opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 02:04:04 +08:00
Code Issues Packages Projects Releases Wiki Activity
48,735 Commits 62 Branches 243 Tags
d3edae0012319dffb4ebac37a3ea165a8e05d91c
Commit Graph
48735 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Sergey Golitsynskiy d3edae0012 Let get_config() handle env override 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
(cherry picked from commit 574fa4cb1f)
 2020-10-08 15:23:19 -04:00
Sergey Golitsynskiy 84c3967ce8 Use passenv to pass env var to tox 
(cherry picked from commit 65ebbce458)
 2020-10-08 15:22:38 -04:00
Sergey Golitsynskiy b98677cd9a Skip client build 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
(cherry picked from commit 7040c0056b)
 2020-10-08 15:21:47 -04:00
Sergey Golitsynskiy de98e1f64e Call common_startup.sh; rebase 
(cherry picked from commit 2cc090847e)
 2020-10-08 15:21:03 -04:00
Sergey Golitsynskiy af0f9bb6ca Add github workflow; env var to override db uri 
(cherry picked from commit f27b4e50f6)
 2020-10-08 15:20:52 -04:00
Sergey Golitsynskiy 08ad0f47c1 Add script to tox.ini 
(cherry picked from commit f11baa411c)
 2020-10-08 15:20:46 -04:00
Sergey Golitsynskiy 7d75f313cf Add environment variable that forces migrations on empty database 
(cherry picked from commit bd8bfdfec6)
 2020-10-08 15:20:38 -04:00
Sergey Golitsynskiy eb89c1f410 Rename missing_index > index_tuple 
(cherry picked from commit 20c7cdb2cb)
 2020-10-08 15:20:31 -04:00
Sergey Golitsynskiy 6e6e3aa757 Update scripts/check_model.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
(cherry picked from commit b9093e33da)
 2020-10-08 15:20:23 -04:00
Sergey Golitsynskiy 9b421aa8c8 Update scripts/check_model.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
(cherry picked from commit 7719f53bca)
 2020-10-08 15:20:09 -04:00
Sergey Golitsynskiy 891bbad041 Add script + wrapper 
(cherry picked from commit 2dbfdce295)
 2020-10-08 15:19:49 -04:00
Dannon Baker 8c8858e3ae Merge remote-tracking branch 'upstream/release_20.05' into release_20.09 2020-10-08 11:16:57 -04:00
Dannon Baker 85e0edbd6b Merge remote-tracking branch 'upstream/release_20.01' into release_20.05 2020-10-08 11:16:27 -04:00
Marius van den Beek 11ea2cb818 Merge pull request #10307 from nuwang/fix_k8s_job_id_clash 
[20.01] Ensure that k8s job ids are unique
 2020-10-08 16:28:07 +02:00
Nate Coraor deae07ec90 Merge pull request #10375 from mvdbeek/data_source_fix_2 
[20.09] Fixes data_source tools
 2020-10-07 12:05:44 -04:00
mvdbeek a1e95411be Fixes data_source tools 
tool_ids may be a list, so need to strip `'/'` in `get_tool_components`
instead.

Broken in https://github.com/galaxyproject/galaxy/pull/10332
 2020-10-07 15:43:56 +02:00
Marius van den Beek 05da1e7739 Merge pull request #10367 from natefoo/defer-metadata-strategy-resolution 
[20.09] Defer metadata strategy resolution in job wrapper
 2020-10-07 09:54:46 +02:00
Nate Coraor 1f4dafbc77 Defer metadata strategy resolution in job wrapper. 2020-10-06 14:02:27 -04:00
Marius van den Beek c6a39d384d Merge pull request #10339 from cat-bro/fix_admin_installed_tool_list_newer_version_tag 
[20.09] Fix 'Newer Version Available' tag in admin tool management section
 2020-10-06 19:31:53 +02:00
Dannon ba6ea1b122 Merge pull request #10362 from hexylena/fix-chrome-gtn-webhook 
[20.09] Bugfix: chrome forgets scroll offset upon show/hide cycle of GTN in Galaxy webhook
 2020-10-06 10:34:00 -04:00
Dannon Baker fe4f81ef66 Standard quotes 2020-10-06 10:33:03 -04:00
Nuwan GoonasekeraandMarius van den Beek 488baee52a Use generated uuid instead of galaxy job id for k8s job name 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2020-10-06 19:02:54 +05:30
Nuwan Goonasekera 3b427177fc Ensure that k8s job ids are unique 2020-10-06 19:02:43 +05:30
mvdbeek 60a83c446d Also order repository revisions on the backend 2020-10-06 19:46:13 +11:00
cat-bro f7697a06cd sort installed tools by ctx_rev prior to selecting the first from each name/owner 
sort installed tools by ctx_rev prior to selecting the first from each name/owner

