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Author SHA1 Message Date
John Davis 9ecea08428 Add migration for index on workflow_request_step_states__workflow_invocation_id 2023-03-07 15:27:20 -05:00
John Davis e16ad29ae4 Add migration helpers for handling indexes 2023-03-07 15:27:16 -05:00
John Davis 1a2c1f4fb3 Add index to WorkflowRequestInputParameter.workflow_invocation_id 2023-03-07 15:27:16 -05:00
John Davis ee112c6d12 Add index to WorkflowRequestStepState.workflow_invocation_id 2023-03-07 15:27:16 -05:00
David LópezandMarius van den Beek d0039b9524 Reduce default polling delay back to 3 seconds 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2023-03-07 12:26:54 +01:00
davelopez 2ae34355d2 Increase polling rate to 10 seconds 
No need to poll that frequently for checking the download status.
 2023-03-07 00:01:25 +01:00
davelopez 397f9a1095 Fix task monitor error handling on export 2023-03-07 00:00:58 +01:00
Marius van den Beek 3e7609ca4e Merge pull request #15710 from nuwang/backport_k8s_dockerfile_changes 
Backport k8s docker changes to match latest playbook
 2023-03-06 17:42:33 +01:00
Nuwan Goonasekera 259cc02271 Changes to match latest playbook 2023-03-06 21:55:57 +05:30
Marius van den Beek 6f945c1ccb Merge pull request #15705 from mvdbeek/history_serialization_improvement 
[23.0] Use more efficient model properties when serializing histories
 2023-03-06 17:09:59 +01:00
Marius van den Beek ab2346ba8c Merge pull request #15706 from dannon/library-sanitization 
[23.0] Data Libraries Sanitization
 2023-03-06 17:03:35 +01:00
mvdbeek a614b61581 Avoid loadind history datasets in 2 more places 2023-03-06 15:30:08 +01:00
Dannon Baker ac0593dbe7 Sanitize displayed text in libraryfolder 2023-03-06 09:04:56 -05:00
mvdbeek 167d16cf4b Use more efficient model properties when serializing histories 2023-03-06 15:02:04 +01:00
Dannon Baker 44fed0dfa5 Sanitize displayed text in libraryeditfield 2023-03-06 08:22:24 -05:00
Dannon 4f52b74549 Merge pull request #15695 from mvdbeek/dont_process_dataset_param 
[23.0] Do not pass dataset keyword parameter into datatype.display_data
 2023-03-06 07:52:11 -05:00
David López c91e4c49f4 Merge pull request #15685 from davelopez/23.0_fix_bco_stock_tool_url_generation 
[23.0] Fix stock tool URL generation in BCOs
 2023-03-06 10:29:06 +01:00
Dannon Baker 89ed8b5852 Add dompurify 2023-03-05 12:27:16 -05:00
mvdbeek d97adf6359 Fix slugified dataset display 
Fixes https://github.com/galaxyproject/galaxy/issues/15676.
 2023-03-03 18:39:34 +01:00
mvdbeek 8992ec3875 Do not pass dataset keyword parameter into datatype.display_data 
Fixes https://github.com/galaxyproject/galaxy/issues/15678.

Krona generates an html dataset that includes a link with dataset as a query param.
