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[BI-2919]: Study Cache 2 - Untangle bi-generated exRefIds from BrAPI studyDbIds #549

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[BI-2919]: Study Cache 2 - Untangle bi-generated exRefIds from BrAPI studyDbIds #549

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d145660
BI-2919: Initial changes made to 2919 ticket.
humsika Aug 21, 2026
78c0863
BI-2919: Removed study external-reference ID overwrites.
humsika Aug 26, 2026
576683e
BI-2919: Added unit tests.
humsika Aug 26, 2026
2d3efd0
Merge remote-tracking branch 'origin/epic/BI-2862' into feature/BI-2919
humsika Aug 27, 2026
12d808b
BI-2919: Pulled latest from epic 2862.
humsika Aug 27, 2026
4b0c6d2
BI-2919: Formatted file.
humsika Aug 27, 2026
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24 changes: 4 additions & 20 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIObservationLevelsController.java
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Expand Up @@ -31,15 +31,13 @@
import org.brapi.client.v2.modules.phenotype.ObservationUnitsApi;
import org.brapi.v2.model.BrAPIIndexPagination;
import org.brapi.v2.model.BrAPIMetadata;
import org.brapi.v2.model.core.BrAPIStudy;
import org.brapi.v2.model.core.BrAPITrial;
import org.brapi.v2.model.pheno.BrAPIObservationUnitHierarchyLevel;
import org.brapi.v2.model.pheno.response.BrAPIObservationLevelListResponse;
import org.brapi.v2.model.pheno.response.BrAPIObservationLevelListResponseResult;
import org.breedinginsight.api.auth.ProgramSecured;
import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
import org.breedinginsight.brapi.v1.controller.BrapiVersion;
import org.breedinginsight.brapi.v2.dao.BrAPIStudyDAO;
import org.breedinginsight.brapi.v2.dao.BrAPITrialDAO;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.model.BrAPIConstants;
Expand All @@ -65,15 +63,13 @@ public class BrAPIObservationLevelsController {
private final ProgramDAO programDAO;
private final ProgramService programService;
private final BrAPITrialDAO trialDAO;
private final BrAPIStudyDAO studyDAO;

@Inject
public BrAPIObservationLevelsController(BrAPIEndpointProvider brAPIEndpointProvider, ProgramDAO programDAO, ProgramService programService, BrAPITrialDAO trialDAO, BrAPIStudyDAO studyDAO) {
public BrAPIObservationLevelsController(BrAPIEndpointProvider brAPIEndpointProvider, ProgramDAO programDAO, ProgramService programService, BrAPITrialDAO trialDAO) {
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.programDAO = programDAO;
this.programService = programService;
this.trialDAO = trialDAO;
this.studyDAO = studyDAO;
}

@Get("/observationlevels")
Expand All @@ -93,25 +89,13 @@ public HttpResponse<BrAPIObservationLevelListResponse> observationlevelsGet(@Pat
}

String programDbId = program.get().getBrapiProgram().getProgramDbId();
String studyDbId = null;
String studyDbId = environmentId;
String trialDbId = null;

if(environmentId != null) {
try {
Optional<BrAPIStudy> study = studyDAO.getStudyByEnvironmentId(UUID.fromString(environmentId), program.get());
if(study.isPresent()) {
studyDbId = study.get().getStudyDbId();
} else {
studyDbId = environmentId;
}
} catch (ApiException e) {
log.error(Utilities.generateApiExceptionLogMessage(e), "Error fetching environment");
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error finding observation levels");
}
} else if(experimentId != null) {
if(environmentId == null && experimentId != null) {
try {
List<BrAPITrial> trial = trialDAO.getTrialsByExperimentIds(List.of(UUID.fromString(experimentId)), program.get());
if(trial.size() == 1) {
if (trial.size() == 1) {
trialDbId = trial.get(0).getTrialDbId();
} else {
trialDbId = experimentId;
Expand Down
3 changes: 0 additions & 3 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIObservationUnitController.java
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Expand Up @@ -220,9 +220,6 @@ public HttpResponse<?> observationunitsTableGet(@PathVariable("programId") UUID
}

