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25171 Commits
Author SHA1 Message Date
mvdbeek eaa64b95c9 Merge branch 'release_20.09' into dev 2020-11-24 10:07:19 +01:00
mvdbeek bdc3ef7001 Fix _make_sizzle_string 
The github action runs on python 3.7. From the python docs:
```
Changed in version 3.7: Only characters that can have special meaning in a regular expression are escaped. As a result, '!', '"', '%', "'", ',', '/', ':', ';', '<', '=', '>', '@', and "`" are no longer escaped.
```
 2020-11-22 18:44:33 +01:00
mvdbeek 1bb1b1da18 Split selenium tests into 3 chunks 
Using pytest-shard
 2020-11-22 18:44:33 +01:00
mvdbeek 0382e64e61 Fix method name 2020-11-22 18:44:33 +01:00
John Chilton 547eb71dff Update selenium histories for sharing changes in #10754. 2020-11-22 18:44:33 +01:00
mvdbeek 1c0a61e022 Fix tool form citation selenium test 
Drops the show as bibtext test as we only offer copying all citations as
bibtext now.
 2020-11-22 18:44:33 +01:00
mvdbeek e1b28b5345 Re-add sleep 2020-11-22 18:44:33 +01:00
mvdbeek 3781304830 Fix non_data_connection selenium test 2020-11-22 18:44:29 +01:00
mvdbeek d47a0661e2 Debounce step label onchange 
Onchange seems to trigger at every character. This migth be a bit heavy
for the reactivity system in Node.vue ?
 2020-11-22 18:38:49 +01:00
mvdbeek e78a0a253f Silence SAWarning 
Silences
```
Got None for value of column workflow_step.id; this is unsupported for a relationship comparison and will not currently produce an IS comparison (but may in a future release) "(but may in a future release)" % column
```
 2020-11-22 18:38:49 +01:00
mvdbeek 15ded641b0 Debounce workflow annotation 
This fixes the flaky selenium tests that check for the `my cool
annotation` annotation.
 2020-11-22 18:38:49 +01:00
Dannon e0e11f67d3 Merge pull request #10754 from guerler/history_clipboard 
Revision of sharing component, adds url copy to clipboard feature
 2020-11-20 09:26:28 -05:00
Dannon 9984d2394f Merge pull request #10529 from OlegZharkov/copy-dataset-btn 
'copy to clipboard' button on datasets
 2020-11-20 09:15:08 -05:00
Marius van den Beek 6b29bdbfee Merge pull request #10767 from jmchilton/script_4 
Allow retrying test output downloads for NFS issues.
 2020-11-20 10:19:20 +01:00
John Chilton af729203a4 Merge pull request #10776 from mvdbeek/reuse_requests_session 
[20.09] Speed up quay.io interaction by using requests session
 2020-11-19 18:04:28 -05:00
Nicola Soranzo a741e155ba Merge pull request #10774 from mvdbeek/singularity_fixes 
[20.09] Fixes for singularity execution and resolution
 2020-11-19 21:21:18 +00:00
guerler 7e4ee13fd5 By default make objects within shared objects accessible 2020-11-19 19:47:52 +01:00
Nicola Soranzo 62ce533470 Merge pull request #10775 from mvdbeek/fix_collectl_plugin 
[20.09] Fix collectl plugin
 2020-11-19 16:43:05 +00:00
mvdbeek 84ddc63937 Fix signature of singularity cached_container_description 2020-11-19 17:02:30 +01:00
Matthias Bernt c0de1c67b6 omit default bind type for singularity 2020-11-19 17:00:06 +01:00
mvdbeek dccb023279 Speed up quay.io interaction by using requests session 
Not sure how much faster this is, but it goes from timeout to no timeout
when I load up usegalaxy.org's toolbox.
 2020-11-19 16:50:58 +01:00
mvdbeek 0a818afaac Fix collectl plugin 
We can't subscript filter objects.
