John Davis
62155b9512
Remove transaction helper from test.integration
2025-01-23 11:39:24 -05:00
mvdbeek
ed8dc4b8e2
Fix dropped when_expression on workflow/tool_upgrade
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Fixes https://github.com/galaxyproject/galaxy/issues/18441
2024-06-27 15:31:30 +02:00
mvdbeek
5050ccde3d
Add test to make sure when_expression is not lost on refactoring
2024-06-27 15:31:29 +02:00
mvdbeek
e3b56f13f4
Adjust integration test for additional conditional
2024-04-09 11:50:52 +02:00
mvdbeek
626baad567
Refactor RuntimeValue utils for re-use
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Moving this to tools.parameters.workflow_utils avoids a circular
dependency when importing is_runtime_value in
tools.parameters.dynamic_options.
2024-04-02 19:10:20 +02:00
mvdbeek
fb0d3453fb
Refactor workflow_buidling_modes so it can be imported in dynamic_options.py
2024-02-16 15:53:13 +01:00
Ahmed Awan
684663360f
fix integrations caused by using tag_handler
2023-11-03 22:25:08 -05:00
mvdbeek
c62da4aa33
Merge branch 'release_23.1' into dev
2023-08-09 16:06:08 +02:00
mvdbeek
c1efbdfa6c
Fix integration tests
2023-07-31 14:03:33 +02:00
John Davis
c6ec1dd12b
Fix SA2.0 syntax in test_workflow_refactoring
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.unique() is required due to joint eager loading specified in the
StoredWorkflow model.
2023-07-21 13:04:23 -04:00
John Davis
5d42685050
Wrap session.flush in test.integration
2023-06-09 13:05:26 -04:00
Nicola Soranzo
30f60493c3
Format Python code with black 23.1.0
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with manual fixes to 3 files to make them compatible with black 22.12.0 .
We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
2023-02-01 23:51:03 +00:00
John Chilton
0180bf67a1
Fixup types surrounding workflow refactoring testing.
2022-12-12 10:18:20 -05:00
mvdbeek
accdea9b14
Always inject all modules, then compute runtime state
2022-10-29 22:11:03 +02:00
Nicola Soranzo
c35d8f2a06
Replace `unittest.TestCase` with pytest-based partial re-implementation
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Also:
- Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected
by pytest only because they were `unittest.TestCase` derived, but normally
pytest collects only test classes whose name starts with `Test`, see
https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
2022-09-27 03:34:58 +01:00
John Chilton
1edee72ce2
Rework uses_shed...
2022-07-05 13:43:04 +01:00
Nicola Soranzo
7466ab89a6
Move `uses_shed.py to galaxy_test.driver`
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to break circular dependency between galaxy-test-base and
galaxy-test-driver packages.
Also:
- Use f-string.
2022-06-28 18:33:05 +01:00
Simon Bray
c3db8271d0
modify update_step_position refactor action to make change relative to previous position
2022-03-31 14:08:57 +02:00
Dannon Baker
623a5e165a
Apply black formatting.
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Apply isort.
2022-02-03 07:42:20 -05:00
Simon Bray
381d218180
ensure tool_id/content_id is updated when refactoring workflows
2022-01-24 13:39:27 +01:00
Nate Coraor
a2d1625780
Merge remote-tracking branch 'upstream/release_21.01' into dev
2021-03-01 16:52:02 -05:00
Simon Bray
b574009c96
small changes to upgrade_all_steps refactor action and add a test
2021-02-23 22:29:32 +01:00
guerler
427594be71
Fix test cases, naming issues
2021-02-19 14:56:49 -05:00
John Chilton
1341c879dd
Establish a best practice for trans type annotations.
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Provide justification and information in docstrings also.
2021-01-12 20:22:54 -05:00
John Chilton
308569fee9
Rename response key actions_executed -> action_executions
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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
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objects were slipping into sa_session in very subtle ways
2021-01-04 00:16:17 -05:00
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
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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.
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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.
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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
f2f12e0966
Refactor action extract_legacy_parameter should work on parameters defined only in rename PJA also.
2020-12-29 22:00:32 -05:00
John Chilton
fc2ce45767
API for structured workflow refactoring.
2020-12-29 22:00:32 -05:00
John Davis