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GEMINI Data Manager is not Python 3 compatible #2408

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natefoo opened this issue May 9, 2019 · 1 comment
Open

GEMINI Data Manager is not Python 3 compatible #2408

natefoo opened this issue May 9, 2019 · 1 comment
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@natefoo
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natefoo commented May 9, 2019

After successfully downloading, it fails with:

/cvmfs/test.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/f57426daa04d/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download.py:50: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  config = yaml.load(fi)
Traceback (most recent call last):
  File "/cvmfs/test.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/f57426daa04d/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download.py", line 91, in <module>
    main()
  File "/cvmfs/test.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/f57426daa04d/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download.py", line 87, in main
    out.write( json.dumps( data_manager_dict ) )
TypeError: a bytes-like object is required, not 'str'

Assuming many DMs are copied from others, there may be other DMs with the same problem.

@nsoranzo
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nsoranzo commented May 9, 2019

As mentioned in the original ticket, this will be fixed by #2032 .

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