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mlm483
requested changes
Oct 9, 2023
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The code looks good and acceptance criterion 2 is met but acceptance criterion 1 is not met; a check for values outside of case insensitive "" (blank => Test), "T", "C", "TEST", "CHECK" should be added, and an appropriate error shown.
Also, please run TAF after making those changes, the test files may need to be updated.
nickpalladino
requested changes
Oct 11, 2023
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During testing I was getting a null pointer exception:
java.lang.RuntimeException: java.lang.NullPointerException
at org.breedinginsight.brapps.importer.services.FileMappingUtil.lambda$sortByField$0(FileMappingUtil.java:90)
at java.base/java.util.TimSort.countRunAndMakeAscending(TimSort.java:355)
at java.base/java.util.TimSort.sort(TimSort.java:220)
at java.base/java.util.Arrays.sort(Arrays.java:1516)
at java.base/java.util.ArrayList.sort(ArrayList.java:1718)
at org.breedinginsight.brapps.importer.services.FileMappingUtil.sortByField(FileMappingUtil.java:84)
at org.breedinginsight.brapps.importer.services.processors.ExperimentProcessor.verifyTraits(ExperimentProcessor.java:439)
at org.breedinginsight.brapps.importer.services.processors.ExperimentProcessor.process(ExperimentProcessor.java:220)
at org.breedinginsight.brapps.importer.services.processors.ProcessorManager.process(ProcessorManager.java:65)
at org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentImportService.process(ExperimentImportService.java:72)
at org.breedinginsight.brapps.importer.services.FileImportService.lambda$processFile$9(FileImportService.java:426)
at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run$$$capture(CompletableFuture.java:1771)
at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.run(CompletableFuture.java)
at java.base/java.util.concurrent.CompletableFuture$AsyncSupply.exec(CompletableFuture.java:1763)
at java.base/java.util.concurrent.ForkJoinTask.doExec$$$capture(ForkJoinTask.java:290)
at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java)
at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1016)
at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1665)
at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1598)
at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:183)
Caused by: java.lang.NullPointerException: null
at org.breedinginsight.brapps.importer.services.FileMappingUtil.lambda$sortByField$0(FileMappingUtil.java:88)
... 19 common frames omitted```
Test files:
[KRSP128_case.xlsx](https://github.com/Breeding-Insight/bi-api/files/12874366/KRSP128_case.xlsx)
[bi_lettuce_ontology_v1.xlsx](https://github.com/Breeding-Insight/bi-api/files/12874371/bi_lettuce_ontology_v1.xlsx)
mlm483
requested changes
Oct 11, 2023
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mlm483
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I'm seeing the Null Pointer Exception as well when uploading Experiment and Observations.
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Bug fixed (and thanks for finding it?) |
nickpalladino
approved these changes
Oct 13, 2023
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BI-1930 - trait names are case sensitive
Description
When importing an experiment in the current system, the observation-variable must match an ontology in a case-sensitive way. If not it will fail validation. The purpose of this story is to allow the matching between the observation-variable and the ontology to be case-insensitive, while still allowing the observation-variable and the observation data to be saved correctly.
Dependencies
bi-web: develop branch
Testing
WHEN An experiment is imported with observations.
AND At least one observation-variable (i.e. the observation column header) differs from an ontology by case (for example: if the ontology is "Color" the observation-variable could be "cOLoR").
THEN The experiment should pass validation.
WHEN Viewing the experiment summary.
THEN the observation-variable should be displayed with the same cases as the ontology (in the above example: "Color")
Checklist: