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[BI-3082] Implement sorting/filtering/pagination on germplasm list items #567

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[BI-3082] Implement sorting/filtering/pagination on germplasm list items #567

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14e1012
Utilize prod server changes to correctly sort/filter/paginate germs b…
jloux-brapi Oct 15, 2026
ece4f54
Force type parametrization serialization on the client
jloux-brapi Oct 16, 2026
8dc5c9e
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jloux-brapi Oct 19, 2026
3abd1a9
Fix broken unit test
jloux-brapi Oct 19, 2026
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28 changes: 23 additions & 5 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 @@ -17,6 +17,8 @@

package org.breedinginsight.brapi.v2.dao;

import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.JsonObject;
import io.micronaut.context.annotation.Property;
import io.micronaut.http.HttpStatus;
Expand All @@ -27,7 +29,9 @@
import org.brapi.client.v2.model.queryParams.germplasm.GermplasmQueryParams;
import org.brapi.client.v2.modules.germplasm.GermplasmApi;
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.core.BrAPIListItemWithFullItem;
import org.brapi.v2.model.core.BrAPIProgram;
import org.brapi.v2.model.core.response.BrAPIListItemsListResponse;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.brapi.v2.model.germ.BrAPIGermplasmSynonyms;
import org.brapi.v2.model.germ.request.BrAPIGermplasmSearchRequest;
Expand All @@ -45,6 +49,7 @@
import org.breedinginsight.utilities.Utilities;

import javax.inject.Inject;
import javax.inject.Named;
import javax.inject.Singleton;
import java.util.*;
import java.util.stream.Collectors;
Expand All @@ -56,6 +61,8 @@ public class BrAPIGermplasmDAO {
private final ProgramDAO programDAO;
private final ImportDAO importDAO;
private final BrAPIDAOUtil brAPIDAOUtil;
private final ObjectMapper objectMapper;
private final BrAPIListDAO brAPIListDAO;

@Property(name = "brapi.server.reference-source")
private String referenceSource;
Expand All @@ -72,12 +79,16 @@ public BrAPIGermplasmDAO(ProgramDAO programDAO,
ImportDAO importDAO,
BrAPIDAOUtil brAPIDAOUtil,
BrAPIEndpointProvider brAPIEndpointProvider,
@Property(name = "brapi.cache.fetch-page-size") int brapiFetchPageSize) {
@Property(name = "brapi.cache.fetch-page-size") int brapiFetchPageSize,
ObjectMapper objectMapper,
BrAPIListDAO brAPIListDAO) {
this.programDAO = programDAO;
this.importDAO = importDAO;
this.brAPIDAOUtil = brAPIDAOUtil;
this.brAPIEndpointProvider = brAPIEndpointProvider;
this.brapiMaxPageSize = brapiFetchPageSize;
this.objectMapper = objectMapper;
this.brAPIListDAO = brAPIListDAO;
}

/**
Expand Down Expand Up @@ -427,13 +438,20 @@ public List<BrAPIGermplasm> getGermplasmByRawName(List<String> germplasmNames, U
.collect(Collectors.toList());
}

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

BrAPIGermplasmSearchRequest searchRequest = new BrAPIGermplasmSearchRequest();
searchRequest.setGermplasmNames(germplasmNames);
BrAPIGermplasmSearchRequest searchRequest = buildSearchRequest(program, null, germplasmQuery);

// Because the list item search endpoint is generalized, a typed BrAPISearchRequest won't work, so convert it to JsonNode.
// The search request type is derived by the client/prod server based off of the type of the submitted list dbId.
JsonNode listRequestBody = objectMapper.valueToTree(searchRequest);

