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peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Use biom export-metadata to check test output #554

Closed peterjc closed 4 months ago

peterjc commented 1 year ago

Failed on Windows,

Checking BIOM output has sequence, and genus-species metadata:
+ biom export-metadata -i /tmp/thapbi_pict/pipeline/output/thapbi-pict.ITS1.onebp.biom --observation-metadata-fp /dev/stdout
+ grep '^.Sequence.genus-species$'

Could it be the metadata order (?)

peterjc commented 1 year ago

Cross reference https://github.com/biocore/biom-format/issues/907 and fix in PR https://github.com/biocore/biom-format/pull/910 - waiting on the next release (after biom 2.1.14) with this change.

peterjc commented 10 months ago

Fails:

+ biom validate-table -i /tmp/thapbi_pict/pipeline/output/thapbi-pict.ITS1.onebp.biom

The input file is a valid BIOM-formatted file.
+ echo 'Checking BIOM output has sequence, genus-species, and taxid metadata:'
Checking BIOM output has sequence, genus-species, and taxid metadata:
+ biom export-metadata -i /tmp/thapbi_pict/pipeline/output/thapbi-pict.ITS1.onebp.biom --observation-metadata-fp /dev/stdout
+ grep '^.Sequence.genus-species.taxid$'
        Sequence        genus-species   taxid
+ echo 'Checking BIOM output has sequence, and genus-species metadata:'
Checking BIOM output has sequence, and genus-species metadata:
+ biom export-metadata -i /tmp/thapbi_pict/pipeline/output/thapbi-pict.ITS1.onebp.biom --observation-metadata-fp /dev/stdout
+ grep '^.Sequence.genus-species$'