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Non-useful error and exit code when resources files corrupt #5

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jfy133 opened this issue Sep 30, 2020 · 0 comments
Open

Non-useful error and exit code when resources files corrupt #5

jfy133 opened this issue Sep 30, 2020 · 0 comments

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@jfy133
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jfy133 commented Sep 30, 2020

I accidently used the wrong link to download the ncbi.tre file from resources/ and this was the HTML github webpage rather than the tree file itself.

When running MaltExtract, I got the error below and this didn't report a recognisable error code. Therefore the pipeline just hung rather than cleanly exiting (until I investigated).

 Sep 29, 2020 3:40:04 PM RMAExtractor.RMAExtractor main
  INFO: Setting up Taxon Name and Taxon ID maps
  Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
  	at org.forester.phylogeny.Phylogeny.createInstanceFromNhxString(Phylogeny.java:312)
  	at NCBI_MapReader.NCBI_TreeReader.<init>(NCBI_TreeReader.java:76)
  	at RMAExtractor.RMAExtractor.main(RMAExtractor.java:92)

Would it be possible to add a validation check of the resources files, and if they are not that MaltExtract reports a useful error message and exit code?

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