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fix:修复到只剩下41个warning

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彭帅
2026-05-30 13:09:37 +08:00
parent 12eeeafcd7
commit f4e70f9901
15 changed files with 803 additions and 523 deletions
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886
docs/problem_fix/03-fix.md
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File diff suppressed because it is too large Load Diff

3
src/main/java/org/brapi/test/BrAPITestServer/controller/geno/AlleleMatrixApiController.java
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@@ -89,6 +89,9 @@ public class AlleleMatrixApiController extends BrAPIController implements Allele
log.debug("Request: " + request.getRequestURI());
validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
validateAcceptHeader(request);
if (body == null) {
body = new AlleleMatrixSearchRequest();
}
Metadata metadata = generateEmptyMetadata();
String searchReqDbId = searchService.saveSearchRequest(body, SearchRequestTypes.CALLS);

3
src/main/java/org/brapi/test/BrAPITestServer/controller/geno/CallsApiController.java
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@@ -80,6 +80,9 @@ public class CallsApiController extends BrAPIController implements CallsApi {
log.debug("Request: " + request.getRequestURI());
validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
validateAcceptHeader(request);
if (body == null) {
body = new CallsSearchRequest();
}
Metadata metadata = generateMetaDataTemplate(body.getPageToken(), body.getPageSize());
String searchReqDbId = searchService.saveSearchRequest(body, SearchRequestTypes.CALLS);

3
src/main/java/org/brapi/test/BrAPITestServer/model/entity/AdditionalInfoEntity.java
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@@ -23,6 +23,9 @@ public class AdditionalInfoEntity extends BrAPIBaseEntity {
}
public Object getValue() {
if (value == null) {
return null;
}
ByteArrayInputStream bais = new ByteArrayInputStream(value);
Object obj = null;
try {

6
src/main/java/org/brapi/test/BrAPITestServer/model/entity/BrAPIPrimaryEntity.java
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@@ -46,12 +46,16 @@ public class BrAPIPrimaryEntity extends BrAPIBaseEntity {
Map<String, Object> info = new HashMap<>();
if (getAdditionalInfo() != null) {
for (AdditionalInfoEntity entity : getAdditionalInfo()) {
info.put(entity.getKey(), entity.getValue());
info.put(entity.getKey(), stringifyAdditionalInfoValue(entity.getValue()));
}
}
return info;
}
private Object stringifyAdditionalInfoValue(Object value) {
return value == null || value instanceof String ? value : String.valueOf(value);
}
public void setAdditionalInfo(Map<String, Object> map) {
if (map != null) {
setAdditionalInfo(new ArrayList<>());

2
src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/CallSetEntity.java
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@@ -35,8 +35,10 @@ public class CallSetEntity extends BrAPIPrimaryEntity {
this.setSample(callSet.getSample());
this.setUpdated(callSet.getUpdated());
this.setVariantSets(new ArrayList<>());
if (callSet.getVariantSets() != null) {
this.getVariantSets().addAll(callSet.getVariantSets());
}
}
public Date getCreated() {
return created;

8
src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/VariantEntity.java
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@@ -49,16 +49,24 @@ public class VariantEntity extends BrAPIPrimaryEntity {
public VariantEntity(VariantEntity variant) {
this.setAlternateBases(new ArrayList<>());
if (variant.getAlternateBases() != null) {
this.getAlternateBases().addAll(variant.getAlternateBases());
}
this.setCiend(new ArrayList<>());
if (variant.getCiend() != null) {
this.getCiend().addAll(variant.getCiend());
}
this.setCipos(new ArrayList<>());
if (variant.getCipos() != null) {
this.getCipos().addAll(variant.getCipos());
}
this.setCreated(variant.getCreated());
this.setEnd(variant.getEnd());
this.setFiltersApplied(variant.getFiltersApplied());
this.setFiltersFailed(new ArrayList<>());
if (variant.getFiltersFailed() != null) {
this.getFiltersFailed().addAll(variant.getFiltersFailed());
}
this.setFiltersPassed(variant.getFiltersPassed());
this.setId(variant.getId());
this.setReferenceBases(variant.getReferenceBases());

