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flake8 contrib/ and lib/tool_shed/ . #708

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merged 2 commits into from
Sep 10, 2015
Merged

flake8 contrib/ and lib/tool_shed/ . #708

merged 2 commits into from
Sep 10, 2015

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nsoranzo
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@nsoranzo nsoranzo commented Sep 9, 2015

Also:

  • use sys.exit() instead of exit()
  • fix sys.path manipulations.

@nsoranzo
flake8 contrib/ .
af2f93b
@nsoranzo
flake8 lib/tool_shed/ .
df808d0 
Also:
- use sys.exit() instead of exit()
- fix sys.path manipulations.
jmchilton
jmchilton reviewed Sep 9, 2015
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lib/tool_shed/scripts/api/common.py
new_path = [ os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir, os.pardir, 'lib' ) ]
new_path.extend( sys.path[ 1: ] )
sys.path = new_path
sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir ) )
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This doesn't have to end with lib?

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No, this file is already in a subdirectory of lib, so I have removed os.pardir, 'lib' .

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👍

@martenson
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This breaks 2 tests for me (./run_tests.sh -toolshed):

======================================================================
ERROR: Verify the exported capsule contents.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/marten/devel/git/galaxy/test/tool_shed/functional/test_0490_export_import_repositories.py", line 82, in test_0015_verify_exported_capsule
    self.verify_capsule_contents( capsule_filepath, owner=common.test_user_1_name )
  File "/Users/marten/devel/git/galaxy/test/tool_shed/base/twilltestcase.py", line 1313, in verify_capsule_contents
    tar_object = tarfile.open( capsule_filepath, 'r:*' )
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tarfile.py", line 1651, in open
    raise ValueError("nothing to open")
ValueError: nothing to open

======================================================================
ERROR: Import the exported repository capsule.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/marten/devel/git/galaxy/test/tool_shed/functional/test_0490_export_import_repositories.py", line 94, in test_0020_import_repository_capsule
    strings_displayed_after_submit=[ 'Import not necessary', 'Exists' ] )
  File "/Users/marten/devel/git/galaxy/test/tool_shed/base/twilltestcase.py", line 829, in import_capsule
    tc.formfile( 'upload_capsule', 'file_data', filename )
  File "/Users/marten/devel/git/galaxy/eggs/twill-0.9-py2.7.egg/twill/commands.py", line 481, in formfile
    fp = open(filename, 'rb')
IOError: [Errno 2] No such file or directory: ''

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seems the tests were failing randomly, 👍

martenson added a commit that referenced this pull request Sep 10, 2015
@martenson
Merge pull request #708 from nsoranzo/flake8_fixes
b1b7109 
flake8 contrib/ and lib/tool_shed/ .
@martenson martenson merged commit b1b7109 into galaxyproject:dev Sep 10, 2015
@martenson martenson added the kind/refactoring cleanup or refactoring of existing code, no functional changes label Sep 10, 2015
@martenson martenson mentioned this pull request Sep 14, 2015
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@nsoranzo
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xref: #391

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@nsoranzo @jmchilton @martenson