Feature/bi 1716

src/main/java/org/breedinginsight/brapi/v2/ExperimentController.java

@@ -24,6 +24,7 @@
 
 import javax.inject.Inject;
 import javax.validation.Valid;
+import java.util.HashMap;
 import java.util.List;
 import java.util.UUID;
 
@@ -61,4 +62,25 @@ public HttpResponse<Response<DataResponse<List<BrAPITrial>>>> getExperiments(
             return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
         }
     }
+
+    @Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/trials/{trialId}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
+    public HttpResponse<Response<BrAPITrial>> getExperimentById(
+            @PathVariable("programId") UUID programId,
+            @PathVariable("trialId") UUID trialId,
+            @QueryValue(defaultValue = "false") Boolean stats){
+        try {
+            String logMsg = "fetching trial id:" +  trialId +" for program: " + programId;
+            if(stats){
+                logMsg += " with stats";
+            }
+            log.debug(logMsg);
+            Response<BrAPITrial> response = new Response<>(experimentService.getTrialDataByUUID(programId, trialId, stats));
+            return HttpResponse.ok(response);
+        } catch (DoesNotExistException e) {
+            log.info(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.NOT_FOUND, e.getMessage());
+        }
+    }
 }

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

@@ -1,13 +1,14 @@
 package org.breedinginsight.brapi.v2.services;
 
-import io.micronaut.context.annotation.Property;
 import io.micronaut.http.server.exceptions.InternalServerException;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import lombok.extern.slf4j.Slf4j;
 import org.brapi.v2.model.core.BrAPITrial;
+import org.brapi.v2.model.pheno.BrAPIObservationUnit;
+import org.breedinginsight.brapps.importer.daos.BrAPIObservationUnitDAO;
 import org.breedinginsight.brapps.importer.daos.BrAPITrialDAO;
-import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.utilities.Utilities;
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
@@ -17,19 +18,38 @@
 @Singleton
 public class BrAPITrialService {
 
-    @Property(name = "brapi.server.reference-source")
-    private String referenceSource;
-
     private final BrAPITrialDAO trialDAO;
-    private final ProgramService programService;
+    private final BrAPIObservationUnitDAO ouDAO;
 
     @Inject
-    public BrAPITrialService(ProgramService programService, BrAPITrialDAO trialDAO) {
-        this.programService = programService;
+    public BrAPITrialService( BrAPITrialDAO trialDAO,BrAPIObservationUnitDAO ouDAO) {
         this.trialDAO = trialDAO;
+        this.ouDAO = ouDAO;
     }
 
     public List<BrAPITrial> getExperiments(UUID programId) throws ApiException, DoesNotExistException {
         return trialDAO.getTrials(programId);
     }
+
+    public BrAPITrial getTrialDataByUUID(UUID programId, UUID trialId, boolean stats) throws DoesNotExistException {
+        try {
+            BrAPITrial trial = trialDAO.getTrialById(programId,trialId).orElseThrow(() -> new DoesNotExistException("Trial does not exist"));
+            //Remove the [program key] from the trial name
+            trial.setTrialName( Utilities.removeUnknownProgramKey( trial.getTrialName()) );
+            if( stats ){
+                int environmentsCount = 1; // For now this is hardcoded to 1, because we are only supporting one environment per experiment
+                long germplasmCount = countGermplasm(programId, trial.getTrialDbId());
+                trial.putAdditionalInfoItem("environmentsCount", environmentsCount);
+                trial.putAdditionalInfoItem("germplasmCount", germplasmCount);
+            }
+            return trial;
+        } catch (ApiException e) {
+            throw new InternalServerException(e.getMessage(), e);
+        }
+    }
+
+    private long countGermplasm(UUID programId, String trialDbId) throws ApiException, DoesNotExistException{
+        List<BrAPIObservationUnit> obUnits = ouDAO.getObservationUnitsForTrialDbId(programId, trialDbId);
+        return obUnits.stream().map(BrAPIObservationUnit::getGermplasmDbId).distinct().count();
+    }
 }