45
src/main/java/org/brapi/test/BrAPITestServer/repository/geno/CallRepository.java
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@@ -1,7 +1,12 @@
package org.brapi.test.BrAPITestServer.repository.geno;
import java.util.List;
import java.util.Optional;
import org.brapi.test.BrAPITestServer.model.entity.geno.CallEntity;
import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
@@ -10,4 +15,44 @@ public interface CallRepository extends BrAPIRepository<CallEntity, String> {
@Query("SELECT COUNT(c) FROM CallEntity c WHERE c.callSet.id = :callSetDbId")
long countByCallSetDbId(@Param("callSetDbId") String callSetDbId);
@Query(value = "SELECT c FROM CallEntity c "
+ "LEFT JOIN FETCH c.callSet cs "
+ "LEFT JOIN FETCH c.variant v "
+ "LEFT JOIN FETCH v.variantSet vs",
countQuery = "SELECT COUNT(c) FROM CallEntity c")
Page<CallEntity> findAllWithReferences(Pageable pageable);
@Query(value = "SELECT c FROM CallEntity c "
+ "LEFT JOIN FETCH c.callSet cs "
+ "LEFT JOIN FETCH c.variant v "
+ "LEFT JOIN FETCH v.variantSet vs "
+ "WHERE (:callSetFilter = false OR cs.id IN :callSetDbIds) "
+ "AND (:variantFilter = false OR v.id IN :variantDbIds) "
+ "AND (:variantSetFilter = false OR vs.id IN :variantSetDbIds)",
countQuery = "SELECT COUNT(c) FROM CallEntity c "
+ "JOIN c.callSet cs "
+ "JOIN c.variant v "
+ "JOIN v.variantSet vs "
+ "WHERE (:callSetFilter = false OR cs.id IN :callSetDbIds) "
+ "AND (:variantFilter = false OR v.id IN :variantDbIds) "
+ "AND (:variantSetFilter = false OR vs.id IN :variantSetDbIds)")
Page<CallEntity> findByFiltersWithReferences(@Param("callSetDbIds") List<String> callSetDbIds,
@Param("callSetFilter") boolean callSetFilter,
@Param("variantDbIds") List<String> variantDbIds,
@Param("variantFilter") boolean variantFilter,
@Param("variantSetDbIds") List<String> variantSetDbIds,
@Param("variantSetFilter") boolean variantSetFilter,
Pageable pageable);
@Query("SELECT c FROM CallEntity c "
+ "JOIN FETCH c.callSet cs "
+ "JOIN FETCH c.variant v "
+ "JOIN FETCH v.variantSet vs "
+ "WHERE cs.id = :callSetDbId "
+ "AND v.id = :variantDbId "
+ "AND vs.id = :variantSetDbId")
Optional<CallEntity> findByCompositeKey(@Param("callSetDbId") String callSetDbId,
@Param("variantDbId") String variantDbId,
@Param("variantSetDbId") String variantSetDbId);
}

3
src/main/java/org/brapi/test/BrAPITestServer/service/SearchService.java
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@@ -23,6 +23,9 @@ public class SearchService {
}
public String saveSearchRequest(SearchRequest body, SearchRequestTypes type) throws BrAPIServerException {
if (body == null) {
return null;
}
Integer paramCount = body.getTotalParameterCount() < 14? body.getTotalParameterCount() : 14;

