Skip to content

Change environment service in deprecated status #335

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
niio972 wants to merge 5 commits into
base: master
Choose a base branch
from
Open

Change environment service in deprecated status #335

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
7d9da83
Add sensor data subservice
niio972 Jan 14, 2020
6c335cd
Merge remote-tracking branch 'origin/master' into sensor-data
niio972 Feb 24, 2020
a15d120
Update remove environment
niio972 Feb 25, 2020
15c7b0c
Update environment service
niio972 Feb 26, 2020
247be64
Update sensor data service
niio972 Mar 11, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions phis2-ws/src/main/java/opensilex/service/dao/DataDAO.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -439,7 +439,7 @@ protected BasicDBObject prepareSearchQuery(String variableUri, String startDate,
}

// Objects filter
if (!objectsUris.isEmpty()) {
if (objectsUris != null && !objectsUris.isEmpty()) {
if (objectsUris.size() > 1) {
BasicDBList or = new BasicDBList();
for (String objectUri : objectsUris) {
Expand All @@ -453,7 +453,7 @@ protected BasicDBObject prepareSearchQuery(String variableUri, String startDate,
}

//Provenance filter
if (!provenancesUris.isEmpty()) {
if (provenancesUris != null && !provenancesUris.isEmpty()) {
if (provenancesUris.size() > 1) {
BasicDBList or = new BasicDBList();
for (String provenanceUri : provenancesUris) {
Expand Down
8 changes: 6 additions & 2 deletions phis2-ws/src/main/java/opensilex/service/documentation/StatusCodeMsg.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
/**
* Web service return messages.
* @see phenomeapi.service.view.brapi.Status
* @author Arnaud Charleroy <arnaud.charleroy@inra.fr>, Morgane Vidal <morgane.vidal@inra.fr>
* @author Arnaud Charleroy, Morgane Vidal
*/
@Singleton
public final class StatusCodeMsg {
Expand All @@ -28,6 +28,7 @@ public final class StatusCodeMsg {
public static final String DATA_ERROR = "Data error";
public static final String DATA_INSERTED = "Data inserted";
public static final String DATA_REJECTED = "Data rejected";
public static final String API_DEPRECATED_INFO_MESSAGE = "This api service should no longer be used. It will be change or removed";
public static final String ERR = "Error";
public static final String ERROR_WHILE_COMMITTING_OR_ROLLING_BACK_TRIPLESTORE_STATEMENT = "Error while committing or rolling back Triplestore statements: ";
public static final String EMPTY_EVENT_LIST = "The event list to create is empty";
Expand All @@ -36,6 +37,7 @@ public final class StatusCodeMsg {
public static final String FILE_ERROR = "File error";
public static final String INFO = "Info";
public static final String INTERNAL_ERROR = "An internal error occured. Please contact the administrator.";
public static final String INVALID_INPUT_PARAMETERS = "Wrong format parameter(s)";
public static final String MALFORMED_CREATE_QUERY = "Malformed create query";
public static final String MALFORMED_UPDATE_QUERY = "Malformed update query";
public static final String MALFORMED_URI = "Malformed URI";
Expand All @@ -57,5 +59,7 @@ public final class StatusCodeMsg {
public static final String UNKNOWN_TYPE = "Unknown type %s";
public static final String UNKNOWN_EVENT_URI = "Unknown event URI";
public static final String WRONG_VALUE = "Wrong value";
public static final String INVALID_INPUT_PARAMETERS = "Wrong format parameter(s)";
public static final String WARNING = "Warning";


}
18 changes: 14 additions & 4 deletions phis2-ws/src/main/java/opensilex/service/resource/EnvironmentResourceService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -49,11 +49,15 @@

/**
* Environmental measure resource service.
* @author Morgane Vidal <morgane.vidal@inra.fr>
* @author Morgane Vidal
*/
@Api("/environments")
@Path("/environments")
@Deprecated
public class EnvironmentResourceService extends ResourceService {

private final Status deprecatedStatus = new Status(StatusCodeMsg.WARNING, StatusCodeMsg.WARNING, StatusCodeMsg.API_DEPRECATED_INFO_MESSAGE);

/**
* Generates environmental measures from a given list of environmental measures DTOs.
* @param environmentMeasureDTOs
Expand Down Expand Up @@ -105,6 +109,7 @@ private List<EnvironmentMeasure> environmentMeasurePostDTOsToEnvironmentMeasure(
})
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
@Deprecated
public Response postEnvironmentMeasures(
@ApiParam(value = DocumentationAnnotation.ENVIRONMENT_POST_DEFINITION) @Valid ArrayList<EnvironmentMeasurePostDTO> environmentMeasures,
@Context HttpServletRequest context) {
Expand All @@ -116,7 +121,8 @@ public Response postEnvironmentMeasures(
environmentDAO.user = userSession.getUser();

