Fix Registry.get_datatype_by_extension() to return None if ext is unknown #4224
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…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.
|
Awesome - thanks a bunch @nsoranzo! |
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peterjc
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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
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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
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Oct 22, 2018
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
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
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
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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Without this fix, the Cheetah expression:
in a tool command would be equivalent to:
meaning that if the dataset datatype is a subclass of
Text, the expression would evaluate toTruewithout any warning.xref. galaxyproject/tools-iuc#1373
Also:
xmldatatype totest/functional/tools/sample_datatypes_conf.xmlwhich is needed by 3 test tools.lib/galaxy/datatypes/registry.pyxref. Python 3 support. #1715The first commit should be backported to fix galaxyproject/tools-iuc#1373 on pre-17.01 releases.