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Remove rest of CRUD operations from BrAPIGermplasmDAO #557

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Merged
jloux-brapi merged 4 commits into from
Oct 6, 2026
Merged

Remove rest of CRUD operations from BrAPIGermplasmDAO #557

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d9d6798
Remove rest of CRUD operations from BrAPIGermplasmDAO
jloux-brapi Sep 14, 2026
536cc8e
Resolve merge conflicts
jloux-brapi Sep 14, 2026
f9fd37d
Remove unused germplasmFetch
jloux-brapi Sep 17, 2026
3eda7eb
Remove imports
jloux-brapi Sep 17, 2026
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80 changes: 2 additions & 78 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,18 +18,14 @@
package org.breedinginsight.brapi.v2.dao;

import com.google.gson.JsonObject;
import io.micronaut.context.annotation.Context;
import io.micronaut.context.annotation.Property;
import io.micronaut.http.HttpStatus;
import io.micronaut.http.server.exceptions.InternalServerException;
import io.micronaut.scheduling.annotation.Scheduled;
import lombok.extern.slf4j.Slf4j;
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.germplasm.GermplasmQueryParams;
import org.brapi.client.v2.modules.germplasm.GermplasmApi;
import org.brapi.v2.model.BrAPIAcceptedSearchResponse;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIProgram;
import org.brapi.v2.model.germ.BrAPIGermplasm;
Expand All @@ -41,10 +37,7 @@
import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
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.ProgramCache;
import org.breedinginsight.daos.cache.ProgramCacheProvider;
import org.breedinginsight.model.Program;
import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
import org.breedinginsight.services.exceptions.DoesNotExistException;
Expand All @@ -54,12 +47,10 @@
import javax.inject.Inject;
import javax.inject.Singleton;
import java.util.*;
import java.util.concurrent.Callable;
import java.util.stream.Collectors;

@Slf4j
@Singleton
@Context
public class BrAPIGermplasmDAO {

private final ProgramDAO programDAO;
Expand All @@ -69,17 +60,9 @@ public class BrAPIGermplasmDAO {
@Property(name = "brapi.server.reference-source")
private String referenceSource;

@Property(name = "micronaut.bi.api.run-scheduled-tasks")
private boolean runScheduledTasks;

@Property(name = "brapi.paginate.germplasm")
private boolean paginateGermplasm;

@Property(name = "data-table.max-size")
private int dataTableMaxSize;

private final ProgramCache<BrAPIGermplasm> programGermplasmCache;

private final BrAPIEndpointProvider brAPIEndpointProvider;

private final int brapiMaxPageSize;
Expand All @@ -88,30 +71,15 @@ public class BrAPIGermplasmDAO {
public BrAPIGermplasmDAO(ProgramDAO programDAO,
ImportDAO importDAO,
BrAPIDAOUtil brAPIDAOUtil,
ProgramCacheProvider programCacheProvider,
BrAPIEndpointProvider brAPIEndpointProvider,
@Property(name = "brapi.cache.fetch-page-size") int brapiFetchPageSize) {
this.programDAO = programDAO;
this.importDAO = importDAO;
this.brAPIDAOUtil = brAPIDAOUtil;
this.programGermplasmCache = programCacheProvider.getProgramCache(this::fetchProgramGermplasm, BrAPIGermplasm.class);
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.brapiMaxPageSize = brapiFetchPageSize;
}

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

/**
* Fetch the germplasm for this program, and process it to remove storage specific values
* @param programId
Expand Down Expand Up @@ -165,47 +133,6 @@ public List<BrAPIGermplasm> getRawGermplasm(UUID programId) throws ApiException
}).collect(Collectors.toList());
}


/**
* Fetch formatted germplasm for this program
* @param programId
* @return Map<Key = string representing germplasm UUID, value = formatted BrAPIGermplasm>
* @throws ApiException
*/
private Map<String, BrAPIGermplasm> fetchProgramGermplasm(UUID programId) throws ApiException {
GermplasmApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), GermplasmApi.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
BrAPIGermplasmSearchRequest germplasmSearch = new BrAPIGermplasmSearchRequest();
germplasmSearch.externalReferenceIDs(List.of(programId.toString()));
germplasmSearch.externalReferenceSources(List.of(Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.PROGRAMS)));

