`, the file will be removed from ODM.
- operationId: deleteData
- parameters:
- - description: Accessions files to be deleted.
- explode: false
- in: query
- name: accessions
- schema:
- items:
- type: string
- type: array
- style: form
- responses:
- "202":
- content:
- application/json:
- schema:
- items:
- $ref: "#/components/schemas/ManagedObject"
- type: array
- description: The deletion of the following files and all linked data has
- started.
- "400":
- content: {}
- description: Deletion could not be performed due to Bad Request.
- "401":
- content: {}
- description: |-
- User is not authenticated. Please supply a valid Access Token in the `Authorization` HTTP header (e.g. Authorization: bearer [token])
- or Genestack API token in the `Genestack-API-Token` header (this token may be obtained from the Genestack UI _Profile_ page).
- "403":
- content: {}
- description: Not enough permissions to call method or the file is not meant to be deleted.
- "404":
- content: {}
- description: Some of the provided accessions could not be found in ODM.
- Deletion will not be preformed. Please review your list and repeat the
- attempt.
- "406":
- content: {}
- description: Some of the provided accessions do not belong to the supported
- object types. Deletion will not be performed. Please review your list
- and repeat the attempt.
- "500":
- content: {}
- description: "An internal server error occurred. This indicates an unexpected\
- \ failure in the Genestack system, please file a bug report to support@genestack.com,\
- \ including the error details."
- security:
- - Access-token: []
- - Genestack-API-Token: []
- summary: Delete objects from ODM
- tags:
- - Manage Data
-components:
- schemas:
- DetachedCollection:
- $ref: "./schemas/manage-data/DetachedCollection.yaml"
- DetachedObject:
- $ref: "./schemas/manage-data/DetachedObject.yaml"
- ManagedObject:
- $ref: "./schemas/manage-data/ManagedObject.yaml"
- securitySchemes:
- Access-token:
- in: header
- name: Authorization
- type: apiKey
- Genestack-API-Token:
- in: header
- name: Genestack-API-Token
- type: apiKey
diff --git a/openapi/v1/odm.yaml b/openapi/v1/odm.yaml
new file mode 100644
index 00000000..e2552d75
--- /dev/null
+++ b/openapi/v1/odm.yaml
@@ -0,0 +1,24810 @@
+---
+openapi: "3.0.3"
+info:
+ description: "This swagger page describes the variantUser API endpoints for ODM.\
+ \ These are typically used to find and retrieve variant data and metadata.\n\n\
+ Before carrying out any API calls you will need an API token. API tokens can be\
+ \ obtained under your profile within the Genestack software.\n\nTo try out calls\
+ \ in this swagger page:\n\n1. Click the 'Authorize' button below to enter your\
+ \ API token\n2. Scroll to the 'Parameters' section for the method you wish to\
+ \ try out and click the 'Try it out' button\n3. Enter parameter values that you\
+ \ wish to try\n4. Scroll to the bottom of the Parameters section and click the\
+ \ 'Execute' bar that appears\n\n\n The server response will be in the section\
+ \ that follows."
+ title: "ODM API"
+ version: "default-released"
+tags:
+- name: "Cells as Curator"
+- name: "Cells as User"
+- name: "Expression SPoT as Curator"
+- name: "Expression SPoT as User"
+- name: "Files as Curator"
+- name: "Files as User"
+- name: "Flow Cytometry SPoT as Curator"
+- name: "Flow Cytometry SPoT as User"
+- name: "Cell integration as Curator"
+- name: "Expression integration as Curator"
+- name: "Files integration as Curator"
+- name: "Flow Cytometry (FACS) integration as Curator"
+- name: "Library integration as Curator"
+- name: "Linkage as Curator"
+- name: "Metadata versioning as Curator"
+- name: "Omics queries as Curator"
+- name: "Preparation integration as Curator"
+- name: "Sample integration as Curator"
+- name: "Study integration as Curator"
+- name: "Validation summary as Curator"
+- name: "Variant integration as Curator"
+- name: "Expression integration as User"
+- name: "Files integration as User"
+- name: "Flow Cytometry (FACS) integration as User"
+- name: "Library integration as User"
+- name: "Linkage as User"
+- name: "Omics queries as User"
+- name: "Preparation integration as User"
+- name: "Sample integration as User"
+- name: "Study integration as User"
+- name: "Variant integration as User"
+- name: "Data import jobs"
+- name: "Data import via direct file upload"
+- name: "Job operations"
+- name: "Library SPoT as Curator"
+- name: "Library SPoT as User"
+- name: "Manage Data"
+- name: "Preparation SPoT as Curator"
+- name: "Preparation SPoT as User"
+- name: "Xrefset queries"
+- name: "Reference genome"
+- name: "Sample SPoT as Curator"
+- name: "Sample SPoT as User"
+- name: "Groups"
+- name: "Users"
+- name: "Study SPoT as Curator"
+- name: "Study SPoT as User"
+- name: "Tasks API"
+- name: "Variant SPoT as Curator"
+- name: "Variant SPoT as User"
+paths:
+ /api/v1/as-curator/cells/{id}:
+ get:
+ operationId: "getCellByIdAsCurator"
+ parameters:
+ - description: "Unique cell identifier. Consists of a cell group accession and\
+ \ a cell barcode, separated by a hyphen, e.g. `GSF123456-AAACCTGAGCGCTCCA-1`."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/Cell"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "Invalid data in the request. See the error message for details."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "Object with provided ID could not be found in ODM."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a cell by ID"
+ tags:
+ - "Cells as Curator"
+ /api/v1/as-curator/cells/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size together with a `cursor` tag.\nTo retrieve\
+ \ the next page of results please supply this `cursor` tag to resume the query\
+ \ from your previous result and get the next page.\nIf there are no more results\
+ \ you will just retrieve an empty result.\n"
+ operationId: "getCellsByGroupAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the cell group."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 10000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "The page tag to resume results from (see Paging above). Cell\
+ \ ID is currently used as a cursor."
+ in: "query"
+ name: "cursor"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/CellListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Cell data cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve cells from a given group"
+ tags:
+ - "Cells as Curator"
+ /api/v1/as-user/cells/{id}:
+ get:
+ operationId: "getCellByIdAsUser"
+ parameters:
+ - description: "Unique cell identifier. Consists of a cell group accession and\
+ \ a cell barcode, separated by a hyphen, e.g. `GSF123456-AAACCTGAGCGCTCCA-1`."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/Cell"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "Invalid data in the request. See the error message for details."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "Object with provided ID could not be found in ODM."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a cell by ID"
+ tags:
+ - "Cells as User"
+ /api/v1/as-user/cells/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size together with a `cursor` tag.\nTo retrieve\
+ \ the next page of results please supply this `cursor` tag to resume the query\
+ \ from your previous result and get the next page.\nIf there are no more results\
+ \ you will just retrieve an empty result.\n"
+ operationId: "getCellsByGroupAsUser"
+ parameters:
+ - description: "Unique identifier (accession) of the cell group."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 10000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "The page tag to resume results from (see Paging above). Cell\
+ \ ID is currently used as a cursor."
+ in: "query"
+ name: "cursor"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/CellListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Cell data cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve cells from a given group"
+ tags:
+ - "Cells as User"
+ /api/v1/as-curator/expressions:
+ get:
+ description: "Retrieve all expression data and metadata objects that match a\
+ \ query.\n\n## Metadata full-text queries\nSingle words can be supplied as\
+ \ is, otherwise use speech marks (`\"`) to quote queries that include whitespace.\
+ \ Speech marks and backslash characters in the query need to be escaped with\
+ \ a backslash (`\\`).\n\n## Metadata filters\nMetadata filters are key-value\
+ \ pairs joined by an operator. The `=` operator matches literal values/string.\
+ \ The `!=` operator matches anything except the literal value/string. The\
+ \ `<` or `>` operators match numerical results that are less or greater than\
+ \ the supplied value. Strings containing whitespace need to be quoted with\
+ \ (`\"`).\n\n## Combinations\nMetadata queries/filters for the same parameter\
+ \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\
+ \ to separate out the terms and operators. Parentheses `( )` can be used for\
+ \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\
+ \ (eg. GCT) can be queried via the useVersions parameter. Different versions\
+ \ of an omics data file are associated via their CHAIN_ID metadata value.\
+ \ This CHAIN_ID can be supplied to the useVersions parameter along with the\
+ \ version number or specific omics data file accessions to include them in\
+ \ the query. If nothing is supplied to the useVersions parameter then only\
+ \ the active version (which is usually the last one imported) is queried.\
+ \ This acts as a filter before the rest of the query is carried out.\n\nExample\
+ \ usage:\nuseVersions=* (query all versions, including those without CHAIN_IDs)\n\
+ useVersions=v2 (query the second version. If there is no second version then\
+ \ the data file is not queried)\nuseVersions=v1,v0 (query the first version\
+ \ and any data files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for\
+ \ omics data files with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size together\
+ \ with a `cursor` tag. To retrieve the next page of results please supply\
+ \ this `cursor` tag to resume the query from your previous result and get\
+ \ the next page. If there are no more results you will just retrieve an empty\
+ \ result.\n\n"
+ operationId: "getExpressionDataAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by expression metadata (key-value metadata pair(s)).\
+ \ E.g. `\"Normalization Method\"=TPM`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for expression objects via a full text query over all\
+ \ expression metadata. E.g. `TPM`. Queries matching dictionary terms are\
+ \ automatically expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "Autogenerated numeric ID that corresponds to the column and\
+ \ is used to link data from the same run to a sample, library or preparation.\
+ \ Multiple values can be provided as a list."
