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[BI-2028] Duplicated accession names getting assigned duplicated GIDs after Exp&Obs upload #320

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Merged
dmeidlin merged 3 commits into from
Dec 20, 2023
Merged

[BI-2028] Duplicated accession names getting assigned duplicated GIDs after Exp&Obs upload #320

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b7f5473
assign existing germplasm to OU PIO by gid instead of by germplasm name
dmeidlin Dec 8, 2023
8852119
remove comment
dmeidlin Dec 8, 2023
0a9181c
cleanup
dmeidlin Dec 8, 2023
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2 changes: 2 additions & 0 deletions ...inginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -228,6 +228,7 @@ public BrAPIObservationUnit constructBrAPIObservationUnit(
String seqVal,
boolean commit,
String germplasmName,
String gid,
String referenceSource,
UUID trialID,
UUID datasetId,
Expand All @@ -250,6 +251,7 @@ public BrAPIObservationUnit constructBrAPIObservationUnit(
germplasmName = getGermplasmName();
}
observationUnit.setGermplasmName(germplasmName);
observationUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GID, gid);

BrAPIObservationUnitPosition position = new BrAPIObservationUnitPosition();
BrAPIObservationUnitLevelRelationship level = new BrAPIObservationUnitLevelRelationship();
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13 changes: 6 additions & 7 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Expand Up @@ -956,7 +956,7 @@ private PendingImportObject<BrAPIObservationUnit> fetchOrCreateObsUnitPIO(Progra
PendingImportObject<BrAPIStudy> studyPIO = this.studyByNameNoScope.get(importRow.getEnv());
UUID studyID = studyPIO.getId();
UUID id = UUID.randomUUID();
BrAPIObservationUnit newObservationUnit = importRow.constructBrAPIObservationUnit(program, envSeqValue, commit, germplasmName, BRAPI_REFERENCE_SOURCE, trialID, datasetId, studyID, id);
BrAPIObservationUnit newObservationUnit = importRow.constructBrAPIObservationUnit(program, envSeqValue, commit, germplasmName, importRow.getGid(), BRAPI_REFERENCE_SOURCE, trialID, datasetId, studyID, id);

// check for existing units if this is an existing study
if (studyPIO.getBrAPIObject().getStudyDbId() != null) {
Expand Down Expand Up @@ -1291,16 +1291,15 @@ private void updateStudyDbId(BrAPIStudy study, String programKey) {
private void updateGermplasmDbId(BrAPIGermplasm germplasm) {
this.observationUnitByNameNoScope.values()
.stream()
.filter(obsUnit -> obsUnit.getBrAPIObject()
.getGermplasmName() != null &&
obsUnit.getBrAPIObject()
.getGermplasmName()
.equals(germplasm.getGermplasmName()))
.filter(obsUnit -> germplasm.getAccessionNumber() != null &&
germplasm.getAccessionNumber().equals(obsUnit
.getBrAPIObject()
.getAdditionalInfo().getAsJsonObject()
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@nickpalladino nickpalladino Dec 8, 2023

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Do we need a migration to add gids to existing observation units additionalinfo?

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@dmeidlin dmeidlin Dec 8, 2023

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Most existing OUs have the correct gemplasm dbId assigned, so a migration adding the GID wouldn't matter either way for them. It's a question more for Alex and Shawn to estimate how many cases of existing OUs using germplasm there are. They haven't com across this until now, so I'm guessing it's a small number where manually fixing it in the species database would make more sense. I'm not sure what a migration would look like. It wouldn't be a case of just adding the GID to the OU additional info since the existing id in the OU germplasmDbId field could be wrong. You couldn't easily tell if it was right or wrong, and if it's wrong, it's not clear which germplasmDbId would be correct? So a migration just looks like re-importing the experiment with bug fix in place.

.get(BrAPIAdditionalInfoFields.GID).getAsString()))
.forEach(obsUnit -> obsUnit.getBrAPIObject()
.setGermplasmDbId(germplasm.getGermplasmDbId()));
}


private void updateStudyDependencyValues(Map<Integer, PendingImport> mappedBrAPIImport, String programKey) {
// update location DbIds in studies for all distinct locations
mappedBrAPIImport.values()
Expand Down