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Author SHA1 Message Date
Sergey Golitsynskiy 8e3c6f65e0 Add troubleshooting section; misc. formating fixes. 2022-05-31 10:30:30 -04:00
Sergey Golitsynskiy 8d1456ef78 Simplify upgrade message 2022-05-31 10:30:30 -04:00
Sergey Golitsynskiy 3de4599f54 Update migrations readme 2022-05-31 10:30:30 -04:00
Sergey Golitsynskiy 7f09898636 Update inline documentation in scripts 2022-05-31 10:30:30 -04:00
Marius van den Beek fd04d1050f Merge pull request #13986 from davelopez/fix_job_cancellation_on_delete_dataset 
Fix job cancellation on delete dataset
 2022-05-30 21:38:09 +02:00
davelopez 3c851fa885 Add explicit parameter to stop job on deleted dataset 
When deleting a dataset through the UI `stop_job` will be true, effectively cancelling the creating job if all its outputs are deleted.
By default the job will not be cancelled.
 2022-05-30 14:48:53 +02:00
davelopez 61615fb8d8 Fix job cancel on deleted output datasets 2022-05-30 11:57:53 +02:00
davelopez 3a784caa05 Add API test for cancel job on deleted outputs 2022-05-30 01:44:24 +02:00
Nicola Soranzo b3b693ea07 Merge pull request #13981 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2022-05-28 09:46:36 +01:00
galaxybot 8874052034 Update Python dependencies 2022-05-28 03:30:11 +00:00
Marius van den Beek f7f9817a77 Merge pull request #13971 from guerler/add_any 
Use colon symbol instead of equal sign in history filters
 2022-05-27 20:14:24 +02:00
Dannon 611c10c231 Merge pull request #13972 from galaxyproject/dependabot/pip/lib/galaxy/dependencies/tensorflow-2.7.2 
Bump tensorflow from 2.6.4 to 2.7.2 in /lib/galaxy/dependencies
 2022-05-27 10:53:11 -07:00
Dannon 5ce81fb586 Merge pull request #13962 from guerler/fix_padding 
Fix padding in history content items
 2022-05-27 08:14:04 -07:00
Marius van den Beek b80c2531d2 Merge pull request #13974 from jdavcs/dev_13177_followup 
Follow-up edits based on #13177 code review
 2022-05-27 16:44:41 +02:00
Sergey Golitsynskiy 258437fdab Follow-up edits based on #13177 code review 2022-05-27 10:41:21 -04:00
Marius van den Beek 61db34aebe Merge pull request #13177 from bernt-matthias/topic/auth-maxretries 
make maximum number of retries for username validation configurable
 2022-05-27 15:58:07 +02:00
Sergey Golitsynskiy 45f5ba6386 Fix linting 2022-05-27 09:44:46 -04:00
John Davis 1818c9e1e5 Merge pull request #12482 from natefoo/papercut-no-spaces-in-email 
Trim spaces from around email addresses and usernames when registering
 2022-05-27 14:02:49 +02:00
Björn Grüning 351a28cc99 Merge pull request #13967 from jmchilton/authentication_service 
Refactor authenticate controller into a services layer.
 2022-05-27 11:23:45 +02:00
Marius van den Beek 14f4ed8de8 Merge pull request #13969 from nsoranzo/fix_13916 
Don't create a BGZF index when running the compressing converter
 2022-05-27 11:10:04 +02:00
guerler f165a206a9 Adjust tour generator webhook 2022-05-27 04:42:56 -04:00
Sergey Golitsynskiy cb3e1ca423 Follow RFC5322 for valid email addresses 
See https://html.spec.whatwg.org/multipage/input.html#valid-e-mail-address
 2022-05-26 18:51:39 -04:00
guerler d0b2d9deb8 Fix comments in filtering.js 2022-05-26 18:12:21 -04:00
guerler cd0890ffc4 Fix filter text in selenium test 2022-05-26 17:24:56 -04:00
dependabot[bot] 81d593665e Bump tensorflow from 2.6.4 to 2.7.2 in /lib/galaxy/dependencies 
Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.6.4 to 2.7.2.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v2.6.4...v2.7.2)

