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5337 Commits
Author SHA1 Message Date
John Chilton 239d6d095e Fix typing issues in galaxy_test.base.populators hierarchy. 
- Consistent abstract methods with consistent implementation signatures.
- Add a bunch of types to methods to ensure mypy gets in there and checks everything it can while also improving the docs.
- Fix a bunch of issues where Base*Populators were using ``galaxy_interactor`` instances directly - which is bad since the whole point is to not require one of those to execute those methods.
 2021-01-16 20:11:39 -05:00
Nicola Soranzo 6df51858e0 Fix test_uninstall_outside_section unit test 2021-01-16 06:38:19 +00:00
Nicola Soranzo 452aba9ee3 Fix remaining issues reported by bugbear; add it to flake8 reqs 2021-01-16 05:58:15 +00:00
Nicola Soranzo 98490490f5 Merge branch 'release_21.01' into dev 2021-01-15 17:30:56 +00:00
Nicola Soranzo 166087ea7a Merge branch 'release_20.09' into release_21.01 2021-01-15 17:05:47 +00:00
mvdbeek 588f2c49b6 Log exception but continue if cli is available but not functional 
That is a good idea, thanks Nicola!
 2021-01-15 15:47:16 +01:00
mvdbeek 40a7cd8f3c Don't attempt to use docker cli if it is not available 
This fixes https://github.com/galaxyproject/galaxy/issues/11125, which
became a problem with https://github.com/galaxyproject/galaxy/pull/10814
and the recent removal of the docker runtime from kubernetes.

This is the quick fix, but I don't like the guessing and disabling
that we do if docker is not available or not functional.

I'm hesitating between adding a config option for the resolver
(`docker_cli_available` or `docker_list_images` + `docker_pull_images`)
and adding a `KubernetesContainerResolver` / `RemoteContainerResolver`
class that doesn't assume docker is available for listing and pulling
iages.

