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[BI-1265-2] Overwrite entity dataset #327

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Merged
dmeidlin merged 3 commits into from
Jan 24, 2024
Merged

[BI-1265-2] Overwrite entity dataset #327

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aee0658
add season to additional info
dmeidlin Jan 18, 2024
e2e6aa0
remove NPE
dmeidlin Jan 18, 2024
b4783e8
remove comments
dmeidlin Jan 18, 2024
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25 changes: 18 additions & 7 deletions ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -383,10 +383,19 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program

mutatedObservationByDbId.forEach((id, observation) -> {
try {
if (observation == null) {
throw new Exception("Null observation");
}
BrAPIObservation updatedObs = brAPIObservationDAO.updateBrAPIObservation(id, observation, program.getId());
if (!observation.getValue().equals(updatedObs.getValue()) || !observation.getObservationTimeStamp().isEqual(updatedObs.getObservationTimeStamp())) {

if (updatedObs == null) {
throw new Exception("Null updated observation");
}

if (!Objects.equals(observation.getValue(), updatedObs.getValue())
|| !Objects.equals(observation.getObservationTimeStamp(), updatedObs.getObservationTimeStamp())) {
String message;
if(!observation.getValue().equals(updatedObs.getValue())) {
if(!Objects.equals(observation.getValue(), updatedObs.getValue())) {
message = String.format("Updated observation, %s, from BrAPI service does not match requested update %s.", updatedObs.getValue(), observation.getValue());
} else {
message = String.format("Updated observation timestamp, %s, from BrAPI service does not match requested update timestamp %s.", updatedObs.getObservationTimeStamp(), observation.getObservationTimeStamp());
Expand All @@ -401,9 +410,7 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program
throw new InternalServerException(e.getMessage(), e);
}
});

log.debug("experiment import complete");

}

private void prepareDataForValidation(List<BrAPIImport> importRows, List<Column<?>> phenotypeCols, Map<Integer, PendingImport> mappedBrAPIImport) {
Expand Down Expand Up @@ -1091,7 +1098,12 @@ private void fetchOrCreateDatasetPIO(ExperimentObservation importRow, Program pr
addObsVarsToDatasetDetails(pio, referencedTraits, program);
}

private PendingImportObject<BrAPIStudy> fetchOrCreateStudyPIO(Program program, boolean commit, String expSequenceValue, ExperimentObservation importRow, Supplier<BigInteger> envNextVal) {
private PendingImportObject<BrAPIStudy> fetchOrCreateStudyPIO(
Program program,
boolean commit,
String expSequenceValue,
ExperimentObservation importRow,
Supplier<BigInteger> envNextVal) {
PendingImportObject<BrAPIStudy> pio;
if (studyByNameNoScope.containsKey(importRow.getEnv())) {
pio = studyByNameNoScope.get(importRow.getEnv());
Expand Down Expand Up @@ -1133,8 +1145,7 @@ private void addYearToStudyAdditionalInfo(Program program, BrAPIStudy study) {

//if it is already there, don't add it.
if(additionalInfo==null || additionalInfo.get(BrAPIAdditionalInfoFields.ENV_YEAR)==null) {
String seasonDbId = study.getSeasons().get(0);
String year = seasonDbIdToYear(seasonDbId, program.getId());
String year = study.getSeasons().get(0);
addYearToStudyAdditionalInfo(program, study, year);
}
}
Expand Down