 2023-03-03 18:14:26 +01:00
Marius van den Beek 0e4dff4e6e Merge pull request #15694 from mvdbeek/release_23.0 
[23.0] Merge 22.05 into 23.0
 2023-03-03 18:04:00 +01:00
Marius van den BeekandNicola Soranzo a9807b710e Remove leftover debugging, fix linting 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-03-03 17:36:05 +01:00
mvdbeek 026b906616 Merge branch 'release_22.05' into release_23.0 2023-03-03 16:40:49 +01:00
Marius van den Beek dd2468a665 Merge pull request #15682 from bernt-matthias/22.05-conda-package-fmt-change 
[22.05] backport #15446: Fix for new style conda packages
 2023-03-03 15:56:20 +01:00
mvdbeek ba4f6de82d Drop unused NamedTuple import 2023-03-03 13:14:35 +01:00
mvdbeek a3a85c5573 Use pinned conda-package-streaming as produced by poetry 2023-03-03 13:13:27 +01:00
mvdbeek b856b35d4f Add conda-package-streaming to pyproject.toml 2023-03-03 13:13:27 +01:00
Dannon cb4ca9721b Merge pull request #15659 from martenson/ep-poll 
[23.0] check for sessionless and userless API access
 2023-03-02 14:57:23 -05:00
Marius van den Beek ed77388619 Merge pull request #15687 from mvdbeek/trs_url_run_form_fix 
[23.0] Fix run_form=true if trs_url is used
 2023-03-02 16:17:20 +01:00
David LópezandNicola Soranzo 554a56b944 Make tool_version match in test 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-03-02 13:49:27 +01:00
davelopez 81b6e9c09a Fix url generation also for tool shed ids 
In the Tool Shed there are tools than can contain spaces in their IDs too.
 2023-03-02 13:31:11 +01:00
Matthias Bernt af4d9cd5f5 guessing around 2023-03-02 12:56:03 +01:00
mvdbeek 15b909de2e Fix run_form=true if trs_url is used 2023-03-02 12:27:44 +01:00
Marius van den Beek 5f9a982e4f Merge pull request #15675 from mvdbeek/sentry_fix_22_05 
[22.05] Fix sentry in WSGI/ASGI context
 2023-03-02 12:15:08 +01:00
Marius van den Beek 52693062ba Merge pull request #15674 from davelopez/23.0_restore_old_bco_export 
[23.0] Temporarily restore old BCO export mechanism (without Celery)
 2023-03-02 11:42:26 +01:00
davelopez f1440723e4 Fix typo 2023-03-02 11:19:21 +01:00
davelopez c0fd449ace Fix gxstocktools url generation for BCOs 2023-03-02 11:18:40 +01:00
davelopez 906d66fe75 Add unit test for stock tool with non-canonical ID 2023-03-02 11:13:53 +01:00
Matthias Bernt 0451ad485b package name with dashes 2023-03-02 09:27:55 +01:00
Matthias Bernt 684ae67bd7 add conda_package_streaming to tool_util setup.cfg 2023-03-01 22:13:15 +01:00
Matthias Bernt 1e05ac0422 move and fix tests 2023-03-01 22:13:00 +01:00
Matthias Bernt 708ea0e08e remove unused imports 2023-03-01 22:12:14 +01:00
Matthias Bernt 7e31d3bb5c attempt to fix 2023-03-01 22:11:59 +01:00
Matthias Bernt b51af0a174 test for extracting conda packages 
for .tar.bz and the new .conda format
 2023-03-01 22:07:53 +01:00
Martin Cech 04c3a7ab73 Merge pull request #15679 from mvdbeek/fix_anonymous_workflow_preview 
[23.0] Fix anonymous workflow preview
 2023-03-01 18:21:09 +01:00
mvdbeek 32abd51dcb Test anon can preview workflow 2023-03-01 17:13:48 +01:00
mvdbeek d768790879 Fix access pattern if no galaxy session found 2023-03-01 17:06:24 +01:00
mvdbeek 70259c3e1c Don't get or create new history for workflow preview 
I don't see why we would do this.
 2023-03-01 17:05:22 +01:00
mvdbeek 045a32e739 Fix sentry in WSGI/ASGI context 
We need to have initialised sentry before building the FastAPI app,
and if we postpone until after forking that won't work.
 2023-03-01 15:04:45 +01:00
davelopez d1a8ca32e1 Temporarily restore old BCO export without Celery 
This allows to export invocations as BCO using the previous non-task based approach instead of completely disable the invocation export options in the UI.
 2023-03-01 13:10:19 +01:00