[20.01] Backport 9175: Update galaxy.tool_util.cwl for latest changes in CWL branch. #9210
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which makes some tools fail by printing to stderr: ``` galaxy.tool_util.output_checker DEBUG 2020-01-07 02:59:07,720 job failed, detected state generic_error, standard error is - [/galaxy_venv/local/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as the Python 2.7 version of cwltool won't be maintained after that date. """, category=CWLToolDeprecationWarning) ] ```
xref. galaxyproject#8558 For other YAML files, `ordered_load()` will raise an exception when it finds a mapping with duplicate keys.
mvdbeek
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| """ Provide a proxy object to cwltool data structures to just | ||
| grab relevant data. | ||
| """ | ||
| ensure_cwltool_available() | ||
| tool = to_cwl_tool_object( | ||
| # if uuid is None: | ||
| # raise Exception("tool_proxy must be called with non-None uuid") |
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Is that something that should be removed or uncommented later?
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This is a last minute change to get the usage from Planemo to pass - I'm happy to remove it I think. Probably should somehow make this required when loading tools from a toolbox and not requires from library behavior but I can just create an issue for that.
| ensure_cwltool_available() | ||
| tool = to_cwl_tool_object(persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation) | ||
| if PERSISTED_REPRESENTATION == "cwl_tool_object": |
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It is an semi-open question in the CWL branch what the persisted representation should be. I think the current setting is right and once the plumbing is all merged and these things work - it will probably be this way - but I'm hesitant to commit to a path until the whole thing is ready to go and working.
Co-Authored-By: Nicola Soranzo <[email protected]>
Co-Authored-By: Nicola Soranzo <[email protected]>
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Thanks for all the work on this. It may seem like a big mess - but it is a huge help to the CWL effort to have this synchronized every so often. I'll try to publish new 20.1 dev packages now |
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galaxy-tool-util-20.1.0.dev0 and galaxy-util-20.1.0.dev0 have been published. I'm not sure I see a reason to publish a galaxy-containers-20.1.0.dev0 since it is unchanged. I've created a minimum dependency of galaxy-util-20.1.0.dev0 on the package galaxy-tool-util-20.1.0.dev0. |
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