BI-2109 - Create Sub-entity Dataset from UI

src/main/java/org/breedinginsight/api/model/v1/request/SubEntityDatasetRequest.java

@@ -0,0 +1,38 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.api.model.v1.request;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.*;
+
+import javax.validation.constraints.NotBlank;
+import javax.validation.constraints.NotNull;
+
+@Getter
+@Setter
+@Builder
+@ToString
+@AllArgsConstructor
+@NoArgsConstructor
+@Introspected
+public class SubEntityDatasetRequest {
+    @NotBlank
+    private String name;
+    @NotNull
+    private int repeatedMeasures;
+}

src/main/java/org/breedinginsight/api/v1/controller/ExperimentController.java

@@ -9,20 +9,25 @@
 import io.micronaut.security.annotation.Secured;
 import io.micronaut.security.rules.SecurityRule;
 import lombok.extern.slf4j.Slf4j;
+import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.api.auth.ProgramSecured;
 import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
+import org.breedinginsight.api.model.v1.request.SubEntityDatasetRequest;
 import org.breedinginsight.api.model.v1.response.Response;
 import org.breedinginsight.brapi.v2.model.request.query.ExperimentExportQuery;
 import org.breedinginsight.brapi.v2.services.BrAPITrialService;
 import org.breedinginsight.model.Dataset;
+import org.breedinginsight.model.DatasetMetadata;
 import org.breedinginsight.model.DownloadFile;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.services.exceptions.UnprocessableEntityException;
 import org.breedinginsight.utilities.response.mappers.ExperimentQueryMapper;
 
 import javax.inject.Inject;
 import javax.validation.Valid;
+import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
 
@@ -89,4 +94,57 @@ public HttpResponse<Response<Dataset>> getDatasetData(
         }
     }
 
+    /**
+     * Creates a sub-entity dataset for a given program and experiment with the specified name and number of repeated measures.
+     * @param programId The UUID of the program.
+     * @param experimentId The UUID of the experiment.
+     * @param datasetRequest The POST body, contains the dataset name and number of repeated measures to create.
+     * @return An HttpResponse with a Response object containing the newly created Dataset.
+     */
+    @Post("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/dataset")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse<Response<Dataset>> createSubEntityDataset(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId,
+            @Body @Valid SubEntityDatasetRequest datasetRequest) {
+        try {
+            Optional<Program> programOptional = programService.getById(programId);
+            if (programOptional.isEmpty()) {
+                return HttpResponse.status(HttpStatus.NOT_FOUND, "Program does not exist");
+            }
+
+            Response<Dataset> response = new Response(experimentService.createSubEntityDataset(programOptional.get(), experimentId, datasetRequest));
+            return HttpResponse.ok(response);
+        } catch (Exception e){
+            log.info(e.getMessage());
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        }
+    }
+
+    /**
+     * Retrieves the datasets for a given program and experiment.
+     *
+     * @param programId The UUID of the program.
+     * @param experimentId The UUID of the experiment.
+     * @return An HttpResponse with a Response object containing a list of DatasetMetadata.
+     * @throws DoesNotExistException if the program does not exist.
+     * @throws ApiException if an error occurs while retrieving the datasets.
+     */
+    @Get("/${micronaut.bi.api.version}/programs/{programId}/experiments/{experimentId}/datasets")
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    @Produces(MediaType.APPLICATION_JSON)
+    public HttpResponse<Response<List<DatasetMetadata>>> getDatasets(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("experimentId") UUID experimentId) throws DoesNotExistException, ApiException {
+
+        Optional<Program> programOptional = programService.getById(programId);
+        if (programOptional.isEmpty()) {
+            return HttpResponse.status(HttpStatus.NOT_FOUND, "Program does not exist");
+        }
+
+        Response<List<DatasetMetadata>> response = new Response(experimentService.getDatasetsMetadata(programOptional.get(), experimentId));
+        return HttpResponse.ok(response);
+
+    }
 }

src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java

@@ -43,7 +43,9 @@ public final class BrAPIAdditionalInfoFields {
     public static final String EXPERIMENT_NUMBER = "experimentNumber";
     public static final String ENVIRONMENT_NUMBER = "environmentNumber";
     public static final String STUDY_NAME = "studyName";
+    @Deprecated
     public static final String OBSERVATION_DATASET_ID = "observationDatasetId";
+    public static final String DATASETS = "datasets";
     public static final String FEMALE_PARENT_UNKNOWN = "femaleParentUnknown";
     public static final String MALE_PARENT_UNKNOWN = "maleParentUnknown";
 	public static final String TREATMENTS = "treatments";

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java

@@ -205,6 +205,24 @@ public List<BrAPIObservation> getObservationsByObservationUnitsAndVariables(Coll
                 .collect(Collectors.toList());
     }
 
+    public List<BrAPIObservation> getObservationsByObservationUnits(Collection<String> ouDbIds, Program program) throws ApiException {
+        if(ouDbIds.isEmpty()) {
+            return Collections.emptyList();
+        }
+        return getProgramObservations(program.getId()).values().stream()
+                .filter(o -> ouDbIds.contains(o.getObservationUnitDbId()))
+                .collect(Collectors.toList());
+    }
+
+    public List<BrAPIObservation> getObservationsByObservationUnitsAndStudies(Collection<String> ouDbIds, Collection<String> studyDbIds, Program program) throws ApiException {
+        if(ouDbIds.isEmpty()) {
+            return Collections.emptyList();
+        }
+        return getProgramObservations(program.getId()).values().stream()
+                .filter(o -> ouDbIds.contains(o.getObservationUnitDbId()) && studyDbIds.contains(o.getStudyDbId()))
+                .collect(Collectors.toList());
+    }
+
     @NotNull
     private ApiResponse<Pair<Optional<BrAPIObservationListResponse>, Optional<BrAPIAcceptedSearchResponse>>> searchObservationsSearchResultsDbIdGet(UUID programId, String searchResultsDbId, Integer page, Integer pageSize) throws ApiException {
         ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationUnitDAO.java