BrAPIListItemsListResponse<BrAPIGermplasm> response = brAPIListDAO.searchBrAPIListItemsByList(listDbId, programId, listRequestBody);

processGermplasmForDisplay(response.getResult().getData().stream().map(BrAPIListItemWithFullItem::getItem).collect(Collectors.toList()), program);

return brapiGermplasmSearchReturnResponse(program, searchRequest, germplasmQuery);
return response;
}

public List<BrAPIGermplasm> brapiGermplasmSearchReturnList(Program program,
Expand Down
47 changes: 38 additions & 9 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIListDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@

package org.breedinginsight.brapi.v2.dao;

import com.fasterxml.jackson.databind.JsonNode;
import io.micronaut.http.HttpResponse;
import lombok.extern.slf4j.Slf4j;
import okhttp3.HttpUrl;
Expand All @@ -27,14 +28,13 @@
import org.brapi.v2.model.BrAPIExternalReference;
import org.brapi.v2.model.BrAPIResponse;
import org.brapi.v2.model.BrAPIResponseResult;
import org.brapi.v2.model.core.BrAPIListItemWithFullItem;
import org.brapi.v2.model.core.BrAPIListSummary;
import org.brapi.v2.model.core.BrAPIListTypes;
import org.brapi.v2.model.core.request.BrAPIListNewRequest;
import org.brapi.v2.model.core.request.BrAPIListSearchRequest;
import org.brapi.v2.model.core.response.BrAPIListDetails;
import org.brapi.v2.model.core.response.BrAPIListsListResponse;
import org.brapi.v2.model.core.response.BrAPIListsListResponseResult;
import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
import org.brapi.v2.model.core.response.*;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.breedinginsight.brapps.importer.daos.ImportDAO;
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.daos.ProgramDAO;
Expand Down Expand Up @@ -71,7 +71,7 @@ public BrAPIListDAO(ProgramDAO programDAO,
}

public List<BrAPIListSummary> getListsByName(List<String> listNames, UUID programId) throws ApiException {
if(listNames.isEmpty()) {
if (listNames.isEmpty()) {
return Collections.emptyList();
}

Expand Down Expand Up @@ -122,11 +122,11 @@ private List<BrAPIListSummary> processListsForProgram(List<BrAPIListSummary> pro
// check that all lists were created via the BI UI in case the BrAPI service silently ignores the search by
// externalReference source and ID
List<BrAPIListSummary> filteredLists = new ArrayList<>();
for (BrAPIListSummary list: programLists) {
for (BrAPIListSummary list : programLists) {
if (list.getExternalReferences() == null || list.getExternalReferences().size() == 0) {
continue;
} else {
for (BrAPIExternalReference ref: list.getExternalReferences()) {
for (BrAPIExternalReference ref : list.getExternalReferences()) {
if (ref.getReferenceID().equals(externalReferenceId.toString()) &&
ref.getReferenceSource().equals(externalReferenceSource)) {
filteredLists.add(list);
Expand All @@ -136,6 +136,7 @@ private List<BrAPIListSummary> processListsForProgram(List<BrAPIListSummary> pro
}
return filteredLists;
}

public List<String> updateBrAPIList(String brAPIListDbId, BrAPIListDetails mutatedList, UUID programId) throws ApiException {
ListsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ListsApi.class);
BrAPIListNewRequest request = new BrAPIListNewRequest();
Expand All @@ -160,7 +161,7 @@ public List<String> updateBrAPIList(String brAPIListDbId, BrAPIListDetails mutat
log.error(Utilities.generateApiExceptionLogMessage(e));
throw e;
}
if(response != null) {
if (response != null) {
BrAPIListsSingleResponse body = response.getBody();
if (body == null) {
throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
Expand Down Expand Up @@ -188,7 +189,7 @@ public List<BrAPIListSummary> createBrAPILists(List<BrAPIListNewRequest> brapiLi
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw e;
}
if(response != null) {
if (response != null) {
BrAPIResponse<BrAPIListsListResponseResult> body = response.getBody();
if (body == null) {
throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
Expand Down Expand Up @@ -220,4 +221,32 @@ public HttpResponse<String> deleteBrAPIList(String listDbId, UUID programId, boo
return brAPIDAOUtil.makeCall(brapiRequest);
}

public <T> BrAPIListItemsListResponse<T> searchBrAPIListItemsByList(String listDbId, UUID programId, JsonNode requestBody) throws ApiException {
ListsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ListsApi.class);
// Do manually, it doesn't like List<Object> to List<BrAPIListNewRequest> for some reason
ApiResponse<BrAPIListItemsListResponse<T>> response;
try {
response = api.searchListItemsByList(listDbId, requestBody);
} catch (ApiException e) {
log.warn(Utilities.generateApiExceptionLogMessage(e));
throw e;
}