+ in: "query"
+ name: "runFilter"
+ schema:
+ $ref: "#/components/schemas/RunFilter"
+ style: "form"
+ - description: "Column name from the file to which all data for a sample, library\
+ \ or preparation is related. Multiple values can be provided as a list to\
+ \ retrieve data from multiple columns."
+ explode: true
+ in: "query"
+ name: "runSourceFilter"
+ schema:
+ items:
+ type: "string"
+ example: "Run Source ID"
+ type: "array"
+ style: "form"
+ - description: "Minimum threshold (inclusive) for returned expression values."
+ in: "query"
+ name: "minExpressionLevel"
+ schema:
+ format: "double"
+ type: "number"
+ - description: "List of features to return. These features must match exactly\
+ \ the probe IDs in the GCT file. Example: `1552269_at`"
+ explode: true
+ in: "query"
+ name: "featureList"
+ schema:
+ items:
+ type: "string"
+ example: "KRAS"
+ type: "array"
+ style: "form"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "The page tag to resume results from (see paging above)."
+ in: "query"
+ name: "cursor"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ExpressionResponse"
+ description: "Retrieved Expression data."
+ "400":
+ content: {}
+ description: "Expression data cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve multiple expression data and metadata objects"
+ tags:
+ - "Expression SPoT as Curator"
+ /api/v1/as-curator/expressions/group:
+ get:
+ description: "Retrieve all group metadata objects that match a query.\n\n##\
+ \ Metadata full-text queries\nSingle words can be supplied as is, otherwise\
+ \ use speech marks (`\"`) to quote queries that include whitespace. Speech\
+ \ marks and backslash characters in the query need to be escaped with a backslash\
+ \ (`\\`).\n\n## Metadata filters\nMetadata filters are key-value pairs joined\
+ \ by an operator. The `=` operator matches literal values/string. The `!=`\
+ \ operator matches anything except the literal value/string. The `<` or `>`\
+ \ operators match numerical results that are less or greater than the supplied\
+ \ value. Strings containing whitespace need to be quoted with (`\"`).\n\n\
+ ## Combinations\nMetadata queries/filters for the same parameter can be combined\
+ \ with `&&`, `AND`, `||` and `OR` operators, using white-space to separate\
+ \ out the terms and operators. Parentheses `( )` can be used for complex expressions.\n\
+ \n## Versioning\nSpecific versions of omics data files (eg. GCT) can be queried\
+ \ via the useVersions parameter. Different versions of an omics data file\
+ \ are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied\
+ \ to the useVersions parameter along with the version number or specific omics\
+ \ data file accessions to include them in the query. If nothing is supplied\
+ \ to the useVersions parameter then only the active version (which is usually\
+ \ the last one imported) is queried. This acts as a filter before the rest\
+ \ of the query is carried out.\n\nExample usage:\nuseVersions=* (query all\
+ \ versions, including those without CHAIN_IDs)\nuseVersions=v2 (query the\
+ \ second version. If there is no second version then the data file is not\
+ \ queried)\nuseVersions=v1,v0 (query the first version and any data files\
+ \ without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files with\
+ \ a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n## List operation\n\nThis endpoint can be called with no `query` parameter.\
+ \ Doing so returns a list of all data objects."
+ operationId: "searchExpressionGroupsAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by expression metadata (key-value metadata pair(s)).\
+ \ E.g. `\"Normalization Method\"=TPM`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for expression objects via a full text query over all\
+ \ expression metadata. E.g. `TPM`. Queries matching dictionary terms are\
+ \ automatically expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve groups that match a query"
+ tags:
+ - "Expression SPoT as Curator"
+ /api/v1/as-curator/expressions/group/by/run/{id}:
+ get:
+ operationId: "getExpressionGroupByRunAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (runId) of the run."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single group object by run ID (runId)"
+ tags:
+ - "Expression SPoT as Curator"
+ /api/v1/as-curator/expressions/group/{id}:
+ get:
+ operationId: "getExpressionGroupAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Expression group identifier (groupId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single expression group by ID (groupId)"
+ tags:
+ - "Expression SPoT as Curator"
+ /api/v1/as-curator/expressions/runs/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size. In order to retrieve all matching results\
+ \ the client needs to request multiple pages starting from an offset to the\
+ \ first result. You can do this using the pageOffset query parameter. A value\
+ \ of 0 (the default) instructs the server to return the first page of results,\
+ \ 100 would return a page of results starting from the 101st result and so\
+ \ on. To return all results iterate through pages using pageOffset values\
+ \ of `n * pageLimit` until the `resultsExhausted` response field is true.\n\
+ \n"
+ operationId: "searchExpressionRunsAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve run objects related to the given group"
+ tags:
+ - "Expression SPoT as Curator"
+ /api/v1/as-curator/expressions/{id}:
+ get:
+ operationId: "getExpressionAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Expression object unique identifier (itemId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ExpressionItem"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single expression object by ID (itemId)"
+ tags:
+ - "Expression SPoT as Curator"
+ patch:
+ description: "## Basic operation\nThe object metadata is updated using the supplied\
+ \ map of attribute names to attribute values. There are three cases:\n1. The\
+ \ attribute name does not already exist in the object metadata. In this case,\
+ \ the attribute and value are added to the object metadata.\n2. The attribute\
+ \ name already exists in the object metadata. In this case, the value is updated.\n\
+ 3. The attribute value is `null`.In this case, the attribute is removed from\
+ \ the object metadata.\n\n## Attribute values\nThe attribute values are intelligently\
+ \ parsed as booleans, integers, etc."
+ operationId: "updateExpressionRunAsCurator"
+ parameters:
+ - description: "Expression object run ID (runId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ requestBody:
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataContent"
+ description: "Metadata in the form of `{key: value, key2: value2, ...}`"
+ required: false
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/SignalRun"
+ description: "The objects was successfully created. The returned value is\
+ \ the updated object, along with any warnings."
+ "400":
+ content: {}
+ description: "The supplied object ID or metadata is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Update metadata object by expression object run ID (runId)"
+ tags:
+ - "Expression SPoT as Curator"
+ x-codegen-request-body-name: "body"
+ /api/v1/as-curator/expressions/{id}/versions:
+ get:
+ operationId: "getExpressionVersionsAsCurator"
+ parameters:
+ - description: "Expression object run ID (runId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ items:
+ $ref: "#/components/schemas/CommitInfo"
+ type: "array"
+ description: "The request was successful. The returned value is the list\
+ \ of object versions."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a list of expression object versions by run ID (runId)"
+ tags:
+ - "Expression SPoT as Curator"
+ /api/v1/as-curator/expressions/{id}/versions/{version}:
+ get:
+ operationId: "getExpressionByVersionAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Expression object run ID (runId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Unique version of the expression object."
+ in: "path"
+ name: "version"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/SignalRun"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single expression object by run ID and its version"
+ tags:
+ - "Expression SPoT as Curator"
+ /api/v1/as-user/expressions:
+ get:
+ description: "Retrieve all expression data and metadata objects that match a\
+ \ query.\n\n## Metadata full-text queries\nSingle words can be supplied as\
+ \ is, otherwise use speech marks (`\"`) to quote queries that include whitespace.\
+ \ Speech marks and backslash characters in the query need to be escaped with\
+ \ a backslash (`\\`).\n\n## Metadata filters\nMetadata filters are key-value\
+ \ pairs joined by an operator. The `=` operator matches literal values/string.\
+ \ The `!=` operator matches anything except the literal value/string. The\
+ \ `<` or `>` operators match numerical results that are less or greater than\
+ \ the supplied value. Strings containing whitespace need to be quoted with\
+ \ (`\"`).\n\n## Combinations\nMetadata queries/filters for the same parameter\
+ \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\
+ \ to separate out the terms and operators. Parentheses `( )` can be used for\
+ \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\
+ \ (eg. GCT) can be queried via the useVersions parameter. Different versions\
+ \ of an omics data file are associated via their CHAIN_ID metadata value.\
+ \ This CHAIN_ID can be supplied to the useVersions parameter along with the\
+ \ version number or specific omics data file accessions to include them in\
+ \ the query. If nothing is supplied to the useVersions parameter then only\
+ \ the active version (which is usually the last one imported) is queried.\
+ \ This acts as a filter before the rest of the query is carried out.\n\nExample\
+ \ usage:\nuseVersions=* (query all versions, including those without CHAIN_IDs)\n\
+ useVersions=v2 (query the second version. If there is no second version then\
+ \ the data file is not queried)\nuseVersions=v1,v0 (query the first version\
+ \ and any data files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for\
+ \ omics data files with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size together\
+ \ with a `cursor` tag. To retrieve the next page of results please supply\
+ \ this `cursor` tag to resume the query from your previous result and get\
+ \ the next page. If there are no more results you will just retrieve an empty\
+ \ result.\n\n"
+ operationId: "getExpressionDataAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by expression metadata (key-value metadata pair(s)).\
+ \ E.g. `\"Normalization Method\"=TPM`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for expression objects via a full text query over all\
+ \ expression metadata. E.g. `TPM`. Queries matching dictionary terms are\
+ \ automatically expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "Autogenerated numeric ID that corresponds to the column and\
+ \ is used to link data from the same run to a sample, library or preparation.\
+ \ Multiple values can be provided as a list."
