John Chilton
ba9d51ccff
Progress toward a stronger typed manager layer.
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ModelManager still needs to use generics to really start providing a lot of benefit.
2021-10-27 13:34:17 -04:00
Marius van den Beek
ae156e3014
Merge pull request #12580 from dannon/localize-directive-improvement
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Update localization directive to trim whitepsace around text content.
2021-10-27 19:13:28 +02:00
Dannon Baker
e888ca21a9
Trim one more localized string
2021-10-27 10:19:32 -04:00
Dannon Baker
01ce29c2cb
Workflow editor tool upgrade fix -- don't rely on whitespace in localized blocks anymore (this is a good thing).
2021-10-27 10:19:32 -04:00
Dannon Baker
dc962cbb17
Update localization directive to trim whitepsace around text content.
2021-10-27 10:19:32 -04:00
Dannon
e7f321bcc4
Merge pull request #12686 from dannon/rxjs-upgrade
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RxJS major version upgrade, client unit testing enhancements.
2021-10-27 09:59:48 -04:00
Nicola Soranzo
2abb6608bc
Merge pull request #12791 from davelopez/fix_api_tests_urls
2021-10-27 14:39:47 +01:00
Dannon
685b146fda
Merge pull request #12674 from dannon/backbone-libraries-removal
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Libraries (legacy) backbone entrypoint and component removal
2021-10-27 08:49:02 -04:00
Dannon
458dd59f56
Merge pull request #12518 from guerler/vueify_form_recursion
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Vueify Form Recursion
2021-10-27 08:23:45 -04:00
Marius van den Beek
cb4997a2ca
Merge pull request #12788 from rhpvorderman/strictchannelpriority
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Force strict channel priority when building images with mulled
2021-10-27 14:04:29 +02:00
davelopez
5b3a734784
Avoid double '/' when generating fully qualified API URLs in API tests
2021-10-27 12:12:05 +02:00
Ruben Vorderman
b043cf86f3
Force strict channel priority when building images
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This is best practice as described here: https://github.com/bioconda/bioconda-recipes/issues/13774
The following command:
conda install -c conda-forge -c bioconda 'changeo=0.4.4' 'biopython=1.72' 'python=3.7.1' 'r-data.table=1.11.4' 'bash=4.4.18' 'xlrd=1.2.0' 'r-reshape2=1.4.3' 'r-seqinr=3.4_5' 'r-scales=0.5.0' 'tar=1.34' 'file=5.39' 'r-ggplot2=3.0.0' 'unzip=6.0' -p /usr/local --copy --yes --strict-channel-priority
Finishes in 10-15 seconds with strict channel priority. Never finishes (at least not within 3 hours) without it.
2021-10-27 10:56:00 +02:00
Marius van den Beek
75975455e7
Merge pull request #12787 from mvdbeek/limit_workflow_runs
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Add various include/exclude patterns for github workflows
2021-10-27 10:50:54 +02:00
mvdbeek
198c59177d
Add various include/exclude patterns for github workflows
2021-10-27 10:15:41 +02:00
mvdbeek
497f6a9835
Merge branch 'release_21.09' into dev
2021-10-26 16:30:19 +02:00
mvdbeek
4262610b71
Merge branch 'release_21.05' into release_21.09
2021-10-26 16:29:37 +02:00
Marius van den Beek
f47d2824ce
Merge pull request #12779 from dannon/fix-welcome-build
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[21.09] Fix new user welcome plugin build status storage/detection
2021-10-26 16:17:27 +02:00
Marius van den Beek
c7ceec917a
Merge pull request #12782 from dannon/fix-msa
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[21.05] Fix msa visualization
2021-10-26 16:12:31 +02:00
Dannon Baker
c8d6d39c5a
Manually hack the built static, too -- this needs followup in dev to be clean and remove artifacts
2021-10-26 08:42:08 -04:00
Dannon Baker
c220f6d55a
The surgical in-place fix to prebuilt msa.js to account for 'at' being in array now in ff/chrome
2021-10-26 08:42:08 -04:00
David López
ef580e88e9
Merge pull request #12780 from jmchilton/type_fixes_managers_2
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Type fixes for HDAs and LDDAs manager.
2021-10-26 11:49:00 +02:00
John Chilton
d8fc9b3ab4
Fixes for LDDA manager - clearly that didn't work at all.
2021-10-25 20:24:01 -04:00
John Chilton
00c30ca493
Strong typing around HDAs manager.
2021-10-25 20:24:01 -04:00
David López
5ed2bbc770
Merge pull request #12778 from jmchilton/type_fixes_managers_1
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More Python type fixes from deferred data branch.
2021-10-25 20:31:49 +02:00
John Chilton
a6c46f9bfc
Typing clarification for datasets manager.
2021-10-25 11:51:40 -04:00
John Chilton
edd15d1d5e
Typing fixes for galaxy.exceptions.
