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31725 Commits
Author SHA1 Message Date
Nicola Soranzo dc0ac34fc4 Merge pull request #14588 from mvdbeek/fix_noisy_exception_logging_when_unicode_null_in_session_key 
[22.05] Ensure guid is hexadecimal value
 2022-09-08 19:05:54 +01:00
Nicola Soranzo 9fa2d71e09 Ignore overlapping type in overlap 2022-09-08 15:54:29 +01:00
mvdbeek d50ec2f3b6 Add unicodify type annotation 2022-09-08 14:34:29 +02:00
mvdbeek aceaa698fc Ensure guid is hexadecimal value 2022-09-08 14:04:35 +02:00
Nicola Soranzo 70b2ea429c Merge branch 'release_22.01' into release_22.05 2022-09-06 12:12:21 +01:00
Nicola Soranzo 9f1d8d053b Merge branch 'release_21.09' into release_22.01 2022-09-06 11:36:36 +01:00
Nicola Soranzo 06baa27d05 Merge branch 'release_21.05' into release_21.09 2022-09-06 11:24:20 +01:00
Nicola Soranzo 8069584d0f Merge branch 'release_21.01' into release_21.05 2022-09-06 11:12:59 +01:00
John Chilton 2b450df90e Merge pull request #14563 from mvdbeek/fix_workflow_parameter_connectability 
[22.05] Fix workflow parameter connectability
 2022-09-02 14:37:56 -04:00
mvdbeek 0abd957659 Fix workflow parameter connectabilty 2022-09-01 21:59:33 +02:00
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 f3eb50369d Merge pull request #14497 from mvdbeek/fix_finding_repository_directory 
[21.05] Fix finding repository directory if repository is repeated in path
 2022-08-31 08:11:58 -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
Matthias Bernt 9b66e46aa0 always use default=0 for strandCol 
just for consistency
 2022-08-26 17:04:01 +02:00
Matthias Bernt fe303085b0 bed, interval: set default for strandCol 
bed and interval datatypes `check element_is_set` before overwriting
metadata. since the having `default=None` and `no_value=0` makes
`element_is_set` return True (since `None!=0`). Therefore metadata
values are never set
 2022-08-26 15:53:40 +02:00
Matthias Bernt 4e23fbb0b1 Revert "set metadata default to no_value if default is None" 
This reverts commit dff9d4087b.
 2022-08-26 12:01:54 +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
Matthias Bernt dff9d4087b set metadata default to no_value if default is None 2022-08-25 17:30:13 +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
mvdbeek 05cad6df38 Fix finding repository directory if repository directory is repeated in path 
As happens for instance for
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/0e3cf9594bb7/ncbi_blast_plus/tools/ncbi_blast_plus
 2022-08-23 15:49:48 +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