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Implement brapi side filtering, sorting, paging for germplasm #561

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13 changes: 9 additions & 4 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIGermplasmController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
import org.brapi.v2.model.BrAPIIndexPagination;
import org.brapi.v2.model.BrAPIMetadata;
import org.brapi.v2.model.BrAPIStatus;
import org.brapi.v2.model.core.BrAPITrial;
import org.brapi.v2.model.germ.*;
import org.brapi.v2.model.germ.request.BrAPIGermplasmSearchRequest;
import org.brapi.v2.model.germ.response.BrAPIGermplasmListResponse;
Expand Down Expand Up @@ -185,7 +186,7 @@ private void batchProcessGermplasm(List<BrAPIGermplasm> germplasmList, String pr
@Get("/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/germplasm{?queryParams*}")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES})
public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
public HttpResponse<Response<DataResponse<BrAPIGermplasm>>> getGermplasm(
@PathVariable("programId") UUID programId,
@QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid GermplasmQuery queryParams) {
try {
Expand All @@ -198,15 +199,19 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
}

// Fetch all germplasm in the program unless a list id is supplied to return only germplasm in that collection
List<BrAPIGermplasm> germplasm = queryParams.getListDbId() == null ? germplasmService.getGermplasm(programId) : germplasmService.getGermplasmByList(programId, queryParams.getListDbId());
SearchRequest searchRequest = queryParams.constructSearchRequest();
return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams, searchRequest);
BrAPIGermplasmListResponse brapiResponse = queryParams.getListDbId() == null ? germplasmService.searchGermplasm(programId, queryParams) : germplasmService.getGermplasmByList(programId, queryParams);

List<BrAPIGermplasm> foundTrials = brapiResponse.getResult().getData();
return ResponseUtils.getBrapiQueryResponse(foundTrials, brapiResponse, queryParams);
} catch (ApiException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving germplasm");
} catch (IllegalArgumentException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, "Error parsing requested date format");
} catch (DoesNotExistException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.NOT_FOUND, "Supplied programId does not exist");
}
}

Expand Down
72 changes: 36 additions & 36 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIGermplasmDAO.java
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Expand Up @@ -135,16 +135,15 @@ public List<BrAPIGermplasm> getRawGermplasm(UUID programId) throws ApiException

/**
* Process germplasm into a format for display
* @param programGermplasm
* @param germplasmToProcess
* @return Map<Key = string representing germplasm UUID, value = formatted BrAPIGermplasm>
* @throws ApiException
*/
private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplasm> programGermplasm,
private List<BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplasm> germplasmToProcess,
Program program) throws ApiException {
// Process the germplasm
Map<String, BrAPIGermplasm> programGermplasmMap = new HashMap<>();
log.trace("processing germ for display: " + programGermplasm);
for (BrAPIGermplasm germplasm: programGermplasm) {
log.trace("processing germ for display: " + germplasmToProcess);
for (BrAPIGermplasm germplasm: germplasmToProcess) {

JsonObject additionalInfo = germplasm.getAdditionalInfo();
if (additionalInfo != null && additionalInfo.has(BrAPIAdditionalInfoFields.GERMPLASM_BREEDING_METHOD_ID)) {
Expand Down Expand Up @@ -177,15 +176,15 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas

// This should ease concerns for extra time pulling this data. The intended usage is for the Germplasm data table,
// but any usage under 200 germs (current data table max size) should not be too large of a hit to the server or database.
boolean pedigreeExRefMutation = programGermplasm.size() <= dataTableMaxSize;
boolean pedigreeExRefMutation = germplasmToProcess.size() <= dataTableMaxSize;

if (pedigreeExRefMutation) {
// Only perform this operation for callers that require it
pedigreeBrAPIGermplasmDbIdByBICreatedExRef = getPedigreeGermplasmDbIdByBICreatedExRef(programGermplasm, program);
pedigreeBrAPIGermplasmDbIdByBICreatedExRef = getPedigreeGermplasmDbIdByBICreatedExRef(germplasmToProcess, program);
}

