opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
61,895 Commits 69 Branches 243 Tags
86e42b54833dbba0c014b888a61ba8d36d5acb7b
Commit Graph
61895 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Nate Coraor 86e42b5483 Update Gravity to 0.13.4 and document setting env vars on dynamic 
handlers.
 2022-09-01 10:40:54 -04:00
Dannon 732ac13f48 Merge pull request #14539 from mvdbeek/post_job_action_state_bug_fix 
[22.05] Fix post job action getting lost when node is made active
 2022-08-30 22:30:08 -04:00
mvdbeek d1b4f05345 Merge branch 'release_22.01' into release_22.05 2022-08-30 20:32:39 +02:00
Marius van den Beek afebb89c2f Merge pull request #14528 from mvdbeek/tool_util_packaging_fixes 
[22.01] Fix tool-util packaging
 2022-08-30 20:22:30 +02:00
Marius van den Beek c39323f20b Merge pull request #14531 from dannon/copy-fix 
[22.05]Fix absolute path generation util
 2022-08-30 17:44:51 +02:00
Marius van den Beek 609c90fa25 Update packages/tool_util/HISTORY.rst 2022-08-30 17:25:10 +02:00
mvdbeek f67ca01a99 Fix post job action getting lost when node is made active 
And many more reactivity fixes.

The core of the issue was that the FormElement would emit a onUpdate
event, which triggers a request to `api/workflows/build_module`.
The FormSection that controls the post job action data is not ready at
this point, so when the data comes back in we have to break the
connection because the post job action that sets the datatype is
missing.

We really don't need to call `build_module` though when change post job
actions, they don't require the backend at all, we just need to bubble
them up to the Index component, which can set the postJobAction on the
active node (let's ignore that we should manipulate the data, not the vue instance
...).

In order for that to be properly reactive I had to remove the majority
of the getNode hacks.

We do still rely on this in the Terminals and Connectors, so those can
get out of sync still, but it fixes an annoying issue where connections
are dropped without notice.
 2022-08-30 17:14:34 +02:00
Nicola Soranzo 6519604620 Add some type annotations 2022-08-30 14:34:54 +01:00
Nicola Soranzo 4faa486c49 Merge pull request #14526 from bernt-matthias/topic/fix-test-linters 
[22.05] Fix typos in test linter
 2022-08-30 12:16:10 +01:00
Nicola Soranzo 61b6eb1ee9 Fix more `discovered_datasets` typos 2022-08-30 09:57:26 +01:00
Martin Cech 5045087f59 Merge pull request #14532 from mvdbeek/datatype_test_fail_hint 
[22.05] Report that (text) datatype test files need to have a final newline
 2022-08-30 04:04:01 +02:00
mvdbeek 3b583a12c7 Give a hint about newlines when datatype test fails 2022-08-29 17:53:00 +02:00
mvdbeek 2f15059543 Skip the quay.io lookup if we have a valid cache entry 
Good thing we had tests that made sure the cache was getting used ...
 2022-08-29 16:54:23 +02:00
Dannon Baker 7e06bb7672 Fix absolute path generation util -- avoid deduplicating '/' in protocol 2022-08-29 10:52:15 -04:00
mvdbeek 60cda23970 Mock quay.io API calls, pass install=False to not pull docker images 2022-08-29 16:38:31 +02:00
mvdbeek c4f576ccf3 Fix cache lookup condition 2022-08-29 16:38:31 +02:00
mvdbeek c4a9050af9 Fix _namespace_has_repo if cache namespace cache key not present 2022-08-29 14:08:49 +02:00
mvdbeek c07fd27806 Touch up tool util packaging fixes 2022-08-29 13:12:01 +02:00
Matthias Bernt 8cc06e9569 fix typo in xsd 2022-08-29 13:11:32 +02:00
Matthias Bernt a8a80cf431 fix typo in test linter 2022-08-29 11:36:59 +02:00
Björn Grüning 6b2678633f Merge pull request #14518 from mvdbeek/always_strip_columns 
[22.05] Always call strip() on data_column column values
 2022-08-28 22:38:54 +02:00
mvdbeek 18ed5116e5 Always call strip() on data_column column values 
Not just when they start with `c`. Should fix running workflows
that were created by manually writing columns in the text area field
and then hitting enter.
 2022-08-27 09:41:22 +02:00
Björn Grüning c096e599ff Merge pull request #14510 from mvdbeek/fix_metadata_action_default_setting_in_conditional 
[22.05] Fix setting metadata elements in conditional tool action
 2022-08-25 20:14:21 +02:00
mvdbeek 94c75a083c Fix setting metadata elements in conditional tool action 
Fixes https://github.com/galaxyproject/galaxy/issues/14509
 2022-08-25 14:27:44 +02:00
John Chilton 83745c3140 Merge pull request #14504 from mvdbeek/patrick/15-castep-datatypes 
[22.05] Add CASTEP datatypes
 2022-08-24 15:16:42 -04:00
Patrick Austin c6989fd149 Update CONTRIBUTORS.md 2022-08-24 17:34:02 +02:00
Patrick Austin 7f794e8f12 Add CASTEP formats to config, sniff typehint for mypy #15 2022-08-24 17:34:02 +02:00
Dannon e1561ad665 Merge pull request #14494 from mvdbeek/fix_refactor_action 
[22.05] Fix refactor action dropping outputs on subworkflow connection
 2022-08-24 07:07:06 -04:00
Dannon 1bd25b1f26 Merge pull request #14498 from mvdbeek/release_script_fixes 
[22.05] Release script fixes
 2022-08-23 17:04:26 -04:00
Marius van den Beek 7a9e83c4ed Merge pull request #14496 from bernt-matthias/topic/lint_level 
[22.01] fix lint context fail function
 2022-08-23 19:06:47 +02:00
mvdbeek 2468629452 Update release.sh script for new packaging layout 2022-08-23 16:04:24 +02:00
Matthias Bernt 0b3f8af25f fix lint context fail function 
error introduced here https://github.com/galaxyproject/galaxy/pull/13186