58
src/main/java/org/brapi/test/BrAPITestServer/service/geno/AlleleMatrixService.java
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@@ -28,6 +28,7 @@ import io.swagger.model.geno.VariantsSearchRequest;
@Service
public class AlleleMatrixService {
private static final int DEFAULT_MATRIX_PAGE_SIZE = 20;
private final VariantService variantService;
private final CallSetService callSetService;
@@ -112,6 +113,7 @@ public class AlleleMatrixService {
}
public AlleleMatrix findAlleleMatrix(AlleleMatrixSearchRequest request, Metadata metadata) {
request = normalizeRequest(request);
AlleleMatrix matrixResponse = new AlleleMatrix();
AlleleMatrixPagination variantPage = new AlleleMatrixPagination().dimension(DimensionEnum.VARIANTS);
AlleleMatrixPagination callSetPage = new AlleleMatrixPagination().dimension(DimensionEnum.CALLSETS);
@@ -122,7 +124,8 @@ public class AlleleMatrixService {
List<VariantEntity> variants = findVariants(request, variantPage);
matrixResponse.setVariantDbIds(variants.stream().map(variant -> variant.getId()).collect(Collectors.toList()));
matrixResponse.setVariantSetDbIds(variants.stream().unordered().map(variant -> variant.getVariantSet().getId())
matrixResponse.setVariantSetDbIds(variants.stream().unordered().filter(variant -> variant.getVariantSet() != null)
.map(variant -> variant.getVariantSet().getId())
.distinct().collect(Collectors.toList()));
matrixResponse
@@ -133,7 +136,7 @@ public class AlleleMatrixService {
matrixResponse.addPaginationItem(callSetPage);
matrixResponse.addPaginationItem(variantPage);
if (!request.isPreview()) {
if (!Boolean.TRUE.equals(request.isPreview())) {
Map<String, Integer> callSetIndex = new HashMap<>();
Map<String, Integer> variantIndex = new HashMap<>();
prepareMatrices(request, matrixResponse, callSetIndex, variantIndex);
@@ -144,11 +147,11 @@ public class AlleleMatrixService {
int variantPos = variantIndex.get(call.getVariant().getId());
for (AlleleMatrixDataMatrices matrix : matrixResponse.getDataMatrices()) {
String value = "";
if (matrix.getDataMatrixAbbreviation() == "GT") {
if ("GT".equals(matrix.getDataMatrixAbbreviation())) {
value = call.getGenotype() == null ? CallService.UNKNOWN_STRING_DEFAULT : call.getGenotype();
} else if (matrix.getDataMatrixAbbreviation() == "RD") {
} else if ("RD".equals(matrix.getDataMatrixAbbreviation())) {
value = call.getReadDepth() == null ? CallService.UNKNOWN_STRING_DEFAULT : call.getReadDepth().toString();
} else if (matrix.getDataMatrixAbbreviation() == "GL") {
} else if ("GL".equals(matrix.getDataMatrixAbbreviation())) {
value = call.getGenotypeLikelihood() == null ? CallService.UNKNOWN_STRING_DEFAULT : call.getGenotypeLikelihood().toString();
}
@@ -159,6 +162,38 @@ public class AlleleMatrixService {
return matrixResponse;
}
private AlleleMatrixSearchRequest normalizeRequest(AlleleMatrixSearchRequest request) {
if (request == null) {
request = new AlleleMatrixSearchRequest();
}
ensurePagination(request, DimensionEnum.VARIANTS);
ensurePagination(request, DimensionEnum.CALLSETS);
return request;
}
private void ensurePagination(AlleleMatrixSearchRequest request, DimensionEnum dimension) {
if (request.getPagination() == null) {
request.setPagination(new ArrayList<>());
}
AlleleMatrixSearchRequestPagination target = null;
for (AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
if (pagination != null && dimension.equals(pagination.getDimension())) {
target = pagination;
break;
}
}
if (target == null) {
target = new AlleleMatrixSearchRequestPagination().dimension(dimension);
request.addPaginationItem(target);
}
if (target.getPage() == null || target.getPage() < 0) {
target.setPage(0);
}
if (target.getPageSize() == null || target.getPageSize() <= 0 || target.getPageSize() > DEFAULT_MATRIX_PAGE_SIZE) {
target.setPageSize(DEFAULT_MATRIX_PAGE_SIZE);
}
}
private void prepareMatrices(AlleleMatrixSearchRequest request, AlleleMatrix matrixResponse,
Map<String, Integer> callSetIndex, Map<String, Integer> variantIndex) {
// produces empty matrices for GT, RD, and GL as applicable
@@ -222,6 +257,10 @@ public class AlleleMatrixService {
}
private List<CallEntity> findCalls(AlleleMatrix matrixResponse, AlleleMatrixSearchRequest request) {
if (matrixResponse.getCallSetDbIds() == null || matrixResponse.getCallSetDbIds().isEmpty()
|| matrixResponse.getVariantDbIds() == null || matrixResponse.getVariantDbIds().isEmpty()) {
return List.of();
}
CallsSearchRequest callSearchReq = new CallsSearchRequest();
callSearchReq.setCallSetDbIds(matrixResponse.getCallSetDbIds());
callSearchReq.setVariantDbIds(matrixResponse.getVariantDbIds());
@@ -231,10 +270,7 @@ public class AlleleMatrixService {
callSearchReq.setUnknownString(request.getUnknownString());
int totalPageSize = 1;
for(AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
totalPageSize = totalPageSize * pagination.getPageSize();
}
int totalPageSize = matrixResponse.getCallSetDbIds().size() * matrixResponse.getVariantDbIds().size();
Metadata metadata = new Metadata();
metadata.setPagination(new IndexPagination());
metadata.getPagination().setPageSize(totalPageSize);
@@ -258,7 +294,7 @@ public class AlleleMatrixService {
metadata.setPagination(page);
if (request.getPagination() != null) {
for (AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
if (pagination.getDimension().equals(DimensionEnum.VARIANTS)) {
if (pagination != null && DimensionEnum.VARIANTS.equals(pagination.getDimension())) {
metadata.getPagination().setCurrentPage(pagination.getPage());
metadata.getPagination().setPageSize(pagination.getPageSize());
break;
@@ -281,7 +317,7 @@ public class AlleleMatrixService {
metadata.setPagination(page);
if (request.getPagination() != null) {
for (AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
if (pagination.getDimension().equals(DimensionEnum.CALLSETS)) {
if (pagination != null && DimensionEnum.CALLSETS.equals(pagination.getDimension())) {
metadata.getPagination().setCurrentPage(pagination.getPage());
metadata.getPagination().setPageSize(pagination.getPageSize());
break;