---
updated-dependencies:
- dependency-name: tensorflow
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
 2022-05-26 21:06:24 +00:00
guerler 3bcae80b7b Update History Counter component 2022-05-26 15:48:45 -04:00
Sergey Golitsynskiy 8dd58897a9 Fix linting 2022-05-26 15:34:28 -04:00
guerler e8654eac91 Fix semicolon in history default filters 2022-05-26 15:34:06 -04:00
guerler 9e33c47abd Fix history tour 2022-05-26 15:32:44 -04:00
guerler 9a2c07b690 Use semicolon instead of equal sign for history filters 2022-05-26 15:31:57 -04:00
Nate Coraor 1f299a5cbf Test with quoted @ in local part of email (technically valid but we're 
not allowing it)
 2022-05-26 15:05:30 -04:00
Nate Coraor d1e79e0441 Test split without @ 2022-05-26 15:05:30 -04:00
Nate Coraor eab84da647 Valid syntax is good 2022-05-26 15:05:27 -04:00
Nate Coraor ab0a90ddca Maybe make validate_email a bit easier to follow? 2022-05-26 15:04:40 -04:00
Nate CoraorandSergey Golitsynskiy 3235e88d9b Apply suggestions from code review 
Co-authored-by: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
 2022-05-26 14:55:28 -04:00
Nate Coraor 37edbaf74c Trim spaces from around email addresses and usernames when registering. 
Additionally, include a stricter email address validation.
 2022-05-26 14:55:27 -04:00
Nicola Soranzo 801fa9415d Don't create a BGZF index when running the compressing converter 
The index file is not used because it is generated again in `set_meta()`
for the `VcfGz` datatype, and ignored for all others.

Additionally, the index file is currently generated alongside the input
dataset, which fails when the input directory is not writeable (such as
when running in a container).

Fix https://github.com/galaxyproject/galaxy/issues/13916 .

Also, replace outdated `tabix` requirement with the latest `htslib`.
 2022-05-26 19:25:09 +01:00
John Chilton 64aea5ef39 Refactor authenticate controller into a services layer. 
Features better typing which did find some issues with Exception handling.
 2022-05-26 11:58:12 -04:00
Dannon 8a6a717418 Merge pull request #13891 from guerler/add_any_default_filter 
Allow disabling default history filters
 2022-05-26 07:23:02 -07:00
guerler 8a009ce093 Increase test coverage for tags 2022-05-26 09:48:44 -04:00
guerler e062dcf468 Use shared iframe helper to load content into window manager 2022-05-26 09:22:04 -04:00
guerler 179e03e417 Fix tag editing 2022-05-26 09:22:01 -04:00
guerler 2e0ee4dab9 Move has tag condition to computed values 2022-05-26 09:22:01 -04:00
guerler 9f34952b38 Use v-if to determine if tag component should exist 2022-05-26 09:22:01 -04:00
guerler 713088cc26 Add test case 2022-05-26 09:22:01 -04:00
guerler db105da271 Fix content item padding for tags 2022-05-26 09:22:01 -04:00
Dannon b27d2d9460 Merge pull request #13963 from mvdbeek/bump_default_milestone 
Bump default milestone to 22.09
 2022-05-26 05:57:37 -07:00
mvdbeek db2a5f5ff6 Bump default milestone to 22.09 2022-05-26 12:50:35 +02:00
Dannon a3b318585e Merge pull request #13961 from nsoranzo/recommend_rebasing_PRs 
Recommend rebasing PRs over merging the target branch
 2022-05-26 02:53:11 -07:00
Dannon 0ef45a3d78 Merge pull request #13922 from guerler/replace_multiview 
Replace scratchbook with window manager
 2022-05-26 02:52:47 -07:00