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Raise detailed exception for broken citation #7891

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merged 1 commit into from May 3, 2019
Merged

Raise detailed exception for broken citation #7891

merged 1 commit into from May 3, 2019

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@nsoranzo
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nsoranzo commented May 3, 2019

For an empty citation, this will result in logging:

Exception: Invalid citation of type 'doi' with content 'None': 'NoneType' object has no attribute 'strip'

instead of:

AttributeError: 'NoneType' object has no attribute 'strip'

xref galaxyproject/planemo#929
@nsoranzo
Raise detailed exception for broken citation
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5ed7722 
For an empty citation, this will result in logging:
```
Exception: Invalid citation of type 'doi' with content 'None': 'NoneType' object has no attribute 'strip'
```

instead of:
```
AttributeError: 'NoneType' object has no attribute 'strip'
```

xref galaxyproject/planemo#929
@nsoranzo nsoranzo added this to the 19.09 milestone May 3, 2019
@mvdbeek
mvdbeek approved these changes May 3, 2019
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@jmchilton
jmchilton approved these changes May 3, 2019
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nsoranzo commented May 3, 2019 •
edited

@jmchilton While working to enhance galaxy/tools/linters/citations.py in galaxy-lib , I noticed that in commit cb9fc09 you added the possibility for a bibtex citation to use a file attribute, but this is not allowed in the XSD and there are no tests for it.
I'm not aware of any tool using this attribute, so should we remove the code allowing it or fix the XSD?
@martenson martenson merged commit a4978e2 into galaxyproject:dev May 3, 2019
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@nsoranzo nsoranzo deleted the nsoranzo:broken_citation_exc branch May 4, 2019
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jmchilton commented May 7, 2019

Hmm... I'm fine with removing the option. Seems undocumented at best.
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nsoranzo commented May 8, 2019

Thanks, I've opened #7911 to remove the attribute.
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