// Update pedigree string
for (BrAPIGermplasm germplasm: programGermplasm) {
for (BrAPIGermplasm germplasm: germplasmToProcess) {
JsonObject additionalInfo = germplasm.getAdditionalInfo();
if(additionalInfo == null) {
additionalInfo = new JsonObject();
Expand Down Expand Up @@ -271,14 +270,10 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME, namePedigreeString);
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_UUID, uuidPedigreeString);

germplasm.setPedigree(gidPedigreeString);

BrAPIExternalReference extRef = germplasm.getExternalReferences().stream().filter(reference -> referenceSource.equals(reference.getReferenceSource())).findFirst().orElseThrow(() -> new IllegalStateException("No BI external reference found"));
String germplasmId = extRef.getReferenceID();
programGermplasmMap.put(germplasmId, germplasm);
germplasm.setPedigree(gidPedigreeString);
}

return programGermplasmMap;
return germplasmToProcess;
}

private Map<String, String> getPedigreeGermplasmDbIdByBICreatedExRef(List<BrAPIGermplasm> brAPIGermplasm, Program program) throws ApiException {
Expand Down Expand Up @@ -320,7 +315,7 @@ private Map<String, String> getPedigreeGermplasmDbIdByBICreatedExRef(List<BrAPIG
searchRequest.setExternalReferenceSources(List.of(referenceSource));

// Reuse some code to properly set searchRequest with brapiProgramDbId, and proper paging
searchRequest = buildSearchRequest(program, null, null, searchRequest);
searchRequest = buildSearchRequest(program, searchRequest, null);

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

Expand Down Expand Up @@ -364,7 +359,7 @@ private List<BrAPIGermplasm> getBrAPIGermplasmUsingBrAPIProgramId(GermplasmQuery
List<BrAPIGermplasm> result = brAPIDAOUtil.get(api::germplasmGet, germplasmQueryParams);

// TODO: Once cache is removed for this class, fix processGermplasmForDisplay to return List<BrAPIGermplasm> [BI-2906]
return new ArrayList<>(processGermplasmForDisplay(result, program).values());
return processGermplasmForDisplay(result, program);
}

// TODO: hack for now, probably should update breedbase
Expand Down Expand Up @@ -401,7 +396,7 @@ public List<BrAPIGermplasm> createBrAPIGermplasm(List<BrAPIGermplasm> postBrAPIG
try {
if (!postBrAPIGermplasmList.isEmpty()) {
List<BrAPIGermplasm> postResponse = brAPIDAOUtil.post(postBrAPIGermplasmList, upload, api::germplasmPost, importDAO::update);
return new ArrayList<>(processGermplasmForDisplay(postResponse, program).values());
return processGermplasmForDisplay(postResponse, program);
}
return new ArrayList<>();
} catch (Exception e) {
Expand All @@ -415,7 +410,7 @@ public List<BrAPIGermplasm> updateBrAPIGermplasm(List<BrAPIGermplasm> putBrAPIGe
try {
if (!putBrAPIGermplasmList.isEmpty()) {
List<BrAPIGermplasm> putResponse = putGermplasm(putBrAPIGermplasmList, api);
return new ArrayList<>(processGermplasmForDisplay(putResponse, program).values());
return processGermplasmForDisplay(putResponse, program);
}
return new ArrayList<>();
} catch (Exception e) {
Expand All @@ -432,39 +427,42 @@ public List<BrAPIGermplasm> getGermplasmByRawName(List<String> germplasmNames, U
.collect(Collectors.toList());
}

public BrAPIGermplasmListResponse searchGermplasmByRawName(List<String> germplasmNames, UUID programId, GermplasmQuery germplasmQuery) throws ApiException {
Program program = new Program(programDAO.fetchOneById(programId));

