[16.07] Backport #4224 #4230
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[16.07] Backport #4224 #4230
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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.
|
I think that integration test failure is to be expected on 16.07. |
mvdbeek
reviewed
Jun 27, 2017
| @@ -14,5 +14,8 @@ | |||
| <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM" /> | |||
| <datatype extension="bcf" type="galaxy.datatypes.binary:Bcf" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bcf' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BCF" /> | |||
| <datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json"/> | |||
| <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://galaxyproject.org/learn/datatypes/#bed"> | |||
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Looks like the indentation is off here
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Yeah, it's a tab. I copy-pasted it from the dev version of this file (was originally added in another commit) and decided to keep it like this to hopefully minimise conflicts when merging forward. But I can fix it here if you want.
mvdbeek
approved these changes
Jun 27, 2017
|
Awesome - thanks for the diligence. |
|
Merged forward all the way to the |
peterjc
added a commit
to peterjc/galaxy_blast
that referenced
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Oct 19, 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 19, 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 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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Fix
Registry.get_datatype_by_extension()to returnNoneifextis unknown.Bugfix-only backport of #4224.
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.Fix galaxyproject/tools-iuc#1373.
Also add missing
bedandxmldatatypes totest/functional/tools/sample_datatypes_conf.xmlwhich are needed by 4 test tools.