2021-10-25 11:51:40 -04:00
Dannon Baker
a53b90fa3a
Fix new user welcome plugin_build_hash.txt location handling -- we'll want to support writing explicitly to static or a more natural js package dist dir here
2021-10-25 11:22:53 -04:00
Oleg Zharkov
13c19ad891
Merge pull request #12774 from nsoranzo/pyupgrade_fixes
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New pyupgrade cleanups
2021-10-25 14:44:14 +02:00
Martin Cech
9c9bfec82d
Merge pull request #12734 from hexylena/2109-release-human
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21.09 Release notes for Users
2021-10-25 14:08:51 +02:00
Martin Cech
57a9dcd746
Merge pull request #12764 from guerler/fix_alert_padding
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[21.09] Use default alert info instead of custom small info style
2021-10-25 14:04:01 +02:00
Helena Rasche
653dd71170
Finish release notes
2021-10-25 12:56:33 +02:00
guerler
9409f1535f
Remove unsued markup and styles from form element
2021-10-24 13:42:56 -04:00
Nicola Soranzo
90a729e431
New pyupgrade fixes
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Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
2021-10-24 12:10:34 +01:00
Marius van den Beek
13e76d2901
Merge pull request #12773 from nsoranzo/add_test_workflow_new_autocreated_history
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Add test for invoking a workflow on a new autocreated history
2021-10-23 21:37:42 +02:00
Nicola Soranzo
8b326e523a
Add test for invoking a workflow on a new autocreated history
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This would fail without commit 397a3a0543
2021-10-23 12:36:04 +01:00
Nicola Soranzo
3cac4cc39e
Merge branch 'release_21.09' into dev
2021-10-23 12:34:40 +01:00
Björn Grüning
61a263fb5f
Merge pull request #12771 from mvdbeek/fix_inputs_to_history
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[21.09] Flush new history before adding items
2021-10-23 04:14:19 +02:00
Nicola Soranzo
258cf8eb3a
Fix invalid framework GH workflow
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Fix:
```
The workflow is not valid. .github/workflows/framework.yaml (Line: 8, Col: 1): 'env' is already defined
```
Also:
- consistently sort top-level `env` and `concurrency` (as in
https://docs.github.com/en/actions/learn-github-actions/workflow-syntax-for-github-actions )
- sort env variables alphabetically
2021-10-23 00:07:40 +01:00
guerler
972ab02163
Add more tests, move element id helper to utilities
2021-10-22 17:59:22 -04:00
mvdbeek
5cfa818207
Merge branch 'release_21.09' into dev
2021-10-22 22:21:17 +02:00
Marius van den Beek
8762475d57
Merge pull request #12772 from mvdbeek/double_scheduling_21_09_forward
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[21.09] merge 21.05 forward
2021-10-22 22:20:51 +02:00
mvdbeek
2e282b1d4c
Merge branch 'release_21.05' into double_scheduling_21_09_forward
2021-10-22 19:39:14 +02:00
Nate Coraor
947d7cf050
Merge pull request #12763 from mvdbeek/fix_job_double_scheduling
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[21.05] Fix double enqueuing of upload jobs
2021-10-22 13:28:40 -04:00
Sergey Golitsynskiy
c3fa79b039
Merge pull request #12765 from ic4f/dev_mapping_tests2
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Mapping tests: restructure, refactor, decouple session and engine, improve
2021-10-22 12:07:36 -04:00
mvdbeek
2a335c981b
Fix double enqueuing of upload jobs
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The canonical place to call enqueue is in
https://github.com/galaxyproject/galaxy/blob/a5bb3e92667b96ef802b378f17788b253a5c0bc6/lib/galaxy/tools/execute.py#L127 .
In the process of enqueue the db-skip-locked assignment method will set
the handler name to the default tag. If you do this more than once the
job might be picked up by compatible handlers.
Fixes https://github.com/galaxyproject/galaxy/issues/11335
2021-10-22 16:49:00 +02:00
mvdbeek
397a3a0543
Flush new history before adding items
2021-10-22 16:06:42 +02:00
Oleg Zharkov and Dannon
16993ab6a8
Remove legacy library code
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removed ununsed library routes and leaving only library-dataset-view.js behind
Co-authored-by: Dannon <dannon.baker@gmail.com >
2021-10-22 14:39:53 +02:00
Marius van den Beek
61810c833f
Merge pull request #12760 from davelopez/improve_directory_uri_parameter_validation
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[21.09] Improve error handling in DirectoryUriToolParameter validation
2021-10-22 10:41:42 +02:00
Sergey Golitsynskiy
f497654ef0
Drop unused fixtures
2021-10-22 00:45:32 -04:00
guerler
4066407536
Add basic validation tests
2021-10-21 23:52:19 -04:00
John Chilton