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[BI-2924] Remove cache.get() dependencies in TraitDAOImpl #572

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[BI-2924] Remove cache.get() dependencies in TraitDAOImpl #572

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ac08461
Remove cache.get() in TraitDAOImpl
jloux-brapi Oct 28, 2026
3c7a06c
Fix revert back to reference_source
jloux-brapi Oct 29, 2026
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67 changes: 50 additions & 17 deletions src/main/java/org/breedinginsight/daos/impl/TraitDAOImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
import org.brapi.v2.model.pheno.*;
import org.brapi.v2.model.pheno.request.BrAPIObservationVariableSearchRequest;
import org.brapi.v2.model.pheno.response.BrAPIObservationVariableListResponse;
import org.brapi.v2.model.pheno.response.BrAPIObservationVariableListResponseResult;
import org.brapi.v2.model.pheno.response.BrAPIObservationVariableSingleResponse;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.dao.db.tables.BiUserTable;
Expand Down Expand Up @@ -61,7 +62,6 @@
import java.util.stream.Stream;

import static org.breedinginsight.dao.db.Tables.*;
import static org.jooq.impl.DSL.lower;

@Singleton
@Slf4j
Expand Down Expand Up @@ -143,15 +143,7 @@ public List<Trait> getTraitsFullByProgramId(UUID programId) {
public List<Trait> getTraitsFullByProgramIds(List<UUID> programIds) {
List<Trait> saturatedTraits = new ArrayList<>();
for(UUID id : programIds) {
Map<String, Trait> programTraits = null;
try {
programTraits = cache.get(id);
} catch (ApiException e) {
throw new RuntimeException(e);
}
if(programTraits != null) {
saturatedTraits.addAll(programTraits.values());
}
saturatedTraits.addAll(fetchTraitsFullByProgramId(id));
}

return saturatedTraits;
Expand Down Expand Up @@ -215,6 +207,53 @@ private List<Trait> fetchTraitsFullByProgramId(UUID programId) {
return saturatedTraits;
}

private Trait fetchTraitFullByBiTraitAndProgramId(UUID traitId, UUID programId) {
// Get our db trait (equivalent to brapi variables)
Optional<Trait> biTraitOpt = getTrait(programId, traitId);
if (biTraitOpt.isEmpty()) {
throw new InternalServerException(String.format("Unable to find BI trait with id [%s]", traitId));
}

Trait trait = biTraitOpt.get();

String brapiProgramDbId;

try {
brapiProgramDbId = brAPIDAOUtil.getBrAPIProgramDbId(programId);
} catch (ApiException e) {
throw new InternalServerException(String.format("While fetching an individual trait in full, unable to retrieve brapi programDbId using bi program ID [%s]", programId), e);
}

// Get brapi variables
VariableQueryParams variablesRequest = new VariableQueryParams();
variablesRequest.programDbId(brapiProgramDbId);
variablesRequest.pageSize(1);

variablesRequest.setExternalReferenceId(traitId.toString());
variablesRequest.externalReferenceSource(referenceSource);

ApiResponse<BrAPIObservationVariableListResponse> brApiVariables = null;
BrAPIObservationVariable brAPIObservationVariable;
try {
brApiVariables = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationVariablesApi.class)
.variablesGet(variablesRequest);
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Error making BrAPI call", e);
} finally {
brAPIObservationVariable = Optional.ofNullable(brApiVariables)
.map(ApiResponse::getBody)
.map(BrAPIObservationVariableListResponse::getResult)
.map(BrAPIObservationVariableListResponseResult::getData)
.orElseThrow()
.get(0);
}

saturateTrait(trait, brAPIObservationVariable);

return trait;
}

@Override
public List<Trait> getTraitsByProgramId(UUID programId) {
return getTraitsByProgramIds(programId);
Expand Down Expand Up @@ -260,13 +299,7 @@ public List<Trait> getTraitsById(UUID... traitIds){

@Override
public Optional<Trait> getTraitFull(UUID programId, UUID traitId){

try {
return Optional.ofNullable(cache.get(programId).get(traitId.toString()));
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw new InternalServerException("Error making BrAPI call", e);
}
return Optional.of(fetchTraitFullByBiTraitAndProgramId(traitId, programId));
}

// could be more efficient to do a single get instead of search in saved search case but less code this way
Expand Down
8 changes: 3 additions & 5 deletions ...test/java/org/breedinginsight/api/v1/controller/TraitUploadControllerIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,18 +30,16 @@
import io.reactivex.Flowable;
import junit.framework.AssertionFailedError;
import org.breedinginsight.BrAPITest;
import org.breedinginsight.DatabaseTest;
import org.breedinginsight.TestUtils;
import org.breedinginsight.api.model.v1.request.ProgramRequest;
import org.breedinginsight.api.model.v1.request.SpeciesRequest;
import org.breedinginsight.api.model.v1.request.query.FilterRequest;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
import org.breedinginsight.api.v1.controller.metadata.SortOrder;
import org.breedinginsight.brapi.v2.dao.BrAPIProgramDAO;
import org.breedinginsight.dao.db.enums.DataType;
import org.breedinginsight.dao.db.enums.TermType;
import org.breedinginsight.dao.db.tables.daos.ProgramDao;
import org.breedinginsight.dao.db.tables.pojos.BiUserEntity;
import org.breedinginsight.dao.db.tables.pojos.ProgramEntity;
import org.breedinginsight.daos.TraitDAO;
import org.breedinginsight.daos.UserDAO;
import org.breedinginsight.model.Program;
Expand All @@ -59,7 +57,6 @@
import java.util.stream.Collectors;

import static io.micronaut.http.HttpRequest.*;
import static org.breedinginsight.TestUtils.insertAndFetchTestProgram;
import static org.junit.jupiter.api.Assertions.*;

@MicronautTest
Expand All @@ -79,6 +76,8 @@ public class TraitUploadControllerIntegrationTest extends BrAPITest {
private TraitDAO traitDAO;
@Inject
private SpeciesService speciesService;
@Inject
private BrAPIProgramDAO programDAO;

private Species validSpecies;

Expand Down Expand Up @@ -135,7 +134,6 @@ public void setup() {
//dsl.execute(fp.get("InsertProgramOntology"));
dsl.execute(fp.get("InsertMethod"));
dsl.execute(fp.get("InsertScale"));
dsl.execute(fp.get("InsertTrait"));

}

Expand Down
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