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BUG: merge doesn't list the offending filename when erroring on file contents #62

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lizgehret opened this issue Dec 5, 2023 · 1 comment · Fixed by #64
Closed

BUG: merge doesn't list the offending filename when erroring on file contents #62

lizgehret opened this issue Dec 5, 2023 · 1 comment · Fixed by #64
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@lizgehret
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Bug Description
When running merge on two different metadata files, if one file contains a formatting issue (i.e. CategoricalMetadataColumn contains floats), the name of the offending file is not listed in the error message. See screenshot below:

Screen Shot 2023-12-05 at 2 32 02 PM

Steps to reproduce the behavior

  1. Go to the Moving Pictures tutorial and download sample-metadata.tsv
  2. Duplicate the sample-metadata.tsv file and save it as two different files (e.g. sample-md1.tsv & sample-md2.tsv)
  3. Modify the month column's comment directive in one of the duplicated files to categorical and change the dtype of this column to float.
  4. Run the following command:
qiime metadata merge \
--m-metadata1-file sample-md1.tsv \
--m-metadata2-file sample-md2.tsv \
--o-merged-metadata merged-md.qza \
--verbose

This will produce the error in the screenshot above, giving no indication of whether the offending file is sample-md1.tsv or sample-md2.tsv.

Expected behavior
The error message above should begin with something like:

There was an issue with loading the file sample-md1.tsv ...etc
@lizgehret
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Another one for you to work on when you're ready @hagenjp 🙂

@lizgehret lizgehret changed the title BUG: merge doesn't list the filename when erroring on file contents BUG: merge doesn't list the offending filename when erroring on file contents Dec 5, 2023
@lizgehret lizgehret added this to 2024.5 May 1, 2024
@github-project-automation github-project-automation bot moved this to Backlog in 2024.5 May 1, 2024
@lizgehret lizgehret moved this from Backlog to Changelog Needed in 2024.5 May 1, 2024
@hagenjp hagenjp moved this from Changelog Needed to Completed in 2024.5 May 22, 2024
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