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30919 Commits
Author SHA1 Message Date
mvdbeek 44b9ddee23 Into schema 2022-04-23 12:09:18 +02:00
mvdbeek 4e98ee9d30 Ensure copied dbkey is a list 
I believe this had been the intention and it fixes
`test_nested_workflow_rerun_with_use_cached_job` and
`test_workflow_rerun_with_use_cached_job`.
 2022-04-23 12:05:54 +02:00
mvdbeek 9abbac0180 Switch most tests to use `__DATA_FETCH__ instead of upload1` 2022-04-23 12:05:54 +02:00
mvdbeek 4cc3f33f30 Skip discovered outputs 
This prevents overwriting discovered metadata with default values,
and is more efficient than doing this twice.
 2022-04-23 12:01:32 +02:00
mvdbeek 02ac5b3c9e Add FastAPI route for tools/fetch 2022-04-23 12:01:32 +02:00
mvdbeek 1d5a52ec05 Schema for fetch_data 2022-04-22 17:08:41 +02:00
Marius van den Beek cf46c5c1fa Merge pull request #13777 from guerler/fix_tour_tests 
Adjust tours and tour tests to new history
 2022-04-22 15:38:27 +02:00
Marius van den Beek 46eb2e6b83 Merge pull request #13602 from bernt-matthias/fix/configfilename 
Fix config file generation if name and filename are given
 2022-04-22 12:31:12 +02:00
Marius van den Beek ed5dd149c4 Merge pull request #13755 from bernt-matthias/fix_mulled_conda 
Respect conda channels in mulled docker container building
 2022-04-22 10:43:31 +02:00
David López e788c3073c Merge pull request #13779 from jmchilton/sharing_error_handling 
Fixes for sharing component error handling.
 2022-04-22 10:39:41 +02:00
Nicola Soranzo 2f0f4c7e08 Replace 2 uses of deprecated `imp` module 
Also:
- Move doctests for `in_directory()` function to unit tests, add test
  for `local_path_module` parameter to exercise the posixpath/ntpath
  import code.
 2022-04-21 19:53:35 +01:00
Matthias Bernt 22c376f8aa hard link 2022-04-21 16:42:35 +02:00
John Chilton 6e4f871cc0 Converge sharing error handling across mako and vue. 2022-04-21 10:12:00 -04:00
John Chilton 59038bc4bf Add navigates_galaxy.py convention for jumping to URLs not via navigating the landing to them. 2022-04-21 10:02:11 -04:00
Nicola Soranzo 6b3c7d38b1 Merge branch 'release_22.01' into dev 2022-04-21 11:43:07 +01:00
Matthias Bernt ad70b9bc4a fix config file generation 
always create the config file in `job_directory/configs/` and
if `filename` is given create a symlink to the actual config file

fixes https://github.com/galaxyproject/galaxy/issues/13586
 2022-04-21 11:15:07 +02:00
guerler 1c643a63ff Adjust tours and tour tests to new history, remove final occurance of use_legacy_history 2022-04-21 04:20:33 -04:00
Matthias Bernt 1794748496 remove superficial slash in bind path 2022-04-20 18:15:40 +02:00
Matthias Bernt 6f7a609665 explicitly set conda channels for CondaInDockerContext 2022-04-20 18:15:40 +02:00
Matthias Bernt 4960e0567a make mulled docker container building respect conda channels 
DEFAULT_MULLED_CONDA_CHANNELS is now respected when building
mulled docker containers.

In addition the change to CondaInDockerContext allows to use
local packages.

