From b7f5473599c95b8981bd7653f31d9b6bef21c6e2 Mon Sep 17 00:00:00 2001 From: dmeidlin <14339308+dmeidlin@users.noreply.github.com> Date: Fri, 8 Dec 2023 11:35:18 -0500 Subject: [PATCH 1/3] assign existing germplasm to OU PIO by gid instead of by germplasm name --- .../ExperimentObservation.java | 2 ++ .../services/processors/ExperimentProcessor.java | 14 +++++++------- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java b/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java index 290c046ad..c2f5926d4 100644 --- a/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java +++ b/src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java @@ -228,6 +228,7 @@ public BrAPIObservationUnit constructBrAPIObservationUnit( String seqVal, boolean commit, String germplasmName, + String gid, String referenceSource, UUID trialID, UUID datasetId, @@ -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(); diff --git a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java index d35da62d8..5989e88f5 100644 --- a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java +++ b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java @@ -956,7 +956,7 @@ private PendingImportObject fetchOrCreateObsUnitPIO(Progra PendingImportObject 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) { @@ -1291,16 +1291,16 @@ 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() + .get(BrAPIAdditionalInfoFields.GID).getAsString())) .forEach(obsUnit -> obsUnit.getBrAPIObject() .setGermplasmDbId(germplasm.getGermplasmDbId())); } - +//obsUnit.getBrAPIObject().getAdditionalInfo().getAsJsonObject().get(BrAPIAdditionalInfoFields.GID).getAsString() private void updateStudyDependencyValues(Map mappedBrAPIImport, String programKey) { // update location DbIds in studies for all distinct locations mappedBrAPIImport.values() From 8852119afff8b1f2b761b6228e7578b85b91aac7 Mon Sep 17 00:00:00 2001 From: dmeidlin <14339308+dmeidlin@users.noreply.github.com> Date: Fri, 8 Dec 2023 11:56:15 -0500 Subject: [PATCH 2/3] remove comment --- .../importer/services/processors/ExperimentProcessor.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java index 5989e88f5..15ae356c3 100644 --- a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java +++ b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java @@ -1299,8 +1299,7 @@ private void updateGermplasmDbId(BrAPIGermplasm germplasm) { .forEach(obsUnit -> obsUnit.getBrAPIObject() .setGermplasmDbId(germplasm.getGermplasmDbId())); } - -//obsUnit.getBrAPIObject().getAdditionalInfo().getAsJsonObject().get(BrAPIAdditionalInfoFields.GID).getAsString() + private void updateStudyDependencyValues(Map mappedBrAPIImport, String programKey) { // update location DbIds in studies for all distinct locations mappedBrAPIImport.values() From 0a9181c0bab31c181fb91a078221de8e346aa2eb Mon Sep 17 00:00:00 2001 From: dmeidlin <14339308+dmeidlin@users.noreply.github.com> Date: Fri, 8 Dec 2023 14:16:13 -0500 Subject: [PATCH 3/3] cleanup --- .../importer/services/processors/ExperimentProcessor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java index 15ae356c3..aded65fe1 100644 --- a/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java +++ b/src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java @@ -1299,7 +1299,7 @@ private void updateGermplasmDbId(BrAPIGermplasm germplasm) { .forEach(obsUnit -> obsUnit.getBrAPIObject() .setGermplasmDbId(germplasm.getGermplasmDbId())); } - + private void updateStudyDependencyValues(Map mappedBrAPIImport, String programKey) { // update location DbIds in studies for all distinct locations mappedBrAPIImport.values()