[BI-1193] Associate phenotypes with experiment observation dataset#247
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[BI-1193] Associate phenotypes with experiment observation dataset#247
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timparsons
requested changes
Apr 27, 2023
| try { | ||
| response = api.listsListDbIdItemsPost(brAPIListDbId, data); | ||
| } catch (ApiException e) { | ||
| log.warn(Utilities.generateApiExceptionLogMessage(e)); |
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This should probably be log.error
| // Do manually, it doesn't like List<Object> to List<BrAPIListNewRequest> for some reason | ||
| ApiResponse<BrAPIListResponse> response; | ||
| try { | ||
| response = api.listsListDbIdItemsPost(brAPIListDbId, data); |
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This method should be changed to use PUT /lists/{listDbId} to allow for full replacement of the contents of the list
| } | ||
| } | ||
| addObsVarsToDatasetDetails(pio, referencedTraits); | ||
| obsVarDatasetByName.put(name, pio); |
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I think this can be done in the else block
| return (T) body.getResult(); | ||
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| } catch (ApiException e) { | ||
| log.warn(Utilities.generateApiExceptionLogMessage(e)); |
davedrp
requested changes
May 1, 2023
src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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src/test/java/org/breedinginsight/brapps/importer/ExperimentFileImportTest.java
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davedrp
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May 2, 2023
timparsons
approved these changes
May 8, 2023
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timparsons
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Looks good! Approving assuming the commented out code is removed.
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| private void processAndCacheTrial(BrAPITrial existingTrial, Program program, String trialRefSource, Map<String, PendingImportObject<BrAPITrial>> trialByNameNoScope) { | ||
| existingTrial.setTrialName(Utilities.removeProgramKey(existingTrial.getTrialName(), program.getKey())); | ||
| //existingTrial.setTrialName(Utilities.removeProgramKey(existingTrial.getTrialName(), program.getKey())); |
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Description
Story: BI-1193
Changes made to
ExperimentProcessor:obsVarDatasetByNameto hold a map for dataset pending import objectsTo handle the case when an import object needs to be updated the following were added:
ImportObjectState.MUTATEDBrAPIDAOUtil#putProcessorData#getMutationsByObjectIdFor updating Trials:
AdditionalInfoField.observationDatasetIdBrAPITrialDAO#updateBrAPITrialFor creating/updating Datasets
ExternalReferenceSource.DATASETExperimentObservation#contructDatasetDetailsBrAPIListDAO#updateBrAPIListDependencies
none
Testing
see acceptance criteria in the card
Checklist: