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[BI-2908] Remove cache.get() dependencies from BrAPIObservationDAO #531

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[BI-2908] Remove cache.get() dependencies from BrAPIObservationDAO #531

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2896356
Add TODOs for cache.get() path involving trial deletion
jloux-brapi Jul 6, 2026
2d3d39c
Remove cache.get calls from ObservationDAO
jloux-brapi Jul 6, 2026
e0baa4a
Remove unused imports, comments on cache usage
jloux-brapi Jul 7, 2026
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1 change: 1 addition & 0 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIObservationsController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,7 @@ public HttpResponse observationsGet(@PathVariable("programId") UUID programId,
}

// Get a filtered list of observations.
// TODO: Handle filtering and pagination of this request entirely on BrAPI side once study and ou cache is removed: [BI-2964]
List<BrAPIObservation> observations = observationDAO.getObservationsByFilters(program.get(), studyDbId);

// If page is not provided, set it to the default value 0.
Expand Down
98 changes: 51 additions & 47 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,11 @@
import org.apache.commons.lang3.tuple.Pair;
import org.brapi.client.v2.ApiResponse;
import org.brapi.client.v2.model.exceptions.ApiException;
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;
Expand All @@ -38,7 +40,6 @@
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.daos.cache.ProgramCacheProvider;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.Trait;
import org.breedinginsight.services.TraitService;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
import org.breedinginsight.services.exceptions.DoesNotExistException;
Expand Down Expand Up @@ -67,6 +68,8 @@ public class BrAPIObservationDAO extends BrAPICachedDAO<BrAPIObservation> {
private boolean runScheduledTasks;
private final TraitService traitService;

private final int brapiMaxPageSize;

@Inject
public BrAPIObservationDAO(ProgramDAO programDAO,
ImportDAO importDAO,
Expand All @@ -75,6 +78,7 @@ public BrAPIObservationDAO(ProgramDAO programDAO,
BrAPIEndpointProvider brAPIEndpointProvider,
@Property(name = "brapi.server.reference-source") String referenceSource,
@Property(name = "micronaut.bi.api.run-scheduled-tasks") boolean runScheduledTasks,
@Property(name = "brapi.cache.fetch-page-size") int brapiFetchPageSize,
ProgramCacheProvider programCacheProvider, TraitService traitService) {
this.programDAO = programDAO;
this.importDAO = importDAO;
Expand All @@ -85,6 +89,7 @@ public BrAPIObservationDAO(ProgramDAO programDAO,
this.runScheduledTasks = runScheduledTasks;
this.traitService = traitService;
this.programCache = programCacheProvider.getProgramCache(this::fetchProgramObservations, BrAPIObservation.class);
this.brapiMaxPageSize = brapiFetchPageSize;
}

@Scheduled(initialDelay = "${startup.delay.observation}")
Expand Down Expand Up @@ -162,14 +167,15 @@ private void processObservations(String programKey, List<BrAPIObservation> obser
}
}

/**
* Get all observations for a program from the cache.
*/
private Map<String, BrAPIObservation> getProgramObservations(UUID programId) throws ApiException {
return programCache.get(programId);
private List<BrAPIObservation> getProgramObservations(UUID programId) throws ApiException {
Program program = programDAO.get(programId)
.stream()
.findFirst()
.orElseThrow();

return getBrAPIObservationsUsingBrAPIProgramId(program);
}

// Note: not using cache, because unique studyName (with "[ProgramKey-ExtraInfo]") is not stored directly on Observation.
public List<BrAPIObservation> getObservationsByStudyName(List<String> studyNames, Program program) throws ApiException {
if(studyNames.isEmpty()) {
return Collections.emptyList();
Expand Down Expand Up @@ -202,7 +208,7 @@ public List<BrAPIObservation> getObservationsByDbIds(List<String> dbIds, Program