POSTResultsReturn result = environmentDAO.checkAndInsert(environmentMeasurePostDTOsToEnvironmentMeasure(environmentMeasures));

result.statusList.add(deprecatedStatus);

if (result.getHttpStatus().equals(Response.Status.CREATED)) {
postResponse = new ResponseFormPOST(result.statusList);
postResponse.getMetadata().setDatafiles(result.getCreatedResources());
Expand All @@ -127,7 +133,10 @@ public Response postEnvironmentMeasures(
}
return Response.status(result.getHttpStatus()).entity(postResponse).build();
} else {
postResponse = new ResponseFormPOST(new Status(StatusCodeMsg.REQUEST_ERROR, StatusCodeMsg.ERR, "Empty environment measure(s) to add"));
List statusList = new ArrayList<>();
statusList.add(new Status(StatusCodeMsg.REQUEST_ERROR, StatusCodeMsg.ERR, "Empty environment measure(s) to add"));
statusList.add(deprecatedStatus);
postResponse = new ResponseFormPOST(statusList);
return Response.status(Response.Status.BAD_REQUEST).entity(postResponse).build();
}
}
Expand Down Expand Up @@ -191,6 +200,7 @@ public Response postEnvironmentMeasures(
example = GlobalWebserviceValues.AUTHENTICATION_SCHEME + " ")
})
@Produces(MediaType.APPLICATION_JSON)
@Deprecated
public Response getEnvironmentMeasures(
@ApiParam(value = DocumentationAnnotation.PAGE_SIZE) @QueryParam(GlobalWebserviceValues.PAGE_SIZE) @DefaultValue(DefaultBrapiPaginationValues.PAGE_SIZE) @Min(0) int pageSize,
@ApiParam(value = DocumentationAnnotation.PAGE) @QueryParam(GlobalWebserviceValues.PAGE) @DefaultValue(DefaultBrapiPaginationValues.PAGE) @Min(0) int page,
Expand Down Expand Up @@ -224,7 +234,7 @@ public Response getEnvironmentMeasures(
ArrayList<EnvironmentMeasureDTO> list = new ArrayList<>();
ArrayList<Status> statusList = new ArrayList<>();
ResultForm<EnvironmentMeasureDTO> getResponse;

statusList.add(deprecatedStatus);
if (measures == null) {
// Request failure
getResponse = new ResultForm<>(0, 0, list, true, 0);
Expand Down
151 changes: 144 additions & 7 deletions phis2-ws/src/main/java/opensilex/service/resource/SensorResourceService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
//******************************************************************************
package opensilex.service.resource;

import com.mongodb.BasicDBObjectBuilder;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiImplicitParam;
import io.swagger.annotations.ApiImplicitParams;
Expand All @@ -18,7 +19,6 @@
import java.util.List;
import javax.servlet.http.HttpServletRequest;
import javax.validation.Valid;
import javax.validation.constraints.Email;
import javax.validation.constraints.Min;
import javax.ws.rs.Consumes;
import javax.ws.rs.DefaultValue;
Expand All @@ -36,11 +36,14 @@
import opensilex.service.configuration.DateFormat;
import opensilex.service.configuration.DefaultBrapiPaginationValues;
import opensilex.service.configuration.GlobalWebserviceValues;
import opensilex.service.dao.DataDAO;
import opensilex.service.dao.ProvenanceDAO;
import opensilex.service.dao.SensorDAO;
import opensilex.service.dao.SensorProfileDAO;
import opensilex.service.dao.exception.DAOPersistenceException;
import opensilex.service.documentation.DocumentationAnnotation;
import opensilex.service.documentation.StatusCodeMsg;
import opensilex.service.model.Data;
import opensilex.service.resource.validation.interfaces.Date;
import opensilex.service.resource.validation.interfaces.Required;
import opensilex.service.resource.validation.interfaces.URL;
Expand All @@ -51,17 +54,19 @@
import opensilex.service.view.brapi.form.ResponseFormPOST;
import opensilex.service.result.ResultForm;
import opensilex.service.model.Sensor;
import opensilex.service.resource.dto.data.DataDTO;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import opensilex.service.resource.dto.sensor.SensorDTO;
import opensilex.service.resource.dto.sensor.SensorDetailDTO;
import opensilex.service.resource.dto.sensor.SensorPostDTO;
import opensilex.service.resource.dto.sensor.SensorProfileDTO;
import opensilex.service.view.model.provenance.Provenance;