if (response != null) {
BrAPIResponse<BrAPIListItemsListResponseResult<T>> body = response.getBody();
if (body == null) {
throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
}
BrAPIResponseResult<BrAPIListItemWithFullItem<T>> result = body.getResult();
if (result == null) {
throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
}
if (result.getData() == null) {
throw new ApiException("Response result is missing data", 0, response.getHeaders(), response.getBody().toString());
}
return response.getBody();
}

throw new ApiException("No response for BrAPI list item search");
}
}
99 changes: 23 additions & 76 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,15 @@
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.v2.model.BrAPIExternalReference;
import lombok.extern.slf4j.Slf4j;
import org.brapi.v2.model.core.BrAPIListItemWithFullItem;
import org.brapi.v2.model.core.request.BrAPIListNewRequest;
import org.brapi.v2.model.core.response.BrAPIListDetails;
import org.brapi.v2.model.core.response.BrAPIListItemsListResponse;
import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.brapi.v2.model.germ.BrAPIGermplasmSynonyms;
import org.brapi.v2.model.germ.response.BrAPIGermplasmListResponse;
import org.brapi.v2.model.germ.response.BrAPIGermplasmListResponseResult;
import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
import org.breedinginsight.brapi.v2.dao.BrAPIListDAO;
import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
Expand Down Expand Up @@ -172,96 +175,40 @@ public BrAPIGermplasmListResponse getGermplasmByList(UUID programId, GermplasmQu
if(Objects.nonNull(listResponse) && Objects.nonNull(listResponse.getResult())) {

// get the list ID stored in the list external references
UUID listId = getGermplasmListId(listResponse.getResult());
// TODO: See if this can be removed/replaced with actual BrAPI list db id
UUID biGermplasmListId = getGermplasmListId(listResponse.getResult());

// get list BrAPI germplasm variables.
// The order of these germplasm names are the exact order/entry number in the list that was imported.
List<String> germplasmNamesFromBrapiList = listResponse.getResult().getData();
// Required for the actual data search in BrAPI
String brapiListDbId = listResponse.getResult().getListDbId();

BrAPIGermplasmListResponse germplasmSearchResponse = germplasmDAO.searchGermplasmByRawName(germplasmNamesFromBrapiList, programId, germplasmQuery);
BrAPIListItemsListResponse<BrAPIGermplasm> listSearchResponse = germplasmDAO.searchGermplasmByList(brapiListDbId, programId, germplasmQuery);

List<BrAPIGermplasm> germplasm = germplasmSearchResponse.getResult().getData();
Map<String, BrAPIGermplasm> germplasmByGid = new HashMap<>();
List<BrAPIListItemWithFullItem<BrAPIGermplasm>> listItemsWithFullItem = listSearchResponse.getResult().getData();

if (germplasm == null || germplasm.isEmpty()) {
return germplasmSearchResponse;
}

for (BrAPIGermplasm g : germplasm) {
// set the list ID in the germplasm additional info
g.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ID, listId);
// Add to map.
germplasmByGid.put(g.getAccessionNumber(), g);
}

// Extract gids from list names
List<String> gids = germplasmNamesFromBrapiList.stream().map(Utilities::extractGid).collect(Collectors.toList());

// Build list from BrAPI list that preserves ordering and duplicates and assigns sequential entry numbers.
List<BrAPIGermplasm> orderByEntryNumber = new ArrayList<>();

Program program = programService.getById(programId).orElseThrow(() -> new DoesNotExistException("Could not find program: " + programId));

for (String gid : gids) {
BrAPIGermplasm germ = germplasmByGid.get(gid);
listItemsWithFullItem.forEach(li -> {
li.getItem().putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_LIST_ID, biGermplasmListId);
// listItem.position start of index is 0 in BrAPI, but in DeltaBreed, it starts at 1. increment result data to account for this.
// The actual sort/filter performs the search on a formula column created on the prod server, so no need to worry about that in the request above.
li.getItem().putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER, li.getListItem().getPosition() + 1);
});

if (germ == null) {
continue;
}

// We can't simply use germ.getGermplasmName here because the BrAPIGermplasmDAO code strips the key and gid via BrAPIGermplasmDAO.processGermplasmForDisplay()
// Rebuild the unique name so we can get the entry number via the order on the germplasmNamesFromBrapiList list which was derived from the list response.
String fullGermplasmName = Utilities.appendProgramKey(germ.getDefaultDisplayName(), program.getKey(), germ.getAccessionNumber());
List<BrAPIGermplasm> germplasm = listItemsWithFullItem.stream().map(BrAPIListItemWithFullItem::getItem).collect(Collectors.toList());