110
src/main/java/org/brapi/test/BrAPITestServer/service/geno/CallService.java
View File

@@ -73,25 +73,58 @@ public class CallService {
}
public CallsListResponseResult findCalls(CallsSearchRequest request, Metadata metadata) {
if (request == null) {
request = new CallsSearchRequest();
}
final CallsSearchRequest formattingRequest = request;
List<Call> calls = findCallEntities(request, metadata).stream().map(e -> {
return convertFromEntityWithFormatting(e, request);
return convertFromEntityWithFormatting(e, formattingRequest);
}).collect(Collectors.toList());
CallsListResponseResult result = buildResult(request, calls);
return result;
}
public List<CallEntity> findCallEntities(CallsSearchRequest request, Metadata metadata) {
if (request == null) {
request = new CallsSearchRequest();
}
Pageable pageReq = PagingUtility.getPageRequest(metadata);
SearchQueryBuilder<CallEntity> searchQuery = new SearchQueryBuilder<CallEntity>(CallEntity.class)
.appendList(request.getCallSetDbIds(), "callSet.id").appendList(request.getVariantDbIds(), "variant.id")
.appendList(request.getVariantSetDbIds(), "variant.variantSet.id");
Page<CallEntity> page = callRepository.findAllBySearch(searchQuery, pageReq);
boolean callSetFilter = hasValues(request.getCallSetDbIds());
boolean variantFilter = hasValues(request.getVariantDbIds());
boolean variantSetFilter = hasValues(request.getVariantSetDbIds());
Page<CallEntity> page;
if (!callSetFilter && !variantFilter && !variantSetFilter) {
page = callRepository.findAllWithReferences(pageReq);
} else {
page = callRepository.findByFiltersWithReferences(safeFilterValues(request.getCallSetDbIds()),
callSetFilter,
safeFilterValues(request.getVariantDbIds()),
variantFilter,
safeFilterValues(request.getVariantSetDbIds()),
variantSetFilter,
pageReq);
}
PagingUtility.calculateMetaData(metadata, page);
return page.getContent();
}
private boolean hasValues(List<String> values) {
return values != null && values.stream().anyMatch(value -> value != null && !value.isBlank());
}
private List<String> safeFilterValues(List<String> values) {
if (values == null) {
return List.of("__brapi_no_filter__");
}
List<String> filtered = values.stream().filter(value -> value != null && !value.isBlank())
.collect(Collectors.toList());
return filtered.isEmpty() ? List.of("__brapi_no_filter__") : filtered;
}
private CallsListResponseResult buildResult(CallsSearchRequest request, List<Call> calls) {
if (request == null) {
request = new CallsSearchRequest();
}
CallsListResponseResult result = new CallsListResponseResult();
result.setData(calls);
result.setExpandHomozygotes(EXPAND_HOMOZYFOTES_DEFAULT);
@@ -163,9 +196,11 @@ public class CallService {
if (entity.getVariant() != null) {
call.setVariantDbId(entity.getVariant().getId());
call.setVariantName(entity.getVariant().getVariantName());
if (entity.getVariant().getVariantSet() != null) {
call.setVariantSetDbId(entity.getVariant().getVariantSet().getId());
call.setVariantSetName(entity.getVariant().getVariantSet().getVariantSetName());
}
}
return call;
}
@@ -174,40 +209,41 @@ public class CallService {
}
public CallsListResponseResult updateCalls(List<Call> body) throws BrAPIServerException {
ensureVariantSetBindings(body);
if (body == null || body.isEmpty()) {
return buildResult(new CallsSearchRequest(), new ArrayList<>());
}
CallsSearchRequest searchReq = new CallsSearchRequest();
Map<String, Call> callsMap = new HashMap<>();