/**
* Sensor resource service.
* @update [Andreas Garcia] 15 Apr. 2019: handle DAO persistence exceptions thrown by property DAO functions.
* @author Morgane Vidal <morgane.vidal@inra.fr>
* @author Morgane Vidal
*/
@Api("/sensors")
@Path("/sensors")
Expand Down Expand Up @@ -175,10 +180,12 @@ public Response getSensorsBySearch(
SensorDAO sensorDAO = new SensorDAO();
//1. Get count
Integer totalCount = sensorDAO.count(uri, rdfType, label, brand, serialNumber, model, inServiceDate, dateOfPurchase, dateOfLastCalibration, personInCharge);

//2. Get sensors
ArrayList<Sensor> sensorsFounded = sensorDAO.find(page, pageSize, uri, rdfType, label, brand, serialNumber, model, inServiceDate, dateOfPurchase, dateOfLastCalibration, personInCharge);

ArrayList<Sensor> sensorsFounded = new ArrayList<>();
//2. Get sensors
if(totalCount > 0){
sensorsFounded = sensorDAO.find(page, pageSize, uri, rdfType, label, brand, serialNumber, model, inServiceDate, dateOfPurchase, dateOfLastCalibration, personInCharge);
}

//3. Return result
ArrayList<Status> statusList = new ArrayList<>();
ArrayList<SensorDTO> sensorsToReturn = new ArrayList<>();
Expand Down Expand Up @@ -649,4 +656,134 @@ public Response putMeasuredVariables(

return Response.status(result.getHttpStatus()).entity(postResponse).build();
}
}

/**
* Sensor Data GET service.
*
* @param pageSize
* @param page
* @param provenanceUri
* @param variablesUri
* @param startDate
* @param endDate
* @param object
* @param uri
* @return list of the data corresponding to the search params given
* @example
* {
* "metadata": {
* "pagination": {
* "pageSize": 20,
* "currentPage": 0,
* "totalCount": 3,
* "totalPages": 1
* },
* "status": [],
* "datafiles": []
* },
* "result": {
* "data": [
* {
* "uri": "http://www.phenome-fppn.fr/diaphen/id/data/d2plf65my4rc2odiv2lbjgukc2zswkqyoddh25jtoy4b5pf3le3q4ec5c332f5cd44ce82977e404cebf83c",
* "provenanceUri": "http://www.phenome-fppn.fr/mtp/2018/pv181515071552",
* "objectUri": "http://www.phenome-fppn.fr/diaphen/2018/o18001199",
* "variableUri": "http://www.phenome-fppn.fr/diaphen/id/variables/v009",
* "date": "2017-06-15T00:00:00+0200",
* "value": 2.4
* },
* {
* "uri": "http://www.phenome-fppn.fr/diaphen/id/data/pttdrrqybxoyku4img323dyrhmpp267mhnpiw3vld2wm6tap3vwq93b344c429ec45bb9b185edfe5bc2b64",
* "provenanceUri": "http://www.phenome-fppn.fr/mtp/2018/pv181515071552",
* "objectUri": "http://www.phenome-fppn.fr/diaphen/2018/o18001199",
* "variableUri": "http://www.phenome-fppn.fr/diaphen/id/variables/v009",
* "date": "2017-06-16T00:00:00+0200",
* "value": "2017-06-15T00:00:00+0200"
* }
* ]
* }
* }
*/
@GET
@Path("{uri}/data")
@ApiOperation(value = "Get data mesured by a sensor")
@ApiResponses(value = {
@ApiResponse(code = 201, message = "Data mesured by a sensor", response = ResponseFormPOST.class),
@ApiResponse(code = 400, message = DocumentationAnnotation.BAD_USER_INFORMATION),
@ApiResponse(code = 401, message = DocumentationAnnotation.USER_NOT_AUTHORIZED),
@ApiResponse(code = 500, message = DocumentationAnnotation.ERROR_SEND_DATA)
})
@ApiImplicitParams({
@ApiImplicitParam(name = GlobalWebserviceValues.AUTHORIZATION, required = true,
dataType = GlobalWebserviceValues.DATA_TYPE_STRING, paramType = GlobalWebserviceValues.HEADER,
value = DocumentationAnnotation.ACCES_TOKEN,
example = GlobalWebserviceValues.AUTHENTICATION_SCHEME + " ")
})
@Consumes(MediaType.APPLICATION_JSON)
@Produces(MediaType.APPLICATION_JSON)
public Response getSensorData(
@PathParam("uri") @Required @URL String uri,
@ApiParam(value = "Search by variable", example = DocumentationAnnotation.EXAMPLE_VARIABLE_URI, required = true) @QueryParam("variable") @Required @URL String variablesUri,
@ApiParam(value = "Search by provenance", example = DocumentationAnnotation.EXAMPLE_PROVENANCE_URI) @QueryParam("provenance") @URL String provenanceUri,
@ApiParam(value = "Search by minimal date", example = DocumentationAnnotation.EXAMPLE_XSDDATETIME) @QueryParam("startDate") @Date({DateFormat.YMDTHMSZ, DateFormat.YMD}) String startDate,
@ApiParam(value = "Search by maximal date", example = DocumentationAnnotation.EXAMPLE_XSDDATETIME) @QueryParam("endDate") @Date({DateFormat.YMDTHMSZ, DateFormat.YMD}) String endDate,
@ApiParam(value = "Search by object uri", example = DocumentationAnnotation.EXAMPLE_SCIENTIFIC_OBJECT_URI) @QueryParam("object") @URL String object,
@ApiParam(value = DocumentationAnnotation.PAGE_SIZE) @QueryParam(GlobalWebserviceValues.PAGE_SIZE) @DefaultValue(DefaultBrapiPaginationValues.PAGE_SIZE) @Min(0) int pageSize,
@ApiParam(value = DocumentationAnnotation.PAGE) @QueryParam(GlobalWebserviceValues.PAGE) @DefaultValue(DefaultBrapiPaginationValues.PAGE) @Min(0) int page
) {
DataDAO dataDAO = new DataDAO();
dataDAO.setPage(page);
dataDAO.setPageSize(pageSize);

