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[BI-1230] Truly Unknown Germplasm #205

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Merged
HMS17 merged 7 commits into from
Sep 21, 2022
Merged

[BI-1230] Truly Unknown Germplasm #205

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744e588
[BI-1230] Unknown Germplasm, saving, display, start of pedigree work
HMS17 Aug 17, 2022
86b0609
[BI-1230] Progeny endpoint attempt
HMS17 Aug 22, 2022
a50223c
Unknown germplasm displays minus 10+ progeny
HMS17 Sep 6, 2022
1f06287
Cleanup
HMS17 Sep 7, 2022
be8697c
Temp page size change due to cache error
HMS17 Sep 7, 2022
3ba5c46
Well that caused a build error
HMS17 Sep 7, 2022
ca7ddf2
Merge branch 'develop' into feature/BI-1230
HMS17 Sep 21, 2022
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169 changes: 166 additions & 3 deletions src/main/java/org/breedinginsight/brapi/v2/GermplasmController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,15 @@
import io.micronaut.security.annotation.Secured;
import io.micronaut.security.rules.SecurityRule;
import lombok.extern.slf4j.Slf4j;
import org.brapi.client.v2.ApiResponse;
import org.brapi.client.v2.model.exceptions.ApiException;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.brapi.client.v2.modules.germplasm.GermplasmApi;
import org.brapi.v2.model.BrAPIIndexPagination;
import org.brapi.v2.model.BrAPIMetadata;
import org.brapi.v2.model.BrAPIStatus;
import org.brapi.v2.model.germ.*;
import org.brapi.v2.model.germ.response.BrAPIGermplasmPedigreeResponse;
import org.brapi.v2.model.germ.response.BrAPIGermplasmProgenyResponse;
import org.breedinginsight.api.auth.ProgramSecured;
import org.breedinginsight.api.auth.ProgramSecuredRoleGroup;
import org.breedinginsight.api.model.v1.request.query.SearchRequest;
Expand All @@ -21,17 +28,20 @@
import org.breedinginsight.api.model.v1.validators.SearchValid;
import org.breedinginsight.brapi.v1.controller.BrapiVersion;
import org.breedinginsight.brapi.v1.model.request.query.BrapiQuery;
import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
import org.breedinginsight.brapi.v2.model.request.query.GermplasmQuery;
import org.breedinginsight.brapi.v2.model.response.mappers.GermplasmQueryMapper;
import org.breedinginsight.brapi.v2.services.BrAPIGermplasmService;
import org.breedinginsight.brapps.importer.model.exports.FileType;
import org.breedinginsight.daos.ProgramDAO;
import org.breedinginsight.model.DownloadFile;
import org.breedinginsight.services.exceptions.DoesNotExistException;
import org.breedinginsight.utilities.response.ResponseUtils;

import javax.inject.Inject;
import javax.validation.Valid;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.UUID;

Expand All @@ -42,11 +52,16 @@ public class GermplasmController {

private final BrAPIGermplasmService germplasmService;
private final GermplasmQueryMapper germplasmQueryMapper;
private final ProgramDAO programDAO;
private final BrAPIGermplasmDAO germplasmDAO;


@Inject
public GermplasmController(BrAPIGermplasmService germplasmService, GermplasmQueryMapper germplasmQueryMapper) {
public GermplasmController(BrAPIGermplasmService germplasmService, GermplasmQueryMapper germplasmQueryMapper, ProgramDAO programDAO, BrAPIGermplasmDAO germplasmDAO) {
this.germplasmService = germplasmService;
this.germplasmQueryMapper = germplasmQueryMapper;
this.programDAO = programDAO;
this.germplasmDAO = germplasmDAO;
}

@Post("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/search/germplasm{?queryParams*}")
Expand Down Expand Up @@ -124,4 +139,152 @@ public HttpResponse<Response<BrAPIGermplasm>> getSingleGermplasm(
return HttpResponse.status(HttpStatus.NOT_FOUND, "Germplasm not found");
}
}

@Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/germplasm/{germplasmId}/pedigree{?notation}{?includeSiblings}")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
public HttpResponse<BrAPIGermplasmPedigreeResponse> getGermplasmPedigreeInfo(
@PathVariable("programId") UUID programId,
@PathVariable("germplasmId") String germplasmId,
@QueryValue(defaultValue = "") String notation,
@QueryValue(defaultValue = "false") Boolean includeSiblings)
{
try {
log.debug("fetching pedigree for germ id:" + germplasmId +" for program: " + programId);
BrAPIPedigreeNode returnNode;
BrAPIGermplasmPedigreeResponse response;
BrAPIMetadata metadata;
if (germplasmId.endsWith("-Unknown")) {
//Unknown germplasm node
returnNode = new BrAPIPedigreeNode();
returnNode.setGermplasmDbId(germplasmId);
returnNode.setGermplasmName("Unknown");

