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Commit Graph
33433 Commits
Author SHA1 Message Date
Dannon Baker 0e4c21ec79 EOF 2023-01-19 15:29:59 -05:00
Dannon Baker 3dba0c9640 Look in main panel and ensure there's an nvd3 *something* 2023-01-19 15:29:59 -05:00
Dannon Baker 7f0684c02b Add basic visualization test exercising nvd3_bar. It exercises most of 
the basic parts of the chart entrypoint and rendering.
 2023-01-19 15:29:59 -05:00
Dannon 0b9a4e5562 Merge pull request #14846 from mvdbeek/galaxy_conditionals 
Implement conditional workflow steps
 2023-01-19 09:36:02 -05:00
Dannon 2c65d8e755 Merge pull request #14035 from dannon/samples-rename 
Rename samples_tool_conf to sample_tool_conf
 2023-01-17 13:03:07 -05:00
Dannon 413ad50afa Merge pull request #15210 from ahmedhamidawan/filter_inputs_in_history 
Filter Inputs and Outputs in HistoryPanel
 2023-01-17 11:57:32 -05:00
Dannon 53e84d5b69 Merge pull request #15291 from mvdbeek/editor_fixes 
Minor workflow editor fixes
 2023-01-17 11:37:05 -05:00
mvdbeek b10cd454a1 Fix regular workflow file upload in UI 2023-01-17 17:07:00 +01:00
mvdbeek acf7a18e3e Make workflow_step_id required for workflow_output_not_found warning 2023-01-17 17:06:59 +01:00
mvdbeek 7dc0bf4b99 Fix dependent workflow step id 2023-01-17 17:06:59 +01:00
mvdbeek bc337ce37c Invocation schema import fixes 2023-01-17 17:06:59 +01:00
mvdbeek 7705038b6c Move InvocationMessage models to own file 2023-01-17 17:06:58 +01:00
mvdbeek ecb160442a Add migration for updated HistoryDatasetCollectionJobStateSummary 2023-01-17 17:06:58 +01:00
mvdbeek 23cc0c483a Avoid Union of GenericModel 
More verbose, but https://github.com/pydantic/pydantic/issues/1194
prevents a more concise setup.
 2023-01-17 17:06:58 +01:00
mvdbeek 7d659bc272 Test invalid expressions and expression results 2023-01-17 17:06:57 +01:00
mvdbeek b9b5f52169 Record execution_tracker.execution_errors on invocation 2023-01-17 17:06:57 +01:00
mvdbeek e59ff1174d Backend for showing invocation failure/cancellation/warning reasons 2023-01-17 17:06:57 +01:00
mvdbeek f911a54841 Fix migration down_revision 2023-01-17 17:06:56 +01:00
mvdbeek a2c66272a7 Test and fix conditional subworkflow steps where subworkflow step produces additional mapping over without being directly connected to a workflow input 2023-01-17 17:06:54 +01:00
mvdbeek ca55ad845d Mark skipped outputs as populated 2023-01-17 17:05:57 +01:00
mvdbeek 22a64fa67b Fix mapping over subworkflow steps without explicit connection to outer workflow 2023-01-17 17:05:57 +01:00
mvdbeek 9cdcde5251 Add subworkflow skip test when tool structure changes 2023-01-17 17:05:57 +01:00
mvdbeek 63549fe034 Stick with CWL syntax and CWL tooling to implement step skipping 2023-01-17 17:05:56 +01:00
mvdbeek bbfc689bfe Implement conditional subwokflow steps 
for mapped over subworkflows and simple subworkflows
 2023-01-17 17:05:56 +01:00
mvdbeek 4ac429c0dc Add skipped to job state summary 2023-01-17 17:05:55 +01:00
mvdbeek a633f1e76c Make sure we're not changing datatypes on skipped outputs 2023-01-17 17:05:55 +01:00
mvdbeek 20d92ad3ee Make new tests robust to job and step order 
which seems to not be stable?!