+ in: "query"
+ name: "runFilter"
+ schema:
+ $ref: "#/components/schemas/RunFilter"
+ style: "form"
+ - description: "Column name from the file to which all data for a sample, library\
+ \ or preparation is related. Multiple values can be provided as a list to\
+ \ retrieve data from multiple columns."
+ explode: true
+ in: "query"
+ name: "runSourceFilter"
+ schema:
+ items:
+ type: "string"
+ example: "Run Source ID"
+ type: "array"
+ style: "form"
+ - description: "Minimum threshold (inclusive) for returned expression values."
+ in: "query"
+ name: "minExpressionLevel"
+ schema:
+ format: "double"
+ type: "number"
+ - description: "List of features to return. These features must match exactly\
+ \ the probe IDs in the GCT file. Example: `1552269_at`"
+ explode: true
+ in: "query"
+ name: "featureList"
+ schema:
+ items:
+ type: "string"
+ example: "KRAS"
+ type: "array"
+ style: "form"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "The page tag to resume results from (see paging above)."
+ in: "query"
+ name: "cursor"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ExpressionResponse"
+ description: "Retrieved Expression data."
+ "400":
+ content: {}
+ description: "Expression data cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve multiple expression data and metadata objects"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-user/expressions/group:
+ get:
+ description: "Retrieve all group metadata objects that match a query.\n\n##\
+ \ Metadata full-text queries\nSingle words can be supplied as is, otherwise\
+ \ use speech marks (`\"`) to quote queries that include whitespace. Speech\
+ \ marks and backslash characters in the query need to be escaped with a backslash\
+ \ (`\\`).\n\n## Metadata filters\nMetadata filters are key-value pairs joined\
+ \ by an operator. The `=` operator matches literal values/string. The `!=`\
+ \ operator matches anything except the literal value/string. The `<` or `>`\
+ \ operators match numerical results that are less or greater than the supplied\
+ \ value. Strings containing whitespace need to be quoted with (`\"`).\n\n\
+ ## Combinations\nMetadata queries/filters for the same parameter can be combined\
+ \ with `&&`, `AND`, `||` and `OR` operators, using white-space to separate\
+ \ out the terms and operators. Parentheses `( )` can be used for complex expressions.\n\
+ \n## Versioning\nSpecific versions of omics data files (eg. GCT) can be queried\
+ \ via the useVersions parameter. Different versions of an omics data file\
+ \ are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied\
+ \ to the useVersions parameter along with the version number or specific omics\
+ \ data file accessions to include them in the query. If nothing is supplied\
+ \ to the useVersions parameter then only the active version (which is usually\
+ \ the last one imported) is queried. This acts as a filter before the rest\
+ \ of the query is carried out.\n\nExample usage:\nuseVersions=* (query all\
+ \ versions, including those without CHAIN_IDs)\nuseVersions=v2 (query the\
+ \ second version. If there is no second version then the data file is not\
+ \ queried)\nuseVersions=v1,v0 (query the first version and any data files\
+ \ without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files with\
+ \ a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n## List operation\n\nThis endpoint can be called with no `query` parameter.\
+ \ Doing so returns a list of all data objects."
+ operationId: "searchExpressionGroupsAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by expression metadata (key-value metadata pair(s)).\
+ \ E.g. `\"Normalization Method\"=TPM`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for expression objects via a full text query over all\
+ \ expression metadata. E.g. `TPM`. Queries matching dictionary terms are\
+ \ automatically expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve groups that match a query"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-user/expressions/group/by/run/{id}:
+ get:
+ operationId: "getExpressionGroupByRunAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (runId) of the run."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single group object by run ID (runId)"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-user/expressions/group/{id}:
+ get:
+ operationId: "getExpressionGroupAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Expression group identifier (groupId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single expression group by ID (groupId)"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-user/expressions/runs/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size. In order to retrieve all matching results\
+ \ the client needs to request multiple pages starting from an offset to the\
+ \ first result. You can do this using the pageOffset query parameter. A value\
+ \ of 0 (the default) instructs the server to return the first page of results,\
+ \ 100 would return a page of results starting from the 101st result and so\
+ \ on. To return all results iterate through pages using pageOffset values\
+ \ of `n * pageLimit` until the `resultsExhausted` response field is true.\n\
+ \n"
+ operationId: "searchExpressionRunsAsUser"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve run objects related to the given group"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-user/expressions/{id}:
+ get:
+ operationId: "getExpressionAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Expression object unique identifier (itemId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ExpressionItem"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single expression object by ID (itemId)"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-user/expressions/{id}/versions:
+ get:
+ operationId: "getExpressionVersionsAsUser"
+ parameters:
+ - description: "Expression object run ID (runId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ items:
+ $ref: "#/components/schemas/CommitInfo"
+ type: "array"
+ description: "The request was successful. The returned value is the list\
+ \ of object versions."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a list of expression object versions by run ID (runId)"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-user/expressions/{id}/versions/{version}:
+ get:
+ operationId: "getExpressionByVersionAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Expression object run ID (runId)."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Unique version of the object."
+ in: "path"
+ name: "version"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/SignalRun"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single expression object by run ID and its version"
+ tags:
+ - "Expression SPoT as User"
+ /api/v1/as-curator/files/{id}/download:
+ head:
+ description: "Check if a file exists by its accession.\n\nThis endpoint can\
+ \ be used to check if a file exists and accessible before downloading it.\n"
+ operationId: "headFileAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ description: "File exists. Additional metadata is provided in the response\
+ \ headers."
+ "400":
+ content: {}
+ description: "File cannot be downloaded."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "406":
+ content: {}
+ description: "File cannot be downloaded."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to"
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ tags:
+ - "Files as Curator"
+ get:
+ description: "Download a file by its accession.\n"
+ operationId: "getFileAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - name: "Range"
+ in: "header"
+ required: false
+ schema:
+ type: "string"
+ example: "bytes=0-"
+ description: "Request a specific range of bytes to support partial downloads.\n\
+ Example: `bytes=0-1024` to download the first 1024 bytes. Supplying several\n\
+ ranges is not supported.\n"
+ responses:
+ "200":
+ description: "File downloaded successfully"
+ content:
+ application/octet-stream:
+ schema:
+ type: "string"
+ format: "binary"
+ "206":
+ description: "Partial content downloaded successfully"
+ content:
+ application/octet-stream:
+ schema:
+ type: "string"
+ format: "binary"
+ "400":
+ content: {}
+ description: "File cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "406":
+ content: {}
+ description: "File cannot be downloaded."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a file by ID (accession)"
+ tags:
+ - "Files as Curator"
+ /api/v1/as-curator/files/{id}:
+ get:
+ operationId: "getFileMetadataByIdAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Select `true` in order to include file structure (contents)\
+ \ for .h5, .h5ad, .zip, .gz to the response."
+ in: "query"
+ name: "includeContents"
+ required: false
+ schema:
+ default: false
+ type: "boolean"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/AFile"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "Invalid data in the request. See the error message for details."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "Object with provided accession could not be found in ODM."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve file's metadata by ID (accession)"
+ tags:
+ - "Files as Curator"
+ /api/v1/as-curator/files:
+ get:
+ operationId: "getFilesMetadataAsCurator"
+ description: "## Metadata full-text queries\nSingle words can be supplied as\
+ \ is, otherwise use speech marks (`\"`) to quote queries that include whitespace.\
+ \ Speech marks and backslash characters in the query need to be escaped with\
+ \ a backslash (`\\`).\n\n## Paging\nFor performance reasons, this endpoint\
+ \ returns results in \"pages\" of limited size. In order to retrieve all matching\
+ \ results the client needs to request multiple pages starting from an offset\
+ \ to the first result. You can do this using the `pageOffset` query parameter.\
+ \ A value of 0 (the default) instructs the server to return the first page\
+ \ of results, 100 would return a page of results starting from the 101st result\
+ \ and so on. To retrieve all results, iterate through pages by increasing\
+ \ the offset in multiples of limit (e.g., `offset = n * limit`), until all\
+ \ results have been retrieved. The total number of pages can be calculated\
+ \ by dividing the total number of results by the limit.\n\n## List operation\n\
+ \nThis endpoint can be called without any query parameters. When called this\
+ \ way, it returns a list of all files metadata objects."
