Apply BrAPI-server side Filtering/Sorting/Pagination to BI Experiments

pom.xml

@@ -89,7 +89,7 @@
         <guava.version>31.0.1-jre</guava.version>
         <okhttp.version>4.9.3</okhttp.version>
         <mockito.version>4.3.1</mockito.version>
-        <brapi-java-client.version>2.2-SNAPSHOT</brapi-java-client.version>
+        <brapi-java-client.version>2.2.1-SNAPSHOT</brapi-java-client.version>
         <commons-io.version>2.11.0</commons-io.version>
         <tika-app.version>2.2.1</tika-app.version>
         <!-- Version of apache-poi depends on version of tika. Tika uses these. -->

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

@@ -46,17 +46,15 @@
 @Secured(SecurityRule.IS_AUTHENTICATED)
 public class ExperimentController {
     private final BrAPITrialService experimentService;
-    private final ExperimentQueryMapper experimentQueryMapper;
     private final ProgramService programService;
     private final ExperimentalCollaboratorService experimentalCollaboratorService;
     private final SecurityService securityService;
     private final ProgramUserService programUserService;
     private final RoleService roleService;
 
     @Inject
-    public ExperimentController(BrAPITrialService experimentService, ExperimentQueryMapper experimentQueryMapper, ProgramService programService, ExperimentalCollaboratorService experimentalCollaboratorService, SecurityService securityService, ProgramUserService programUserService, RoleService roleService) {
+    public ExperimentController(BrAPITrialService experimentService, ProgramService programService, ExperimentalCollaboratorService experimentalCollaboratorService, SecurityService securityService, ProgramUserService programUserService, RoleService roleService) {
         this.experimentService = experimentService;
-        this.experimentQueryMapper = experimentQueryMapper;
         this.programService = programService;
         this.experimentalCollaboratorService = experimentalCollaboratorService;
         this.securityService = securityService;

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

@@ -114,7 +114,7 @@ public HttpResponse<Response<DataResponse<List<BrAPIStudy>>>> getStudies(
                 return ResponseUtils.getBrapiQueryResponse(authorizedStudies, studyQueryMapper, queryParams, searchRequest);
             }
 
-            // TODO: Instead of getting all studies for a program and filtering, doing the filtering on brapi side
+            // TODO: Instead of getting all studies for a program and filtering, doing the filtering on brapi side [BI-2922]
             List<BrAPIStudy> studies = studyService.getStudies(programId)
                         .stream()
                         .peek(this::setDbIds)

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

@@ -26,8 +26,8 @@
 import io.micronaut.security.rules.SecurityRule;
 import lombok.extern.slf4j.Slf4j;
 import org.brapi.client.v2.model.exceptions.ApiException;
-import org.brapi.v2.model.BrAPIExternalReference;
 import org.brapi.v2.model.core.BrAPITrial;
+import org.brapi.v2.model.core.response.BrAPITrialListResponse;
 import org.brapi.v2.model.core.response.BrAPITrialSingleResponse;
 import org.breedinginsight.api.auth.*;
 import org.breedinginsight.api.model.v1.request.query.SearchRequest;
@@ -43,16 +43,13 @@
 import org.breedinginsight.services.ExperimentalCollaboratorService;
 import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.ProgramUserService;
-import org.breedinginsight.model.ProgramUser;
-import org.breedinginsight.model.Role;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.utilities.Utilities;
 import org.breedinginsight.utilities.response.ResponseUtils;
 import org.breedinginsight.utilities.response.mappers.ExperimentQueryMapper;
 
 import javax.inject.Inject;
 import javax.validation.Valid;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
@@ -65,22 +62,19 @@ public class BrAPITrialsController {
 
     private final String referenceSource;
     private final BrAPITrialService experimentService;
-    private final ExperimentQueryMapper experimentQueryMapper;
     private final SecurityService securityService;
     private final ProgramUserService programUserService;
     private final ExperimentalCollaboratorService experimentalCollaboratorService;
     private final ProgramService programService;
 
