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Author SHA1 Message Date
Marius van den Beek ee25cfc511 Merge pull request #10691 from bernt-matthias/topic/fix_metadatawrapper 
Fix element_is_set for MetadataWrapper
 2020-11-12 15:51:33 +01:00
Marius van den Beek 690e5b57ca Merge pull request #10620 from jmchilton/refine_client_test_config 
Enhancements for galaxy-tool-test script.
 2020-11-12 13:11:10 +01:00
Nicola Soranzo 068440daaf Merge pull request #10702 from mvdbeek/flake8_ignorelist 
Rename flake8 ignorelist
 2020-11-12 10:41:53 +00:00
mvdbeek d6c07fd9bd Rename flake8 ignorelist 2020-11-12 10:38:52 +01:00
Marius van den Beek e79dc5e17d Merge pull request #10694 from jmchilton/null_handling 
Harden, formalize 'null' handling around boolean tool parameters.
 2020-11-12 09:58:40 +01:00
John Chilton 1cf6c980f2 More fixes for tool test script. 2020-11-11 22:21:27 -05:00
mvdbeek 64682ebde7 Parse --test-index and --retries as integer 2020-11-11 22:21:27 -05:00
mvdbeek 406c3acdcb verify_quiet is already in verify_kwds 2020-11-11 22:21:27 -05:00
mvdbeek 050141a5f6 Store test id 2020-11-11 22:21:27 -05:00
John Chilton 9467106ee0 Or maybe this? 2020-11-11 22:21:27 -05:00
John Chilton ab142bf9c5 Rebase into handling multiple versions. 2020-11-11 22:21:27 -05:00
John Chilton be2f25c8b8 Enhancements for galaxy-tool-test script. 
- Option to skip if reference data is annotated.
- Try to build more abstractions to allow reuse with ephemeris.
- Enhance to allow parallelization and enhnaced reporting like ephemeris.
- Allow testing a whole tool panel.
- Fix bugs in imported ephemeris logic (skipped failed tests and skipped tests for in counts/reporting for instance).
- Unit tests for abstractions.
 2020-11-11 22:21:27 -05:00
John Chilton 4d33251943 Allow test_data API to get tests for all tool versions. 2020-11-11 22:21:27 -05:00
John Chilton a7a8754e24 Harden, formalize 'null' handling around booelan tool parameters and between workflow steps. 
Important for expression tools and implementing CWL-style conditionals.
 2020-11-11 19:44:16 -05:00
Matthias Bernt 51315a296b revert previous and add element_is_set to MetadataWrapper 2020-11-11 16:46:03 +01:00
Matthias Bernt 56df6160da allow access to metadata collection attributes 
follow up to https://github.com/galaxyproject/galaxy/pull/8599

in the planemo tests in the line https://github.com/bernt-matthias/galaxy/blob/1882aa641cdde1c51c077fd983f2241971308377/lib/galaxy/tools/parameters/dynamic_options.py#L205

