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31237 Commits
Author SHA1 Message Date
John Chilton 6bde989e16 Merge pull request #13983 from jmchilton/package_tests_203 
Run CI on test_base so we can catch issues with packaging
 2022-06-03 09:16:57 -04:00
John Chilton d27459a767 Merge pull request #13993 from jmchilton/workflow_jest_tests 
More workflow Jest tests.
 2022-06-03 08:53:36 -04:00
Björn Grüning c373861fac Merge pull request #14003 from jmchilton/tours_validation 
Script to validate tours structure.
 2022-06-03 09:36:58 +02:00
Dannon 724b0c4eb7 Merge pull request #13997 from jdavcs/dev_jobstatehistory 
Drop update_time from JobStateHistory
 2022-06-02 13:49:55 -07:00
John Chilton 1c795891e3 Tour validation. 2022-06-02 14:53:55 -04:00
Sergey Golitsynskiy 3b745b7893 Drop redundant import 2022-06-01 18:30:30 -04:00
Sergey Golitsynskiy bf91dc5b75 Remove column update_time from model, tests 2022-06-01 18:30:30 -04:00
Sergey Golitsynskiy 512572d3f1 Add revision: drop update_time column 2022-06-01 18:30:24 -04:00
John Chilton 6d743a18fc More workflow Jest tests. 
- Add tests for WorkflowRunButton.
- Allow using navigation.yml selectors to Vue test utils.
 2022-06-01 16:46:39 -04:00
John Chilton c2e350a804 Workflow deletion selenium tests. 2022-06-01 16:27:13 -04:00
Björn Grüning 23a21340bf Merge pull request #13975 from jmchilton/remove_tool_dependencies_packages_5 
Remove can_eliminate_tool_dependency from tool shed code.
 2022-06-01 20:04:10 +02:00
Sergey Golitsynskiy 320821ce14 Update OudatedDatabaseError message 
Drop redundant warning;
Do not list database_auto_migrate as an option (too risky; use this as
an option for development only).
 2022-05-31 10:30:30 -04:00
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
Nicola Soranzo 385b665ce2 Transform pseudo-code in doc test 2022-05-30 22:41:37 +01:00
Nicola Soranzo f2a42ba67e Run mypy on all packages' files 
Also:
- mypy fixes.
- Use `with` statement to open/close files.
 2022-05-30 22:38:55 +01:00
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
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
John Chilton 64cf8bfe62 Remove can_eliminate_tool_dependency from tool shed code. 2022-05-27 12:44:32 -04:00
John Chilton 84dfd9540b Remove a bunch of tool dependency utility code now unused. 2022-05-27 12:26:41 -04:00
John Chilton cad6ff35c1 Remove unused attribute in twilltestcase. 2022-05-27 10:57:45 -04:00
John Chilton 362a1807ee More cleanup tool_dependencies.xml handling. 2022-05-27 10:57:45 -04:00
John Chilton 5c807f6b6b Remove tool shed tool_dependencies.xml handling on the client side. 2022-05-27 10:57:44 -04:00
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
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 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
Sergey Golitsynskiy 8dd58897a9 Fix linting 2022-05-26 15:34:28 -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 0ef45a3d78 Merge pull request #13922 from guerler/replace_multiview 
Replace scratchbook with window manager
 2022-05-26 02:52:47 -07:00
Enis Afgan e977f8289c Merge pull request #13636 from nuwang/add_tpv_optional 
Add optional dependency on total-perspective-vortex
 2022-05-25 22:15:36 +00:00
Nicola Soranzo 16f691b42d Merge branch 'release_22.01' into dev 2022-05-25 19:07:33 +01:00
Marius van den Beek d42a149de6 Merge pull request #13583 from bernt-matthias/lint-ftype-action 
[22.01] linter: allow setting output format with actions
 2022-05-25 16:31:49 +02:00
Marius van den Beek 251e01dc1c Merge pull request #13927 from gallardoalba/Add_compression_gfa_files 
Add support for gz-compressed gfa1 and gfa2 files
 2022-05-25 16:11:39 +02:00
Marius van den Beek a5724ff0cd Merge pull request #13953 from qiagu/metrics 
Fix job metrics route is missing
 2022-05-25 16:04:08 +02:00
Marius van den Beek ad873032b8 Merge pull request #12604 from bernt-matthias/topic/yaml-extensions 
Check prefix before complete loading when checking yaml and cwl tools
 2022-05-25 15:54:18 +02:00