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31218 Commits
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
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
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
Marius van den Beek 7cb3f76c6e Merge pull request #12232 from bernt-matthias/topic/drilldown 
fix `drill_down` parameters
 2022-05-25 15:52:50 +02:00
Marius van den Beek aa33272d21 Merge pull request #12533 from jmchilton/deferred_data 
Add DEFERRED datasets to Galaxy.
 2022-05-25 15:50:33 +02:00
Dannon 570b30e9d7 Merge pull request #13848 from ahmedhamidawan/Show_only_name_tags_#13747 
Display name tags only in dataset items
 2022-05-25 06:42:05 -07:00
Marius van den Beek 574a0d42ea Merge pull request #13893 from jmchilton/jobs_grid_tweaks 
Jobs Index and Grid Improvements
 2022-05-25 15:36:12 +02:00
Marius van den Beek ac510bc8dc Merge pull request #7894 from bernt-matthias/topic/count-pairs-correctly 
Fix docs for `expect_num_outputs` and add `count` attribute for test `output` and `element` tags
 2022-05-25 15:23:10 +02:00
mvdbeek ae69c5224c Tighten xyz sniffer 2022-05-25 13:38:55 +02:00
mvdbeek dd156d08a5 Tighten phylip sniffer 2022-05-25 12:51:08 +02:00
Nuwan Goonasekera 76de85c7f3 Change sample file for TPV 2022-05-25 11:11:23 +05:30
Nuwan Goonasekera 163e429abc Fix handling of yaml job_conf optional rule modules 2022-05-25 11:11:23 +05:30
Nuwan Goonasekera 268235e512 Added conditional requirement on TPV 2022-05-25 11:11:21 +05:30
mvdbeek 72e16548a4 Use INFO log level for irods 
We've run out of disk space on usegalaxy.org due to these log messages.
 2022-05-24 23:47:32 +02:00
Ahmed Awan 08933ee497 stateless tags replace nametags, clicking tag emits filterText 2022-05-24 13:59:58 -04:00
dependabot[bot] 1f8f39664c Bump tensorflow from 2.5.3 to 2.6.4 in /lib/galaxy/dependencies 
Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 2.5.3 to 2.6.4.
- [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/v2.5.3...v2.6.4)

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

Signed-off-by: dependabot[bot] <support@github.com>
 2022-05-24 17:27:49 +00:00
guerler 4f6397f41e Adjust renaming in localization 2022-05-24 10:48:12 -04:00
John Chilton c5bf63bc91 Add DEFERRED datasets to Galaxy 
- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
 2022-05-23 19:48:47 -04:00
qiagu b0161986db Merge branch 'dev' of https://github.com/galaxyproject/galaxy into metrics 2022-05-23 16:44:41 -07:00
John Chilton d2204b656b Task status API for celery. 2022-05-23 19:19:18 -04:00
John Chilton c796dec0f2 Rework galaxy.model.store.discover to not require unique paths for incoming files. 2022-05-23 18:54:19 -04:00
qiagu feb3aeba6e Add route for job metrics 2022-05-23 14:41:19 -07:00