 2020-11-19 15:44:15 +01:00
Marius van den Beek 3a31aca11e Merge pull request #10761 from assuntad23/bugfix/papercut/copy_dataset_tags_when_copying_collection 
changed copy_tags to an array in copy_tags_to and added copy_tags par…
 2020-11-19 10:53:30 +01:00
Marius van den Beek ed2fa3eb39 Merge pull request #10760 from mvdbeek/more_verbose_exception 
[20.09] Include dataset and state in valid state exception
 2020-11-19 10:53:09 +01:00
John Chilton 788f805039 Allow retrying test output downloads for NFS issues. 2020-11-18 16:32:50 -05:00
Assunta DeSanto 012f9c1332 fixing a test and other use case of copy_tags_to 2020-11-18 15:11:11 -05:00
Nicola Soranzo 2b0383a8a9 Merge branch 'release_20.09' into dev 2020-11-18 19:50:15 +00:00
Assunta DeSanto 92e95fd70a changed copy_tags to an array in copy_tags_to and added copy_tags parameter in copy call 2020-11-18 13:56:20 -05:00
Dannon d76dbcec19 Merge pull request #10759 from mvdbeek/hide_hidden_workflows 
[20.09] Don't preload editor mako with hidden workflows
 2020-11-18 13:56:01 -05:00
Marius van den BeekandNicola Soranzo 40e20a40f1 Better exception message 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-18 19:43:50 +01:00
mvdbeek c27a01e293 Include dataset and state in valid state exception 2020-11-18 19:35:24 +01:00
mvdbeek 8968e0a256 Don't preload editor mako with hidden workflows 
Fixes https://github.com/galaxyproject/galaxy/issues/10746
 2020-11-18 17:33:43 +01:00
Nicola Soranzo 17be68361b Replace deprecated isAlive() method of Thread 2020-11-18 16:22:52 +00:00
Nicola Soranzo ec90e35eb0 Fix flake8 bugbear errors, remove Py2 import 2020-11-18 16:16:46 +00:00
Nicola Soranzo e40e5aef7e Upgrade syntax using pyupgrade --py36-plus 2020-11-18 16:16:46 +00:00
Dannon e65bf7d97c Merge pull request #10735 from jmchilton/script_3 
More tool test script fixes.
 2020-11-18 08:46:42 -05:00
Marius van den Beek df0ac05577 Merge pull request #10505 from jmchilton/rules_dataset_selector 
Use dataset selector in rules input dialog.
 2020-11-18 14:30:43 +01:00
Marius van den Beek c140c7749b Merge pull request #10660 from nsoranzo/update_dependencies 
Full Python dependencies update
 2020-11-18 14:25:22 +01:00
Björn Grüning 3a96dcea30 Merge pull request #10748 from simonbray/wf-api 
Add/document API for publishing/tagging workflows
 2020-11-18 14:00:21 +01:00
Marius van den Beek 554e17e0ba Merge pull request #10212 from jmchilton/quota_interface 
Implement quota interface - with better logic isolation and unit tests.
 2020-11-18 12:36:34 +01:00
Marius van den Beek 670081cbf8 Merge pull request #10408 from jmchilton/author_license_2009 
Microdata for tools and workflows.
 2020-11-18 12:31:36 +01:00
Marius van den Beek 2513c38bed Merge pull request #10546 from gregvonkuster/dzi_datatype 
Add support for the dzi (Deep Zoom Image) data format
 2020-11-18 12:16:33 +01:00
Marius van den Beek 641b7e9f73 Merge pull request #10608 from bernt-matthias/topic/drop-iuc-channel 
Remove IUC conda channel from default configuration
 2020-11-18 12:09:54 +01:00
Marius van den Beek 2473a434b1 Merge pull request #10667 from brinkmanlab/fix_dbkeys 
Add default dbkey when collecting builds
 2020-11-18 12:07:57 +01:00
Simon Bray dd992a67f2 add API test for publishing workflows 2020-11-18 11:52:15 +01:00
John Chilton 7f4339ff4e Use dataset selector in rules input dialog. 2020-11-18 11:38:13 +01:00
Marius van den Beek ae1b7b9a8e Merge pull request #10666 from dannon/admin-user-diskusage 
Display user disk usage in admin user panel
 2020-11-18 11:33:39 +01:00
Marius van den Beek 15d79444b5 Merge pull request #10712 from jmchilton/pick_value_1 
Implement expression tool for picking non-null values for CWL-style merging of conditional branches in native Galaxy workflows
 2020-11-18 11:29:34 +01:00
mvdbeek 6c76cf8178 Fix anonymous user uploads if file sources configured 
To get both file source uploads to work and anonymous uploads
you would need to use something like
```
${user.preferences.get('dropbox|access_token') if $user.preferences else ''}
```
This simplifies that back to the documented
```
${user.preferences['dropbox|access_token']
```

Overall I don't think we benefit from KeyErrors in the extra file
preferences, so I've made this `defaultdict(lambda: None)`, but we could
limit that to just the ProvidesUserFileSourcesUserContext.

Fixes https://github.com/galaxyproject/galaxy/issues/10595.
 2020-11-18 10:40:49 +01:00
Simon Bray 7fcd6db83f add/document API for publishing/tagging workflows 2020-11-18 10:11:05 +01:00