- 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)
setup-data-librariescommand is run ephemeris fails with the error message.folder_idfrom 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 themouse genomein the data libraries of my test Galaxy instance, just like it was described in the GTN training material)