Ideally planemo users would be able to set the channels via
a command line option, but I could not find a way.
 2022-04-20 18:15:40 +02:00
John Chilton 4dc6820e30 Merge pull request #13762 from jmchilton/selenium_fixes_98 
More robust is_beta_history() testing check.
 2022-04-20 10:14:46 -04:00
Sergey Golitsynskiy e50078306e Merge pull request #13767 from jmchilton/jobs_index_fastapi 
[WIP] Migrate jobs index to FastAPI controller.
 2022-04-20 08:33:13 -04:00
Marius van den Beek f5c511beed Merge pull request #13768 from kxk302/main_irods_fixes 
[22.01] Fix race condition in object store dir creation
 2022-04-20 10:20:35 +02:00
Nicola Soranzo 6656633a54 Merge pull request #13759 from jmchilton/cli_test_output_improvement 
Improve error handling for CLI job runner.
 2022-04-20 07:29:04 +01:00
Kaivan Kamali 5dcb129490 Added exist_ok flag so creating an directory that already exists does not error out 2022-04-19 16:39:01 -04:00
John Chilton fc3595370e Migrate jobs index to FastAPI controller. 2022-04-19 16:05:02 -04:00
David LópezandNicola Soranzo 5e8eea6759 Add type hint suggestion 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-04-19 15:44:44 -04:00
davelopez 99025c770b Fix mypy error 2022-04-19 15:44:38 -04:00
John ChiltonandNicola Soranzo 9b72b20495 Update lib/galaxy/jobs/runners/cli.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-04-19 12:36:33 -04:00
John Chilton 3aeeb47e8d More robust is_beta_history() check. 
Given error on https://github.com/galaxyproject/galaxy/runs/6068791674?check_suite_focus=true, I assume what happened is the beta history panel wasn't on the page so the test tried to act on the old history panel.
 2022-04-19 12:13:55 -04:00
Dannon 83b3ff32e4 Merge pull request #13735 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2022-04-19 08:53:47 -07:00
Kaivan Kamali e83a691293 Update python-irodsclient 2022-04-19 11:43:34 -04:00
Kaivan Kamali d3afc0b6a1 Merge branch 'release_22.01' of https://github.com/galaxyproject/galaxy into release_22.01 2022-04-19 11:40:40 -04:00
Kaivan Kamali b621f83d0e Update python-irodsclient 2022-04-19 11:38:44 -04:00
John Chilton f25ca4600e Improve error handling for CLI job runner. 
Saw this in the logs for a failed test. I'm sure the test would still have failed but at least we'd be handling things in the error path we're meant to.

ERROR    galaxy.jobs.runners:__init__.py:149 (1) Unhandled exception calling queue_job
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/__init__.py", line 146, in run_next
    method(arg)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/cli.py", line 107, in queue_job
    external_job_id = stdout.strip().split()[-1]
IndexError: list index out of range
DEBUG    galaxy.jobs.runners.cli:cli.py:249 (1/None) Terminated at user's request

https://github.com/galaxyproject/galaxy/runs/6068791433?check_suite_focus=true
 2022-04-19 11:36:58 -04:00
David López 3f8c9356ed Merge pull request #13754 from davelopez/fix_import_workflow 
Fix import workflow file and UX enhancements
 2022-04-19 17:31:35 +02:00
Sergey Golitsynskiy bcaeef01fe Merge pull request #13730 from ic4f/dev_unquote_url 
Unquote url before using it
 2022-04-19 11:25:44 -04:00
davelopez ee6034cf15 Fix WorkflowCreateOptions validation 
When importing a workflow by file upload directly `archive_source` has to be present in the payload, but its value can be None since we're not importing from a URI
 2022-04-19 14:07:22 +02:00
Nicola Soranzo faeba22f30 Stricter maximum Python version to appease numpy and scipy 
xref.: https://github.com/scipy/scipy/pull/12862
 2022-04-19 12:36:43 +01:00
guerler b4d11a042a Remove use_legacy_history helper from sharing tests, thx @jmchilton 2022-04-18 17:22:22 -04:00
guerler 4e04393b70 Adjust tool tour generator plugin, remove legacy history dependence 2022-04-18 17:09:05 -04:00
guerler a48e3977f5 Remove final use_legacy_history helper from selenium upload tests 2022-04-18 17:09:05 -04:00
John Chilton d5283ea2bd Converge testing and classes for history options across new and old history panel. 
Add TODO for different behavior between menus.
 2022-04-18 12:21:03 -04:00
galaxybot e2e1c4a6d2 Update Python dependencies 2022-04-16 03:21:15 +00:00
guerler 35d6b927a6 Fix hidden dataset and published histories testing, use more stringent rule for history watcher 2022-04-15 23:07:11 -04:00
guerler b9cc163a48 Remove use_legacy_history from published histories test 2022-04-15 17:32:54 -04:00
guerler 96a5d32314 Apply rerun test to new history 2022-04-15 17:32:54 -04:00
guerler 8108d7e749 remove use_legacy_history from library and anon tests 2022-04-15 17:32:54 -04:00
guerler 8477105699 Remove two use_legacy calls from custom build selenium tests 2022-04-15 17:32:54 -04:00
guerler ca4981e781 Avoid update local props while user is editing corresponding fields 2022-04-15 17:32:54 -04:00