r.metadata is sometimes a MetadataWrapper and sometimes a MetadataCollection

in the former case acccess to the `element_is_set` function defined in MetadataCollection is not possible.
 2020-11-11 13:57:07 +01:00
John Chilton f236a73e16 Merge pull request #10674 from nsoranzo/api_tests_gh_wf 
Migrate API tests to GitHub workflow
 2020-11-10 23:23:35 -05:00
John Chilton 53843634c6 Merge pull request #10676 from mvdbeek/fix_empty_collection_dataset_listing 
Produce a clean list of dataset instances if not datasets in collection
 2020-11-10 23:22:06 -05:00
Nicola Soranzo efa9e0fdd1 Fix command line for tools using interpreter when galaxy root contains spaces 2020-11-10 19:29:22 +00:00
Nicola Soranzo 1e9f83b53e Add missing single-quotes in tools Cheetah 2020-11-10 19:29:22 +00:00
Nicola Soranzo be1e21bffc Migrate API tests to GitHub workflow 2020-11-10 19:29:22 +00:00
Marius van den Beek ba2ba1ed27 Merge pull request #8599 from bernt-matthias/topic/data_meta_improvements 
dynamic options and metadata filter for collections and metadata filter fix
 2020-11-10 19:35:18 +01:00
mvdbeek 92a76e9fd4 Produce a clean list of dataset instances if not datasets in collection 2020-11-10 15:30:29 +01:00
Matthias Bernt 1882aa641c revert change to to_hda_representative 2020-11-10 14:02:50 +01:00
John Chilton 39c7c3dfd4 Merge pull request #10668 from jmchilton/assert_ok_invocation 
wait_for_invocation should take in an assert_ok flag like other wait methods.
 2020-11-10 07:47:59 -05:00
Nicola Soranzo 719df27150 Merge pull request #10673 from galaxyproject/bernt-matthias-patch-1 
fix link to job config sample in docs
 2020-11-10 12:13:50 +00:00
Nicola Soranzo 41c649d667 Merge pull request #10669 from jmchilton/optional_inputs_api_test 
API workflow test showing structure of default/optionals parameters.
 2020-11-10 11:56:09 +00:00
M Bernt 963fb994dd fix link to job config sample in docs 2020-11-10 11:34:31 +01:00
John Chilton 08a4ddafd1 API workflow test showing structure of default/optionals parameters. 
- Shows how to find them, name of parameters, odd double encoding of tool_state, and shows parameters with default values are implicitly optional = True.
 2020-11-09 23:12:21 -05:00
John Chilton 220d441844 wait_for_invocation should take in an assert_ok flag like other wait methods. 2020-11-09 20:42:52 -05:00
Dannon 3337e249f5 Merge pull request #10489 from guerler/radio_buttons 
Revise style of radio button groups to improve visibility
 2020-11-09 15:20:17 -05:00
Marius van den Beek e2977fd24c Merge pull request #10659 from nsoranzo/merge_20.05 
Merge forward release_20.09
 2020-11-09 16:12:55 +01:00
Marius van den Beek 7eb7e6be54 Merge pull request #10658 from jmchilton/cwltool_rev 
Rev cwltool to 3.0.20201109103151
 2020-11-09 16:06:28 +01:00
Marius van den Beek fd627e3091 Merge pull request #10657 from jmchilton/workflow_step_type 
Refactor logic for workflow_step.input_type into model.
 2020-11-09 14:50:55 +01:00
Nicola Soranzo 9f4dcc924f Update cwltool 3.0.20201109103151 requirements 2020-11-09 13:40:17 +00:00
Dannon 38623472af Merge pull request #10583 from hexylena/extract-wf-primary 
Make extract wf action more visible
 2020-11-09 08:37:05 -05:00
Nicola Soranzo cb8a310e74 Merge branch 'release_20.09' into dev 2020-11-09 12:53:53 +00:00
mvdbeek cae46bd415 Rev cwltool with fix for opaque strings 2020-11-09 12:46:23 +01:00
John Chilton 15c81f8869 Rev cwltool. 2020-11-08 22:11:45 -05:00
John Chilton f1d601a138 Move logic for workflow_step.input_type into model. 2020-11-08 13:57:50 -05:00
John Chilton cef3b9ab5c Merge pull request #10619 from OlegZharkov/trs-auto-import 
auto-import workflow with trs
 2020-11-08 08:02:42 -05:00
Marius van den Beek 3519db8698 Merge pull request #10652 from OlegZharkov/fix-race-20.09 
[20.09] fix dataset_manipulation and logged_dataset_manipulation
 2020-11-07 19:44:06 +01:00
Marius van den Beek 44c99169ac Merge pull request #10650 from jmchilton/upload_object 
Fix ObjectUploadTarget handling in tool util staging code.
 2020-11-07 19:30:52 +01:00
John Chilton 177bd9f7fe Fix ObjectUploadTarget handling in tool util staging code. 
With test cases.
 2020-11-07 08:44:46 -05:00
Oleg Zharkov e95246cbcb move logged_dataset_manipulation and dataset_manipulation to computed 2020-11-07 13:07:07 +01:00
Marius van den Beek bcc7ea0afc Merge pull request #10637 from assuntad23/bugfix/SavedRulesSelectorIssues 
Fix saving rule builder rules when uploading in rule editing view
 2020-11-07 13:03:12 +01:00
Dannon 08e839538b Merge pull request #10499 from guerler/upload_button_revision 
Move upload button below Tool panel header, increase size, add label
 2020-11-07 06:58:44 -05:00
John Chilton 85d196e0e8 Merge pull request #10649 from nsoranzo/release_20.09_fix_lint.yaml 
[20.09] Fix cache key for lint CI workflow
 2020-11-06 20:33:52 -05:00
Nicola Soranzo c86989826a Fix cache key for lint CI workflow 
Also:
- test on Python 3.9 instead of 3.8
- update some action versions

xref. https://github.com/galaxyproject/galaxy/pull/10615#pullrequestreview-521926167
 2020-11-06 18:47:31 +00:00
Assunta DeSanto 7e18d65492 Merge branch 'bugfix/SavedRulesSelectorIssues' of https://github.com/assuntad23/galaxy into bugfix/SavedRulesSelectorIssues 2020-11-06 11:55:26 -05:00