BrAPIPedigreeNodeParents emptyParents = new BrAPIPedigreeNodeParents();
returnNode.addParentsItem(emptyParents);

returnNode.setSiblings(new ArrayList<>());
returnNode.setPedigree("/");
metadata = new BrAPIMetadata();
BrAPIStatus status = new BrAPIStatus();
status.setMessage("Complete");
status.setMessageType(BrAPIStatus.MessageTypeEnum.INFO);
BrAPIIndexPagination pagination = new BrAPIIndexPagination();
pagination.setTotalPages(1);
pagination.setTotalCount(1);
pagination.setPageSize(1);
pagination.setCurrentPage(0);
metadata.setStatus(Collections.singletonList(status));
metadata.setPagination(pagination);
response = new BrAPIGermplasmPedigreeResponse();
} else {
BrAPIGermplasm germplasm = germplasmService.getGermplasmByDBID(programId, germplasmId);
//Forward the pedigree call to the backing BrAPI system of the program passing the germplasmDbId that came in the request
GermplasmApi api = new GermplasmApi(programDAO.getCoreClient(programId));
ApiResponse<BrAPIGermplasmPedigreeResponse> pedigreeResponse = api.germplasmGermplasmDbIdPedigreeGet(germplasmId, notation, includeSiblings);
returnNode = pedigreeResponse.getBody().getResult();
metadata = pedigreeResponse.getBody().getMetadata();
response = pedigreeResponse.getBody();

//Add nodes for unknown parents if applicable
if (germplasm.getAdditionalInfo().has("femaleParentUnknown") && germplasm.getAdditionalInfo().get("femaleParentUnknown").getAsBoolean()) {
BrAPIPedigreeNodeParents unknownFemale = new BrAPIPedigreeNodeParents();
unknownFemale.setGermplasmDbId(germplasm.getGermplasmDbId()+"-F-Unknown");
unknownFemale.setGermplasmName("Unknown");
unknownFemale.setParentType(BrAPIParentType.FEMALE);
returnNode.addParentsItem(unknownFemale);
}
if (germplasm.getAdditionalInfo().has("maleParentUnknown") && germplasm.getAdditionalInfo().get("maleParentUnknown").getAsBoolean()) {
BrAPIPedigreeNodeParents unknownMale = new BrAPIPedigreeNodeParents();
unknownMale.setGermplasmDbId(germplasm.getGermplasmDbId()+"-M-Unknown");
unknownMale.setGermplasmName("Unknown");
unknownMale.setParentType(BrAPIParentType.MALE);
returnNode.addParentsItem(unknownMale);
}

//If no parents, need to add empty parents for display to work
if (returnNode.getParents().isEmpty()) {
BrAPIPedigreeNodeParents emptyParents = new BrAPIPedigreeNodeParents();
returnNode.addParentsItem(emptyParents);
}
}
response.setResult(returnNode);
response.setMetadata(metadata);
return HttpResponse.ok(response);
} catch (InternalServerException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
} catch (DoesNotExistException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.NOT_FOUND, "Pedigree node not found");
} catch (ApiException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
}
}

@Get("/${micronaut.bi.api.version}/programs/{programId}" + BrapiVersion.BRAPI_V2 + "/germplasm/{germplasmId}/progeny")
@Produces(MediaType.APPLICATION_JSON)
@ProgramSecured(roleGroups = {ProgramSecuredRoleGroup.ALL})
public HttpResponse<BrAPIGermplasmProgenyResponse> getGermplasmProgenyInfo(
@PathVariable("programId") UUID programId,
@PathVariable("germplasmId") String germplasmId) {
try {
log.debug("fetching progeny for germ id:" + germplasmId +" for program: " + programId);
BrAPIProgenyNode returnNode;
BrAPIGermplasmProgenyResponse response;
BrAPIMetadata metadata;
if (germplasmId.endsWith("-Unknown")) {
//Unknown germplasm node, only has one child
//We know progeny and parent type based on germplasmId
returnNode = new BrAPIProgenyNode();
returnNode.setGermplasmDbId(germplasmId);
returnNode.setGermplasmName("Unknown [-0]");
ArrayList<BrAPIProgenyNodeProgeny> progeny = new ArrayList<>();
BrAPIProgenyNodeProgeny singleProgeny = new BrAPIProgenyNodeProgeny();
singleProgeny.setGermplasmDbId(germplasmId.split("-")[0]);
singleProgeny.setGermplasmName("Name"); //does not seem necessary, preferable to avoid longer id string/making more endpoint calls
if (germplasmId.endsWith("F-Unknown")) {
singleProgeny.setParentType(BrAPIParentType.FEMALE);
} else {
singleProgeny.setParentType(BrAPIParentType.MALE);
}
returnNode.setProgeny(Collections.singletonList(singleProgeny));