private void setDbIds(BrAPIObservationUnit ou) {
ou.studyDbId(Utilities.getExternalReference(ou.getExternalReferences(), Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.STUDIES))
.orElseThrow(() -> new IllegalStateException("No BI external reference found"))
.getReferenceID());
ou.programDbId(Utilities.getExternalReference(ou.getExternalReferences(), Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS))
.orElseThrow(() -> new IllegalStateException("No BI external reference found"))
.getReferenceID());
Expand Down
13 changes: 0 additions & 13 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIObservationsController.java
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Expand Up @@ -61,20 +61,17 @@ public class BrAPIObservationsController {

private final ProgramService programService;
private final ProgramDAO programDAO;
private final BrAPIStudyDAO brAPIStudyDAO;
private final BrAPIEndpointProvider brAPIEndpointProvider;
private final BrAPIObservationDAO observationDAO;

@Inject
public BrAPIObservationsController(ProgramService programService,
ProgramDAO programDAO,
ProgramDAO programDAO1,
BrAPIStudyDAO brAPIStudyDAO,
BrAPIEndpointProvider brAPIEndpointProvider,
BrAPIObservationDAO brAPIObservationDAO) {
this.programService = programService;
this.programDAO = programDAO1;
this.brAPIStudyDAO = brAPIStudyDAO;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.observationDAO = brAPIObservationDAO;
}
Expand Down Expand Up @@ -254,16 +251,6 @@ public HttpResponse<BrAPIObservationTableResponse> observationsTableGet(
}

try {
// Translate studyDbId if provided.
if (queryParams.getStudyDbId() != null) {
Optional<BrAPIStudy> study = brAPIStudyDAO.getStudyByEnvironmentId(UUID.fromString(queryParams.getStudyDbId()), program.get());
if (study.isEmpty()) {
return HttpResponse.notFound();
}
queryParams.setStudyDbId(study.get().getStudyDbId());
}
// TODO: Translate other DbIds if provided as well (but studyDbId is sufficient for Mr. Bean).

ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
ApiResponse<BrAPIObservationTableResponse> response = api.observationsTableGet(BrAPIWSMIMEDataTypes.APPLICATION_JSON, queryParams.toBrAPIQueryParams());

Expand Down
55 changes: 23 additions & 32 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIStudiesController.java
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Expand Up @@ -17,7 +17,6 @@

package org.breedinginsight.brapi.v2;

import io.micronaut.context.annotation.Property;
import io.micronaut.http.HttpResponse;
import io.micronaut.http.HttpStatus;
import io.micronaut.http.MediaType;
Expand All @@ -30,21 +29,22 @@
import org.brapi.v2.model.BrAPIStatus;
import org.brapi.v2.model.core.BrAPIStudy;
import org.brapi.v2.model.core.response.BrAPIStudySingleResponse;
import org.breedinginsight.api.auth.*;
import org.breedinginsight.api.auth.ProgramSecured;
import org.breedinginsight.api.auth.ProgramSecuredRole;
import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
import org.breedinginsight.api.auth.SecurityService;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
import org.breedinginsight.api.model.v1.response.DataResponse;
import org.breedinginsight.api.model.v1.response.Response;
import org.breedinginsight.api.model.v1.validators.QueryValid;
import org.breedinginsight.brapi.v1.controller.BrapiVersion;
import org.breedinginsight.brapi.v2.model.request.query.StudyQuery;
import org.breedinginsight.brapi.v2.services.BrAPIStudyService;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.ProgramUser;
import org.breedinginsight.services.ExperimentalCollaboratorService;
import org.breedinginsight.services.ProgramService;
import org.breedinginsight.services.ProgramUserService;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.utilities.Utilities;
import org.breedinginsight.utilities.response.ResponseUtils;
import org.breedinginsight.utilities.response.mappers.StudyQueryMapper;
Expand All @@ -54,14 +54,12 @@
import java.util.List;
import java.util.Optional;
import java.util.UUID;
import java.util.stream.Collectors;