BrAPIGermplasmSearchRequest searchRequest = new BrAPIGermplasmSearchRequest();
searchRequest.setGermplasmNames(germplasmNames);

return brapiGermplasmSearchReturnResponse(program, searchRequest, germplasmQuery);
}

public List<BrAPIGermplasm> brapiGermplasmSearchReturnList(Program program,
List<String> brapiGermplasmIds) throws ApiException {
return brapiGermplasmSearchReturnResponse(program, brapiGermplasmIds, null).getResult().getData();
BrAPIGermplasmSearchRequest searchRequest) throws ApiException {
return brapiGermplasmSearchReturnResponse(program, searchRequest, null).getResult().getData();
}

public BrAPIGermplasmListResponse brapiGermplasmSearchReturnResponse(Program program,
List<String> brapiGermplasmIds,
BrAPIGermplasmSearchRequest searchRequest,
GermplasmQuery germplasmQuery) throws ApiException {

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

BrAPIGermplasmSearchRequest brAPIGermplasmSearchRequest = buildSearchRequest(program, brapiGermplasmIds, germplasmQuery);
BrAPIGermplasmSearchRequest brAPIGermplasmSearchRequest = buildSearchRequest(program, searchRequest, germplasmQuery);

BrAPIGermplasmListResponse brAPIResponse =
brAPIDAOUtil.simpleSearch(
api::searchGermplasmPost,
brAPIGermplasmSearchRequest
);

// TODO: Once cache is removed for this class, fix processGermplasmForDisplay to return List<BrAPIGermplasm> [BI-2906]
List<BrAPIGermplasm> processedGermplasm =
new ArrayList<>(processGermplasmForDisplay(brAPIDAOUtil.getListResult(brAPIResponse), program).values());
List<BrAPIGermplasm> processedGermplasm = processGermplasmForDisplay(brAPIDAOUtil.getListResult(brAPIResponse), program);

brAPIResponse.getResult().setData(processedGermplasm);

return brAPIResponse;
}

private BrAPIGermplasmSearchRequest buildSearchRequest(Program program, List<String> brapiGermplasmIds, GermplasmQuery query) throws ApiException {
return buildSearchRequest(program, brapiGermplasmIds, query, null);
}

private BrAPIGermplasmSearchRequest buildSearchRequest(Program program, List<String> brapiGermplasmIds, GermplasmQuery germplasmQuery, BrAPIGermplasmSearchRequest searchRequestPassThru) throws ApiException {
private BrAPIGermplasmSearchRequest buildSearchRequest(Program program, BrAPIGermplasmSearchRequest searchRequestPassThru, GermplasmQuery germplasmQuery) throws ApiException {
BrAPIGermplasmSearchRequest searchRequest;

if (searchRequestPassThru == null) {
Expand All @@ -475,10 +473,6 @@ private BrAPIGermplasmSearchRequest buildSearchRequest(Program program, List<Str

searchRequest.programDbIds(List.of(brAPIDAOUtil.getBrAPIProgramDbId(program.getId())));

if (brapiGermplasmIds != null && !brapiGermplasmIds.isEmpty()) {
searchRequest.setGermplasmDbIds(new ArrayList<>(brapiGermplasmIds));
}

brAPIDAOUtil.setGenericSearchParameters(searchRequest, germplasmQuery);

return searchRequest;
Expand All @@ -487,7 +481,10 @@ private BrAPIGermplasmSearchRequest buildSearchRequest(Program program, List<Str
public BrAPIGermplasm getGermplasmByUUID(String germplasmId, UUID programId) throws ApiException, DoesNotExistException {
Program program = new Program(programDAO.fetchOneById(programId));

List<BrAPIGermplasm> result = brapiGermplasmSearchReturnList(program, List.of(germplasmId));
BrAPIGermplasmSearchRequest searchRequest = new BrAPIGermplasmSearchRequest();
searchRequest.setGermplasmDbIds(List.of(germplasmId));

