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BI-2921 - Study Cache 4 Remove rest of CRUD operations from BrAPIStudyDAO #555

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Merged
jloux-brapi merged 2 commits into from
Sep 14, 2026
Merged

BI-2921 - Study Cache 4 Remove rest of CRUD operations from BrAPIStudyDAO #555

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6ce44fe
BI-2921: Removed remaining ProgramCache operations from BrAPIStudyDAO.
humsika Sep 11, 2026
5bef696
BI-2921: Formatted the file.
humsika Sep 14, 2026
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15 changes: 0 additions & 15 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPICachedDAO.java
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87 changes: 15 additions & 72 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIStudyDAO.java
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Expand Up @@ -19,7 +19,6 @@
import com.google.gson.JsonObject;
import io.micronaut.context.annotation.Property;
import io.micronaut.http.server.exceptions.InternalServerException;
import io.micronaut.scheduling.annotation.Scheduled;
import lombok.extern.slf4j.Slf4j;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.client.v2.model.queryParams.core.StudyQueryParams;
Expand All @@ -32,7 +31,6 @@
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.daos.cache.ProgramCacheProvider;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
import org.breedinginsight.utilities.BrAPIDAOUtil;
Expand All @@ -42,16 +40,14 @@
import javax.inject.Singleton;
import javax.validation.constraints.NotNull;
import java.util.*;
import java.util.concurrent.Callable;
import java.util.stream.Collectors;

@Slf4j
@Singleton
public class BrAPIStudyDAO extends BrAPICachedDAO<BrAPIStudy> {
public class BrAPIStudyDAO {
@Property(name = "brapi.server.reference-source")
private String referenceSource;
@Property(name = "micronaut.bi.api.run-scheduled-tasks")
private boolean runScheduledTasks;

@Property(name = "brapi.cache.fetch-page-size")
private int brapiMaxPageSize;

Expand All @@ -61,52 +57,15 @@ public class BrAPIStudyDAO extends BrAPICachedDAO<BrAPIStudy> {
private final BrAPIEndpointProvider brAPIEndpointProvider;

@Inject
public BrAPIStudyDAO(ProgramDAO programDAO, ImportDAO importDAO, BrAPIDAOUtil brAPIDAOUtil, BrAPIEndpointProvider brAPIEndpointProvider, ProgramCacheProvider programCacheProvider) {
public BrAPIStudyDAO(
ProgramDAO programDAO,
ImportDAO importDAO,
BrAPIDAOUtil brAPIDAOUtil,
BrAPIEndpointProvider brAPIEndpointProvider) {
this.programDAO = programDAO;
this.importDAO = importDAO;
this.brAPIDAOUtil = brAPIDAOUtil;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.programCache = programCacheProvider.getProgramCache(this::fetchProgramStudy, BrAPIStudy.class);
}

@Scheduled(initialDelay = "${startup.delay.study}")
public void setup() {
if(!runScheduledTasks) {
return;
}
// Populate study cache for all programs on startup
log.debug("populating study cache");
List<Program> programs = programDAO.getActive();
if(programs != null) {
programCache.populate(programs.stream().map(Program::getId).collect(Collectors.toList()));
}
}


/**
* Fetch formatted study for this program
* @param programId
* @return Map - Key = string representing study UUID, value = formatted BrAPIStudy
* @throws ApiException
*/
private Map<String, BrAPIStudy> fetchProgramStudy(UUID programId) throws ApiException {
StudiesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), StudiesApi.class);
// Get the program key
List<Program> programs = programDAO.get(programId);
if (programs.size() != 1) {
throw new InternalServerException("Program was not found for given key");
}
Program program = programs.get(0);

// Set query params and make call
BrAPIStudySearchRequest studySearch = new BrAPIStudySearchRequest();
studySearch.externalReferenceIDs(List.of(programId.toString()));
studySearch.externalReferenceSources(List.of(Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS)));
return processStudyForDisplay(brAPIDAOUtil.search(
api::searchStudiesPost,
api::searchStudiesSearchResultsDbIdGet,
studySearch
), program.getKey());
}

