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phac-nml / irida-plugin-amr-detection

IRIDA Plugin for AMR Detection
Apache License 2.0
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Metadata table not updated if not results for RGI #8

Closed apetkau closed 3 years ago

apetkau commented 4 years ago

If no results for RGI are found, instead of updating the metadata table with the staramr results, I get the following exception:

16 Aug 2019 14:42:01,629 ERROR ca.corefacility.bioinformatics.irida.service.analysis.execution.galaxy.AnalysisExecutionServiceGalaxyAsync:229 - Error updating corresponding samples with analysis results for Anal
ysisSubmission = [8]. Skipping this step.                                               
ca.corefacility.bioinformatics.irida.exceptions.PostProcessingException: No results found in rgi output file [/Drives/W/Temporary/aaron/output-files/73/0/rgi-summary.tsv]
        at ca.corefacility.bioinformatics.irida.plugin.amrdetection.AMRDetectionUpdater.getRgiResults(AMRDetectionUpdater.java:174)
        at ca.corefacility.bioinformatics.irida.plugin.amrdetection.AMRDetectionUpdater.update(AMRDetectionUpdater.java:204)    
        at ca.corefacility.bioinformatics.irida.pipeline.results.impl.AnalysisSubmissionSampleProcessorImpl.updateSamples(AnalysisSubmissionSampleProcessorImpl.java:88)
...
apetkau commented 3 years ago

Fixed in #13

Released as 0.2.0 - https://github.com/phac-nml/irida-plugin-amr-detection/releases/tag/0.2.0