Deduplicate spec

build.gradle.kts

@@ -6,6 +6,7 @@
  * actual or intended publication of such source code.
  */
 
+import com.genestack.openapi.TemplateSpecification
 import com.genestack.openapi.DownloadSpecification
 import org.openapitools.generator.gradle.plugin.tasks.GenerateTask
 import com.genestack.openapi.MergeSpecifications
@@ -27,13 +28,13 @@ val openApiVersion: String = System.getenv("OPENAPI_VERSION")
 val mergedFileName = "odmApi.yaml"
 val mergedFilePath = "${sourceDirectory}/${mergedFileName}"
 
-val sourceFileList = KotlinPath(sourceDirectory)
-    .listDirectoryEntries("*.yaml")
-    .sorted()
-    .map { layout.projectDirectory.file("${sourceDirectory}/${it.name}") }
-
 tasks {
+    val templateSpecs by registering(TemplateSpecification::class) {
+        inputDir = layout.projectDirectory.file(sourceDirectory)
+        outputDir = layout.projectDirectory.file(sourceDirectory)
+    }
     val downloadSpec by registering(DownloadSpecification::class) {
+        dependsOn(templateSpecs)
         version.set(processorsControllerVersion)
         registryUsername.set(System.getenv("NEXUS_USER"))
         registryPassword.set(System.getenv("NEXUS_PASSWORD"))
@@ -43,7 +44,7 @@ tasks {
     }
     val mergeSpecifications by registering(MergeSpecifications::class) {
         dependsOn(downloadSpec)
-        inputFiles = sourceFileList
+        inputDir = layout.projectDirectory.file(sourceDirectory)
         outputFile = layout.projectDirectory.file(mergedFilePath)
     }
     val generateOdmApiPython by registering(GenerateTask::class) {

buildSrc/src/main/kotlin/com/genestack/openapi/MergeSpecifications.kt

@@ -6,26 +6,26 @@ import org.gradle.api.file.RegularFileProperty
 import org.gradle.api.provider.ListProperty
 import org.gradle.api.tasks.OutputFile
 import org.gradle.api.tasks.TaskAction
-import org.gradle.api.tasks.InputFiles
+import org.gradle.api.tasks.InputDirectory
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory
 
 
 abstract class MergeSpecifications : DefaultTask() {
 
-    @get:InputFiles
-    abstract val inputFiles: ListProperty<RegularFile>
+    @get:InputDirectory
+    abstract val inputDir: RegularFileProperty
 
     @get:OutputFile
     abstract val outputFile: RegularFileProperty
 
     @TaskAction
     fun merge() {
         val objectMapper = ObjectMapper(YAMLFactory())
-        val mergedNode = inputFiles
-            .get().map { it.asFile }
-            .filterNot { it == outputFile.get().asFile }
+        val mergedNode = inputDir.get().asFile.listFiles { file ->
+            !file.name.contains("{Role}") && file.name.endsWith(".yaml")
+        }.sorted()
             .map { objectMapper.readTree(it) }
             .reduce { acc, node -> objectMapper.updateValue(acc, node) }
         objectMapper.writeValue(outputFile.get().asFile, mergedNode)

