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Allow include source to be a list of filenames/patterns. #185

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merged 2 commits into from May 6, 2015

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peterjc commented May 6, 2015

This allows nesting within the include setting of .shed.yml for example if you have a batch of files with the same strip_components setting.

See GitHub issue #180, and #160 which would no longer be needed for my use cases https://github.com/peterjc/galaxy_blast and https://github.com/peterjc/pico_galaxy ).

The relative_dest == "." check was needed for this example .shed.yml to work, otherwise the four files under tools/venn_list/* were ignored:

$ tail  ~/repositories/pico_galaxy/tools/venn_list/.shed.yml
include:
- strip_components: 2
  source:
  - ../../tools/venn_list/README.rst
  - ../../tools/venn_list/venn_list.py
  - ../../tools/venn_list/venn_list.xml
  - ../../tools/venn_list/tool_dependencies.xml
  - ../../test-data/magic.pdf
  - ../../test-data/venn_list.tabular
  - ../../test-data/rhodopsin_proteins.fasta
$ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/venn_list/ && tar -tzf shed_upload.tar.gz 
cp '/tmp/tmpkASHOo' 'shed_upload.tar.gz'
README.rst
test-data/magic.pdf
test-data/rhodopsin_proteins.fasta
test-data/venn_list.tabular
tool_dependencies.xml
venn_list.py
venn_list.xml

As per the suggestion on #180, this approach leaves the missing include detection added in #158 working:

$ tail  ~/repositories/pico_galaxy/tools/venn_list/.shed.yml
include:
- strip_components: 2
  source:
  - ../../tools/venn_list/README.rst
  - ../../tools/venn_list/venn_list_with_typo.py
  - ../../tools/venn_list/venn_list.xml
  - ../../tools/venn_list/tool_dependencies.xml
  - ../../test-data/magic.pdf
  - ../../test-data/venn_list.tabular
  - ../../test-data/rhodopsin_proteins.fasta
(.venv)[galaxy@ppserver planemo]$ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/venn_list/ && tar -tzf shed_upload.tar.gz 
Failed to include files for [{'source': '../../tools/venn_list/venn_list_with_typo.py', 'strip_components': 2}]
Problem encountered executing action for one or more repositories.
Allow include source to be a list of filenames/patterns.
This allows nesting within the include setting of .shed.yml
for example if you have a batch of files with the same
strip_components setting. See GitHub issue #180.
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peterjc commented May 6, 2015

Hmm. An interesting platform specific failure according to TravisCI, Exception ['str' object has no attribute 'get']. with TOXENV=py26 and TOXENV=py27.

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jmchilton commented May 6, 2015

Awesome - thanks!

jmchilton added a commit that referenced this pull request May 6, 2015

Merge pull request #185 from peterjc/source_list
Allow include source to be a list of filenames/patterns.

@jmchilton jmchilton merged commit 7ac2e70 into galaxyproject:master May 6, 2015

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