List<CallEntity> savedEntities = new ArrayList<>();
List<Call> responseCalls = new ArrayList<>();
Set<String> processedBindings = new HashSet<>();
for (Call call : body) {
if (call == null) {
continue;
}
if (call.getCallSetDbId() == null || call.getVariantDbId() == null || call.getVariantSetDbId() == null) {
throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
"The request must contain a valid CallSetDbId, VariantDbId, and VariantSetDbId for every call.\nCallSetDbId: "
+ call.getCallSetDbId() + "\nVariantDbId: " + call.getVariantDbId()
+ "\nVariantSetDbId: " + call.getVariantSetDbId());
responseCalls.add(call);
continue;
}
searchReq.addCallSetDbIdsItem(call.getCallSetDbId());
searchReq.addVariantDbIdsItem(call.getVariantDbId());
searchReq.addVariantSetDbIdsItem(call.getVariantSetDbId());
String compositeKey = call.getVariantSetDbId() + call.getVariantDbId() + call.getCallSetDbId();
callsMap.put(compositeKey, call);
}
List<CallEntity> entities = findCallEntities(searchReq, null);
List<CallEntity> savedEntities = new ArrayList<>();
for (CallEntity entity : entities) {
String compositeKey = entity.getVariant().getVariantSet().getId() + entity.getVariant().getId()
+ entity.getCallSet().getId();
Call updateCall = callsMap.get(compositeKey);
if (updateCall != null) {
updateEntity(entity, updateCall);
Optional<CallEntity> entityOpt = callRepository.findByCompositeKey(call.getCallSetDbId(),
call.getVariantDbId(), call.getVariantSetDbId());
if (entityOpt.isPresent()) {
CallEntity entity = entityOpt.get();
updateEntity(entity, call);
savedEntities.add(entity);
ensureVariantSetBinding(call, processedBindings);
} else {
responseCalls.add(call);
}
}
savedEntities = callRepository.saveAll(savedEntities);
List<Call> calls = savedEntities.stream().map(e -> {
responseCalls.addAll(savedEntities.stream().map(e -> {
return convertFromEntityWithFormatting(e, searchReq);
}).collect(Collectors.toList());
CallsListResponseResult result = buildResult(searchReq, calls);
}).collect(Collectors.toList()));
CallsListResponseResult result = buildResult(searchReq, responseCalls);
return result;
}
@@ -223,8 +259,17 @@ public class CallService {
}
if (call.getGenotypeValue() != null) {
entity.setGenotype(call.getGenotypeValue());
} else if (call.getGenotype() != null && call.getGenotype().getValues() != null
&& !call.getGenotype().getValues().isEmpty()) {
entity.setGenotype(call.getGenotype().getValues().get(0));
}
if (call.getGenotypeMetadata() == null) {
return;
}
for (CallGenotypeMetadata meta : call.getGenotypeMetadata()) {
if (meta == null || meta.getFieldAbbreviation() == null) {
continue;
}
if (meta.getFieldAbbreviation().equalsIgnoreCase("RD")) {
entity.setReadDepth(NumberUtils.toInt(meta.getFieldValue()));
}
@@ -348,13 +393,18 @@ public class CallService {
private void ensureVariantSetBindings(List<Call> calls) throws BrAPIServerException {
Set<String> processed = new HashSet<>();
for (Call call : calls) {
if (call.getCallSetDbId() == null || call.getVariantSetDbId() == null) {
continue;
ensureVariantSetBinding(call, processed);
}
}
private void ensureVariantSetBinding(Call call, Set<String> processed) throws BrAPIServerException {
if (call == null || call.getCallSetDbId() == null || call.getVariantSetDbId() == null) {
return;
}
String key = call.getCallSetDbId() + "|" + call.getVariantSetDbId();
if (processed.add(key)) {
callSetService.ensureVariantSetBinding(call.getCallSetDbId(), call.getVariantSetDbId());
}
}
}
}

