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cmd to export an existing invocations as an archive for storage or later import.#1534

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mvdbeek merged 6 commits intogalaxyproject:masterfrom
Smeds:export-invocation-as-ro-crate-command
Jun 19, 2025
Merged

cmd to export an existing invocations as an archive for storage or later import.#1534
mvdbeek merged 6 commits intogalaxyproject:masterfrom
Smeds:export-invocation-as-ro-crate-command

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@Smeds Smeds commented Jun 3, 2025

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@Smeds Smeds marked this pull request as draft June 3, 2025 18:36
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Smeds commented Jun 3, 2025

I need to see if it's possible to turn on 'asynchronous tasks' for the test. It will currently fail with the following error:

AssertionError: Planemo command [invocation_export --galaxy_url http://localhost:55043 --galaxy_user_key e4ca85cc22bac6a37c7e885640a3a0bc --output /tmp/tmp_0mov935/temp.rocrate.zip 7f117ef222b8a072] resulted in unexpected exit code [1], expected exit code [0]]. Command output [] Exception [Unexpected HTTP status code: 403: {"err_msg":"This operation requires asynchronous tasks to be enabled on the Galaxy server and they are not, please contact the server admin.","err_code":403004}], Traceback [['Traceback (most recent call last):\n', '  File "/home/pks5769/workspace/planemo/.venv/lib/python3.12/site-packages/click/testing.py", line 412, in invoke\n    return_value = cli.main(args=args or (), prog_name=prog_name, **extra)\n                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/.venv/lib/python3.12/site-packages/click/core.py", line 1082, in main\n    rv = self.invoke(ctx)\n         ^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/.venv/lib/python3.12/site-packages/click/core.py", line 1697, in invoke\n    return _process_result(sub_ctx.command.invoke(sub_ctx))\n                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/.venv/lib/python3.12/site-packages/click/core.py", line 1443, in invoke\n    return ctx.invoke(self.callback, **ctx.params)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/.venv/lib/python3.12/site-packages/click/core.py", line 788, in invoke\n    return __callback(*args, **kwargs)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/.venv/lib/python3.12/site-packages/click/decorators.py", line 92, in new_func\n    return ctx.invoke(f, obj, *args, **kwargs)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/.venv/lib/python3.12/site-packages/click/core.py", line 788, in invoke\n    return __callback(*args, **kwargs)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/planemo/cli.py", line 103, in handle_blended_options\n    return f(*args, **kwds)\n           ^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/planemo/planemo/commands/cmd_invocation_export.py", line 25, in cli\n    export_invocation_as_archive(\n', '  File "/home/pks5769/workspace/planemo/planemo/galaxy/api.py", line 131, in export_invocation_as_archive\n    response = inv_gi.invocations.get_invocation_archive(invocation_id=invocation_id, model_store_format=export_format)\n               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/bioblend/bioblend/galaxy/invocations/__init__.py", line 517, in get_invocation_archive\n    psd = self._post(url=url, payload=payload)\n          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/bioblend/bioblend/galaxy/client.py", line 197, in _post\n    return self.gi.make_post_request(url, payload=payload, files_attached=files_attached)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n', '  File "/home/pks5769/workspace/bioblend/bioblend/galaxyclient.py", line 202, in make_post_request\n    raise ConnectionError(\n', 'bioblend.ConnectionError: Unexpected HTTP status code: 403: {"err_msg":"This operation requires asynchronous tasks to be enabled on the Galaxy server and they are not, please contact the server admin.","err_code":403004}\n']]

@Smeds Smeds force-pushed the export-invocation-as-ro-crate-command branch from e96c57b to 809bda9 Compare June 3, 2025 18:39
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mvdbeek commented Jun 18, 2025

Is there a specific bioblend branch I need to install ?

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mvdbeek commented Jun 18, 2025

Test is passing fine with #1541 and bioblend from the master branch

@mvdbeek mvdbeek force-pushed the export-invocation-as-ro-crate-command branch from 570c69f to 6a7879c Compare June 19, 2025 08:00
@mvdbeek mvdbeek marked this pull request as ready for review June 19, 2025 08:58
@mvdbeek mvdbeek changed the title cmd use to export an existing invocations as an archive for storage or later import. cmd to export an existing invocations as an archive for storage or later import. Jun 19, 2025
@mvdbeek mvdbeek merged commit e278d2f into galaxyproject:master Jun 19, 2025
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