+ parameters:
+ - in: "query"
+ name: "filter"
+ description: "Filter by files metadata (key-value metadata pair(s))."
+ schema:
+ type: "string"
+ - in: "query"
+ name: "query"
+ description: "Search for files via a full-text query over all file metadata."
+ schema:
+ type: "string"
+ - in: "query"
+ name: "includeContents"
+ description: "Select `true` in order to include file structure (contents)\
+ \ for .h5, .h5ad, .zip, .gz to the response."
+ required: false
+ schema:
+ default: false
+ type: "boolean"
+ - in: "query"
+ name: "pageLimit"
+ description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ schema:
+ format: "int32"
+ type: "integer"
+ - in: "query"
+ name: "pageOffset"
+ description: "Show the page {pageOffset + 1} results from the start of the\
+ \ results. E.g. 100 will show a page of results starting from the 101st\
+ \ result. The default value is 0."
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ text/tab-separated-values:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Invalid data in the request. See the error message for details."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve file's metadata by its fields"
+ tags:
+ - "Files as Curator"
+ /api/v1/as-user/files/{id}/download:
+ head:
+ description: "Check if a file exists by its accession.\n\nThis endpoint can\
+ \ be used to check if a file exists and accessible before downloading it.\n"
+ operationId: "headFileAsUser"
+ summary: "Check if a file exists by ID (accession)."
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ description: "File exists. Additional metadata is provided in the response\
+ \ headers."
+ "400":
+ content: {}
+ description: "File cannot be downloaded."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "406":
+ content: {}
+ description: "File cannot be downloaded."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to"
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ tags:
+ - "Files as User"
+ get:
+ description: "Download a file by its accession.\n"
+ operationId: "getFileAsUser"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - name: "Range"
+ in: "header"
+ required: false
+ schema:
+ type: "string"
+ example: "bytes=0-"
+ description: "Request a specific range of bytes to support partial downloads.\n\
+ Example: `bytes=0-1024` to download the first 1024 bytes. Supplying several\n\
+ ranges is not supported.\n"
+ responses:
+ "200":
+ description: "File downloaded successfully"
+ content:
+ application/octet-stream:
+ schema:
+ type: "string"
+ format: "binary"
+ "206":
+ description: "Partial content downloaded successfully"
+ content:
+ application/octet-stream:
+ schema:
+ type: "string"
+ format: "binary"
+ "400":
+ content: {}
+ description: "File cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "406":
+ content: {}
+ description: "File cannot be downloaded."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a file by ID (accession)"
+ tags:
+ - "Files as User"
+ /api/v1/as-user/files/{id}:
+ get:
+ operationId: "getFileMetadataByIdAsUser"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Select `true` in order to include file structure (contents)\
+ \ for .h5, .h5ad, .zip, .gz to the response."
+ in: "query"
+ name: "includeContents"
+ required: false
+ schema:
+ default: false
+ type: "boolean"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/AFile"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "Invalid data in the request. See the error message for details."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "Object with provided accession could not be found in ODM."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve file's metadata by ID (accession)"
+ tags:
+ - "Files as User"
+ /api/v1/as-user/files:
+ get:
+ operationId: "getFilesMetadataAsUser"
+ description: "## Metadata full-text queries\nSingle words can be supplied as\
+ \ is, otherwise use speech marks (`\"`) to quote queries that include whitespace.\
+ \ Speech marks and backslash characters in the query need to be escaped with\
+ \ a backslash (`\\`).\n\n## Paging\nFor performance reasons, this endpoint\
+ \ returns results in \"pages\" of limited size. In order to retrieve all matching\
+ \ results the client needs to request multiple pages starting from an offset\
+ \ to the first result. You can do this using the `pageOffset` query parameter.\
+ \ A value of 0 (the default) instructs the server to return the first page\
+ \ of results, 100 would return a page of results starting from the 101st result\
+ \ and so on. To retrieve all results, iterate through pages by increasing\
+ \ the offset in multiples of limit (e.g., `offset = n * limit`), until all\
+ \ results have been retrieved. The total number of pages can be calculated\
+ \ by dividing the total number of results by the limit.\n\n## List operation\n\
+ \nThis endpoint can be called without any query parameters. When called this\
+ \ way, it returns a list of all files metadata objects."
+ parameters:
+ - in: "query"
+ name: "filter"
+ description: "Filter by files metadata (key-value metadata pair(s))."
+ schema:
+ type: "string"
+ - in: "query"
+ name: "query"
+ description: "Search for files via a full-text query over all file metadata."
+ schema:
+ type: "string"
+ - in: "query"
+ name: "includeContents"
+ description: "Select `true` in order to include file structure (contents)\
+ \ for .h5, .h5ad, .zip, .gz to the response."
+ required: false
+ schema:
+ default: false
+ type: "boolean"
+ - in: "query"
+ name: "pageLimit"
+ description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ schema:
+ format: "int32"
+ type: "integer"
+ - in: "query"
+ name: "pageOffset"
+ description: "Show the page {pageOffset + 1} results from the start of the\
+ \ results. E.g. 100 will show a page of results starting from the 101st\
+ \ result. The default value is 0."
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ text/tab-separated-values:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Invalid data in the request. See the error message for details."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve file's metadata by its fields"
+ tags:
+ - "Files as User"
+ /api/v1/as-curator/flow-cytometries:
+ get:
+ description: "Retrieve all flow cytometry data and metadata objects that match\
+ \ a query.\n\n## Metadata full-text queries\nSingle words can be supplied\
+ \ as is, otherwise use speech marks (`\"`) to quote queries that include whitespace.\
+ \ Speech marks and backslash characters in the query need to be escaped with\
+ \ a backslash (`\\`).\n\n## Metadata filters\nMetadata filters are key-value\
+ \ pairs joined by an operator. The `=` operator matches literal values/string.\
+ \ The `!=` operator matches anything except the literal value/string. The\
+ \ `<` or `>` operators match numerical results that are less or greater than\
+ \ the supplied value. Strings containing whitespace need to be quoted with\
+ \ (`\"`).\n\n## Combinations\nMetadata queries/filters for the same parameter\
+ \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\
+ \ to separate out the terms and operators. Parentheses `( )` can be used for\
+ \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\
+ \ (eg. GCT) can be queried via the useVersions parameter. Different versions\
+ \ of an omics data file are associated via their CHAIN_ID metadata value.\
+ \ This CHAIN_ID can be supplied to the useVersions parameter along with the\
+ \ version number or specific omics data file accessions to include them in\
+ \ the query. If nothing is supplied to the useVersions parameter then only\
+ \ the active version (which is usually the last one imported) is queried.\
+ \ This acts as a filter before the rest of the query is carried out.\n\nExample\
+ \ usage:\nuseVersions=* (query all versions, including those without CHAIN_IDs)\n\
+ useVersions=v2 (query the second version. If there is no second version then\
+ \ the data file is not queried)\nuseVersions=v1,v0 (query the first version\
+ \ and any data files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for\
+ \ omics data files with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size together\
+ \ with a `cursor` tag. To retrieve the next page of results please supply\
+ \ this `cursor` tag to resume the query from your previous result and get\
+ \ the next page. If there are no more results you will just retrieve an empty\
+ \ result.\n\n"
+ operationId: "getFlowCytometryDataAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
+ \ E.g. `Organ=blood`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for flow cytometry objects via a full text query over\
+ \ all flow cytometry metadata. Queries matching dictionary terms are automatically\
+ \ expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "Autogenerated numeric ID that identifies a set of rows related\
+ \ to one run and is used to link data from the run to a sample. Multiple\
+ \ values can be provided as a list."
+ in: "query"
+ name: "runFilter"
+ schema:
+ $ref: "#/components/schemas/RunFilter"
+ style: "form"
+ - description: "Sample name from the file which allows retrieval of all the\
+ \ rows related to the sample. Multiple values can be provided as a list."
+ explode: true
+ in: "query"
+ name: "runSourceFilter"
+ schema:
+ items:
+ type: "string"
+ example: "Run Source ID"
+ type: "array"
+ style: "form"
+ - description: "Required value of \"Readout type\" column. E.g.: `Count`, `Median`"
+ in: "query"
+ name: "readoutType"
+ schema:
+ type: "string"
+ - description: "Value of \"Cell Population\" column. E.g.: `\"total cells\"\
+ `, `CD45+,live/CD45+`, `CD3+`.\n\nNote that if this value contains special\
+ \ characters like `/` which is used as a URI path separator, such characters\
+ \ should be escaped manually before sending request. For example, `/` should\
+ \ be escaped as `%2F`."
