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Merged
nickpalladino merged 3 commits into from
Jun 2, 2023
Merged

BI-1798 #255

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30878c4
Use additional info for pedigree gids
nickpalladino May 25, 2023
a0e5766
Accounted for entry number of 0
nickpalladino Jun 1, 2023
27b2593
Merge branch 'develop' into bug/BI-1798
nickpalladino Jun 2, 2023
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2 changes: 2 additions & 0 deletions src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,4 +41,6 @@ public final class BrAPIAdditionalInfoFields {
public static final String ENVIRONMENT_NUMBER = "environmentNumber";
public static final String STUDY_NAME = "studyName";
public static final String OBSERVATION_DATASET_ID = "observationDatasetId";
public static final String FEMALE_PARENT_UNKNOWN = "femaleParentUnknown";
public static final String MALE_PARENT_UNKNOWN = "maleParentUnknown";
}
25 changes: 19 additions & 6 deletions src/main/java/org/breedinginsight/brapi/v2/services/BrAPIGermplasmService.java
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Expand Up @@ -138,14 +138,27 @@ public List<Map<String, Object>> processListData(List<BrAPIGermplasm> germplasm,
}
}

if ((germplasmEntry.getPedigree() != null) && (!germplasmEntry.getPedigree().isEmpty())) {
Pedigree germPedigree = Pedigree.parsePedigreeString(germplasmEntry.getPedigree());
if (!germPedigree.maleParent.isEmpty()) {
row.put("Male Parent GID", Integer.parseInt(germPedigree.maleParent));
// Try getting parentGID otherwise look for unknownParent flag
if (germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID) != null) {
row.put("Male Parent GID", germplasmEntry.getAdditionalInfo()
.get(BrAPIAdditionalInfoFields.GERMPLASM_MALE_PARENT_GID).getAsInt());
} else if (germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN) != null) {
if (germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN).getAsBoolean()) {
row.put("Male Parent GID", 0);
}
if (!germPedigree.femaleParent.isEmpty()) {
row.put("Female Parent GID", Integer.parseInt(germPedigree.femaleParent));
} else {
log.error("Male Parent missing expected value");
}

if (germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID) != null) {
row.put("Female Parent GID", germplasmEntry.getAdditionalInfo()
.get(BrAPIAdditionalInfoFields.GERMPLASM_FEMALE_PARENT_GID).getAsInt());
} else if (germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN) != null) {
if (germplasmEntry.getAdditionalInfo().get(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN).getAsBoolean()) {
row.put("Female Parent GID", 0);
}
} else {
log.error("Female Parent missing expected value");
}

// Synonyms
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4 changes: 2 additions & 2 deletions ...main/java/org/breedinginsight/brapps/importer/services/processors/GermplasmProcessor.java
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Expand Up @@ -584,8 +584,8 @@ else if (germplasmIndexByEntryNo.containsKey(germplasm.getFemaleParentEntryNo())
if (existingPedigree.isEmpty()) {
mappedBrAPIImport.get(i).getGermplasm().getBrAPIObject().setPedigree(pedigreeString.length() > 0 ? pedigreeString.toString() : null);
//Simpler to just always add boolean, but consider for logic that previous imported values won't have that additional info value
mappedBrAPIImport.get(i).getGermplasm().getBrAPIObject().putAdditionalInfoItem("femaleParentUnknown", femaleParentUnknown);
mappedBrAPIImport.get(i).getGermplasm().getBrAPIObject().putAdditionalInfoItem("maleParentUnknown", maleParentUnknown);
mappedBrAPIImport.get(i).getGermplasm().getBrAPIObject().putAdditionalInfoItem(BrAPIAdditionalInfoFields.FEMALE_PARENT_UNKNOWN, femaleParentUnknown);
mappedBrAPIImport.get(i).getGermplasm().getBrAPIObject().putAdditionalInfoItem(BrAPIAdditionalInfoFields.MALE_PARENT_UNKNOWN, maleParentUnknown);
}
}
}
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