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Patch for metadata setting of minimal BIOM1 files #7696

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merged 1 commit into from Apr 9, 2019

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commented Apr 9, 2019

Hi,

As reported in #7625, the upload and generation of BIOM file are raising errors on 19.01, not on 18.09. This issue happens only with minimal BIOM files (not rich ones).

The minimal BIOM1 files may have column = {u'id': u'sth', u'metadata': None}, raising then the following error:

ERROR:galaxy.datatypes.text:Something in the metadata detection for biom1 went wrong.
Traceback (most recent call last):
  File "/opt/galaxy/server/lib/galaxy/datatypes/text.py", line 259, in set_meta
    for k, v in column['metadata'].items():
AttributeError: 'NoneType' object has no attribute 'items'

This PR checks if column['metadata'] is not None before the for loop. It should fix #7625.

@nsoranzo @Slugger70 could you check this patch? Should I add some tests? If yes, how/where?

Thanks a lot

Bérénice


See BIOM1 specs for examples of minimal and rich BIOM1 files

@galaxybot galaxybot added the triage label Apr 9, 2019

@galaxybot galaxybot added this to the 19.05 milestone Apr 9, 2019

@bgruening

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commented Apr 9, 2019

Should that target 19.01?

@nsoranzo nsoranzo merged commit b32626d into galaxyproject:dev Apr 9, 2019

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@nsoranzo

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commented Apr 9, 2019

Feel free to open a backport PR to 19.01 if that's worth.

@bebatut bebatut deleted the bebatut:fix_biom1 branch Apr 9, 2019

jmchilton added a commit that referenced this pull request Apr 29, 2019

mvdbeek added a commit that referenced this pull request Apr 30, 2019

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