+ in: "query"
+ name: "population"
+ schema:
+ type: "string"
+ - description: "Marker value. E.g.: `PD1`, `BV786`"
+ in: "query"
+ name: "marker"
+ schema:
+ type: "string"
+ - description: "Minimum threshold (inclusive) for returned expression values."
+ in: "query"
+ name: "minValue"
+ schema:
+ type: "number"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "The page tag to resume results from (see paging above)."
+ in: "query"
+ name: "cursor"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/FlowCytometryResponse"
+ description: "Retrieved Flow Cytometry data."
+ "400":
+ content: {}
+ description: "Flow Cytometry data cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve multiple flow cytometry data and metadata objects"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ /api/v1/as-curator/flow-cytometries/group:
+ get:
+ description: "Retrieve all group metadata objects that match a query.\n\n##\
+ \ Metadata full-text queries\nSingle words can be supplied as is, otherwise\
+ \ use speech marks (`\"`) to quote queries that include whitespace. Speech\
+ \ marks and backslash characters in the query need to be escaped with a backslash\
+ \ (`\\`).\n\n## Metadata filters\nMetadata filters are key-value pairs joined\
+ \ by an operator. The `=` operator matches literal values/string. The `!=`\
+ \ operator matches anything except the literal value/string. The `<` or `>`\
+ \ operators match numerical results that are less or greater than the supplied\
+ \ value. Strings containing whitespace need to be quoted with (`\"`).\n\n\
+ ## Combinations\nMetadata queries/filters for the same parameter can be combined\
+ \ with `&&`, `AND`, `||` and `OR` operators, using white-space to separate\
+ \ out the terms and operators. Parentheses `( )` can be used for complex expressions.\n\
+ \n## Versioning\nSpecific versions of omics data files (eg. GCT) can be queried\
+ \ via the useVersions parameter. Different versions of an omics data file\
+ \ are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied\
+ \ to the useVersions parameter along with the version number or specific omics\
+ \ data file accessions to include them in the query. If nothing is supplied\
+ \ to the useVersions parameter then only the active version (which is usually\
+ \ the last one imported) is queried. This acts as a filter before the rest\
+ \ of the query is carried out.\n\nExample usage:\nuseVersions=* (query all\
+ \ versions, including those without CHAIN_IDs)\nuseVersions=v2 (query the\
+ \ second version. If there is no second version then the data file is not\
+ \ queried)\nuseVersions=v1,v0 (query the first version and any data files\
+ \ without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files with\
+ \ a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n## List operation\n\nThis endpoint can be called with no `query` parameter.\
+ \ Doing so returns a list of all data objects."
+ operationId: "searchFlowCytometryGroupsAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
+ \ E.g. `Organ=blood`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for flow cytometry objects via a full text query over\
+ \ all flow cytometry metadata. Queries matching dictionary terms are automatically\
+ \ expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve groups that match a query"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ /api/v1/as-curator/flow-cytometries/group/by/run/{id}:
+ get:
+ operationId: "getFlowCytometryGroupByRunAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single group object by run ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ /api/v1/as-curator/flow-cytometries/group/{id}:
+ get:
+ operationId: "getFlowCytometryGroupAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single group object by ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ /api/v1/as-curator/flow-cytometries/runs/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size. In order to retrieve all matching results\
+ \ the client needs to request multiple pages starting from an offset to the\
+ \ first result. You can do this using the pageOffset query parameter. A value\
+ \ of 0 (the default) instructs the server to return the first page of results,\
+ \ 100 would return a page of results starting from the 101st result and so\
+ \ on. To retrieve all results, iterate through pages using `pageOffset` values\
+ \ of `n * pageLimit` until a page returns fewer results than the page limit,\
+ \ which indicates there are no more results.\n\n"
+ operationId: "searchFlowCytometryRunsAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve run objects related to the given group"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ /api/v1/as-curator/flow-cytometries/{id}:
+ get:
+ operationId: "getFlowCytometryAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/FlowCytometryItem"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single sample flow cytometry by ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ patch:
+ description: "## Basic operation\nThe object metadata is updated using the supplied\
+ \ map of attribute names to attribute values. There are three cases:\n1. The\
+ \ attribute name does not already exist in the object metadata. In this case,\
+ \ the attribute and value are added to the object metadata.\n2. The attribute\
+ \ name already exists in the object metadata. In this case, the value is updated.\n\
+ 3. The attribute value is `null`.In this case, the attribute is removed from\
+ \ the object metadata.\n\n## Attribute values\nThe attribute values are intelligently\
+ \ parsed as booleans, integers, etc."
+ operationId: "updateFlowCytometryAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ requestBody:
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataContent"
+ description: "Metadata in the form of `{key: value, key2: value2, ...}`"
+ required: false
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/SignalRun"
+ description: "The objects was successfully created. The returned value is\
+ \ the updated object, along with any warnings."
+ "400":
+ content: {}
+ description: "The supplied object ID or metadata is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Update object metadata"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ x-codegen-request-body-name: "body"
+ /api/v1/as-curator/flow-cytometries/{id}/versions:
+ get:
+ operationId: "getFlowCytometryVersionsAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ items:
+ $ref: "#/components/schemas/CommitInfo"
+ type: "array"
+ description: "The request was successful. The returned value is the list\
+ \ of object versions."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a list of object versions by ID"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ /api/v1/as-curator/flow-cytometries/{id}/versions/{version}:
+ get:
+ operationId: "getFlowCytometryByVersionAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Unique version of the object."
+ in: "path"
+ name: "version"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/SignalRun"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single sample flow cytometry by ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as Curator"
+ /api/v1/as-user/flow-cytometries:
+ get:
+ description: "Retrieve all flow cytometry data and metadata objects that match\
+ \ a query.\n\n## Metadata full-text queries\nSingle words can be supplied\
+ \ as is, otherwise use speech marks (`\"`) to quote queries that include whitespace.\
+ \ Speech marks and backslash characters in the query need to be escaped with\
+ \ a backslash (`\\`).\n\n## Metadata filters\nMetadata filters are key-value\
+ \ pairs joined by an operator. The `=` operator matches literal values/string.\
+ \ The `!=` operator matches anything except the literal value/string. The\
+ \ `<` or `>` operators match numerical results that are less or greater than\
+ \ the supplied value. Strings containing whitespace need to be quoted with\
+ \ (`\"`).\n\n## Combinations\nMetadata queries/filters for the same parameter\
+ \ can be combined with `&&`, `AND`, `||` and `OR` operators, using white-space\
+ \ to separate out the terms and operators. Parentheses `( )` can be used for\
+ \ complex expressions.\n\n## Versioning\nSpecific versions of omics data files\
+ \ (eg. GCT) can be queried via the useVersions parameter. Different versions\
+ \ of an omics data file are associated via their CHAIN_ID metadata value.\
+ \ This CHAIN_ID can be supplied to the useVersions parameter along with the\
+ \ version number or specific omics data file accessions to include them in\
+ \ the query. If nothing is supplied to the useVersions parameter then only\
+ \ the active version (which is usually the last one imported) is queried.\
+ \ This acts as a filter before the rest of the query is carried out.\n\nExample\
+ \ usage:\nuseVersions=* (query all versions, including those without CHAIN_IDs)\n\
+ useVersions=v2 (query the second version. If there is no second version then\
+ \ the data file is not queried)\nuseVersions=v1,v0 (query the first version\
+ \ and any data files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for\
+ \ omics data files with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size together\
+ \ with a `cursor` tag. To retrieve the next page of results please supply\
+ \ this `cursor` tag to resume the query from your previous result and get\
+ \ the next page. If there are no more results you will just retrieve an empty\
+ \ result.\n\n"
+ operationId: "getFlowCytometryDataAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
+ \ E.g. `Organ=blood`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for flow cytometry objects via a full text query over\
+ \ all flow cytometry metadata. Queries matching dictionary terms are automatically\
+ \ expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "Autogenerated numeric ID that identifies a set of rows related\
+ \ to one run and is used to link data from the run to a sample. Multiple\
+ \ values can be provided as a list."
+ in: "query"
+ name: "runFilter"
+ schema:
+ $ref: "#/components/schemas/RunFilter"
+ style: "form"
+ - description: "Sample name from the file which allows retrieval of all the\
+ \ rows related to the sample. Multiple values can be provided as a list."