ProvenanceDAO provenanceDAO = new ProvenanceDAO();
provenanceDAO.setPage(0);
provenanceDAO.setPageSize(500);

//1. Get associated sensors
ArrayList<String> provenanceUrisAssociatedToSensor = new ArrayList<>();
if (provenanceUri != null) {
provenanceUrisAssociatedToSensor.add(provenanceUri);
} else {
Provenance searchProvenance = new Provenance();
String jsonFilter = BasicDBObjectBuilder.start("metadata.prov:Agent.prov:id", uri).get().toString();
ArrayList<Provenance> provenances = provenanceDAO.getProvenances(searchProvenance, jsonFilter);

for (Provenance provenance : provenances) {
provenanceUrisAssociatedToSensor.add(provenance.getUri());
}
}
List<String> objectsUris = new ArrayList<>();
List<Data> dataFounded = new ArrayList<>();
Integer totalCount = 0;
if (!provenanceUrisAssociatedToSensor.isEmpty()) {
if (object != null) {
objectsUris.add(object);
}
//2. Get sensor data count
totalCount = dataDAO.count(variablesUri, startDate, endDate, objectsUris, provenanceUrisAssociatedToSensor);
//3. Get sensor data
if (totalCount > 0) {
dataFounded = dataDAO.find(page, pageSize, variablesUri, startDate, endDate, objectsUris, provenanceUrisAssociatedToSensor);
}
}
//4. Return result
ArrayList<Status> statusList = new ArrayList<>();
ArrayList<DataDTO> sensorsToReturn = new ArrayList<>();
ResultForm<DataDTO> getResponse;
if (dataFounded == null) { //Request failure
getResponse = new ResultForm<>(0, 0, sensorsToReturn, true);
return noResultFound(getResponse, statusList);
} else if (dataFounded.isEmpty()) { //No result found
getResponse = new ResultForm<>(0, 0, sensorsToReturn, true);
return noResultFound(getResponse, statusList);
} else { //Results
//Convert all objects to DTOs
dataFounded.forEach((data) -> {
sensorsToReturn.add(new DataDTO(data));
});

getResponse = new ResultForm<>(pageSize, page, sensorsToReturn, true, totalCount);
getResponse.setStatus(statusList);
return Response.status(Response.Status.OK).entity(getResponse).build();
}
}
}
5 changes: 2 additions & 3 deletions phis2-ws/src/main/java/opensilex/service/resource/dto/data/DataPostDTO.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,8 +56,7 @@ public class DataPostDTO extends AbstractVerifiedClass {
protected Object value;

@URL
@Required
@ApiModelProperty(example = DocumentationAnnotation.EXAMPLE_SENSOR_URI)
@ApiModelProperty(example = DocumentationAnnotation.EXAMPLE_SCIENTIFIC_OBJECT_URI)
public String getObjectUri() {
return objectUri;
}
Expand Down Expand Up @@ -161,4 +160,4 @@ private BigDecimal getBigDecimalOrNullIfInvalid(String value) {
return null;
}
}
}
}