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPIObservationUnitDAO.java

@@ -26,7 +26,9 @@
 import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
 import org.breedinginsight.daos.ProgramDAO;
 import org.breedinginsight.model.Program;
+import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
+import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.utilities.BrAPIDAOUtil;
 
 import javax.inject.Inject;
@@ -36,44 +38,24 @@
 
 @Singleton
 public class BrAPIObservationUnitDAO {
-
-    public static String OU_ID_REFERENCE_SOURCE = "ou_id";
-
-    private ProgramDAO programDAO;
-    private ImportDAO importDAO;
+    private final ProgramDAO programDAO;
+    private final ImportDAO importDAO;
     private final BrAPIDAOUtil brAPIDAOUtil;
     private final BrAPIEndpointProvider brAPIEndpointProvider;
+    private final ProgramService programService;
 
     private final String referenceSource;
 
     @Inject
-    public BrAPIObservationUnitDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil brAPIDAOUtil, BrAPIEndpointProvider brAPIEndpointProvider, @Property(name = "brapi.server.reference-source") String referenceSource) {
+    public BrAPIObservationUnitDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil brAPIDAOUtil, BrAPIEndpointProvider brAPIEndpointProvider, ProgramService programService, @Property(name = "brapi.server.reference-source") String referenceSource) {
         this.programDAO = programDAO;
         this.importDAO = importDAO;
         this.brAPIDAOUtil = brAPIDAOUtil;
         this.brAPIEndpointProvider = brAPIEndpointProvider;
         this.referenceSource = referenceSource;
+        this.programService = programService;
     }
 
-    /*
-    public List<BrAPIObservationUnit> getObservationUnitsByNameAndStudyName(List<Pair<String, String>> nameStudyPairs, BrAPIProgram brAPIProgram) throws ApiException {
-
-        List<String> observationUnitNames = nameStudyPairs.stream().map(Pair::getLeft).collect(Collectors.toList());
-        BrAPIObservationUnitSearchRequest observationUnitSearchRequest = new BrAPIObservationUnitSearchRequest();
-        observationUnitSearchRequest.setObservationUnitNames(new ArrayList<>(observationUnitNames));
-        observationUnitSearchRequest.setProgramDbIds(List.of(brAPIProgram.getProgramDbId()));
-        ObservationUnitsApi api = brAPIProvider.getObservationUnitApi(BrAPIClientType.CORE);
-        List<BrAPIObservationUnit> observationUnits = BrAPIDAOUtil.search(
-                api::searchObservationunitsPost,
-                api::searchObservationunitsSearchResultsDbIdGet,
-                observationUnitSearchRequest
-        );
-
-        // TODO: Select for study as well
-        return observationUnits;
-    }
-     */
-
     public List<BrAPIObservationUnit> getObservationUnitByName(List<String> observationUnitNames, Program program) throws ApiException {
         if(observationUnitNames.isEmpty()) {
             return Collections.emptyList();
@@ -115,12 +97,25 @@ public List<BrAPIObservationUnit> getObservationUnitsById(Collection<String> obs
     public List<BrAPIObservationUnit> getObservationUnitsForStudyDbId(@NotNull String studyDbId, Program program) throws ApiException {
         BrAPIObservationUnitSearchRequest observationUnitSearchRequest = new BrAPIObservationUnitSearchRequest();
         observationUnitSearchRequest.programDbIds(List.of(program.getBrapiProgram()
-                                                                 .getProgramDbId()));
+                .getProgramDbId()));
         observationUnitSearchRequest.studyDbIds(List.of(studyDbId));
 
         ObservationUnitsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationUnitsApi.class);
         return brAPIDAOUtil.search(api::searchObservationunitsPost,
-                                   api::searchObservationunitsSearchResultsDbIdGet,
-                                   observationUnitSearchRequest);
+                api::searchObservationunitsSearchResultsDbIdGet,
+                observationUnitSearchRequest);
+    }
+    public List<BrAPIObservationUnit> getObservationUnitsForTrialDbId(@NotNull UUID programId, @NotNull String trialDbId) throws ApiException, DoesNotExistException {
+        Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
+
+        BrAPIObservationUnitSearchRequest observationUnitSearchRequest = new BrAPIObservationUnitSearchRequest();
+        observationUnitSearchRequest.programDbIds(List.of(program.getBrapiProgram()
+                .getProgramDbId()));
+        observationUnitSearchRequest.trialDbIds(List.of(trialDbId));
+
+        ObservationUnitsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationUnitsApi.class);
+        return brAPIDAOUtil.search(api::searchObservationunitsPost,
+                api::searchObservationunitsSearchResultsDbIdGet,
+                observationUnitSearchRequest);
     }
 }

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPITrialDAO.java

@@ -21,9 +21,6 @@
 import org.brapi.client.v2.modules.core.TrialsApi;
 import org.brapi.v2.model.core.BrAPITrial;
 import org.brapi.v2.model.core.request.BrAPITrialSearchRequest;
-import org.brapi.v2.model.core.response.BrAPIListDetails;
-import org.brapi.v2.model.core.response.BrAPIListResponse;
-import org.brapi.v2.model.core.response.BrAPITrialSingleResponse;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
 import org.breedinginsight.daos.ProgramDAO;
@@ -40,11 +37,13 @@
 
 @Singleton
 public class BrAPITrialDAO {
+    @Property(name = "brapi.server.reference-source")
+    private String BRAPI_REFERENCE_SOURCE;
 
-    private ProgramDAO programDAO;
-    private ImportDAO importDAO;
+    private final ProgramDAO programDAO;
+    private final ImportDAO importDAO;
     private final BrAPIDAOUtil brAPIDAOUtil;
-    private ProgramService programService;
+    private final ProgramService programService;
     private final BrAPIEndpointProvider brAPIEndpointProvider;
 
     private final String referenceSource;
@@ -75,6 +74,19 @@ public List<BrAPITrial> getTrialsByName(List<String> trialNames, Program program
         );
     }
 
+    private List<BrAPITrial> getTrialsByExRef(String referenceSource, String referenceId, Program program) throws ApiException {
+        BrAPITrialSearchRequest trialSearch = new BrAPITrialSearchRequest();
+        trialSearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
+        trialSearch.externalReferenceSources(List.of(referenceSource));
+        trialSearch.externalReferenceIDs(List.of(referenceId));
+        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), TrialsApi.class);
+        return brAPIDAOUtil.search(
+                api::searchTrialsPost,
+                api::searchTrialsSearchResultsDbIdGet,
+                trialSearch
+        );
+    }
+
     public List<BrAPITrial> createBrAPITrials(List<BrAPITrial> brAPITrialList, UUID programId, ImportUpload upload) throws ApiException {
         TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), TrialsApi.class);
         return brAPIDAOUtil.post(brAPITrialList, upload, api::trialsPost, importDAO::update);
@@ -123,12 +135,18 @@ private List<BrAPITrial> processExperimentsForDisplay(List<BrAPITrial> trials, S
         return displayExperiments;
     }
 
-    public Optional<BrAPITrial> getTrialByDbId(String trialDbId, Program program) throws ApiException {
-        List<BrAPITrial> trials = getTrialsByDbIds(List.of(trialDbId), program);
+    public Optional<BrAPITrial> getTrialById(UUID programId, UUID trialDbId) throws ApiException, DoesNotExistException {
+        Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Program id does not exist"));
+        String refSoure = Utilities.generateReferenceSource(BRAPI_REFERENCE_SOURCE, ExternalReferenceSource.TRIALS);
+        List<BrAPITrial> trials = getTrialsByExRef(refSoure, trialDbId.toString(), program);
 
         return Utilities.getSingleOptional(trials);
     }
 
+    public Optional<BrAPITrial> getTrialByDbId(String trialDbId, Program program) throws ApiException {
+        List<BrAPITrial> trials = getTrialsByDbIds(List.of(trialDbId), program);
+        return Utilities.getSingleOptional(trials);
+    }
     public List<BrAPITrial> getTrialsByDbIds(Collection<String> trialDbIds, Program program) throws ApiException {
         if(trialDbIds.isEmpty()) {
             return Collections.emptyList();

src/main/java/org/breedinginsight/utilities/Utilities.java

@@ -71,6 +71,17 @@ public static String appendProgramKey( String original, String programKey ){
         return appendProgramKey( original, programKey, null);
     }
 
+    /**
+     * Remove unknown program key from a string. Returns a new value instead of altering original string.
+     *
+     * @param original - The string with a [program key]
+     * @return - the original string without the [program key]
+     */
+    public static String removeUnknownProgramKey(String original) {
+        return original.replaceAll("\\[.*\\]", "").trim();
+    }
+
+
     /**
      * Remove program key from a string. Returns a new value instead of altering original string.
      *