+ explode: true
+ in: "query"
+ name: "runSourceFilter"
+ schema:
+ items:
+ type: "string"
+ example: "Run Source ID"
+ type: "array"
+ style: "form"
+ - description: "Required value of \"Readout type\" column. E.g.: `Count`, `Median`"
+ in: "query"
+ name: "readoutType"
+ schema:
+ type: "string"
+ - description: "Value of \"Cell Population\" column. E.g.: `\"total cells\"\
+ `, `CD45+,live/CD45+`, `CD3+`.\n\nNote that if this value contains special\
+ \ characters like `/` which is used as a URI path separator, such characters\
+ \ should be escaped manually before sending request. For example, `/` should\
+ \ be escaped as `%2F`."
+ in: "query"
+ name: "population"
+ schema:
+ type: "string"
+ - description: "Marker value. E.g.: `PD1`, `BV786`"
+ in: "query"
+ name: "marker"
+ schema:
+ type: "string"
+ - description: "Minimum threshold (inclusive) for returned expression values."
+ in: "query"
+ name: "minValue"
+ schema:
+ type: "number"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "The page tag to resume results from (see paging above)."
+ in: "query"
+ name: "cursor"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/FlowCytometryResponse"
+ description: "Retrieved Flow Cytometry data."
+ "400":
+ content: {}
+ description: "Flow Cytometry data cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve multiple flow cytometry data and metadata objects"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-user/flow-cytometries/group:
+ get:
+ description: "Retrieve all group metadata objects that match a query.\n\n##\
+ \ Metadata full-text queries\nSingle words can be supplied as is, otherwise\
+ \ use speech marks (`\"`) to quote queries that include whitespace. Speech\
+ \ marks and backslash characters in the query need to be escaped with a backslash\
+ \ (`\\`).\n\n## Metadata filters\nMetadata filters are key-value pairs joined\
+ \ by an operator. The `=` operator matches literal values/string. The `!=`\
+ \ operator matches anything except the literal value/string. The `<` or `>`\
+ \ operators match numerical results that are less or greater than the supplied\
+ \ value. Strings containing whitespace need to be quoted with (`\"`).\n\n\
+ ## Combinations\nMetadata queries/filters for the same parameter can be combined\
+ \ with `&&`, `AND`, `||` and `OR` operators, using white-space to separate\
+ \ out the terms and operators. Parentheses `( )` can be used for complex expressions.\n\
+ \n## Versioning\nSpecific versions of omics data files (eg. GCT) can be queried\
+ \ via the useVersions parameter. Different versions of an omics data file\
+ \ are associated via their CHAIN_ID metadata value. This CHAIN_ID can be supplied\
+ \ to the useVersions parameter along with the version number or specific omics\
+ \ data file accessions to include them in the query. If nothing is supplied\
+ \ to the useVersions parameter then only the active version (which is usually\
+ \ the last one imported) is queried. This acts as a filter before the rest\
+ \ of the query is carried out.\n\nExample usage:\nuseVersions=* (query all\
+ \ versions, including those without CHAIN_IDs)\nuseVersions=v2 (query the\
+ \ second version. If there is no second version then the data file is not\
+ \ queried)\nuseVersions=v1,v0 (query the first version and any data files\
+ \ without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files with\
+ \ a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n## List operation\n\nThis endpoint can be called with no `query` parameter.\
+ \ Doing so returns a list of all data objects."
+ operationId: "searchFlowCytometryGroupsAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Filter by flow cytometry metadata (key-value metadata pair(s)).\
+ \ E.g. `Organ=blood`."
+ in: "query"
+ name: "filter"
+ schema:
+ type: "string"
+ - description: "Search for flow cytometry objects via a full text query over\
+ \ all flow cytometry metadata. Queries matching dictionary terms are automatically\
+ \ expanded to include synonyms."
+ in: "query"
+ name: "query"
+ schema:
+ type: "string"
+ - description: "If the full-text query term is present in an ODM dictionary,\
+ \ enabling this parameter will modify the query to include child terms of\
+ \ the full-text query.\n\nFor example, the search query \"Body fluid\" can\
+ \ be expanded to include the term \"Blood\" (a child term of \"Body fluid\"\
+ ) so files containing either \"Body fluid\" or \"Blood\" in their metadata\
+ \ will be returned in the search results.\n\nThe parent-child relationship\
+ \ is defined by the key \"broaders\" or \"subClassOf\" in the dictionary.\n\
+ \nIf the full query term is not present in a dictionary then this parameter\
+ \ has no effect."
+ in: "query"
+ name: "searchSpecificTerms"
+ schema:
+ type: "boolean"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve groups that match a query"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-user/flow-cytometries/group/by/run/{id}:
+ get:
+ operationId: "getFlowCytometryGroupByRunAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single group object by run ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-user/flow-cytometries/group/{id}:
+ get:
+ operationId: "getFlowCytometryGroupAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/MetadataWithId"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single group object by ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-user/flow-cytometries/runs/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size. In order to retrieve all matching results\
+ \ the client needs to request multiple pages starting from an offset to the\
+ \ first result. You can do this using the pageOffset query parameter. A value\
+ \ of 0 (the default) instructs the server to return the first page of results,\
+ \ 100 would return a page of results starting from the 101st result and so\
+ \ on. To retrieve all results, iterate through pages using `pageOffset` values\
+ \ of `n * pageLimit` until a page returns fewer results than the page limit,\
+ \ which indicates there are no more results.\n\n"
+ operationId: "searchFlowCytometryRunsAsUser"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Maximum number of results to return per page (see Paging above).\
+ \ This value must be between 0 and 2000 (inclusive). The default is 2000."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve run objects related to the given group"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-user/flow-cytometries/{id}:
+ get:
+ operationId: "getFlowCytometryAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/FlowCytometryItem"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single sample flow cytometry by ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-user/flow-cytometries/{id}/versions:
+ get:
+ operationId: "getFlowCytometryVersionsAsUser"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ items:
+ $ref: "#/components/schemas/CommitInfo"
+ type: "array"
+ description: "The request was successful. The returned value is the list\
+ \ of object versions."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a list of object versions by ID"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-user/flow-cytometries/{id}/versions/{version}:
+ get:
+ operationId: "getFlowCytometryByVersionAsUser"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Unique version of the object."
+ in: "path"
+ name: "version"
+ required: true
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template, default\
+ \ template will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/SignalRun"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve a single sample flow cytometry by ID (accession)"
+ tags:
+ - "Flow Cytometry SPoT as User"
+ /api/v1/as-curator/data-types:
+ get:
+ description: "This endpoint is for instructional uses and can be used to get\
+ \ the latest list of Data Types."
+ operationId: "getDataTypesAsCurator"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ items:
+ type: "string"
+ type: "array"
+ uniqueItems: true
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Lists all available data types."
+ tags:
+ - "Linkage as Curator"
+ /api/v1/as-curator/data-types/links:
+ get:
+ description: "This endpoint should be used for instructional needs, and can\
+ \ be used in order to get the links between the Data Types."
+ operationId: "getDataTypesLinksAsCurator"
+ parameters:
+ - description: "Return only links with the specified data type."
+ in: "query"
+ name: "type"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ items:
+ $ref: "#/components/schemas/SourceTypePair"
+ type: "array"
+ uniqueItems: true
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "List all possible links between data types that match the specified\
+ \ criteria."
