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Fix Registry.get_datatype_by_extension() to return None if ext is unknown #4224

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merged 3 commits into from Jun 26, 2017

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commented Jun 26, 2017

Without this fix, the Cheetah expression:

$dataset.is_of_type('unknown_ext')

in a tool command would be equivalent to:

$dataset.is_of_type('txt')

meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning.

xref. galaxyproject/tools-iuc#1373

Also:

  • add missing xml datatype to test/functional/tools/sample_datatypes_conf.xml which is needed by 3 test tools.
  • fix import order and Python3 compatibility for lib/galaxy/datatypes/registry.py xref. #1715
  • small fixes.

The first commit should be backported to fix galaxyproject/tools-iuc#1373 on pre-17.01 releases.

nsoranzo added some commits Jun 25, 2017

Fix Registry.get_datatype_by_extension() to return None if ext is unk…
…nown

Without this fix, the Cheetah expression:

$dataset.is_of_type('unknown_ext')

in a tool command would be equivalent to:

$dataset.is_of_type('txt')

meaning that if the dataset datatype is a subclass of Text, the expression
would evaluate to True without any warning.

xref. galaxyproject/tools-iuc#1373

Also add missing `xml` datatype to
`test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test
tools.
@jmchilton

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commented Jun 26, 2017

Awesome - thanks a bunch @nsoranzo!

@jmchilton jmchilton merged commit 3ec2c78 into galaxyproject:dev Jun 26, 2017

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@nsoranzo nsoranzo deleted the nsoranzo:fix_get_datatype_by_extension branch Jun 26, 2017

@nsoranzo nsoranzo referenced this pull request Jun 26, 2017

Merged

[16.07] Backport #4224 #4230

jmchilton added a commit that referenced this pull request Jul 5, 2017

peterjc added a commit to peterjc/galaxy_blast that referenced this pull request Oct 19, 2018

Workaround for gzip support breaking on Galaxy 16.01
See galaxyproject/tools-iuc#1373
which was fixed and back-ported to Galaxy 16.07,
galaxyproject/galaxy#4224
galaxyproject/galaxy#4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.

peterjc added a commit to peterjc/galaxy_blast that referenced this pull request Oct 19, 2018

Workaround for gzip support breaking on Galaxy 16.01
See galaxyproject/tools-iuc#1373
which was fixed and back-ported to Galaxy 16.07,
galaxyproject/galaxy#4224
galaxyproject/galaxy#4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.

peterjc added a commit to peterjc/galaxy_blast that referenced this pull request Oct 22, 2018

Workaround for gzip support breaking on Galaxy 16.01
See galaxyproject/tools-iuc#1373
which was fixed and back-ported to Galaxy 16.07,
galaxyproject/galaxy#4224
galaxyproject/galaxy#4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.

peterjc added a commit to peterjc/galaxy_blast that referenced this pull request Oct 22, 2018

Workaround for gzip support breaking on Galaxy 16.01
See galaxyproject/tools-iuc#1373
which was fixed and back-ported to Galaxy 16.07,
galaxyproject/galaxy#4224
galaxyproject/galaxy#4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.

peterjc added a commit to peterjc/galaxy_blast that referenced this pull request Oct 23, 2018

Workaround for gzip support breaking on Galaxy 16.01
See galaxyproject/tools-iuc#1373
which was fixed and back-ported to Galaxy 16.07,
galaxyproject/galaxy#4224
galaxyproject/galaxy#4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.

peterjc added a commit to peterjc/galaxy_blast that referenced this pull request Oct 23, 2018

Workaround for gzip support breaking on Galaxy 16.01
See galaxyproject/tools-iuc#1373
which was fixed and back-ported to Galaxy 16.07,
galaxyproject/galaxy#4224
galaxyproject/galaxy#4230

This would still break with other non-compressed FASTA
subclasses, but this is intended as a stop-gap until
the last few elderly Galaxy servers in use are updated.
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