@Slf4j
@Controller("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2)
@Secured(SecurityRule.IS_AUTHENTICATED)
public class BrAPIStudiesController {

private final String referenceSource;
private final BrAPIStudyService studyService;
private final StudyQueryMapper studyQueryMapper;
private final ProgramService programService;
Expand All @@ -73,14 +71,12 @@ public class BrAPIStudiesController {
@Inject
public BrAPIStudiesController(BrAPIStudyService studyService,
StudyQueryMapper studyQueryMapper,
@Property(name = "brapi.server.reference-source") String referenceSource,
ProgramService programService,
SecurityService securityService,
ProgramUserService programUserService,
ExperimentalCollaboratorService experimentalCollaboratorService) {
this.studyService = studyService;
this.studyQueryMapper = studyQueryMapper;
this.referenceSource = referenceSource;
this.programService = programService;
this.securityService = securityService;
this.programUserService = programUserService;
Expand All @@ -107,18 +103,14 @@ public HttpResponse<Response<DataResponse<List<BrAPIStudy>>>> getStudies(
Optional<ProgramUser> experimentalCollaborator = programUserService.getIfExperimentalCollaborator(programId, securityService.getUser().getId());
if (experimentalCollaborator.isPresent()) {
List<UUID> authorizedExperimentIds = experimentalCollaboratorService.getAuthorizedExperimentIds(experimentalCollaborator.get().getId());
List<BrAPIStudy> authorizedStudies = studyService.getStudiesByExperimentIds(program.get(), authorizedExperimentIds)
.stream()
.peek(this::setDbIds)
.collect(Collectors.toList());
List<BrAPIStudy> authorizedStudies = studyService.getStudiesByExperimentIds(
program.get(),
authorizedExperimentIds);
return ResponseUtils.getBrapiQueryResponse(authorizedStudies, studyQueryMapper, queryParams, searchRequest);
}

// 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)
.collect(Collectors.toList());
List<BrAPIStudy> studies = studyService.getStudies(programId);
return ResponseUtils.getBrapiQueryResponse(studies, studyQueryMapper, queryParams, searchRequest);
} catch (ApiException e) {
log.info(e.getMessage(), e);
Expand All @@ -138,25 +130,31 @@ public HttpResponse studiesPost(@PathVariable("programId") UUID programId, @Body

@Get("/studies/{studyDbId}")
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
public HttpResponse<BrAPIStudySingleResponse> studiesStudyDbIdGet(@PathVariable("programId") UUID programId, @PathVariable("studyDbId") String environmentId) {
public HttpResponse<BrAPIStudySingleResponse> studiesStudyDbIdGet(@PathVariable("programId") UUID programId, @PathVariable("studyDbId") String studyDbId) {
Optional<Program> program = programService.getById(programId);
if(program.isEmpty()) {
if (program.isEmpty()) {
log.warn("program id: " + programId + " not found");
return HttpResponse.notFound();
}

try {
Optional<BrAPIStudy> study = studyService.getStudyByEnvironmentId(program.get(), UUID.fromString(environmentId));
if(study.isPresent()) {
setDbIds(study.get());
return HttpResponse.ok(new BrAPIStudySingleResponse().result(study.get()));
Optional<BrAPIStudy> study = studyService.getStudyByDbId(program.get(), studyDbId);

if (study.isPresent()) {
return HttpResponse.ok(
new BrAPIStudySingleResponse()
.result(study.get()));
} else {
log.warn("studyDbId: " + environmentId + " not found");
log.warn("studyDbId: " + studyDbId + " not found");
return HttpResponse.notFound();
}
} catch (ApiException e) {
log.error(Utilities.generateApiExceptionLogMessage(e), e);
return HttpResponse.serverError(new BrAPIStudySingleResponse().metadata(new BrAPIMetadata().addStatusItem(new BrAPIStatus().message("Error fetching study")
.messageType(BrAPIStatus.MessageTypeEnum.ERROR))));
return HttpResponse.serverError(new BrAPIStudySingleResponse()
.metadata(new BrAPIMetadata()
.addStatusItem(new BrAPIStatus()
.message("Error fetching study")
.messageType(BrAPIStatus.MessageTypeEnum.ERROR))));
}
}

Expand All @@ -168,11 +166,4 @@ public HttpResponse studiesStudyDbIdPut(@PathVariable("programId") UUID programI
return HttpResponse.notFound();
}

private void setDbIds(BrAPIStudy study) {
study.studyDbId(Utilities.getExternalReference(study.getExternalReferences(), Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.STUDIES))
.orElseThrow(() -> new IllegalStateException("No BI external reference found"))
.getReferenceID());