+ tags:
+ - "Linkage as Curator"
+ /api/v1/as-curator/integration/link/expression/by/library/{id}:
+ get:
+ description: "## Versioning\nSpecific versions of omics data files (eg. GCT)\
+ \ can be queried via the useVersions parameter. Different versions of an omics\
+ \ data file are associated via their CHAIN_ID metadata value. This CHAIN_ID\
+ \ can be supplied to the useVersions parameter along with the version number\
+ \ or specific omics data file accessions to include them in the query. If\
+ \ nothing is supplied to the useVersions parameter then only the active version\
+ \ (which is usually the last one imported) is queried. This acts as a filter\
+ \ before the rest of the query is carried out.\n\nExample usage:\nuseVersions=*\
+ \ (query all versions, including those without CHAIN_IDs)\nuseVersions=v2\
+ \ (query the second version. If there is no second version then the data file\
+ \ is not queried)\nuseVersions=v1,v0 (query the first version and any data\
+ \ files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files\
+ \ with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n"
+ operationId: "getExpressionByLibraryAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return. This value must be between\
+ \ 0 and 2000 (inclusive)."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template default template\
+ \ will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ text/tab-separated-values:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve expression run-level data by querying related library ID\
+ \ (accession)"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/by/preparation/{id}:
+ get:
+ description: "## Versioning\nSpecific versions of omics data files (eg. GCT)\
+ \ can be queried via the useVersions parameter. Different versions of an omics\
+ \ data file are associated via their CHAIN_ID metadata value. This CHAIN_ID\
+ \ can be supplied to the useVersions parameter along with the version number\
+ \ or specific omics data file accessions to include them in the query. If\
+ \ nothing is supplied to the useVersions parameter then only the active version\
+ \ (which is usually the last one imported) is queried. This acts as a filter\
+ \ before the rest of the query is carried out.\n\nExample usage:\nuseVersions=*\
+ \ (query all versions, including those without CHAIN_IDs)\nuseVersions=v2\
+ \ (query the second version. If there is no second version then the data file\
+ \ is not queried)\nuseVersions=v1,v0 (query the first version and any data\
+ \ files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files\
+ \ with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n"
+ operationId: "getExpressionByPreparation"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return. This value must be between\
+ \ 0 and 2000 (inclusive)."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template default template\
+ \ will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ text/tab-separated-values:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve expression run-level data by querying related preparation\
+ \ ID (accession)"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/by/sample/{id}:
+ get:
+ description: "## Versioning\nSpecific versions of omics data files (eg. GCT)\
+ \ can be queried via the useVersions parameter. Different versions of an omics\
+ \ data file are associated via their CHAIN_ID metadata value. This CHAIN_ID\
+ \ can be supplied to the useVersions parameter along with the version number\
+ \ or specific omics data file accessions to include them in the query. If\
+ \ nothing is supplied to the useVersions parameter then only the active version\
+ \ (which is usually the last one imported) is queried. This acts as a filter\
+ \ before the rest of the query is carried out.\n\nExample usage:\nuseVersions=*\
+ \ (query all versions, including those without CHAIN_IDs)\nuseVersions=v2\
+ \ (query the second version. If there is no second version then the data file\
+ \ is not queried)\nuseVersions=v1,v0 (query the first version and any data\
+ \ files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files\
+ \ with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n"
+ operationId: "getExpressionBySampleAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return. This value must be between\
+ \ 0 and 2000 (inclusive)."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template default template\
+ \ will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ text/tab-separated-values:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve expression run-level data by querying related sample ID (accession)"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/group/by/study/{id}:
+ get:
+ description: "## Versioning\nSpecific versions of omics data files (eg. GCT)\
+ \ can be queried via the useVersions parameter. Different versions of an omics\
+ \ data file are associated via their CHAIN_ID metadata value. This CHAIN_ID\
+ \ can be supplied to the useVersions parameter along with the version number\
+ \ or specific omics data file accessions to include them in the query. If\
+ \ nothing is supplied to the useVersions parameter then only the active version\
+ \ (which is usually the last one imported) is queried. This acts as a filter\
+ \ before the rest of the query is carried out.\n\nExample usage:\nuseVersions=*\
+ \ (query all versions, including those without CHAIN_IDs)\nuseVersions=v2\
+ \ (query the second version. If there is no second version then the data file\
+ \ is not queried)\nuseVersions=v1,v0 (query the first version and any data\
+ \ files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files\
+ \ with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n"
+ operationId: "getExpressionGroupsByStudyAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or ``:`v` or ``:``"
+ in: "query"
+ name: "useVersions"
+ schema:
+ type: "string"
+ - description: "The parameter defines amount of metadata attributes to return:\n\
+ \n1. `minimal_data` - return metadata attributes according to the default\
+ \ template.\n2. `extended_data_included` - return metadata attributes according\
+ \ to applied template, if object doesn’t have applied template default template\
+ \ will be used. This is the default for User endpoints.\n3. `original_data_included`\
+ \ - return all metadata attributes with values and null attributes, if they\
+ \ are present in the applied template. This is the default for Curator endpoints."
+ in: "query"
+ name: "returnedMetadataFields"
+ schema:
+ enum:
+ - "minimal_data"
+ - "extended_data_included"
+ - "original_data_included"
+ type: "string"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ items:
+ $ref: "#/components/schemas/MetadataWithId"
+ type: "array"
+ description: "The request was successful. The returned value is the object."
+ "400":
+ content: {}
+ description: "The supplied object ID is invalid."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve group metadata by querying study ID (accession)"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/library/group/{targetId}:
+ delete:
+ description: "Delete link between a group of expression objects and a group\
+ \ of library objects"
+ operationId: "deleteExpressionGroupLibraryGroupLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the group of run-level objects (corresponding\
+ \ to a GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the library group object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link deleted."
+ "400":
+ content: {}
+ description: "Link cannot be deleted."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Delete link between a group of expression objects and a group of library\
+ \ objects"
+ tags:
+ - "Expression integration as Curator"
+ post:
+ description: "Create a link between a group of expression objects and a group\
+ \ of library objects.\n\nAn expression object can be linked to one object\
+ \ only. If an expression object is already linked to another object, this\
+ \ link will be deleted and a new link with the specified object will be created.\n\
+ Expression objects of the same group can only be linked to objects of the\
+ \ same study."
+ operationId: "createExpressionGroupLibraryGroupLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the group of run-level objects (corresponding\
+ \ to a GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the library group object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content: {}
+ description: "Some (not all) sample links created."
+ "204":
+ content: {}
+ description: "Link created."
+ "400":
+ content: {}
+ description: "Library group, signal group or libraries to link not found"
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Create a link between a group of expression objects and a group of\
+ \ library objects"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/preparation/group/{targetId}:
+ delete:
+ description: "Delete link between a group of expression objects and a group\
+ \ of preparation objects"
+ operationId: "deleteExpressionGroupPreparationGroupLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the group of run-level objects (corresponding\
+ \ to a GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the preparation group object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link deleted."
+ "400":
+ content: {}
+ description: "Link cannot be deleted."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Delete link between a group of expression objects and a group of preparation\
+ \ objects"
+ tags:
+ - "Expression integration as Curator"
+ post:
+ description: "Create a link between a group of expression objects and a group\
+ \ of preparation objects.\n\nAn expression object can be linked to one object\
+ \ only. If an expression object is already linked to another object, this\
+ \ link will be deleted and a new link with the specified object will be created.\n\
+ Expression objects of the same group can only be linked to objects of the\
+ \ same study."
+ operationId: "createExpressionGroupPreparationGroupLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the group of run-level objects (corresponding\
+ \ to a GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the preparation group object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content: {}
+ description: "Some (not all) sample links created."
+ "204":
+ content: {}
+ description: "Link created."
+ "400":
+ content: {}
+ description: "Preparation group, signal group or preparations to link not\
+ \ found"
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Create a link between a group of expression objects and a group of\
+ \ preparation objects"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/group/{sourceId}/to/sample/group/{targetId}:
+ delete:
+ description: "Delete link between a group of expression objects and a group\
+ \ of sample objects"
+ operationId: "deleteExpressionGroupSampleGroupLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the group of run-level objects (corresponding\
+ \ to a GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the sample group object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link deleted."
+ "400":
+ content: {}
+ description: "Link cannot be deleted."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Delete link between a group of expression objects and a group of sample\
+ \ objects"
+ tags:
+ - "Expression integration as Curator"
+ post:
+ description: "Create a link between a group of expression objects and a group\
+ \ of sample objects.\n\nAn expression object can be linked to one object only.\
+ \ If an expression object is already linked to another object, this link will\
+ \ be deleted and a new link with the specified object will be created.\nExpression\
+ \ objects of the same group can only be linked to objects of the same study.\n\
+ \n Users can specify a custom metadata field for linking omics data to samples\
+ \ via the “linkingAttribute” parameter, if not specified the “Sample Source\
+ \ ID“ sample metadata attribute will be used by default."
+ operationId: "createExpressionGroupSampleGroupLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the group of run-level objects (corresponding\
+ \ to a GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the sample group object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ - description: "Metadata field containing sample IDs to link omics data to samples.\
+ \ The template applied to the study must contain this field in the sample\
+ \ section."
+ in: "query"
+ name: "linkingAttribute"
+ schema:
+ type: "string"
+ responses:
+ "200":
+ content: {}
+ description: "Not all signal data were linked to the samples."
+ "204":
+ content: {}
+ description: "All signal data were linked to the samples from the specified\
+ \ sample group."
+ "400":
+ content: {}
+ description: "Sample group, signal group or samples to the link were not\
+ \ found, or the specified linking attribute was not found."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Create a link between a group of expression objects and a group of\
+ \ sample objects"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/run-to-libraries/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size. In order to retrieve all matching results\
+ \ the client needs to request multiple pages starting from an offset to the\
+ \ first result. You can do this using the pageOffset query parameter. A value\
+ \ of 0 (the default) instructs the server to return the first page of results,\
+ \ 100 would return a page of results starting from the 101st result and so\
+ \ on. To retrieve all results, iterate through pages using `pageOffset` values\
+ \ of `n * pageLimit` until a page returns fewer results than the page limit,\
+ \ which indicates there are no more results.\n\n"
+ operationId: "getExpressionRunToLibraryPairsAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return. This value must be between\
+ \ 0 and 2000 (inclusive)."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve run-library pairs by group id. Pagination is based on unique\
+ \ runs, not unique pairs."