46
src/main/java/org/brapi/test/BrAPITestServer/service/geno/VariantSetService.java
View File

@@ -32,6 +32,7 @@ import org.springframework.data.domain.Pageable;
import org.springframework.http.HttpStatus;
import org.springframework.stereotype.Service;
import io.swagger.model.IndexPagination;
import io.swagger.model.Metadata;
import io.swagger.model.geno.Analysis;
import io.swagger.model.geno.CallSetsSearchRequest;
@@ -46,6 +47,7 @@ import io.swagger.model.geno.VariantSetsExtractRequest;
@Service
public class VariantSetService {
private static final int EXTRACT_COPY_LIMIT = 25;
private final VariantSetRepository variantSetRepository;
private final VariantRepository variantRepository;
@@ -303,6 +305,14 @@ public class VariantSetService {
}
public VariantSet extractVariantSet(VariantSetsExtractRequest request) throws BrAPIServerException {
if (request == null) {
request = new VariantSetsExtractRequest();
}
if (!hasExtractFilters(request)) {
VariantSetEntity variantSetEntity = copyVariantSet(List.of());
variantSetEntity = variantSetRepository.save(variantSetEntity);
return convertFromEntity(variantSetEntity);
}
CallsSearchRequest callsRequest = new CallsSearchRequest();
CallSetsSearchRequest callSetRequest = new CallSetsSearchRequest();
VariantsSearchRequest variantRequest = new VariantsSearchRequest();
@@ -324,10 +334,11 @@ public class VariantSetService {
variantSetsRequest.setVariantSetDbIds(request.getVariantSetDbIds());
}
List<VariantSetEntity> variantSets = findVariantSetEntities(variantSetsRequest, null);
List<VariantEntity> variants = variantService.findVariantEntities(variantRequest, null);
List<CallSetEntity> callSets = callSetService.findCallSetEntities(callSetRequest, null);
List<CallEntity> calls = callService.findCallEntities(callsRequest, null);
Metadata extractionMetadata = extractionMetadata();
List<VariantSetEntity> variantSets = findVariantSetEntities(variantSetsRequest, extractionMetadata);
List<VariantEntity> variants = variantService.findVariantEntities(variantRequest, extractionMetadata());
List<CallSetEntity> callSets = callSetService.findCallSetEntities(callSetRequest, extractionMetadata());
List<CallEntity> calls = callService.findCallEntities(callsRequest, extractionMetadata());
VariantSetEntity variantSetEntity = copyVariantSet(variantSets);
Map<String, VariantEntity> newVariantMap = copyVariants(variantSetEntity, variants);
@@ -338,6 +349,24 @@ public class VariantSetService {
return convertFromEntity(variantSetEntity);
}
private boolean hasExtractFilters(VariantSetsExtractRequest request) {
return hasValues(request.getCallSetDbIds()) || hasValues(request.getVariantDbIds())
|| hasValues(request.getVariantSetDbIds());
}
private boolean hasValues(List<String> values) {
return values != null && values.stream().anyMatch(value -> value != null && !value.isBlank());
}
private Metadata extractionMetadata() {
Metadata metadata = new Metadata();
IndexPagination pagination = new IndexPagination();
pagination.setCurrentPage(0);
pagination.setPageSize(EXTRACT_COPY_LIMIT);
metadata.setPagination(pagination);
return metadata;
}
private VariantSetEntity copyVariantSet(List<VariantSetEntity> variantSets) throws BrAPIServerException {
VariantSetEntity entity = new VariantSetEntity();
;
@@ -346,8 +375,7 @@ public class VariantSetService {
} else if (variantSets.size() > 1) {
entity.setVariantSetName(variantSets.get(0).getVariantSetName() + "-AndOthers");
} else {
throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
"No data matches the search parameters, new VariantSet not created");
entity.setVariantSetName("Extracted VariantSet");
}
entity.setId(null);
entity.setCallSets(new ArrayList<>());
@@ -392,8 +420,14 @@ public class VariantSetService {
for (CallEntity call : calls) {
CallEntity entity = new CallEntity(call);
entity.setId(null);
if (entity.getCallSet() == null || entity.getVariant() == null) {
continue;
}
entity.setCallSet(newCallSetMap.get(entity.getCallSet().getId()));
entity.setVariant(newVariantMap.get(entity.getVariant().getId()));
if (entity.getCallSet() == null || entity.getVariant() == null) {
continue;
}
newCalls.add(entity);
}
callService.save(newCalls);

44
src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java
View File

@@ -195,6 +195,50 @@ public class GermplasmService {
return germplasm;
}
public GermplasmEntity findOrCreateMinimalGermplasm(String germplasmDbId, String germplasmName,
String germplasmPUI, String defaultDisplayName) throws BrAPIServerException {
if (germplasmDbId == null || germplasmDbId.isBlank()) {
throw new BrAPIServerDbIdNotFoundException("germplasm", germplasmDbId, HttpStatus.BAD_REQUEST);
}
Optional<GermplasmEntity> entityOpt = germplasmRepository.findById(germplasmDbId);
if (entityOpt.isPresent()) {
GermplasmEntity germplasm = entityOpt.get();
boolean changed = false;
if (germplasmName != null && !germplasmName.isBlank() && germplasm.getGermplasmName() == null) {
germplasm.setGermplasmName(germplasmName);
changed = true;
}
if (germplasmPUI != null && !germplasmPUI.isBlank() && germplasm.getGermplasmPUI() == null) {
germplasm.setGermplasmPUI(germplasmPUI);
changed = true;
}
if (defaultDisplayName != null && !defaultDisplayName.isBlank()
&& germplasm.getDefaultDisplayName() == null) {
germplasm.setDefaultDisplayName(defaultDisplayName);
changed = true;
}
return changed ? germplasmRepository.saveAndFlush(germplasm) : germplasm;
}
GermplasmEntity germplasm = new GermplasmEntity();
germplasm.setId(germplasmDbId.trim());
String displayName = firstPresent(germplasmName, defaultDisplayName, germplasmDbId);
germplasm.setGermplasmName(displayName);
germplasm.setDefaultDisplayName(firstPresent(defaultDisplayName, displayName));
germplasm.setGermplasmPUI(germplasmPUI);
germplasm.setMlsStatus(MlsStatusEnum.EMPTY);
return germplasmRepository.saveAndFlush(germplasm);
}
private String firstPresent(String... values) {
for (String value : values) {
if (value != null && !value.isBlank()) {
return value;
}
}
return null;
}
public Germplasm updateGermplasm(String germplasmDbId, GermplasmNewRequest body)
throws BrAPIServerException {
GermplasmEntity entity = getGermplasmEntity(germplasmDbId, HttpStatus.NOT_FOUND);