if (paginateGermplasm) {
log.debug("Fetching germplasm with pagination to BrAPI");
return processGermplasmForDisplay(brAPIDAOUtil.search(
api::searchGermplasmPost,
api::searchGermplasmSearchResultsDbIdGet,
germplasmSearch),
program);
} else {
log.debug("Fetching germplasm without pagination to BrAPI");
return processGermplasmForDisplay(brAPIDAOUtil.searchNoPaging(
api::searchGermplasmPost,
api::searchGermplasmSearchResultsDbIdGet,
germplasmSearch),
program);
}
}

public void repopulateGermplasmCacheForProgram(UUID programId) {
programGermplasmCache.populate(programId);
}
/**
* Process germplasm into a format for display
* @param programGermplasm
Expand Down Expand Up @@ -487,11 +414,8 @@ public List<BrAPIGermplasm> updateBrAPIGermplasm(List<BrAPIGermplasm> putBrAPIGe
var program = new Program(programDAO.fetchOneById(programId));
try {
if (!putBrAPIGermplasmList.isEmpty()) {
Callable<Map<String, BrAPIGermplasm>> postFunction = () -> {
List<BrAPIGermplasm> putResponse = putGermplasm(putBrAPIGermplasmList, api);
return processGermplasmForDisplay(putResponse, program);
};
return programGermplasmCache.post(programId, postFunction);
List<BrAPIGermplasm> putResponse = putGermplasm(putBrAPIGermplasmList, api);
return new ArrayList<>(processGermplasmForDisplay(putResponse, program).values());
}
return new ArrayList<>();
} catch (Exception e) {
Expand Down
2 changes: 0 additions & 2 deletions ...org/breedinginsight/brapps/importer/services/processors/germplasm/GermplasmProcessor.java
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Expand Up @@ -724,8 +724,6 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program
try {
// Create germplasm list
brAPIListDAO.createBrAPILists(List.of(importList), program.getId(), upload);
// Now that we have finished uploading, fetch all the data posted to BrAPI to the cache so it is up-to-date.
brAPIGermplasmDAO.repopulateGermplasmCacheForProgram(program.getId());
} catch (ApiException e) {
throw new InternalServerException(e.toString(), e);
}
Expand Down
3 changes: 0 additions & 3 deletions src/test/java/org/breedinginsight/brapps/importer/GermplasmFileImportTest.java
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Expand Up @@ -1257,8 +1257,5 @@ private void seedExistingGermplasm(String accessionNumber, String displayName, S
germplasm.setExternalReferences(externalReferences);

germplasmDAO.createBrAPIGermplasm(List.of(germplasm), validProgram.getId(), null);

//Refresh cache so importer lookup sees the seeded germplasm immediately.
germplasmDAO.repopulateGermplasmCacheForProgram(validProgram.getId());
}
}
9 changes: 1 addition & 8 deletions src/test/java/org/breedinginsight/services/BrAPIGermplasmServiceUnitTest.java
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Expand Up @@ -51,7 +51,6 @@ public class BrAPIGermplasmServiceUnitTest extends DatabaseTest {
private BrAPIGermplasmService germplasmService;
private BrAPIDAOUtil brAPIDAOUtil;
private String referenceSource;
private ProgramCacheProvider cacheProvider;

@SneakyThrows
@BeforeEach
Expand All @@ -61,8 +60,7 @@ void setup() {
listDAO = mock(BrAPIListDAO.class);
programDAO = mock(ProgramDAO.class);
brAPIDAOUtil = mock(BrAPIDAOUtil.class);
cacheProvider = new ProgramCacheProvider(super.getRedisConnection());
germplasmDAO = new BrAPIGermplasmDAO(programDAO, mock(ImportDAO.class), brAPIDAOUtil, cacheProvider, new BrAPIEndpointProvider(), 65000);
germplasmDAO = new BrAPIGermplasmDAO(programDAO, mock(ImportDAO.class), brAPIDAOUtil, new BrAPIEndpointProvider(), 65000);
programService = mock(ProgramService.class);

Field externalReferenceSource = BrAPIGermplasmDAO.class.getDeclaredField("referenceSource");
Expand Down Expand Up @@ -157,11 +155,6 @@ public void getGermplasmListExport() {
any(GermplasmQueryParams.class))).thenReturn(germplasm);
when(brAPIDAOUtil.getBrAPIProgramDbId(any())).thenReturn(brapiProgramDbId);

//Create germplasm cache of stub data
Method setupMethod = BrAPIGermplasmDAO.class.getDeclaredMethod("setup");
setupMethod.setAccessible(true);
setupMethod.invoke(germplasmDAO);

//Create test instance of service, injecting spy- and mock-dependencies
germplasmService = new BrAPIGermplasmService(brAPIListSpy, programSpy, germplasmDAO);

Expand Down
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