BrAPIGermplasm listEntry = cloneBrAPIGermplasm(germ);
BrAPIGermplasmListResponse germplasmSearchResponse = new BrAPIGermplasmListResponse();
BrAPIGermplasmListResponseResult germplasmListResponseResult = new BrAPIGermplasmListResponseResult();

int entryNumber = germplasmNamesFromBrapiList.indexOf(fullGermplasmName) + 1;

// Set entry number.
listEntry.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER, entryNumber);
germ.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER, entryNumber);
orderByEntryNumber.add(listEntry);
}
germplasmSearchResponse.setMetadata(listSearchResponse.getMetadata());
germplasmListResponseResult.setData(germplasm);
germplasmSearchResponse.setResult(germplasmListResponseResult);

if (germplasmQuery.getSortField() == null || germplasmQuery.getSortField().equals("importEntryNumber")) {
// This should order by entry number when germplasm list details page displays
germplasmSearchResponse.getResult().setData(orderByEntryNumber);
} else {
// In all other cases it will order by the other selected data
germplasmSearchResponse.getResult().setData(germplasm);
if (germplasm.isEmpty()) {
return germplasmSearchResponse;
}

return germplasmSearchResponse;
} else throw new ApiException();
}

// private BrAPIGermplasmListResponse orderByListImportEntryNumber() {
// for (String gid : gids) {
// BrAPIGermplasm germ = germplasmByGid.get(gid);
//
// if (germ == null) {
// continue;
// }
//
// // We can't simply use germ.getGermplasmName here because the BrAPIGermplasmDAO code strips the key and gid via BrAPIGermplasmDAO.processGermplasmForDisplay()
// // Rebuild the unique name so we can get the entry number via the order on the germplasmNamesFromBrapiList list which was derived from the list response.
// String fullGermplasmName = Utilities.appendProgramKey(germ.getDefaultDisplayName(), program.getKey(), germ.getAccessionNumber());
//
// BrAPIGermplasm listEntry = cloneBrAPIGermplasm(germ);
//
// int entryNumber = germplasmNamesFromBrapiList.indexOf(fullGermplasmName) + 1;
//
// // Set entry number.
// listEntry.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GERMPLASM_IMPORT_ENTRY_NUMBER, entryNumber);
// orderByEntryNumber.add(listEntry);
// }
// }

private BrAPIGermplasm cloneBrAPIGermplasm(BrAPIGermplasm germplasm) {
// Serialize then deserialize to deep copy.
return (BrAPIGermplasm) gson.fromJson(gson.toJson(germplasm), BrAPIGermplasm.class);
}

public DownloadFile exportGermplasm(UUID programId, FileType fileExtension) throws IllegalArgumentException, ApiException, IOException, DoesNotExistException {
List<Column> columns = GermplasmFileColumns.getOrderedColumns();

Expand Down
3 changes: 2 additions & 1 deletion src/test/java/org/breedinginsight/services/BrAPIGermplasmServiceUnitTest.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package org.breedinginsight.services;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.JsonObject;
import io.reactivex.functions.Function;
import io.reactivex.functions.Function3;
Expand Down Expand Up @@ -60,7 +61,7 @@ void setup() {
listDAO = mock(BrAPIListDAO.class);
programDAO = mock(ProgramDAO.class);
brAPIDAOUtil = mock(BrAPIDAOUtil.class);
germplasmDAO = new BrAPIGermplasmDAO(programDAO, mock(ImportDAO.class), brAPIDAOUtil, new BrAPIEndpointProvider(), 65000);
germplasmDAO = new BrAPIGermplasmDAO(programDAO, mock(ImportDAO.class), brAPIDAOUtil, new BrAPIEndpointProvider(), 65000, new ObjectMapper(), listDAO);
programService = mock(ProgramService.class);

Field externalReferenceSource = BrAPIGermplasmDAO.class.getDeclaredField("referenceSource");
Expand Down
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