/**
Expand Down Expand Up @@ -201,39 +160,23 @@ public List<BrAPIStudy> getStudiesByExperimentIds(@NotNull Collection<UUID> expe

public List<BrAPIStudy> createBrAPIStudies(List<BrAPIStudy> brAPIStudyList, UUID programId, ImportUpload upload) throws ApiException {
StudiesApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), StudiesApi.class);
List<BrAPIStudy> createdStudies = new ArrayList<>();

try {
if (!brAPIStudyList.isEmpty()) {
Callable<Map<String, BrAPIStudy>> postCallback = () -> {
List<BrAPIStudy> postedStudies = brAPIDAOUtil
.post(brAPIStudyList, upload, api::studiesPost, importDAO::update);
return environmentById(postedStudies);
};
createdStudies.addAll(programCache.post(programId, postCallback));
//Create studies directly through BrAPI.
List<BrAPIStudy> postedStudies = brAPIDAOUtil.post(brAPIStudyList, upload, api::studiesPost, importDAO::update);

// Return the BrAPI response without updating Redis.
return postedStudies;
}

return createdStudies;
// Preserve the existing empty-input behavior.
return new ArrayList<>();
} catch (Exception e) {
throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
}
}

/**
* @return Map - Key = BI external reference ID, Value = BrAPIStudy
* */
private Map<String, BrAPIStudy> environmentById(List<BrAPIStudy> studies) {
Map<String, BrAPIStudy> environmentById = new HashMap<>();
for (BrAPIStudy environment: studies) {
BrAPIExternalReference xref = environment
.getExternalReferences()
.stream()
.filter(reference -> String.format("%s/%s", referenceSource, ExternalReferenceSource.STUDIES.getName()).equals(reference.getReferenceSource()))
.findFirst().orElseThrow(() -> new IllegalStateException("No BI external reference found"));
environmentById.put(xref.getReferenceID(), environment);
}
return environmentById;
}

public List<BrAPIStudy> getStudiesByStudyDbId(Collection<String> studyDbIds, Program program) throws ApiException {
if(studyDbIds.isEmpty()) {
return Collections.emptyList();
Expand Down
2 changes: 0 additions & 2 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -814,8 +814,6 @@ public int deleteExperiment(Program program, UUID experimentId, boolean hard) th
for (BrAPIListSummary list : lists) {
listDAO.deleteBrAPIList(list.getListDbId(), program.getId(), hard);
}
// TODO: if performance is poor, implement more precise invalidation, possibly using hierarchical cache keys.
studyDAO.repopulateCache(program.getId());
}

// Successful or not, return the number of observations in this experiment.
Expand Down
3 changes: 3 additions & 0 deletions src/test/java/org/breedinginsight/api/v1/controller/ExperimentControllerIntegrationTest.java
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Expand Up @@ -16,6 +16,7 @@
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIStudy;
import org.brapi.v2.model.core.BrAPITrial;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.breedinginsight.BrAPITest;
Expand Down Expand Up @@ -218,6 +219,8 @@ void setup() throws Exception {

envIds.clear();
brAPIStudyDAO.getStudies(program.getId())
.stream()
.sorted(Comparator.comparing(BrAPIStudy::getStudyName))
.forEach(study -> envIds.add(study.getStudyDbId()));
}