//TODO update locationDbId
}
}
38 changes: 11 additions & 27 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
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Expand Up @@ -26,15 +26,13 @@
import org.brapi.client.v2.model.queryParams.phenotype.ObservationQueryParams;
import org.brapi.client.v2.modules.phenotype.ObservationsApi;
import org.brapi.v2.model.BrAPIAcceptedSearchResponse;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIProgram;
import org.brapi.v2.model.pheno.BrAPIObservation;
import org.brapi.v2.model.pheno.BrAPIObservationUnit;
import org.brapi.v2.model.pheno.request.BrAPIObservationSearchRequest;
import org.brapi.v2.model.pheno.response.BrAPIObservationListResponse;
import org.breedinginsight.brapps.importer.daos.ImportDAO;
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.TraitService;
Expand All @@ -60,7 +58,6 @@ public class BrAPIObservationDAO {
private BrAPIObservationUnitDAO observationUnitDAO;
private final BrAPIDAOUtil brAPIDAOUtil;
private final BrAPIEndpointProvider brAPIEndpointProvider;
private final String referenceSource;
private final TraitService traitService;

private final int brapiMaxPageSize;
Expand All @@ -71,15 +68,13 @@ public BrAPIObservationDAO(ProgramDAO programDAO,
BrAPIObservationUnitDAO observationUnitDAO,
BrAPIDAOUtil brAPIDAOUtil,
BrAPIEndpointProvider brAPIEndpointProvider,
@Property(name = "brapi.server.reference-source") String referenceSource,
@Property(name = "brapi.cache.fetch-page-size") int brapiFetchPageSize,
TraitService traitService) {
this.programDAO = programDAO;
this.importDAO = importDAO;
this.observationUnitDAO = observationUnitDAO;
this.brAPIDAOUtil = brAPIDAOUtil;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.referenceSource = referenceSource;
this.traitService = traitService;
this.brapiMaxPageSize = brapiFetchPageSize;
}
Expand Down Expand Up @@ -184,32 +179,21 @@ public List<BrAPIObservation> getObservationsByObservationUnits(Collection<Strin
.collect(Collectors.toList());
}

// TODO: implement other filters in BI-2506.
public List<BrAPIObservation> getObservationsByFilters(Program program, String studyDbId) throws ApiException, DoesNotExistException {

String studySource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.STUDIES);

// Get all observations for the program.
Collection<BrAPIObservation> observations = getProgramObservations(program.getId());
// Build a hashmap of traits for fast lookup. The key is ObservationVariableDbId, the value is the Trait Id.
HashMap<String, String> traitIdsByObservationVariableDbId = traitService.getIdsByObservationVariableDbIds(program.getId(), observations.stream().map(BrAPIObservation::getObservationVariableDbId).collect(Collectors.toList()));

// Lookup studyDbId.
HashMap<String, String> traitIdsByObservationVariableDbId =
traitService.getIdsByObservationVariableDbIds(
program.getId(),
observations.stream()
.map(BrAPIObservation::getObservationVariableDbId)
.collect(Collectors.toList()));

return observations.stream()
.filter(o -> {
// Short circuit if filter is null.
if (studyDbId == null) return true;
Optional<BrAPIExternalReference> xref = Utilities.getExternalReference(o.getExternalReferences(), studySource);
return xref.filter(brAPIExternalReference -> studyDbId.equals(brAPIExternalReference.getReferenceId())).isPresent();
})
.peek(o -> {
// Translate ObservationVariableDbId.
o.setObservationVariableDbId(traitIdsByObservationVariableDbId.get(o.getObservationVariableDbId()));
// Translate StudyDbId.
o.setStudyDbId(Utilities.getExternalReference(o.getExternalReferences(), studySource)
.orElseThrow(() -> new RuntimeException("study xref not found on observation")).getReferenceId());
// TODO: consider translating germplasmDbId in BI-2506.
}).collect(Collectors.toList());
.filter(o -> studyDbId == null || studyDbId.equals(o.getStudyDbId()))
.peek(o ->
o.setObservationVariableDbId(traitIdsByObservationVariableDbId.get(o.getObservationVariableDbId())))
.collect(Collectors.toList());
}

@NotNull
Expand Down
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