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Fix an issue when you run shed_diff --shed_target local#375

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jmchilton merged 1 commit intogalaxyproject:masterfrom
gwenandres:bugfix_shed_diff_with_local_toolshed
Nov 18, 2015
Merged

Fix an issue when you run shed_diff --shed_target local#375
jmchilton merged 1 commit intogalaxyproject:masterfrom
gwenandres:bugfix_shed_diff_with_local_toolshed

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@gwenandres
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@gwenandres gwenandres commented Nov 18, 2015

Hi,

We are a developer team in Roscoff in France.

We have detected a bug when you run planemo shed_diff --shed_target local.
The directories, which are compared, have the same name local for both files from the localtoolshed and files from the working tested directory.

BEFORE

$ planemo shed_diff -t local
Diffing repository package_fastme_1_0_0 
wget -q --recursive -O - 'http://localhost:9009/repository/download?repository_id=d9abeb98649a6a7e&changeset_revision=default&file_type=gz' | tar -xzf - -C /tmp/tool_shed_diff_bQBFCC/_local_ --strip-components 1
mkdir "/tmp/tool_shed_diff_bQBFCC/_local_"; tar -xzf "/tmp/tmpLl2Gh5" -C "/tmp/tool_shed_diff_bQBFCC/_local_"; rm -rf /tmp/tmpLl2Gh5
mkdir: cannot create directory `/tmp/tool_shed_diff_bQBFCC/_local_': File exists
[...]
  File "/usr/local/galaxy/galaxy/.venv/lib/python2.7/site-packages/planemo/shed/diff.py", line 11, in diff_and_remove
    assert label_a != label_b

We propose a fix changing the working tested directory name: workingdir instead of local

AFTER

$ planemo shed_diff -t local
Diffing repository package_fastme_1_0_0 
wget -q --recursive -O - 'http://localhost:9009/repository/download?repository_id=d9abeb98649a6a7e&changeset_revision=default&file_type=gz' | tar -xzf - -C /tmp/tool_shed_diff_Jh4HoN/_local_ --strip-components 1
mkdir "/tmp/tool_shed_diff_Jh4HoN/_workingdir_"; tar -xzf "/tmp/tmpGHqMci" -C "/tmp/tool_shed_diff_Jh4HoN/_workingdir_"; rm -rf /tmp/tmpGHqMci
cd "/tmp/tool_shed_diff_Jh4HoN"; diff -r _workingdir_ _local_ >> '/tmp/tmpiX8fW2'

If you have any questions about this fix don't hesitate to contact us.

Cheers

Gwendoline Andres and Gildas Le Corguillé - ABiMS Roscoff - CNRS/UPMC - France

@jmchilton
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jmchilton commented Nov 18, 2015

Fantastic, thanks for the fix!

jmchilton added a commit that referenced this pull request Nov 18, 2015
@jmchilton
Merge pull request #375 from gwenandres/bugfix_shed_diff_with_local_t…
ea0d69b 
…oolshed

Fix an issue when you run shed_diff --shed_target local
@jmchilton jmchilton merged commit ea0d69b into galaxyproject:master Nov 18, 2015
@hexylena hexylena added the bug label Nov 18, 2015
jmchilton added a commit that referenced this pull request Nov 18, 2015
@jmchilton
Fix tests for PR #375.
0e4f70a
@gwenandres
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gwenandres commented Nov 19, 2015

Great !

Thanks a lot

2015-11-18 16:36 GMT+01:00 John Chilton notifications@github.com:

Merged #375 #375.

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@gwenandres @jmchilton @hexylena