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BI-2306 - Helium BrAPI integration filter by accessionNumber #412

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Merged
nickpalladino merged 1 commit into from
Oct 15, 2024
Merged

BI-2306 - Helium BrAPI integration filter by accessionNumber #412

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15 changes: 8 additions & 7 deletions src/main/java/org/breedinginsight/brapi/v2/BrAPIPedigreeController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -95,13 +95,14 @@ public HttpResponse<BrAPIPedigreeListResponse> pedigreeGet(@PathVariable("progra
try {
List<BrAPIPedigreeNode> pedigree = pedigreeDAO.getPedigree(
program.get(),
Optional.ofNullable(includeParents),
Optional.ofNullable(includeSiblings),
Optional.ofNullable(includeProgeny),
Optional.ofNullable(includeFullTree),
Optional.ofNullable(pedigreeDepth),
Optional.ofNullable(progenyDepth),
Optional.ofNullable(germplasmName));
includeParents,
includeSiblings,
includeProgeny,
includeFullTree,
pedigreeDepth,
progenyDepth,
germplasmName,
accessionNumber);

return HttpResponse.ok(
new BrAPIPedigreeListResponse()
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30 changes: 16 additions & 14 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIPedigreeDAO.java
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Expand Up @@ -73,13 +73,14 @@ public BrAPIPedigreeDAO(ProgramDAO programDAO, BrAPIDAOUtil brAPIDAOUtil,
*/
public List<BrAPIPedigreeNode> getPedigree(
Program program,
Optional<Boolean> includeParents,
Optional<Boolean> includeSiblings,
Optional<Boolean> includeProgeny,
Optional<Boolean> includeFullTree,
Optional<Integer> pedigreeDepth,
Optional<Integer> progenyDepth,
Optional<String> germplasmName
Boolean includeParents,
Boolean includeSiblings,
Boolean includeProgeny,
Boolean includeFullTree,
Integer pedigreeDepth,
Integer progenyDepth,
String germplasmName,
String accessionNumber
) throws ApiException {

PedigreeQueryParams pedigreeRequest = new PedigreeQueryParams();
Expand All @@ -94,13 +95,14 @@ public List<BrAPIPedigreeNode> getPedigree(
pedigreeRequest.externalReferenceId(extRefId);
pedigreeRequest.externalReferenceSource(extRefSrc);

includeParents.ifPresent(pedigreeRequest::includeParents);
includeSiblings.ifPresent(pedigreeRequest::includeSiblings);
includeProgeny.ifPresent(pedigreeRequest::includeProgeny);
includeFullTree.ifPresent(pedigreeRequest::includeFullTree);
pedigreeDepth.ifPresent(pedigreeRequest::pedigreeDepth);
progenyDepth.ifPresent(pedigreeRequest::progenyDepth);
germplasmName.ifPresent(pedigreeRequest::germplasmName);
if (includeParents != null) pedigreeRequest.includeParents(includeParents);
if (includeSiblings != null) pedigreeRequest.includeSiblings(includeSiblings);
if (includeProgeny != null) pedigreeRequest.includeProgeny(includeProgeny);
if (includeFullTree != null) pedigreeRequest.includeFullTree(includeFullTree);
if (pedigreeDepth != null) pedigreeRequest.pedigreeDepth(pedigreeDepth);
if (progenyDepth != null) pedigreeRequest.progenyDepth(progenyDepth);
if (germplasmName != null) pedigreeRequest.germplasmName(germplasmName);
if (accessionNumber != null) pedigreeRequest.accessionNumber(accessionNumber);
// TODO: other parameters

// TODO: write utility to do paging instead of hardcoding
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