Expand Down
38 changes: 25 additions & 13 deletions src/test/java/org/breedinginsight/brapi/v2/dao/BrAPIStudyDAOUnitTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
*/
package org.breedinginsight.brapi.v2.dao;

import io.reactivex.functions.Consumer;
import io.reactivex.functions.Function;
import io.reactivex.functions.Function3;
import lombok.SneakyThrows;
Expand All @@ -26,11 +27,9 @@
import org.brapi.v2.model.core.BrAPIStudy;
import org.brapi.v2.model.core.request.BrAPIStudySearchRequest;
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.daos.cache.FetchFunction;
import org.breedinginsight.daos.cache.ProgramCache;
import org.breedinginsight.daos.cache.ProgramCacheProvider;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
import org.breedinginsight.utilities.BrAPIDAOUtil;
Expand All @@ -56,7 +55,6 @@ public class BrAPIStudyDAOUnitTest {
private BrAPIStudyDAO studyDAO;
private ProgramDAO programDAO;
private BrAPIDAOUtil brAPIDAOUtil;
private ProgramCache<BrAPIStudy> programCache;
private Program program;
private UUID programId;
private UUID environmentId;
Expand All @@ -76,11 +74,7 @@ void setup() {

programDAO = mock(ProgramDAO.class);
brAPIDAOUtil = mock(BrAPIDAOUtil.class);
ProgramCacheProvider programCacheProvider = mock(ProgramCacheProvider.class);
programCache = mock(ProgramCache.class);

when(programCacheProvider.getProgramCache(any(FetchFunction.class), eq(BrAPIStudy.class)))
.thenReturn(programCache);
when(programDAO.get(programId)).thenReturn(List.of(program));
when(programDAO.getCoreClient(programId)).thenReturn(mock(BrAPIClient.class));
when(programDAO.getProgramBrAPI(program)).thenReturn(brapiProgram);
Expand All @@ -89,8 +83,7 @@ void setup() {
programDAO,
mock(ImportDAO.class),
brAPIDAOUtil,
new BrAPIEndpointProvider(),
programCacheProvider
new BrAPIEndpointProvider()
);

Field referenceSource = BrAPIStudyDAO.class.getDeclaredField("referenceSource");
Expand Down Expand Up @@ -119,7 +112,6 @@ void getStudiesUsesDirectBrAPIGetInsteadOfProgramCache() {
assertEquals("brapi-program-1", queryParamsCaptor.getValue().programDbId());
assertEquals(0, queryParamsCaptor.getValue().page());
assertEquals(1000, queryParamsCaptor.getValue().pageSize());
verify(programCache, never()).get(any(UUID.class));
}

@Test
Expand All @@ -143,8 +135,6 @@ void getStudiesByStudyDbIdUsesDirectBrAPISearch() {

assertEquals(List.of("brapi-program-1"), requestCaptor.getValue().getProgramDbIds());
assertEquals(List.of(studyDbId), requestCaptor.getValue().getStudyDbIds());

verify(programCache, never()).get(any(UUID.class));
}

@Test
Expand All @@ -158,6 +148,28 @@ void getStudyByDbIdReturnsEmptyWhenBrAPIDoesNotFindStudy() {
assertTrue(result.isEmpty());
}

@Test
@SneakyThrows
void createBrAPIStudiesReturnsDirectBrAPIPostResponse() {

BrAPIStudy requestedStudy = new BrAPIStudy().studyName("Env1 [TEST-1]");
List<BrAPIStudy> requestedStudies = List.of(requestedStudy);

BrAPIStudy createdStudy = new BrAPIStudy().studyDbId("study-db-id").studyName("Env1 [TEST-1]");
ImportUpload upload = mock(ImportUpload.class);

doReturn(List.of(createdStudy))
.when(brAPIDAOUtil)
.post(eq(requestedStudies),eq(upload),any(Function.class),any(Consumer.class));

List<BrAPIStudy> result = studyDAO.createBrAPIStudies(requestedStudies,programId,upload);

assertEquals(1, result.size());
assertEquals("study-db-id",result.get(0).getStudyDbId());

verify(brAPIDAOUtil).post(eq(requestedStudies),eq(upload),any(Function.class),any(Consumer.class));
}

private BrAPIStudy study(UUID environmentId, String studyName) {
BrAPIExternalReference studyReference = new BrAPIExternalReference()
.referenceSource(Utilities.generateReferenceSource(REFERENCE_SOURCE, ExternalReferenceSource.STUDIES))
Expand Down
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