     @Inject
     public BrAPITrialsController(BrAPITrialService experimentService,
-                                 ExperimentQueryMapper experimentQueryMapper,
                                  @Property(name = "brapi.server.reference-source") String referenceSource,
                                  SecurityService securityService,
                                  ProgramUserService programUserService,
                                  ExperimentalCollaboratorService experimentalCollaboratorService,
                                  ProgramService programService) {
         this.experimentService = experimentService;
-        this.experimentQueryMapper = experimentQueryMapper;
         this.referenceSource = referenceSource;
         this.securityService = securityService;
         this.programUserService = programUserService;
@@ -92,7 +86,7 @@ public BrAPITrialsController(BrAPITrialService experimentService,
     @Produces(MediaType.APPLICATION_JSON)
     @ProgramSecured(roles = {ProgramSecuredRole.SYSTEM_ADMIN, ProgramSecuredRole.READ_ONLY, ProgramSecuredRole.PROGRAM_ADMIN
             ,ProgramSecuredRole.EXPERIMENTAL_COLLABORATOR })
-    public HttpResponse<Response<DataResponse<List<BrAPITrial>>>> getExperiments(
+    public HttpResponse<Response<DataResponse<BrAPITrial>>> getExperiments(
             @PathVariable("programId") UUID programId,
             @QueryValue @QueryValid(using = ExperimentQueryMapper.class) @Valid ExperimentQuery queryParams) {
         try {
@@ -105,13 +99,21 @@ public HttpResponse<Response<DataResponse<List<BrAPITrial>>>> getExperiments(
             // If the program user is an experimental collaborator, filter results for only authorized experiments.
             Optional<ProgramUser> experimentalCollaborator = programUserService.getIfExperimentalCollaborator(programId, securityService.getUser().getId());
             if (experimentalCollaborator.isPresent()) {
-                List<UUID> experimentIds = experimentalCollaboratorService.getAuthorizedExperimentIds(experimentalCollaborator.get().getId());
-                List<BrAPITrial> authorizedExperiments = experimentService.getTrialsByExperimentIds(program.get(), experimentIds).stream().peek(this::setDbIds).collect(Collectors.toList());
-                return ResponseUtils.getBrapiQueryResponse(authorizedExperiments, experimentQueryMapper, queryParams, searchRequest);
+                List<UUID> authorizedExperimentIds = experimentalCollaboratorService.getAuthorizedExperimentIds(experimentalCollaborator.get().getId());
+
+                BrAPITrialListResponse brapiResponse = experimentService.searchTrials(program.get(), authorizedExperimentIds, queryParams);
+
+                List<BrAPITrial> foundTrials = brapiResponse.getResult().getData();
+                foundTrials.forEach(this::setDbIds);
+
+                return ResponseUtils.getBrapiQueryResponse(foundTrials, brapiResponse, queryParams);
             }
 
-            List<BrAPITrial> experiments = experimentService.getExperiments(programId).stream().peek(this::setDbIds).collect(Collectors.toList());
-            return ResponseUtils.getBrapiQueryResponse(experiments, experimentQueryMapper, queryParams, searchRequest);
+            BrAPITrialListResponse brapiResponse = experimentService.searchTrials(program.get(), queryParams);
+
+            List<BrAPITrial> foundTrials = brapiResponse.getResult().getData();
+            foundTrials.forEach(this::setDbIds);
+            return ResponseUtils.getBrapiQueryResponse(foundTrials, brapiResponse, queryParams);
         } catch (ApiException e) {
             log.info(e.getMessage(), e);
             return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving experiments");
@@ -159,7 +161,7 @@ public HttpResponse<?> trialsTrialDbIdPut(@PathVariable("programId") UUID progra
         return HttpResponse.notFound();
     }
 
-    // TODO: Remove for trialDbId once cache is removed for that entity
+    // TODO: Verify that the programDbId does not need to be reset and that the BrAPI programDbId can be used instead [BI-2931]
     private void setDbIds(BrAPITrial trial) {
         trial.programDbId(Utilities.getExternalReference(trial.getExternalReferences(), Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS))
                                  .orElseThrow(() -> new IllegalStateException("No BI external reference found"))

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

@@ -136,11 +136,11 @@ public List<BrAPIStudy> getStudiesByName(List<String> studyNames, Program progra
         );
     }
 
-    public List<BrAPIStudy> getStudiesByExperimentID(@NotNull UUID experimentId, Program program) throws ApiException {
-        // TODO: This should look up on trialDbId, and the trialDbId should be passed thru
+    public List<BrAPIStudy> getStudiesByBrAPITrialExRefId(@NotNull UUID brapiTrialExRefId, Program program) throws ApiException {
+        // TODO: If external references are removed for trial for studies, this method should look up on trialDbId, and the trialDbId should be passed through. [BI-2933]
         BrAPIStudySearchRequest studySearch = new BrAPIStudySearchRequest();
         studySearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
-        studySearch.addExternalReferenceIdsItem(experimentId.toString());
+        studySearch.addExternalReferenceIdsItem(brapiTrialExRefId.toString());
         studySearch.addExternalReferenceSourcesItem(Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.TRIALS));
         StudiesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), StudiesApi.class);
         return brAPIDAOUtil.search(

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

@@ -19,6 +19,9 @@
 
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.v2.model.core.BrAPITrial;
+import org.brapi.v2.model.core.request.BrAPITrialSearchRequest;
+import org.brapi.v2.model.core.response.BrAPITrialListResponse;
+import org.breedinginsight.brapi.v2.model.request.query.ExperimentQuery;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
@@ -45,4 +48,9 @@ List<BrAPITrial> createBrAPITrials(List<BrAPITrial> brAPITrialList, UUID program
     List<BrAPITrial> getTrialsByExperimentIds(Collection<UUID> experimentIds, Program program) throws ApiException;
 
     void deleteBrAPITrial(Program program, BrAPITrial trial, boolean hard) throws ApiException;
+
+    BrAPITrialListResponse brapiTrialSearch(Program program, ExperimentQuery experimentQuery) throws ApiException;
+
+    BrAPITrialListResponse brapiTrialSearch(Program program, List<UUID> brapiTrialIds, ExperimentQuery experimentQuery) throws ApiException;
+
 }