opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
61,895 Commits 69 Branches 243 Tags
86e42b54833dbba0c014b888a61ba8d36d5acb7b
Commit Graph
31708 Commits
Author SHA1 Message Date
Nate Coraor 86e42b5483 Update Gravity to 0.13.4 and document setting env vars on dynamic 
handlers.
 2022-09-01 10:40:54 -04:00
Dannon 732ac13f48 Merge pull request #14539 from mvdbeek/post_job_action_state_bug_fix 
[22.05] Fix post job action getting lost when node is made active
 2022-08-30 22:30:08 -04:00
mvdbeek d1b4f05345 Merge branch 'release_22.01' into release_22.05 2022-08-30 20:32:39 +02:00
mvdbeek f67ca01a99 Fix post job action getting lost when node is made active 
And many more reactivity fixes.

The core of the issue was that the FormElement would emit a onUpdate
event, which triggers a request to `api/workflows/build_module`.
The FormSection that controls the post job action data is not ready at
this point, so when the data comes back in we have to break the
connection because the post job action that sets the datatype is
missing.

We really don't need to call `build_module` though when change post job
actions, they don't require the backend at all, we just need to bubble
them up to the Index component, which can set the postJobAction on the
active node (let's ignore that we should manipulate the data, not the vue instance
...).

In order for that to be properly reactive I had to remove the majority
of the getNode hacks.

We do still rely on this in the Terminals and Connectors, so those can
get out of sync still, but it fixes an annoying issue where connections
are dropped without notice.
 2022-08-30 17:14:34 +02:00
Nicola Soranzo 6519604620 Add some type annotations 2022-08-30 14:34:54 +01:00
Nicola Soranzo 4faa486c49 Merge pull request #14526 from bernt-matthias/topic/fix-test-linters 
[22.05] Fix typos in test linter
 2022-08-30 12:16:10 +01:00
Nicola Soranzo 61b6eb1ee9 Fix more `discovered_datasets` typos 2022-08-30 09:57:26 +01:00
mvdbeek 2f15059543 Skip the quay.io lookup if we have a valid cache entry 
Good thing we had tests that made sure the cache was getting used ...
 2022-08-29 16:54:23 +02:00
mvdbeek 60cda23970 Mock quay.io API calls, pass install=False to not pull docker images 2022-08-29 16:38:31 +02:00
mvdbeek c4f576ccf3 Fix cache lookup condition 2022-08-29 16:38:31 +02:00
mvdbeek c4a9050af9 Fix _namespace_has_repo if cache namespace cache key not present 2022-08-29 14:08:49 +02:00
Matthias Bernt 8cc06e9569 fix typo in xsd 2022-08-29 13:11:32 +02:00
Matthias Bernt a8a80cf431 fix typo in test linter 2022-08-29 11:36:59 +02:00
mvdbeek 18ed5116e5 Always call strip() on data_column column values 
Not just when they start with `c`. Should fix running workflows
that were created by manually writing columns in the text area field
and then hitting enter.
 2022-08-27 09:41:22 +02:00
Björn Grüning c096e599ff Merge pull request #14510 from mvdbeek/fix_metadata_action_default_setting_in_conditional 
[22.05] Fix setting metadata elements in conditional tool action
 2022-08-25 20:14:21 +02:00
mvdbeek 94c75a083c Fix setting metadata elements in conditional tool action 
Fixes https://github.com/galaxyproject/galaxy/issues/14509
 2022-08-25 14:27:44 +02:00
John Chilton 83745c3140 Merge pull request #14504 from mvdbeek/patrick/15-castep-datatypes 
[22.05] Add CASTEP datatypes
 2022-08-24 15:16:42 -04:00
Patrick Austin 7f794e8f12 Add CASTEP formats to config, sniff typehint for mypy #15 2022-08-24 17:34:02 +02:00
Matthias Bernt 0b3f8af25f fix lint context fail function 
error introduced here https://github.com/galaxyproject/galaxy/pull/13186

found this while working on https://github.com/galaxyproject/planemo/pull/1264
 2022-08-23 15:46:16 +02:00
mvdbeek 8a8acc625f Fix refactor action dropping outputs on subworkflow connection 
I thought it would be cleaner to make a distinction between the output
name and the output label when reasoning about a subworkflow step in
the context of a parent workflow
(https://github.com/galaxyproject/galaxy/pull/14473/commits/b0727be9e0b096a2dacacb767a1f4ac0fc3e6540#diff-a50bcc5c08ade11249449c4100ea8c286727df601b52a5b9588eb2a385d97da7R543),
in case we'd later want to do something with the label.

I don't think I thought about this correctly though,
and it breaks connections between steps that were made by referencing
the subworkflow's output name.

This wasn't necessary for the main goal of
https://github.com/galaxyproject/galaxy/pull/14473, so I'm partially
reverting that here.