List<BrAPIGermplasm> result = brapiGermplasmSearchReturnList(program, searchRequest);

if (result.size() > 1) {
throw new ApiException(String.format("Multiple germplasms found for germplasm with ID: [%s]", germplasmId));
Expand All @@ -502,7 +499,10 @@ public List<BrAPIGermplasm> getGermplasmsByDBID(Collection<String> germplasmDbId
// TODO: This method is mainly used by the download experiment export tool. This method will fail until we address the parameter limit for async Germplasm requests for germplasmDbIds > 4. Return to this use case during [BI-3021]
Program program = new Program(programDAO.fetchOneById(programId));

return brapiGermplasmSearchReturnList(program, new ArrayList<>(germplasmDbIds));
BrAPIGermplasmSearchRequest searchRequest = new BrAPIGermplasmSearchRequest();
searchRequest.setGermplasmDbIds(new ArrayList<>(germplasmDbIds));

return brapiGermplasmSearchReturnList(program, searchRequest);
}

public List<BrAPIGermplasm> putGermplasm(List<BrAPIGermplasm> germplasmList, GermplasmApi api) throws ApiException {
Expand Down
40 changes: 40 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/model/request/query/GermplasmQuery.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,9 @@
import org.jooq.tools.StringUtils;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

@Getter
@Introspected
Expand Down Expand Up @@ -67,4 +69,42 @@ public SearchRequest constructSearchRequest() {
}
return new SearchRequest(filters);
}

@Override
public Map<String, String> getFilterValuesByBrAPIColumnName() {
Map<String, String> filterValuesByBrAPIColumnName = new HashMap<>();

filterValuesByBrAPIColumnName.put("importEntryNumber", getImportEntryNumber());
filterValuesByBrAPIColumnName.put("accessionNumber", getAccessionNumber());
filterValuesByBrAPIColumnName.put("defaultDisplayName", getDefaultDisplayName());
filterValuesByBrAPIColumnName.put("breedingMethod", getBreedingMethod());
filterValuesByBrAPIColumnName.put("seedSource", getSeedSource());
filterValuesByBrAPIColumnName.put("pedigree", getPedigree());
filterValuesByBrAPIColumnName.put("femaleParentGID", getFemaleParentGID());
filterValuesByBrAPIColumnName.put("maleParentGID", getMaleParentGID());
filterValuesByBrAPIColumnName.put("createdDate", getCreatedDate());
filterValuesByBrAPIColumnName.put("createdBy", getCreatedByUserName());
filterValuesByBrAPIColumnName.put("synonyms", getSynonym());

return filterValuesByBrAPIColumnName;
}

@Override
public Map<String, String> getBrAPIColumnNamesByBiColumnName() {
Map<String, String> brAPIColumnNamesByBiColumnName = new HashMap<>();

brAPIColumnNamesByBiColumnName.put("importEntryNumber", "importEntryNumber");
brAPIColumnNamesByBiColumnName.put("accessionNumber", "accessionNumber");
brAPIColumnNamesByBiColumnName.put("defaultDisplayName", "defaultDisplayName");
brAPIColumnNamesByBiColumnName.put("breedingMethod", "breedingMethod");
brAPIColumnNamesByBiColumnName.put("seedSource", "seedSource");
brAPIColumnNamesByBiColumnName.put("pedigree", "pedigree");
brAPIColumnNamesByBiColumnName.put("femaleParentGID", "femaleParentGID");
brAPIColumnNamesByBiColumnName.put("maleParentGID", "maleParentGID");
brAPIColumnNamesByBiColumnName.put("createdDate", "createdDate");
brAPIColumnNamesByBiColumnName.put("createdBy", "createdByUserName");
brAPIColumnNamesByBiColumnName.put("synonyms", "synonyms");

return brAPIColumnNamesByBiColumnName;
}
}
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