buildSrc/src/main/kotlin/com/genestack/openapi/TemplateSpecification.kt

@@ -0,0 +1,121 @@
+package com.genestack.openapi
+
+import org.gradle.api.DefaultTask
+import org.gradle.api.file.RegularFile
+import org.gradle.api.file.RegularFileProperty
+import org.gradle.api.provider.ListProperty
+import org.gradle.api.tasks.OutputFile
+import org.gradle.api.tasks.TaskAction
+import org.gradle.api.tasks.InputDirectory
+import org.gradle.api.tasks.OutputDirectory
+import java.io.File
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory
+
+
+abstract class TemplateSpecification : DefaultTask() {
+
+    @get:InputDirectory
+    abstract val inputDir: RegularFileProperty
+
+    @get:OutputDirectory
+    abstract val outputDir: RegularFileProperty
+
+    @TaskAction
+    fun template() {
+        inputDir.get().asFile.listFiles { file ->
+            file.name.contains("{Role}") && file.name.endsWith(".yaml")
+        }.forEach {
+            writeTemplated(it, "User")
+            writeTemplated(it, "Curator")
+        }
+    }
+
+    private fun writeTemplated(spec: File, role: String) {
+        val content = spec.readText()
+        val outputContent = StringBuilder()
+
+        // Role in lowercase for substitutions
+        val roleLowercase = role.lowercase()
+
+        // Define regex patterns for role matching
+        val rolePattern = """\{Role=([^}]+)\}""".toRegex()
+        val sectionStartPattern = """##\s*\{Role=([^}]+)\}""".toRegex()
+        val sectionEndPattern = """##\s*end\s*\{Role=([^}]+)\}""".toRegex()
+        val lineCommentPattern = """#\{Role=([^}]+)\}""".toRegex()
+
+        // Flag to track if we're inside a conditional section
+        var insideConditionalSection = false
+        var shouldIncludeSection = false
+        var sectionRole = ""
+
+        // Process line by line
+        content.lineSequence().withIndex().forEach { (index, line) ->
+            // Check if this line is the start of a conditional section
+            val sectionStartMatch = sectionStartPattern.find(line)
+            if (sectionStartMatch != null) {
+                if (insideConditionalSection) {
+                    throw IllegalStateException("Nested conditional sections are not allowed. Error in file: ${spec.name}, line ${index}")
+                }
+
+                insideConditionalSection = true
+                sectionRole = sectionStartMatch.groupValues[1]
+                shouldIncludeSection = (sectionRole == role)
+                // Skip this marker line
+                return@forEach
+            }
+
+            // Check if this line is the end of a conditional section
+            val sectionEndMatch = sectionEndPattern.find(line)
+            if (sectionEndMatch != null) {
+                if (!insideConditionalSection) {
+                    throw IllegalStateException("Found end marker without start marker. Error in file: ${spec.name}, line ${index}")
+                }
+
+                val endRole = sectionEndMatch.groupValues[1]
+                if (endRole != sectionRole) {
+                    throw IllegalStateException("Mismatched roles in section markers: $sectionRole vs $endRole. Error in file: ${spec.name}, line ${index}")
+                }
+
+                insideConditionalSection = false
+                shouldIncludeSection = false
+                // Skip this marker line
+                return@forEach
+            }
+
+            // If we're inside a conditional section and shouldn't include it, skip this line
+            if (insideConditionalSection && !shouldIncludeSection) {
+                return@forEach
+            }
+
+            // Handle single line conditional comments: #{Role=X}
+            val lineCommentMatch = lineCommentPattern.find(line)
+            if (lineCommentMatch != null) {
+                val commentRole = lineCommentMatch.groupValues[1]
+                if (commentRole == role) {
+                    // Keep the line but remove the comment
+                    val processedLine = line.replace(lineCommentPattern, "").trimEnd()
+                    outputContent.appendLine(processedLine)
+                }
+                // If role doesn't match, skip this line
+                return@forEach
+            }
+
+            // Process regular lines with substitutions
+            val processedLine = line.replace("{Role}", role).replace("{role}", roleLowercase)
+            outputContent.appendLine(processedLine)
+        }
+
+        // Check if we ended with an unclosed section
+        if (insideConditionalSection) {
+            throw IllegalStateException("Unclosed conditional section for role: $sectionRole. Error in file: ${spec.name}")
+        }
+
+        // Create output file with appropriate name
+        val outputFileName = spec.name.replace("{Role}", role)
+        val outputFile = File(outputDir.get().asFile, outputFileName)
+        outputFile.parentFile.mkdirs()
+        outputFile.writeText(outputContent.toString())
+    }
+}

openapi/v1/cellUser.yaml → openapi/v1/cell{Role}.yaml

@@ -5,11 +5,11 @@ info:
   title: ODM API
   version: default-released
 tags:
-  - name: Cells as User
+  - name: Cells as {Role}
 paths:
-  /api/v1/as-user/cells/{id}:
+  /api/v1/as-{role}/cells/{id}:
     get:
-      operationId: getCellByIdAsUser
+      operationId: getCellByIdAs{Role}
       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
@@ -45,15 +45,15 @@ paths:
         - Genestack-API-Token: [ ]
       summary: Retrieve a cell by ID
       tags:
-        - Cells as User
-  /api/v1/as-user/cells/by/group/{id}:
+        - Cells as {Role}
+  /api/v1/as-{role}/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
+      operationId: getCellsByGroupAs{Role}
       parameters:
         - description: Unique identifier (accession) of the cell group.
           in: path
@@ -102,7 +102,7 @@ paths:
         - Genestack-API-Token: [ ]
       summary: Retrieve cells from a given group
       tags:
-        - Cells as User
+        - Cells as {Role}
 components:
   schemas:
     Cell: