BI-1195 - 4.3 Exp Preview: Append Experiment with Observations

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

@@ -24,6 +24,7 @@
 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.*;
 import org.breedinginsight.api.model.v1.request.*;
 import org.breedinginsight.api.model.v1.request.query.QueryParams;
@@ -37,6 +38,7 @@
 import org.breedinginsight.model.*;
 import org.breedinginsight.services.ProgramObservationLevelService;
 import org.breedinginsight.services.exceptions.*;
+import org.breedinginsight.utilities.Utilities;
 import org.breedinginsight.utilities.response.mappers.ProgramLocationQueryMapper;
 import org.breedinginsight.utilities.response.mappers.ProgramQueryMapper;
 import org.breedinginsight.api.model.v1.response.DataResponse;
@@ -302,6 +304,9 @@ public HttpResponse<Response<DataResponse<ProgramLocation>>> getProgramLocations
         } catch (DoesNotExistException e){
             log.info(e.getMessage());
             return HttpResponse.notFound();
+        } catch (ApiException e) {
+            log.error("Error fetching program locations: " + Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
         }
     }
 
@@ -318,8 +323,11 @@ public HttpResponse<Response<DataResponse<ProgramLocation>>> postProgramLocation
             return ResponseUtils.getQueryResponse(programLocations, programLocationQueryMapper, searchRequest, queryParams);
 
         } catch (DoesNotExistException e){
-            log.info(e.getMessage());
+            log.error(e.getMessage(), e);
             return HttpResponse.notFound();
+        } catch (ApiException e) {
+            log.error("Error fetching program locations: " + Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
         }
 
     }
@@ -332,7 +340,13 @@ public HttpResponse<Response<DataResponse<ProgramLocation>>> postProgramLocation
     public HttpResponse<Response<ProgramLocation>> getProgramLocations(@PathVariable UUID programId,
                                                                        @PathVariable UUID locationId) {
 
-        Optional<ProgramLocation> programLocation = programLocationService.getById(programId, locationId);
+        Optional<ProgramLocation> programLocation = null;
+        try {
+            programLocation = programLocationService.getById(programId, locationId);
+        } catch (ApiException e) {
+            log.error("Error fetching program location: " + Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.serverError();
+        }
 
         if(programLocation.isPresent()) {
             Response<ProgramLocation> response = new Response(programLocation.get());

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

@@ -30,6 +30,7 @@
 import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
 import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
 import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
+import org.breedinginsight.utilities.Utilities;
 import org.breedinginsight.utilities.response.mappers.GermplasmQueryMapper;
 import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
 import org.breedinginsight.brapps.importer.model.exports.FileType;
@@ -44,10 +45,7 @@
 
 import javax.inject.Inject;
 import javax.validation.Valid;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.UUID;
+import java.util.*;
 
 @Slf4j
 @Controller("/${micronaut.bi.api.version}")
@@ -205,7 +203,9 @@ public HttpResponse<BrAPIGermplasmPedigreeResponse> getGermplasmPedigreeInfo(
                 metadata.setPagination(pagination);
                 response = new BrAPIGermplasmPedigreeResponse();
             } else {
-                BrAPIGermplasm germplasm = germplasmService.getGermplasmByDBID(programId, germplasmId);
+                BrAPIGermplasm germplasm = germplasmService.getGermplasmByDBID(programId, germplasmId)
+                                                                             .orElseThrow(() -> new DoesNotExistException("DBID for this germplasm does not exist"));
+
                 //Forward the pedigree call to the backing BrAPI system of the program passing the germplasmDbId that came in the request
                 GermplasmApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), GermplasmApi.class);
                 ApiResponse<BrAPIGermplasmPedigreeResponse> pedigreeResponse = api.germplasmGermplasmDbIdPedigreeGet(germplasmId, notation, includeSiblings);
@@ -238,12 +238,15 @@ public HttpResponse<BrAPIGermplasmPedigreeResponse> getGermplasmPedigreeInfo(
             response.setResult(returnNode);
             response.setMetadata(metadata);
             return HttpResponse.ok(response);
-        } catch (InternalServerException | ApiException e) {
+        } catch (InternalServerException e) {
             log.error(e.getMessage(), e);
             return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
         } catch (DoesNotExistException e) {
             log.error(e.getMessage(), e);
             return HttpResponse.status(HttpStatus.NOT_FOUND, "Pedigree node not found");
+        } catch (ApiException e) {
+            log.info(Utilities.generateApiExceptionLogMessage(e), e);
+            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
         }
     }
 
@@ -302,8 +305,11 @@ public HttpResponse<BrAPIGermplasmProgenyResponse> getGermplasmProgenyInfo(
                 }
                 return HttpResponse.ok(progenyResponse.getBody());
             }
-        } catch (InternalServerException | ApiException e) {
-            log.info(e.getMessage(), e);
+        } catch (InternalServerException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e), e);
             return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
         }
     }

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

@@ -273,15 +273,22 @@ public BrAPIGermplasm getGermplasmByUUID(String germplasmId, UUID programId) thr
         return germplasm;
     }
 
-    public BrAPIGermplasm getGermplasmByDBID(String germplasmDbId, UUID programId) throws ApiException, DoesNotExistException {
+    public Optional<BrAPIGermplasm> getGermplasmByDBID(String germplasmDbId, UUID programId) throws ApiException {
         Map<String, BrAPIGermplasm> cache = programGermplasmCache.get(programId);
         //key is UUID, want to filter by DBID
         BrAPIGermplasm germplasm = null;
         if (cache != null) {
             germplasm = cache.values().stream().filter(x -> x.getGermplasmDbId().equals(germplasmDbId)).collect(Collectors.toList()).get(0);
         }
-        if (germplasm == null) {
-            throw new DoesNotExistException("DBID for this germplasm does not exist");
+        return Optional.ofNullable(germplasm);
+    }
+
+    public List<BrAPIGermplasm> getGermplasmsByDBID(Collection<String> germplasmDbIds, UUID programId) throws ApiException {
+        Map<String, BrAPIGermplasm> cache = programGermplasmCache.get(programId);
+        //key is UUID, want to filter by DBID
+        List<BrAPIGermplasm> germplasm = new ArrayList<>();
+        if (cache != null) {
+            germplasm = cache.values().stream().filter(x -> germplasmDbIds.contains(x.getGermplasmDbId())).collect(Collectors.toList());
         }
         return germplasm;
     }

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

@@ -73,12 +73,8 @@ public BrAPIGermplasm getGermplasmByUUID(UUID programId, String germplasmId) thr
         }
     }
 
-    public BrAPIGermplasm getGermplasmByDBID(UUID programId, String germplasmId) throws DoesNotExistException {
-        try {
-            return germplasmDAO.getGermplasmByDBID(germplasmId, programId);
-        } catch (ApiException e) {
-            throw new InternalServerException(e.getMessage(), e);
-        }
+    public Optional<BrAPIGermplasm> getGermplasmByDBID(UUID programId, String germplasmId) throws ApiException {
+        return germplasmDAO.getGermplasmByDBID(germplasmId, programId);
     }
 
     public List<BrAPIListSummary> getGermplasmListsByProgramId(UUID programId, HttpRequest<String> request) throws DoesNotExistException, ApiException {

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

@@ -21,7 +21,9 @@
 import org.breedinginsight.utilities.Utilities;
 
 import javax.inject.Inject;
+import javax.validation.constraints.NotNull;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.UUID;
 
@@ -42,6 +44,10 @@ public BrAPIListDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil brA
     }
 
     public List<BrAPIListSummary> getListByName(List<String> listNames, UUID programId) throws ApiException {
+        if(listNames.isEmpty()) {
+            return Collections.emptyList();
+        }
+
         BrAPIListSearchRequest listSearch = new BrAPIListSearchRequest();
         listSearch.listNames(listNames);
         ListsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ListsApi.class);
@@ -58,7 +64,7 @@ public BrAPIListsSingleResponse getListById(String listId, UUID programId) throw
         return response.getBody();
     }
 
-    public List<BrAPIListSummary> getListByTypeAndExternalRef(BrAPIListTypes listType, UUID programId, String externalReferenceSource, UUID externalReferenceId) throws ApiException {
+    public List<BrAPIListSummary> getListByTypeAndExternalRef(@NotNull BrAPIListTypes listType, UUID programId, String externalReferenceSource, UUID externalReferenceId) throws ApiException {
         BrAPIListSearchRequest searchRequest = new BrAPIListSearchRequest()
                 .externalReferenceIDs(List.of(externalReferenceId.toString()))
                 .externalReferenceSources(List.of(externalReferenceSource))

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

@@ -28,9 +28,7 @@
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.UUID;
+import java.util.*;
 
 @Singleton
 public class BrAPILocationDAO {
@@ -49,6 +47,9 @@ public BrAPILocationDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil
     }
 
     public List<BrAPILocation> getLocationsByName(List<String> locationNames, UUID programId) throws ApiException {
+        if(locationNames.isEmpty()) {
+            return Collections.emptyList();
+        }
 
         BrAPILocationSearchRequest locationSearchRequest = new BrAPILocationSearchRequest();
         locationSearchRequest.setLocationNames(new ArrayList<>(locationNames));
@@ -61,9 +62,24 @@ public List<BrAPILocation> getLocationsByName(List<String> locationNames, UUID p
         );
     }
 
-    public List<BrAPILocation> createBrAPILocation(List<BrAPILocation> brAPILocationList, UUID programId, ImportUpload upload) throws ApiException {
+    public List<BrAPILocation> createBrAPILocations(List<BrAPILocation> brAPILocationList, UUID programId, ImportUpload upload) throws ApiException {
         LocationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), LocationsApi.class);
         return brAPIDAOUtil.post(brAPILocationList, upload, api::locationsPost, importDAO::update);
     }
 
+    public List<BrAPILocation> getLocationsByDbId(Collection<String> locationDbIds, UUID programId) throws ApiException {
+        if(locationDbIds.isEmpty()) {
+            return Collections.emptyList();
+        }
+
+        BrAPILocationSearchRequest locationSearchRequest = new BrAPILocationSearchRequest();
+        locationSearchRequest.setLocationDbIds(new ArrayList<>(locationDbIds));
+        //TODO: Locations don't connect to programs. How to get locations for the program?
+        LocationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), LocationsApi.class);
+        return brAPIDAOUtil.search(
+                api::searchLocationsPost,
+                api::searchLocationsSearchResultsDbIdGet,
+                locationSearchRequest
+        );
+    }
 }

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

@@ -25,7 +25,6 @@
 import org.brapi.v2.model.pheno.request.BrAPIObservationSearchRequest;
 import org.brapi.v2.model.pheno.response.BrAPIObservationListResponse;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
-import org.breedinginsight.daos.ObservationDAO;
 import org.breedinginsight.daos.ProgramDAO;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
@@ -34,10 +33,7 @@
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
-import java.util.UUID;
+import java.util.*;
 
 import static org.brapi.v2.model.BrAPIWSMIMEDataTypes.APPLICATION_JSON;
 
@@ -58,6 +54,9 @@ public BrAPIObservationDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOU
     }
 
     public List<BrAPIObservation> getObservationsByStudyName(List<String> studyNames, Program program) throws ApiException {
+        if(studyNames.isEmpty()) {
+            return Collections.emptyList();
+        }
 
         BrAPIObservationSearchRequest observationSearchRequest = new BrAPIObservationSearchRequest();
         observationSearchRequest.setProgramDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
@@ -70,14 +69,30 @@ public List<BrAPIObservation> getObservationsByStudyName(List<String> studyNames
         );
     }
 
+    public List<BrAPIObservation> getObservationsByObservationUnitsAndVariables(Collection<String> ouDbIds, Collection<String> variableDbIds, Program program) throws ApiException {
+        if(ouDbIds.isEmpty() || variableDbIds.isEmpty()) {
+            return Collections.emptyList();
+        }
+
+        BrAPIObservationSearchRequest observationSearchRequest = new BrAPIObservationSearchRequest();
+        observationSearchRequest.setProgramDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
+        observationSearchRequest.setObservationUnitDbIds(new ArrayList<>(ouDbIds));
+        observationSearchRequest.setObservationVariableDbIds(new ArrayList<>(variableDbIds));
+        ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationsApi.class);
+        return brAPIDAOUtil.search(
+                api::searchObservationsPost,
+                (brAPIWSMIMEDataTypes, searchResultsDbId, page, pageSize) -> searchObservationsSearchResultsDbIdGet(program.getId(), searchResultsDbId, page, pageSize),
+                observationSearchRequest
+        );
+    }
+
     @NotNull
-    private ApiResponse<Pair<Optional<BrAPIObservationListResponse>, Optional<BrAPIAcceptedSearchResponse>>>
-    searchObservationsSearchResultsDbIdGet(UUID programId, String searchResultsDbId, Integer page, Integer pageSize) throws ApiException {
+    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);
         return api.searchObservationsSearchResultsDbIdGet(APPLICATION_JSON, searchResultsDbId, page, pageSize);
     }
 
-    public List<BrAPIObservation> createBrAPIObservation(List<BrAPIObservation> brAPIObservationList, UUID programId, ImportUpload upload) throws ApiException {
+    public List<BrAPIObservation> createBrAPIObservations(List<BrAPIObservation> brAPIObservationList, UUID programId, ImportUpload upload) throws ApiException {
         ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
         return brAPIDAOUtil.post(brAPIObservationList, upload, api::observationsPost, importDAO::update);
     }