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Remove folder id from get_folders function call in setup-data-libraries#196

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mvdbeek merged 1 commit intogalaxyproject:masterfrom
sanjaysrikakulam:setup-data-libraries
Apr 18, 2023
Merged

Remove folder id from get_folders function call in setup-data-libraries#196
mvdbeek merged 1 commit intogalaxyproject:masterfrom
sanjaysrikakulam:setup-data-libraries

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@sanjaysrikakulam
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- Using the deprecated ``folder_id`` parameter of the
  ``LibraryClient.get_folders()`` method now raises a ``ValueError``
  exception."
  • Therefore when the setup-data-libraries command is run ephemeris fails with the error message.
+ setup-data-libraries -g https://galaxy-example.org -a key --training -i /libraries/example-library.yaml --legacy
Library name: Mouse sequencing project
Traceback (most recent call last):
  File "/usr/local/bin/setup-data-libraries", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/dist-packages/ephemeris/setup_data_libraries.py", line 214, in main
    setup_data_libraries(gi, args.infile, training=args.training, legacy=args.legacy)
  File "/usr/local/lib/python3.10/dist-packages/ephemeris/setup_data_libraries.py", line 158, in setup_data_libraries
    jobs = list(create_func(gi, library_def))
  File "/usr/local/lib/python3.10/dist-packages/ephemeris/setup_data_libraries.py", line 84, in create_legacy
    populate_items(folder_id, desc)
  File "/usr/local/lib/python3.10/dist-packages/ephemeris/setup_data_libraries.py", line 62, in populate_items
    populate_items(folder_id, item)
  File "/usr/local/lib/python3.10/dist-packages/ephemeris/setup_data_libraries.py", line 51, in populate_items
    folder = gi.libraries.get_folders(lib_id, folder_id)
  File "/usr/local/lib/python3.10/dist-packages/bioblend/galaxy/libraries/__init__.py", line 295, in get_folders
    raise ValueError(
ValueError: The folder_id parameter has been removed, use the show_folder() method to view details of a folder for which you know the ID.
  • Removing folder_id from the function call would fix the issue (I hope it's correct, when I manually changed it in my environment the command worked fine and I was able to see the mouse genome in the data libraries of my test Galaxy instance, just like it was described in the GTN training material)

- BioBlend Release 1.1.0 made the following change
"- Using the deprecated ``folder_id`` parameter of the
  ``LibraryClient.get_folders()`` method now raises a ``ValueError``
  exception."
- Therefore when the `setup-data-libraries` command is run ephemeris fails
with the deprecated error message.
- Removing `folder_id` from the function call would fix the issue
@mvdbeek mvdbeek merged commit 62b6fa6 into galaxyproject:master Apr 18, 2023
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3 participants