 2023-01-17 17:05:55 +01:00
mvdbeek bfc4801e6d Fix type annotation for temp_input_connections 2023-01-17 17:05:54 +01:00
mvdbeek 0fb4118faf Drop unused function 2023-01-17 17:05:54 +01:00
mvdbeek d39674396a Drop unreachable SkipWorkflowStepEvaluation except statement 2023-01-17 17:05:54 +01:00
mvdbeek c146f1771a Assert skipped state in tests 2023-01-17 17:05:53 +01:00
mvdbeek f087608f6a Fix up map_over of conditional output 2023-01-17 17:05:53 +01:00
mvdbeek b194db6100 WIP: Produce json null on skip, load expression.json null as null in json_wrap 
Should probably avoid the object store assignment here, but I would also
like to avoid the extra pass through the job handler. OTOH a skipped job
might be nice ?
 2023-01-17 17:05:53 +01:00
mvdbeek a7e392d0da Fix up migration 2023-01-17 17:05:52 +01:00
mvdbeek b06444fb24 WIP: test map over and pick_value 2023-01-17 17:05:52 +01:00
mvdbeek fbdc45f7f6 Add when_expression migration 2023-01-17 17:05:52 +01:00
mvdbeek 1f44e44873 Into map-over 2023-01-17 17:05:51 +01:00
mvdbeek 20f9b6feec Attempt to skip mapped-over steps 2023-01-17 17:05:11 +01:00
John Chilton 0a79d23150 Implement conditionals via boolean step parameter 
For tool steps only right now. This side-steps user-defined javascript
expressions in favor of boolean input parameters.
 2023-01-17 17:05:11 +01:00
Marius van den Beek a92901d97d Merge pull request #15310 from mvdbeek/fix_subworkflow_export_tool_id 
[22.05] Ensure tool_id is null for subworkflow steps
 2023-01-17 17:00:54 +01:00
Marius van den Beek cf446dce5d Merge pull request #15320 from davelopez/fix_tool_shed_tests 
Revert check for new legacy API routes
 2023-01-17 15:06:28 +01:00
Nicola Soranzo 4178266659 Merge pull request #15315 from nsoranzo/ruff 
Add linting with ruff
 2023-01-17 13:53:21 +00:00
davelopez 8f0ecc6b7f Revert check for new legacy routes 2023-01-17 12:45:02 +01:00
Nicola Soranzo cc3f5b82db Merge pull request #15308 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2023-01-17 00:31:45 +00:00
Nicola Soranzo 7fee81607c Add linting with ruff 
ruff (https://github.com/charliermarsh/ruff) is a new and extremely fast
Python linter, written in Rust.
Ruff can be used to replace Flake8 (plus a variety of plugins), isort,
pydocstyle, yesqa, eradicate, pyupgrade, and autoflake.
Here ruff is added to our current linters (flake8, flake8-bugbear and isort)
while we assess its reliability.
I've not enabled the isort rules because many of the options we use are not
implemented yet. I have instead enabled the pyupgrade rules (a tool which I
run manually every few months).

Also:
- Fix new linting errors reported by ruff.
 2023-01-16 14:34:56 +00:00
Nicola Soranzo 921e5da2e6 Lint 2 previously excluded files with black and isort 2023-01-16 14:34:56 +00:00
Nicola Soranzo 2a2f244ca3 Replace deprecated `@abc.abstractproperty` decorator 
See https://docs.python.org/3/library/abc.html#abc.abstractproperty
 2023-01-16 14:34:55 +00:00
Nicola Soranzo b4c1119f00 Code cleanups from pyupgrade 
Found by running:

```
ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|^tools/' | xargs pyupgrade --py37-plus
```
 2023-01-16 14:34:55 +00:00
mvdbeek c7a89bb6d7 Use content_id if upgrades allowed 2023-01-16 14:57:04 +01:00
davelopez 498491e548 Fail if new legacy API routes get added 2023-01-16 13:34:47 +01:00