Not wanting to list/pull images on the Galaxy node is probably a
reasonable thing outside of kubernetes as well, so I tend to
go with a `RemoteContainerResolver` class in dev ?
 2021-01-14 17:43:25 +01:00
John Chilton 58620c0602 Merge pull request #11113 from jmchilton/types_and_trans 
Establish a best practice for trans dependency management.
 2021-01-13 18:11:57 -05:00
Marius van den Beek c148445e6c Merge pull request #10880 from bernt-matthias/topic/options-fallback-name 
Dynamic select parameters: also allow to choose legal options by name
 2021-01-13 12:00:08 +01:00
John Chilton 1341c879dd Establish a best practice for trans type annotations. 
Provide justification and information in docstrings also.
 2021-01-12 20:22:54 -05:00
Matthias Bernt 5f67c2075b fix name and value column in select_from_dataset.xml 2021-01-12 19:27:07 +01:00
Marius van den Beek 520e097771 Merge pull request #11063 from bernt-matthias/topic/validate-collections 
add validation for collection parameters
 2021-01-12 16:40:06 +01:00
Matthias Bernt 0c8c403bf4 add tests 
showing that dynamic selects can be chosen by name for
from_data_table and from_dataset
 2021-01-12 13:45:45 +01:00
Matthias Bernt d512049a4a more specific functional tool tests involving fasta_indexes.loc 
rename entries such that they are suffixed by the column name
(execpt for dbkey).
this makes tests more specific, because this ensures that always
the correct column is used.
 2021-01-12 13:44:58 +01:00
John Chilton 0482543402 Merge pull request #10822 from jmchilton/conda_readonly_2 
Implement read-only conda resolver (alternative)
 2021-01-10 12:43:59 -05:00
Marius van den Beek af4d041dc9 Merge pull request #10592 from hexylena/edam-tool-panel 
EDAM tool panel
 2021-01-08 18:56:28 +01:00
Helena Rasche 4044d76e35 Expect test data in correct location 
thanks @ic4f
 2021-01-08 17:30:13 +01:00
John Chilton 22aa23e1db Implement read-only conda resolver. 2021-01-08 11:09:10 -05:00
Matthias Bernt fd97fd4b5b fix output assertion in test tool 2021-01-08 12:44:39 +01:00
Matthias Bernt 5a01f060d9 add explicit formats to validation_empty_dataset.xml 2021-01-08 12:43:37 +01:00
Matthias Bernt 4343014792 add validation for collection parameters 2021-01-08 12:43:37 +01:00
Nicola Soranzo f99fbd4981 Merge pull request #11073 from mvdbeek/empty_work_dir_outputs_v3 2021-01-07 19:01:05 +00:00
Helena Rasche f5a3545541 Merge branch 'dev' into edam-tool-panel 2021-01-07 19:54:12 +01:00
Marius van den Beek e966f5abed Update test class docstring 2021-01-07 17:53:29 +01:00
Nicola Soranzo 3be6e1805e Lint collection_creates_pair_from_work_dir tool 2021-01-07 16:51:18 +00:00
Nicola Soranzo 82a66c59d2 Lint output_empty_work_dir tool 2021-01-07 16:47:15 +00:00
John Chilton 144ebce8f4 Verify behavior of non-existent from_work_dir outputs. 2021-01-07 15:29:23 +01:00
Marius van den Beek ca8435681a Merge pull request #11032 from jmchilton/workflow_refactor_polish_2 
Implement edit & upgrade subworkflow buttons in workflow editor.
 2021-01-07 10:11:01 +01:00
Nicola Soranzo 2c9e89a398 Lint a bunch of test tools 2021-01-05 12:39:53 +00:00
John Chilton 308569fee9 Rename response key actions_executed -> action_executions 
When dry_run=True actions_executed feels mislabeld.
 2021-01-04 00:16:58 -05:00
John Chilton 4dde704d55 wf refactor API - fix dry_run=True subworkflow upgrades 
objects were slipping into sa_session in very subtle ways
 2021-01-04 00:16:17 -05:00
Nicola Soranzo c38cdb9dcf Use bash for run_tests.sh 2021-01-04 02:59:48 +00:00
John Chilton 7b46cfead5 subworkflow upgrade - catch and record dropped workflow output labels 2021-01-03 19:59:37 -05:00
John Chilton 869633d116 wf refactor API - subworkflow upgrade - dropping connections 2021-01-03 19:59:37 -05:00
John Chilton 9d710f2afd wf refactor API - implement update_output_label action 2021-01-03 19:59:37 -05:00
John Chilton a8de0cdfc8 Implement much more complete dry_run workflow refactor API. 2021-01-03 19:59:37 -05:00
John Chilton c578a710c7 refactor action - upgrade_subworkflow - report dropped inputs 2021-01-03 19:52:28 -05:00
John Chilton d8080bcd70 wf refactor API - add upgrade_tool action 2021-01-03 19:52:28 -05:00
John Chilton 7dc53d0daa wf refactor API - add upgrade_subworkflow action 2021-01-03 19:52:28 -05:00
John Chilton 2868690368 wf refactor API - add fill_defaults action 
Fills step defaults on all tool steps.
 2021-01-03 19:52:28 -05:00
John Chilton ce9240e921 Rework refactor responses for structured messages... 2021-01-03 19:52:28 -05:00
John Chilton 6be4e2bdbd Rework refactoring API for better separation of concerns. 
Thinner controller, pydantic model to separate options available for manager (which has to render a response) from those of the refactoring executor.
 2021-01-03 19:52:28 -05:00
John Chilton 87090e479d wf refactor API - add fill_step_defaults action 2021-01-03 19:52:28 -05:00
John Chilton 0c7cc4679c Ensure the workflow refactor API works around incomplete tool state information. 
Test cases and one small fix to ensure this.

This should allow the API (or at least many of the actions) to work without knowledge of a toolbox potentially and I think it will allow use to track the tool state upgrades the workflow editor does automatically more formally.
 2021-01-03 19:52:28 -05:00
John Chilton 194a3c15eb integration test for tool state handling around fill_defaults option 2021-01-03 19:52:28 -05:00
John Chilton 38fbd87c88 Use existing workflow_manager to load subworkflows in wf modules. 2021-01-03 19:52:28 -05:00
Bjoern Gruening 2cd2777746 adopt to code review 2021-01-02 18:48:32 +00:00
Bjoern Gruening dfba28a443 fix mutable arguments in tests 2021-01-02 18:48:31 +00:00
Nicola Soranzo 1a9b210300 Iterate over schema dict only once 2021-01-02 02:42:44 +00:00
John Chilton f2f12e0966 Refactor action extract_legacy_parameter should work on parameters defined only in rename PJA also. 2020-12-29 22:00:32 -05:00