Fixes https://github.com/galaxyproject/planemo/pull/1262#issuecomment-1223874571
 2022-08-23 14:12:29 +02:00
mvdbeek 36f049410b Update version to 22.05.1 2022-08-22 23:14:31 +02:00
mvdbeek 88a986c578 Update version to 22.05.1.dev0 2022-08-22 23:14:27 +02:00
mvdbeek 0a69d3d882 Update version to 22.1.2.dev0 2022-08-22 21:57:17 +02:00
mvdbeek dc56fc4e61 Update version to 22.01.1 2022-08-22 21:47:47 +02:00
Nicola Soranzo 4fcbe80268 Doc fixes 2022-08-19 18:33:20 +01:00
Nicola Soranzo b5a75cac27 Merge branch 'release_22.01' into release_22.05 2022-08-19 15:28:58 +01:00
Marius van den Beek cccdb496b8 Merge pull request #14482 from davelopez/22.05_fix_query_parameter_lists 
[22.05] Fix Jobs API index to accept query parameters as lists
 2022-08-19 13:23:32 +02:00
Dannon d1c66d61b5 Merge pull request #14473 from mvdbeek/change_datatype_problems 
[22.05] Fix effective datatype in workflow editor node terminals
 2022-08-19 06:32:49 -04:00
davelopez 1545b9da99 Simplify query_parameter_as_list 
And render the repeated parameter input in the docs.
The first parameter can be a comma-separated list of values
 2022-08-19 12:30:53 +02:00
Marius van den Beek 65c724ec66 Merge pull request #14475 from jancrichter/patch-1 
[22.05] Grep1 tool: fix keep_header option
 2022-08-19 11:43:38 +02:00
Matthias Bernt b1e7b895b5 fix deprection warning 
which pops up at every `planemo lint`:

```
galaxy/tool_util/deps/requirements.py:348: FutureWarning: The behavior of this method will change in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
```
 2022-08-19 10:29:06 +02:00
davelopez 05ed92688c Fix Jobs API index endpoint 
Use the `query_parameter_as_list` dependency to support multiple ways of providing lists of values while rendering the API docs as a single string query parameter.
 2022-08-18 18:39:34 +02:00
davelopez 1a103279af Add query_parameter_as_list dependable 
Supports declaring query parameters as 'listified'
 2022-08-18 18:37:10 +02:00
mvdbeek 446b07b4c0 Adjust workflow safe tool version update range for Grep1 2022-08-18 17:50:21 +02:00
Marius van den Beek 01a4915e29 Merge pull request #14476 from bernt-matthias/topic/linter-fixes 
[22.05] Tool linter bug fixes
 2022-08-18 17:35:51 +02:00
M BerntandMarius van den Beek 2bd8044a4d Remove comment 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-08-18 17:18:36 +02:00
Matthias Bernt d7006d2429 add scool datatype 
used in IUC schicexplorer
 2022-08-18 16:50:47 +02:00
Matthias Bernt df81e5568c explicitly test for None 
found one tool where argument was "" due to macro usage
 2022-08-18 14:35:11 +02:00
Matthias Bernt d8036a8418 f-string fix 2022-08-18 14:35:11 +02:00
Matthias Bernt b41bc6d336 allow no_options validator for data and data_collection 2022-08-18 14:35:11 +02:00
Matthias Bernt 1ede9e839d xsd: allow 0 for bytes 2022-08-18 14:35:11 +02:00
Matthias Bernt 5f0fbb061b fix docs 2022-08-18 14:30:14 +02:00
qiagu ea85cab75a Revert startswith of tool parameter options 2022-08-18 11:04:12 +02:00
Patrick Austin 3df9444799 Add Datatypes for CASTEP files #15 2022-08-18 08:32:01 +00:00
mvdbeek 685ac29018 Fix qunit tests 2022-08-18 10:18:46 +02:00
mvdbeek e35b82aef1 Selenium test for changing datatype 
In subworkflows and outside. All asserts terminal label.
 2022-08-18 10:18:10 +02:00
Nate Coraor 1ec5909b98 Merge pull request #14471 from natefoo/gravity-0.13.3 
[22.05] Bump Gravity version to 0.13.3
 2022-08-17 16:35:13 -04:00
Nicola Soranzo 9915a6eeeb Merge pull request #14456 from mvdbeek/drop_tzinfo_when_parsing_datetime 
[22.05] Fix data_range_{min,max} parsing
 2022-08-17 20:06:43 +01:00
Nate Coraor 69ca03e99a Bump Gravity version to 0.13.3 2022-08-17 13:48:39 -04:00
Marius van den Beek cd94ccb6c5 Merge pull request #14457 from natefoo/log-rotation 
[22.05] Add log rotation options and update logging documentation
 2022-08-17 19:24:07 +02:00