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[BI-1632] - Unknown Pedigree not displaying for BrAPI-server programs #217

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Merged
HMS17 merged 4 commits into from
Oct 14, 2022
Merged

[BI-1632] - Unknown Pedigree not displaying for BrAPI-server programs #217

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7bdc21e
[BI-1632] - Unknown Pedigree not displaying for BrAPI-server programs
HMS17 Oct 7, 2022
931a105
[BI-1632] - Clean up spacing
HMS17 Oct 7, 2022
cb4d0ef
[BI-1632] - Unit test fix
HMS17 Oct 7, 2022
0bf1ae3
Merge branch 'develop' into bug/BI-1632
HMS17 Oct 14, 2022
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15 changes: 8 additions & 7 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 @@ -108,8 +108,8 @@ public List<BrAPIGermplasm> getRawGermplasm(UUID programId) throws ApiException
List<BrAPIGermplasm> cacheList = new ArrayList<>(programGermplasmCache.get(programId).values());
return cacheList.stream().map(germplasm -> {
germplasm.setGermplasmName(Utilities.appendProgramKey(germplasm.getDefaultDisplayName(), program.getKey(), germplasm.getAccessionNumber()));
if(germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo()
.has(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE)) {
if(germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().has(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE)
&& !(germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE).isJsonNull())) {
germplasm.setPedigree(germplasm.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_RAW_PEDIGREE).getAsString());
}

Expand Down Expand Up @@ -178,7 +178,6 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas

// Update pedigree string
for (BrAPIGermplasm germplasm: programGermplasm) {
if (germplasm.getPedigree() != null) {
JsonObject additionalInfo = germplasm.getAdditionalInfo();
if(additionalInfo == null) {
additionalInfo = new JsonObject();
Expand All @@ -188,7 +187,10 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
String newPedigreeString = "";
String namePedigreeString = "";
String uuidPedigreeString = "";
List<String> parents = Arrays.asList(germplasm.getPedigree().split("/"));
List<String> parents = Arrays.asList("","");
if (germplasm.getPedigree() != null) {
parents = Arrays.asList(germplasm.getPedigree().split("/"));
}
if (parents.size() >= 1) {
if (programGermplasmByFullName.containsKey(parents.get(0))) {
String femaleParentAccessionNumber = programGermplasmByFullName.get(parents.get(0)).getAccessionNumber();
Expand All @@ -212,18 +214,17 @@ private Map<String,BrAPIGermplasm> processGermplasmForDisplay(List<BrAPIGermplas
}
}
//Add Unknown germplasm for display
if (germplasm.getAdditionalInfo().has("femaleParentUnknown") && germplasm.getAdditionalInfo().get("femaleParentUnknown").getAsBoolean()) {
if (additionalInfo.has("femaleParentUnknown") && additionalInfo.get("femaleParentUnknown").getAsBoolean()) {
namePedigreeString = "Unknown";
}
if (germplasm.getAdditionalInfo().has("maleParentUnknown") && germplasm.getAdditionalInfo().get("maleParentUnknown").getAsBoolean()) {
if (additionalInfo.has("maleParentUnknown") && additionalInfo.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);

germplasm.setPedigree(newPedigreeString);
}

BrAPIExternalReference extRef = germplasm.getExternalReferences().stream().filter(reference -> referenceSource.equals(reference.getReferenceSource())).findFirst().orElseThrow(() -> new IllegalStateException("No BI external reference found"));
String germplasmId = extRef.getReferenceID();
Expand Down