found this while working on https://github.com/galaxyproject/planemo/pull/1264
 2022-08-23 15:46:16 +02:00
mvdbeek 8a8acc625f Fix refactor action dropping outputs on subworkflow connection 
I thought it would be cleaner to make a distinction between the output
name and the output label when reasoning about a subworkflow step in
the context of a parent workflow
(https://github.com/galaxyproject/galaxy/pull/14473/commits/b0727be9e0b096a2dacacb767a1f4ac0fc3e6540#diff-a50bcc5c08ade11249449c4100ea8c286727df601b52a5b9588eb2a385d97da7R543),
in case we'd later want to do something with the label.

I don't think I thought about this correctly though,
and it breaks connections between steps that were made by referencing
the subworkflow's output name.

This wasn't necessary for the main goal of
https://github.com/galaxyproject/galaxy/pull/14473, so I'm partially
reverting that here.

Fixes https://github.com/galaxyproject/planemo/pull/1262#issuecomment-1223874571
 2022-08-23 14:12:29 +02:00
mvdbeek 36f049410b Update version to 22.05.1 v22.05 2022-08-22 23:14:31 +02:00
mvdbeek 88a986c578 Update version to 22.05.1.dev0 v22.05.1.dev0 2022-08-22 23:14:27 +02:00
mvdbeek b5b63da659 Merge branch 'release_22.01' into release_22.05 2022-08-22 21:59:39 +02:00
mvdbeek 0a69d3d882 Update version to 22.1.2.dev0 2022-08-22 21:57:17 +02:00
mvdbeek dc56fc4e61 Update version to 22.01.1 2022-08-22 21:47:47 +02:00
Marius van den Beek 4258b4e075 Merge pull request #14492 from mvdbeek/missing_image 
[22.05] Add missing image to user facing release notes
 2022-08-22 21:06:54 +02:00
mvdbeek a8ff8c62b1 Add missing image 2022-08-22 21:05:59 +02:00
Marius van den Beek c5a2d38c26 Merge pull request #14211 from mvdbeek/22.05_release_notes 
[22.05] 22.05 release notes
 2022-08-22 18:42:24 +02:00
mvdbeek aa577230f8 Drop placeholders 2022-08-22 17:47:37 +02:00
mvdbeek 3d24ef2d91 Add last PR 2022-08-22 17:37:48 +02:00
Marius van den Beek b5ae0ac5d8 Apply Magda's typo and spelling fixes 2022-08-22 17:02:39 +02:00
Marius van den BeekandJohn Davis 0d40797e03 Add Alembic to admin announcement 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2022-08-22 16:34:03 +02:00
Marius van den Beek 0ac10db716 Merge pull request #14488 from nsoranzo/release_22.05_fix_docs 
[22.05] Doc fixes
 2022-08-21 14:52:48 +02:00
Nicola Soranzo 4fcbe80268 Doc fixes 2022-08-19 18:33:20 +01:00
Nicola Soranzo 95326249cd Update application documentation 
with:

```
make -C doc/ updaterst
```
 2022-08-19 17:37:27 +01:00
mvdbeek 2f34e4070c Drop overly verbose changes 2022-08-19 17:11:57 +02:00
Nicola Soranzo b5a75cac27 Merge branch 'release_22.01' into release_22.05 2022-08-19 15:28:58 +01:00