metadata = new BrAPIMetadata();
BrAPIStatus status = new BrAPIStatus();
status.setMessage("Complete");
status.setMessageType(BrAPIStatus.MessageTypeEnum.INFO);
BrAPIIndexPagination pagination = new BrAPIIndexPagination();
pagination.setTotalPages(1);
pagination.setTotalCount(1);
pagination.setPageSize(1);
pagination.setCurrentPage(0);
metadata.setStatus(Collections.singletonList(status));
metadata.setPagination(pagination);
response = new BrAPIGermplasmProgenyResponse();
response.setResult(returnNode);
response.setMetadata(metadata);
return HttpResponse.ok(response);
} else {
//Forward the progeny call to the backing BrAPI system of the program passing the germplasmDbId that came in the request
GermplasmApi api = new GermplasmApi(programDAO.getCoreClient(programId));
ApiResponse<BrAPIGermplasmProgenyResponse> progenyResponse = api.germplasmGermplasmDbIdProgenyGet(germplasmId);

//If no progeny, need to add empty progeny for display to work
if (progenyResponse.getBody().getResult().getProgeny().isEmpty()) {
BrAPIProgenyNodeProgeny emptyProgeny = new BrAPIProgenyNodeProgeny();
progenyResponse.getBody().getResult().addProgenyItem(emptyProgeny);
}
return HttpResponse.ok(progenyResponse.getBody());
}
} catch (InternalServerException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
} catch (ApiException e) {
log.info(e.getMessage(), e);
return HttpResponse.status(HttpStatus.INTERNAL_SERVER_ERROR, "Error retrieving pedigree node");
}
}

}
19 changes: 19 additions & 0 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 @@ -195,6 +195,13 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID, maleParentAccessionNumber);
}
}
//Add Unknown germplasm for display
if (germplasm.getAdditionalInfo().has("femaleParentUnknown") && germplasm.getAdditionalInfo().get("femaleParentUnknown").getAsBoolean()) {
namePedigreeString = "Unknown";
}
if (germplasm.getAdditionalInfo().has("maleParentUnknown") && germplasm.getAdditionalInfo().get("maleParentUnknown").getAsBoolean()) {
namePedigreeString += "/Unknown";
}
//For use in individual germplasm display
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_NAME, namePedigreeString);
additionalInfo.addProperty(BrAPIAdditionalInfoFields.GERMPLASM_PEDIGREE_BY_UUID, uuidPedigreeString);
Expand Down Expand Up @@ -242,4 +249,16 @@ public BrAPIGermplasm getGermplasmByUUID(String germplasmId, UUID programId) thr
return germplasm;
}

public BrAPIGermplasm getGermplasmByDBID(String germplasmDbId, UUID programId) throws ApiException, DoesNotExistException {
Map<String, BrAPIGermplasm> cache = programGermplasmCache.get(programId);
//key is UUID, want to filter by DBID
BrAPIGermplasm germplasm = null;
if (cache != null) {
germplasm = cache.values().stream().filter(x -> x.getGermplasmDbId().equals(germplasmDbId)).collect(Collectors.toList()).get(0);
}
if (germplasm == null) {
throw new DoesNotExistException("DBID for this germplasm does not exist");
}
return germplasm;
}
}
8 changes: 8 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java
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Expand Up @@ -70,6 +70,14 @@ public BrAPIGermplasm getGermplasmByUUID(UUID programId, String germplasmId) thr
}
}

public BrAPIGermplasm getGermplasmByDBID(UUID programId, String germplasmId) throws DoesNotExistException {
try {
return germplasmDAO.getGermplasmByDBID(germplasmId, programId);
} catch (ApiException e) {
throw new InternalServerException(e.getMessage(), e);
}
}

public List<BrAPIListSummary> getGermplasmListsByProgramId(UUID programId, HttpRequest<String> request) throws DoesNotExistException, ApiException {

if (!programService.exists(programId)) {
Expand Down
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