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BI-2134 Fix error message displayed for wrong observation variable headers #391

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Merged
dmeidlin merged 1 commit into from
Aug 16, 2024
Merged

BI-2134 Fix error message displayed for wrong observation variable headers #391

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1 change: 1 addition & 0 deletions ...g/breedinginsight/brapps/importer/services/processors/experiment/ExperimentUtilities.java
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Expand Up @@ -69,6 +69,7 @@ public class ExperimentUtilities {
public static final String MULTIPLE_EXP_TITLES = "File contains more than one Experiment Title";
public static final String PREEXISTING_EXPERIMENT_TITLE = "Experiment Title already exists";
public static final String MISSING_OBS_UNIT_ID_ERROR = "Experimental entities are missing ObsUnitIDs";
public static final String UNMATCHED_COLUMN = "Ontology term(s) not found: ";



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2 changes: 1 addition & 1 deletion ...services/processors/experiment/appendoverwrite/middleware/process/ImportTableProcess.java
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Expand Up @@ -375,7 +375,7 @@ public AppendOverwriteMiddlewareContext process(AppendOverwriteMiddlewareContext
context.getAppendOverwriteWorkflowContext().setPendingObservationByHash(pendingObservationByHash);

return processNext(context);
} catch (DoesNotExistException | ApiException | UnprocessableEntityException | ValidatorException e) {
} catch (DoesNotExistException | ApiException | UnprocessableEntityException | ValidatorException | IllegalStateException e) {
context.getAppendOverwriteWorkflowContext().setProcessError(new MiddlewareException(e));
return this.compensate(context);
}
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2 changes: 1 addition & 1 deletion ...nsight/brapps/importer/services/processors/experiment/service/ObservationUnitService.java
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Expand Up @@ -75,7 +75,7 @@ public List<BrAPIObservationUnit> getObservationUnitsByDbId(Set<String> expUnitI
missingIds.removeAll(brapiUnits.stream().map(BrAPIObservationUnit::getObservationUnitDbId).collect(Collectors.toSet()));

// Throw exception with missing IDs information
throw new IllegalStateException("Observation unit not found for unit dbid(s): " + String.join(COMMA_DELIMITER, missingIds));
throw new IllegalStateException(ExperimentUtilities.UNMATCHED_COLUMN + String.join(COMMA_DELIMITER, missingIds));
}

return brapiUnits;
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3 changes: 2 additions & 1 deletion ...ht/brapps/importer/services/processors/experiment/service/ObservationVariableService.java
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Expand Up @@ -20,6 +20,7 @@
import io.micronaut.http.HttpStatus;
import org.apache.commons.lang3.StringUtils;
import org.breedinginsight.api.model.v1.response.ValidationError;
import org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentUtilities;
import org.breedinginsight.brapps.importer.services.processors.experiment.model.ExpImportProcessConstants;
import org.breedinginsight.model.Program;
import org.breedinginsight.model.Trait;
Expand Down Expand Up @@ -69,7 +70,7 @@ public List<Trait> fetchTraitsByName(Set<String> varNames, Program program) thro
if (varNames.size() != traits.size()) {
Set<String> missingVarNames = new HashSet<>(varNames);
missingVarNames.removeAll(traits.stream().map(TraitEntity::getObservationVariableName).collect(Collectors.toSet()));
throw new IllegalStateException("Observation variables not found for name(s): " + String.join(ExpImportProcessConstants.COMMA_DELIMITER, missingVarNames));
throw new DoesNotExistException(ExperimentUtilities.UNMATCHED_COLUMN + String.join(ExpImportProcessConstants.COMMA_DELIMITER, missingVarNames));
}

return traits;
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