// Filter the observations based on the provided program ID and the provided list of dbIds
// Collect the filtered observations into a List and return the result
return getProgramObservations(program.getId()).values().stream()
return getProgramObservations(program.getId()).stream()
.filter(o -> dbIds.contains(o.getObservationDbId()))
.collect(Collectors.toList());
}
Expand All @@ -212,10 +218,12 @@ public List<BrAPIObservation> getObservationsByTrialDbId(List<String> trialDbIds
return Collections.emptyList();
}
// First, get all ObservationUnits for the given trialDbIds.
// TODO: Once OUDAO removes cache, investigate utilizing observationUnit GET param to includeObservations instead of making an extra call for the observations. This should offer performance gains. [BI-2963]
List<String> observationUnitDbIds = observationUnitDAO.getObservationUnitsForTrialDbIds(program.getId(), trialDbIds)
.stream().map(BrAPIObservationUnit::getObservationUnitDbId).collect(Collectors.toList());
// Finally, return all Observations for those ObservationUnits (Observations are linked to Trial through ObservationUnits).
return getProgramObservations(program.getId()).values().stream()
// TODO: This gets all observations for the program and filters, which is extremely inefficient. If above TODO suggestion doesn't work, another improvement would be to search on OU ids directly in BrAPI instead. [BI-2963]
return getProgramObservations(program.getId()).stream()
.filter(o -> observationUnitDbIds.contains(o.getObservationUnitDbId()))
.collect(Collectors.toList());
}
Expand All @@ -224,29 +232,22 @@ public List<BrAPIObservation> getObservationsByObservationUnitsAndVariables(Coll
if(ouDbIds.isEmpty() || variableDbIds.isEmpty()) {
return Collections.emptyList();
}
return getProgramObservations(program.getId()).values().stream()
// TODO: Once OUDAO removes cache, change to BrAPI Observation search request on program, observation var ids, and ouDbId [BI-2963]
return getProgramObservations(program.getId()).stream()
.filter(o -> ouDbIds.contains(o.getObservationUnitDbId()) && variableDbIds.contains(o.getObservationVariableDbId()))
.collect(Collectors.toList());
}

public List<BrAPIObservation> getObservationsByObservationUnits(Collection<String> ouDbIds, Program program) throws ApiException {
// TODO: Once OUDAO removes cache, change to BrAPI Observation search request on program and ouDbIds [BI-2963]
if(ouDbIds.isEmpty()) {
return Collections.emptyList();
}
return getProgramObservations(program.getId()).values().stream()
return getProgramObservations(program.getId()).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());
}

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

Expand All @@ -255,7 +256,7 @@ public List<BrAPIObservation> getObservationsByFilters(Program program, String s
String observationSource = Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.OBSERVATIONS);

// Get all observations for the program.
Collection<BrAPIObservation> observations = getProgramObservations(program.getId()).values();
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()));

Expand All @@ -267,6 +268,7 @@ public List<BrAPIObservation> getObservationsByFilters(Program program, String s
Optional<BrAPIExternalReference> xref = Utilities.getExternalReference(o.getExternalReferences(), studySource);
return xref.filter(brAPIExternalReference -> studyDbId.equals(brAPIExternalReference.getReferenceId())).isPresent();
})
// Try to figure out why/how this translation is used.
.peek(o -> {
// Translate ObservationVariableDbId.
o.setObservationVariableDbId(traitIdsByObservationVariableDbId.get(o.getObservationVariableDbId()));
Expand Down Expand Up @@ -306,33 +308,35 @@ public List<BrAPIObservation> createBrAPIObservations(List<BrAPIObservation> brA
}
}

public BrAPIObservation updateBrAPIObservation(String dbId, BrAPIObservation observation, UUID programId) throws ApiException {
ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
var program = programDAO.fetchOneById(programId);
try {
Callable<Map<String, BrAPIObservation>> postFunction = () -> {
ApiResponse<BrAPIObservationSingleResponse> response = api.observationsObservationDbIdPut(dbId, observation);
if (response == null)
{
throw new ApiException("Response is null", 0, null, null);
}
BrAPIObservationSingleResponse body = response.getBody();
if (body == null) {
throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
}
BrAPIObservation updatedObservation = body.getResult();
if (updatedObservation == null) {
throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
}
return processObservationsForCache(List.of(updatedObservation), program.getKey());
};
return programCache.post(programId, postFunction).get(0);
} catch (ApiException e) {
log.error(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
} catch (Exception e) {
throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
private List<BrAPIObservation> getBrAPIObservationsUsingBrAPIProgramId(Program program) throws ApiException {

if (program == null || program.getId() == null) {
throw new InternalServerException("BI-API Program or Program ID is null");
}

String brapiProgramDbId = Optional.of(program)
.map(Program::getBrapiProgram)
.map(BrAPIProgram::getProgramDbId)
.orElse(null);

if (brapiProgramDbId == null) {
brapiProgramDbId = programDAO.getProgramBrAPI(program).getProgramDbId();
}

ObservationQueryParams observationQueryParams =
ObservationQueryParams.builder()
.programDbId(brapiProgramDbId)
.pageSize(brapiMaxPageSize)
.page(0)
.build();

ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(program.getId()), ObservationsApi.class);

List<BrAPIObservation> result = brAPIDAOUtil.get(api::observationsGet, observationQueryParams);

processObservations(program.getKey(), result);

return result;
}

// This method overloads updateBrAPIObservation(String dbId, BrAPIObservation observation, UUID programId)
Expand Down
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