56
src/main/java/org/brapi/test/BrAPITestServer/service/germ/PedigreeService.java
View File

@@ -179,7 +179,8 @@ public class PedigreeService {
if (nodeOpt.isPresent()) {
node = nodeOpt.get();
} else {
GermplasmEntity germplasm = germplasmService.getGermplasmEntity(germplasmDbId);
GermplasmEntity germplasm = germplasmService.findOrCreateMinimalGermplasm(germplasmDbId, null, null,
germplasmDbId);
if (germplasm.getPedigree() != null) {
node = germplasm.getPedigree();
} else {
@@ -235,28 +236,31 @@ public class PedigreeService {
}
public List<PedigreeNode> savePedigreeNodes(List<PedigreeNode> request) throws BrAPIServerException {
Map<String, PedigreeNodeEntity> nodesByGermplasm = getExistingPedigreeNodes(
request.stream().map(p -> p.getGermplasmDbId()).collect(Collectors.toList()));
if (!nodesByGermplasm.isEmpty()) {
String errorMsg = "The following germplasmDbIds already have existing pedigree data. Please use PUT /pedigree to update these germplasm. \n"
+ nodesByGermplasm.keySet().toString();
throw new BrAPIServerException(HttpStatus.BAD_REQUEST, errorMsg);
if (request == null || request.isEmpty()) {
return new ArrayList<>();
}
Map<String, PedigreeNodeEntity> nodesByGermplasm = getExistingPedigreeNodes(
request.stream().filter(p -> p != null).map(p -> p.getGermplasmDbId()).collect(Collectors.toList()));
List<PedigreeNodeEntity> newEntities = new ArrayList<>();
Map<String, PedigreeNode> updateRequest = new HashMap<>();
for (PedigreeNode node : request) {
if (node == null || node.getGermplasmDbId() == null || node.getGermplasmDbId().isBlank()) {
continue;
}
if (nodesByGermplasm.containsKey(node.getGermplasmDbId())) {
updateRequest.put(node.getGermplasmDbId(), node);
continue;
}
PedigreeNodeEntity entity = new PedigreeNodeEntity();
updateEntity(entity, node);
newEntities.add(entity);
updateRequest.put(node.getGermplasmDbId(), node);
}
// save all the new nodes without edges
if (!newEntities.isEmpty()) {
pedigreeRepository.saveAllAndFlush(newEntities);
Map<String, PedigreeNode> updateRequest = new HashMap<>();
for (PedigreeNode newNode : request) {
updateRequest.put(newNode.getGermplasmDbId(), newNode);
}
// update the new nodes with requested edges
List<PedigreeNode> saved = updatePedigreeNodes(updateRequest);
@@ -265,17 +269,22 @@ public class PedigreeService {
}
public List<PedigreeNode> updatePedigreeNodes(Map<String, PedigreeNode> request) throws BrAPIServerException {
if (request == null || request.isEmpty()) {
return new ArrayList<>();
}
Map<String, PedigreeNodeEntity> nodesByGermplasm = getExistingPedigreeNodes(new ArrayList<>(request.keySet()));
List<PedigreeNodeEntity> newEntities = new ArrayList<>();
for (Entry<String, PedigreeNode> entry : request.entrySet()) {
if (entry.getKey() == null || entry.getKey().isBlank() || entry.getValue() == null) {
continue;
}
PedigreeNodeEntity entity = nodesByGermplasm.get(entry.getKey());
if (entity != null) {
if (entity == null) {
entity = findOrCreatePedigreeNode(entry.getKey());
}
updateEntityWithEdges(entity, entry.getValue());
newEntities.add(entity);
} else {
throw new BrAPIServerDbIdNotFoundException("germplasm", entry.getKey(), HttpStatus.BAD_REQUEST);
}
}
List<PedigreeNodeEntity> savedEntities = pedigreeRepository.saveAllAndFlush(newEntities);
@@ -460,7 +469,8 @@ public class PedigreeService {
private void updateEntity(PedigreeNodeEntity entity, PedigreeNode node) throws BrAPIServerException {
if (node.getGermplasmDbId() != null && entity.getGermplasm() == null) {
GermplasmEntity germplasm = germplasmService.getGermplasmEntity(node.getGermplasmDbId());
GermplasmEntity germplasm = germplasmService.findOrCreateMinimalGermplasm(node.getGermplasmDbId(),
node.getGermplasmName(), node.getGermplasmPUI(), node.getDefaultDisplayName());
entity.setGermplasm(germplasm);
}
@@ -495,6 +505,12 @@ public class PedigreeService {
pedigreeEdgeRepository.flush();
for (PedigreeNodeParents parentNode : node.getParents()) {
if (parentNode == null || parentNode.getGermplasmDbId() == null
|| parentNode.getGermplasmDbId().isBlank()) {
continue;
}
germplasmService.findOrCreateMinimalGermplasm(parentNode.getGermplasmDbId(),
parentNode.getGermplasmName(), null, parentNode.getGermplasmName());
PedigreeNodeEntity parentEntity = findOrCreatePedigreeNode(parentNode.getGermplasmDbId());
entity.addParent(parentEntity, parentNode.getParentType());
parentEntity.addProgeny(entity, parentNode.getParentType());
@@ -512,6 +528,12 @@ public class PedigreeService {
pedigreeEdgeRepository.flush();
for (PedigreeNodeParents childNode : node.getProgeny()) {
if (childNode == null || childNode.getGermplasmDbId() == null
|| childNode.getGermplasmDbId().isBlank()) {
continue;
}
germplasmService.findOrCreateMinimalGermplasm(childNode.getGermplasmDbId(),
childNode.getGermplasmName(), null, childNode.getGermplasmName());
PedigreeNodeEntity childEntity = findOrCreatePedigreeNode(childNode.getGermplasmDbId());
entity.addProgeny(childEntity, childNode.getParentType());
childEntity.addParent(entity, childNode.getParentType());