@@ -170,7 +170,8 @@ public List<BrAPIObservationUnit> getObservationUnitByName(List<String> observat
     }
 
     /**
-     * Create observation units, mutates brAPIObservationUnitList
+     * Create observation units with import progress.
+     * Mutates brAPIObservationUnitList.
      */
     public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservationUnit> brAPIObservationUnitList, UUID programId, ImportUpload upload) throws ApiException, DoesNotExistException {
         Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
@@ -190,6 +191,28 @@ public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservat
         }
     }
 
+    /**
+     * Create observation units without import progress.
+     * Mutates brAPIObservationUnitList.
+     */
+    public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservationUnit> brAPIObservationUnitList, UUID programId) throws ApiException, DoesNotExistException {
+        Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
+        ObservationUnitsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationUnitsApi.class);
+        try {
+            if (!brAPIObservationUnitList.isEmpty()) {
+                Callable<Map<String, BrAPIObservationUnit>> postFunction = () -> {
+                    preprocessObservationUnits(brAPIObservationUnitList);
+                    List<BrAPIObservationUnit> ous = brAPIDAOUtil.post(brAPIObservationUnitList, api::observationunitsPost);
+                    return processObservationUnitsForCache(ous, program, false);
+                };
+                return programObservationUnitCache.post(programId, postFunction);
+            }
+            return new ArrayList<>();
+        } catch (Exception e) {
+            throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
+        }
+    }
+
     public List<BrAPIObservationUnit> getObservationUnitsById(Collection<String> observationUnitExternalIds, Program program) throws ApiException {
         if(observationUnitExternalIds.isEmpty()) {
             return Collections.emptyList();
@@ -231,6 +254,21 @@ public List<BrAPIObservationUnit> getObservationUnitsForDataset(@NotNull String
                 .collect(Collectors.toList());
     }
 
+    public List<BrAPIObservationUnit> getObservationUnitsForDatasetAndEnvs(@NotNull String datasetId, Collection<String> envIds, @NotNull Program program) throws ApiException {
+        String datasetReferenceSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.DATASET);
+        String studyReferenceSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.STUDIES);
+        return getProgramObservationUnits(program.getId()).values().stream()
+                .filter(ou -> {
+                    Optional<BrAPIExternalReference> datasetExRef = Utilities.getExternalReference(ou.getExternalReferences(), datasetReferenceSource);
+                    Optional<BrAPIExternalReference> studyExRef = Utilities.getExternalReference(ou.getExternalReferences(), studyReferenceSource);
+                    return Boolean.logicalAnd(
+                            datasetExRef.map(x -> x.getReferenceId().equals(datasetId)).orElse(false),
+                            studyExRef.map(x -> envIds.contains(x.getReferenceId())).orElse(false)
+                    );
+                })
+                .collect(Collectors.toList());
+    }
+
     // Note: does not use cache, impractical to implement all search parameters client-side.
     public List<BrAPIObservationUnit> getObservationUnits(Program program,
                                                           Optional<String> observationUnitId,

src/main/java/org/breedinginsight/brapi/v2/model/request/query/ExperimentExportQuery.java

@@ -12,7 +12,7 @@
 @ToString
 public class ExperimentExportQuery {
     private FileType fileExtension;
-    private String dataset;
+    private String datasetId;
     private String environments;
     @NotNull
     private boolean includeTimestamps;

src/main/java/org/breedinginsight/brapi/v2/services/BrAPIObservationVariableService.java

@@ -31,6 +31,7 @@
 import org.breedinginsight.model.*;
 import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.utilities.DatasetUtil;
 import org.breedinginsight.utilities.Utilities;
 import org.jetbrains.annotations.NotNull;
 
@@ -55,6 +56,8 @@ public BrAPIObservationVariableService(
         this.referenceSource = referenceSource;
     }
 
+    // TODO: support sub-entity datasets.
+    // This gets the observation variables for the top-level dataset in an experiment.
     public List<Trait> getBrAPIObservationVariablesForExperiment(
             UUID programId,
             Optional<String> experimentId,
@@ -78,12 +81,10 @@ public List<Trait> getBrAPIObservationVariablesForExperiment(
         }
 
         BrAPITrial experiment = trialService.getExperiment(program.get(), expId);
-        if(experiment
-                .getAdditionalInfo().getAsJsonObject()
-                .has(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID)) {
-            String obsDatasetId = experiment
-                    .getAdditionalInfo().getAsJsonObject()
-                    .get(BrAPIAdditionalInfoFields.OBSERVATION_DATASET_ID).getAsString();
+        if(!experiment.getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS).isEmpty()) {
+            String obsDatasetId = DatasetUtil
+                    .getTopLevelDatasetFromJson(experiment.getAdditionalInfo().getAsJsonArray(BrAPIAdditionalInfoFields.DATASETS))
+                    .getId().toString();
             return trialService.getDatasetObsVars(obsDatasetId, program.get());
         }