add some ;;;;;

prettier --write

another prettier file
 2020-10-06 19:46:13 +11:00
Helena Rasche a681ebfa3f Fix chrome-only scrolling bug with GTN webhook 
Content is reflown upon display changes, meaning that in chrome the iframe fails to retain it's original scroll offset. This fixes it by using visibility in place of display, thus preventing a content reflow.
 2020-10-06 10:45:35 +02:00
John Chilton d99b7eddb0 Merge pull request #10360 from mvdbeek/skip_workflow_invocation_step_update_subquery 
[20.09] Don't use subquery to update workflow invocation step update time
 2020-10-05 13:04:07 -04:00
Marius van den BeekandDannon 1c76fbd18d Drop parens 
Thanks Dannon!

Co-authored-by: Dannon <dannon.baker@gmail.com>
 2020-10-05 17:18:12 +02:00
mvdbeek ecf34f3b37 Don't use subquery to update workflow invocation step update time 
Thanks Nate, I don't think the subqeury was needed.
 2020-10-05 15:55:49 +02:00
mvdbeek 048e3b7c4f Merge branch 'release_20.05' into release_20.09 2020-10-02 17:41:29 +02:00
Marius van den Beek dcb329be00 Merge pull request #10284 from OlegZharkov/quickfix_20.09 
[20.09] fix folder path
 2020-10-02 17:04:21 +02:00
John Chilton 076e640206 Merge pull request #10321 from nsoranzo/release_20.05_fix_use_shared_home_with_docker 
[20.05] Respect ``use_shared_home="false"`` when running tools in container
 2020-10-02 10:57:38 -04:00
Marius van den Beek 9a15b1a6b5 Merge pull request #10344 from mvdbeek/add_missing_index_migrations 
[20.09] Add missing index migrations
 2020-10-02 15:39:35 +02:00
mvdbeek 79a018f861 Merge branch 'release_20.05' into release_20.09 2020-10-02 15:37:45 +02:00
mvdbeek 71e01da20f Merge branch 'release_20.01' into release_20.05 2020-10-02 15:32:35 +02:00
Marius van den Beek 311cbe430a Merge pull request #10248 from dannon/refactor-logout 
[20.09] Logout fix and refactoring
 2020-10-02 15:31:07 +02:00
Dannon Baker 70060df180 Expect a transition here in selenium test when logout_all happens 2020-10-02 08:42:34 -04:00
Marius van den Beek 6f495fceb3 Merge pull request #10335 from simonbray/staging-with-id-20.09 
[20.09] Allow 'planemo run' to stage in existing datasets without reuploading
 2020-10-02 12:29:47 +02:00
Marius van den Beek 535e4c52a5 Merge pull request #10308 from nuwang/fix_k8s_job_cleanup_loop 
[20.01] Prevent endless cleanup loops when duplicate job or k8s job not found
 2020-10-02 12:28:31 +02:00
Marius van den Beek 1a8e271e01 Merge pull request #10342 from dannon/fix-toolbox-wrap-20.05 
[20.05] Use block elements for labels to handle wrapping indentation
 2020-10-02 12:25:35 +02:00
mvdbeek 3af877573a Cleanup add_index/drop_index 2020-10-02 11:41:37 +02:00
Dannon 1af5d5d45b Merge pull request #10341 from blankenberg/itsvalid20.09 
[20.09] enable validation of ITs
 2020-10-01 15:06:55 -04:00
Nuwan Goonasekera e0d221a97b Also check for expected output in k8s delete test 2020-10-02 00:11:50 +05:30
mvdbeek d97606186c Add missing indexes 2020-10-01 20:21:08 +02:00
mvdbeek 04186715e9 Drop unused models 2020-10-01 20:21:08 +02:00
Nuwan Goonasekera ada9ee648d Minor refactoring of k8s tests 2020-10-01 23:46:18 +05:30
Nuwan Goonasekera 5d1b54cf6c Added test to check that jobs fail when deleted directly via k8s api 2020-10-01 23:46:18 +05:30
Nuwan Goonasekera 9d311d4557 Prevent endless cleanup loops when duplicate k8s job or k8s job not found 2020-10-01 23:46:18 +05:30
Dannon Baker 5c00766d86 Use block elements for labels to handle wrapping indentation 2020-10-01 14:00:35 -04:00
John Chilton 341b80b63b Merge pull request #10337 from dannon/pytest_pin 
[20.01] Pin pytest < 6.1
 2020-10-01 09:44:29 -04:00