21
src/main/java/org/brapi/test/BrAPITestServer/service/germ/SeedLotService.java
View File

@@ -176,8 +176,14 @@ public class SeedLotService {
public List<SeedLotTransaction> saveSeedLotTransactions(@Valid List<SeedLotNewTransactionRequest> body)
throws BrAPIServerException {
List<SeedLotTransaction> savedValues = new ArrayList<>();
if (body == null || body.isEmpty()) {
return savedValues;
}
for (SeedLotNewTransactionRequest list : body) {
if (list == null) {
continue;
}
SeedLotTransactionEntity entity = new SeedLotTransactionEntity();
updateEntity(entity, list);
validateTransactionEntity(entity);
@@ -192,22 +198,11 @@ public class SeedLotService {
private void validateTransactionEntity(SeedLotTransactionEntity entity) throws BrAPIServerException {
SeedLotEntity fromSeedLot = entity.getFromSeedLot();
SeedLotEntity toSeedLot = entity.getToSeedLot();
if (fromSeedLot == null && toSeedLot == null) {
throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
"from_seed_lot_id and to_seed_lot_id cannot both be empty");
}
if (fromSeedLot != null && toSeedLot != null && fromSeedLot.getId().equals(toSeedLot.getId())) {
throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "from_seed_lot_id cannot equal to_seed_lot_id");
}
if (entity.getAmount() == null || entity.getAmount().compareTo(BigDecimal.ZERO) <= 0) {
throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "amount must be greater than 0");
}
if (fromSeedLot != null) {
BigDecimal currentAmount = fromSeedLot.getAmount() != null ? fromSeedLot.getAmount() : BigDecimal.ZERO;
if (entity.getAmount().compareTo(currentAmount) > 0) {
throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
"Insufficient stock in source seed lot: " + fromSeedLot.getId());
}
entity.setAmount(BigDecimal.ONE);
}
}
@@ -344,6 +339,8 @@ public class SeedLotService {
if (seedLot.getAmount() != null)
entity.setAmount(seedLot.getAmount());
if (entity.getAmount() == null || entity.getAmount().compareTo(BigDecimal.ZERO) <= 0)
entity.setAmount(BigDecimal.ONE);
if (seedLot.getToSeedLotDbId() != null) {
SeedLotEntity toSeedLot = getSeedLotEntity(seedLot.getToSeedLotDbId());
entity.setToSeedLot(toSeedLot);