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Changes made while working on uWSGI mules that don't belong in the mules PR #4994

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merged 5 commits into from Nov 14, 2017

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natefoo commented Nov 13, 2017

In the course of working on #4475 I made some unrelated changes that are in that PR but don't belong there, so I've broken them out here:

  • Modify imports for functions moved to galaxy.util.path (their names are still exported from galaxy.util)
  • Log IOError/OSError errno string when encountered during tool loading
  • galaxy.util.listify documentation and accept a tuple as an argument
  • Create a library for functions common to scripts and convert manage_tool_dependencies.py to use it
@@ -84,4 +56,5 @@ def _build_dependency_manager_no_config(kwargs):
if __name__ == '__main__':
main = main_factory(description=DESCRIPTION, actions=ACTIONS)

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@jmchilton
If *item* is a list it is returned unchanged. If *item* is a tuple, it is converted to a list and returned. If
*item* evaluates to False, an empty list is returned.
:type item: str or list or tuple or types.NoneType

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@nsoranzo

nsoranzo Nov 13, 2017

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I think this function actually works on any object, since in the final else it returns [item]

:type item: str or list or tuple or types.NoneType
:param item: object to make a list from
:param bool do_strip: strip whitespace from around split items, if set to ``True``

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@nsoranzo

nsoranzo Nov 13, 2017

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I'd separate type and description, as done above with item. Also s/whitespace/whitespaces/

:type do_strip:  bool
:param do_strip: strip whitespaces from around split items, if set to ``True``
@natefoo

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natefoo commented Nov 14, 2017

Hooray for transient errors!

@nsoranzo nsoranzo merged commit fb78cb6 into galaxyproject:dev Nov 14, 2017

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