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/run-to-preparations/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size. In order to retrieve all matching results\
+ \ the client needs to request multiple pages starting from an offset to the\
+ \ first result. You can do this using the pageOffset query parameter. A value\
+ \ of 0 (the default) instructs the server to return the first page of results,\
+ \ 100 would return a page of results starting from the 101st result and so\
+ \ on. To retrieve all results, iterate through pages using `pageOffset` values\
+ \ of `n * pageLimit` until a page returns fewer results than the page limit,\
+ \ which indicates there are no more results.\n\n"
+ operationId: "getExpressionRunToPreparationPairsAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return. This value must be between\
+ \ 0 and 2000 (inclusive)."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve run-preparation pairs by group id. Pagination is based on\
+ \ unique runs, not unique pairs."
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/run-to-samples/by/group/{id}:
+ get:
+ description: "## Paging\nFor performance reasons this endpoint returns results\
+ \ in \"pages\" of limited size. In order to retrieve all matching results\
+ \ the client needs to request multiple pages starting from an offset to the\
+ \ first result. You can do this using the pageOffset query parameter. A value\
+ \ of 0 (the default) instructs the server to return the first page of results,\
+ \ 100 would return a page of results starting from the 101st result and so\
+ \ on. To retrieve all results, iterate through pages using `pageOffset` values\
+ \ of `n * pageLimit` until a page returns fewer results than the page limit,\
+ \ which indicates there are no more results.\n\n"
+ operationId: "getExpressionRunToSamplePairsAsCurator"
+ parameters:
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return. This value must be between\
+ \ 0 and 2000 (inclusive)."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ responses:
+ "200":
+ content:
+ application/json:
+ schema:
+ $ref: "#/components/schemas/ListResponse"
+ description: "The request was successful. The returned value is a list of\
+ \ objects."
+ "400":
+ content: {}
+ description: "Entities cannot be retrieved."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "404":
+ content: {}
+ description: "No object exists with the given ID."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Retrieve run-sample pairs by group id. Pagination is based on unique\
+ \ runs, not unique pairs."
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/{sourceId}/to/library/{targetId}:
+ delete:
+ description: "Delete link between an expression object and a library"
+ operationId: "deleteExpressionLibraryLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the run-level object (corresponding to\
+ \ the column in a VCG/GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the library object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link deleted."
+ "400":
+ content: {}
+ description: "Link cannot be deleted."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Delete link between an expression object and a library"
+ tags:
+ - "Expression integration as Curator"
+ post:
+ description: "Create a link between an expression object and a library.\n\n\
+ An expression object can be linked to one object only. If an expression object\
+ \ is already linked to another object, this link will be deleted and a new\
+ \ link with the specified object will be created.\nExpression objects of the\
+ \ same group can only be linked to objects of the same study."
+ operationId: "createExpressionLibraryLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the run-level object (corresponding to\
+ \ the column in a VCG/GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the library object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link created."
+ "400":
+ content: {}
+ description: "Link cannot be created."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Create a link between an expression object and a library"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/{sourceId}/to/preparation/{targetId}:
+ delete:
+ description: "Delete link between an expression object and a preparation"
+ operationId: "deleteExpressionPreparationLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the run-level object (corresponding to\
+ \ the column in a VCG/GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the preparation object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link deleted."
+ "400":
+ content: {}
+ description: "Link cannot be deleted."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Delete link between an expression object and a preparation"
+ tags:
+ - "Expression integration as Curator"
+ post:
+ description: "Create a link between an expression object and a preparation.\n\
+ \nAn expression object can be linked to one object only. If an expression\
+ \ object is already linked to another object, this link will be deleted and\
+ \ a new link with the specified object will be created.\nExpression objects\
+ \ of the same group can only be linked to objects of the same study."
+ operationId: "createExpressionPreparationLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the run-level object (corresponding to\
+ \ the column in a VCG/GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the preparation object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link created."
+ "400":
+ content: {}
+ description: "Link cannot be created."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Create a link between an expression object and a preparation"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/expression/{sourceId}/to/sample/{targetId}:
+ delete:
+ description: "Delete link between an expression object and a sample"
+ operationId: "deleteExpressionSampleLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the run-level object (corresponding to\
+ \ the column in a VCG/GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the sample object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link deleted."
+ "400":
+ content: {}
+ description: "Link cannot be deleted."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Delete link between an expression object and a sample"
+ tags:
+ - "Expression integration as Curator"
+ post:
+ description: "Create a link between an expression object and a sample.\n\nAn\
+ \ expression object can be linked to one object only. If an expression object\
+ \ is already linked to another object, this link will be deleted and a new\
+ \ link with the specified object will be created.\nExpression objects of the\
+ \ same group can only be linked to objects of the same study."
+ operationId: "createExpressionSampleLinkAsCurator"
+ parameters:
+ - description: "The ID (accession) of the run-level object (corresponding to\
+ \ the column in a VCG/GCT file)"
+ in: "path"
+ name: "sourceId"
+ required: true
+ schema:
+ type: "string"
+ - description: "The ID (accession) of the sample object"
+ in: "path"
+ name: "targetId"
+ required: true
+ schema:
+ type: "string"
+ responses:
+ "204":
+ content: {}
+ description: "Link created."
+ "400":
+ content: {}
+ description: "Link cannot be created."
+ "401":
+ content: {}
+ description: "User is not authenticated. Please supply a valid Access Token\
+ \ in the `Authorization` HTTP header (e.g. Authorization: bearer [token])\n\
+ \ or Genestack API token in the `Genestack-API-Token` header (this token\
+ \ may be obtained from the Genestack UI _Profile_ page)."
+ "500":
+ content: {}
+ description: "An internal server error occurred. This indicates an unexpected\
+ \ failure in the Genestack system, please file a bug report to support@genestack.com,\
+ \ including the error details."
+ security:
+ - Access-token: []
+ - Genestack-API-Token: []
+ summary: "Create a link between an expression object and a sample"
+ tags:
+ - "Expression integration as Curator"
+ /api/v1/as-curator/integration/link/flow-cytometry/by/sample/{id}:
+ get:
+ description: "## Versioning\nSpecific versions of omics data files (eg. GCT)\
+ \ can be queried via the useVersions parameter. Different versions of an omics\
+ \ data file are associated via their CHAIN_ID metadata value. This CHAIN_ID\
+ \ can be supplied to the useVersions parameter along with the version number\
+ \ or specific omics data file accessions to include them in the query. If\
+ \ nothing is supplied to the useVersions parameter then only the active version\
+ \ (which is usually the last one imported) is queried. This acts as a filter\
+ \ before the rest of the query is carried out.\n\nExample usage:\nuseVersions=*\
+ \ (query all versions, including those without CHAIN_IDs)\nuseVersions=v2\
+ \ (query the second version. If there is no second version then the data file\
+ \ is not queried)\nuseVersions=v1,v0 (query the first version and any data\
+ \ files without CHAIN_IDs(v0) )\nuseVersions=GSVC002:v3 (for omics data files\
+ \ with a CHAIN_ID of GSCV002 query the third version)\nuseVersions=GSVC002:GSF00494,GSF000496\
+ \ (for omics data files with a CHAIN_ID of GSCV002 query only the specific\
+ \ accessions GSF00494 and GSF000496)\n\nRules for multiple CHAIN_IDs can be\
+ \ supplied to the parameter using the ; separator.\n\n## Paging\nFor performance\
+ \ reasons this endpoint returns results in \"pages\" of limited size. In order\
+ \ to retrieve all matching results the client needs to request multiple pages\
+ \ starting from an offset to the first result. You can do this using the pageOffset\
+ \ query parameter. A value of 0 (the default) instructs the server to return\
+ \ the first page of results, 100 would return a page of results starting from\
+ \ the 101st result and so on. To retrieve all results, iterate through pages\
+ \ using `pageOffset` values of `n * pageLimit` until a page returns fewer\
+ \ results than the page limit, which indicates there are no more results.\n\
+ \n"
+ operationId: "getFlowCytometryBySampleAsCurator"
+ parameters:
+ - description: "Supply this parameter with the value `term_id` as part of the\
+ \ query to return extended information including IDs for values and dictionaries."
+ in: "query"
+ name: "responseFormat"
+ schema:
+ $ref: "#/components/schemas/ResponseFormat"
+ - description: "Unique identifier (accession) of the object."
+ in: "path"
+ name: "id"
+ required: true
+ schema:
+ type: "string"
+ - description: "Maximum number of results to return. This value must be between\
+ \ 0 and 2000 (inclusive)."
+ in: "query"
+ name: "pageLimit"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Show the page {pageOffset+1} results from the start of the results.\
+ \ E.g. 100 will show a page of results starting from the 101st result.\
+ \ The default value is 0."
+ in: "query"
+ name: "pageOffset"
+ schema:
+ format: "int32"
+ type: "integer"
+ - description: "Specify which versions of omics data files are used in the query.\
+ \ By default the active version is used. See Versioning above. Syntax:\n\
+ \n\\* or `v` or `