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Author SHA1 Message Date
John Chilton 4cd0883b0f Allow returning error messages from Galaxy-flavored expression tools. 2020-11-17 11:46:36 +01:00
John Chilton 6640c1c3f1 Skip filtered outputs when collecting HDAs from expression tools. 2020-11-17 11:46:36 +01:00
John Chilton 724305de51 More informative error messages around macros. 2020-11-17 11:46:36 +01:00
Dannon 60388e0a67 Merge pull request #10633 from brinkmanlab/doc_repo 
Document toolshed repository response object
 2020-11-16 21:10:35 -05:00
John Chilton 2da7aab7ea Starting work on tool-util 21.1.0.dev2 2020-11-16 14:53:58 -05:00
Marius van den Beek cb42d3513e Merge pull request #10725 from jmchilton/script_2 
More fixes/enhancements for tool testing script.
 2020-11-16 20:27:40 +01:00
John Chilton 2b5486e45d Bug fix and error handling for tool util verify script. 2020-11-16 11:32:43 -05:00
John Chilton 8d52b0a3f6 Allow paginating tool test script. 2020-11-16 11:01:13 -05:00
John Chilton 53e448f5e7 Starting work on tool-util 21.1.0.dev1 2020-11-16 09:32:06 -05:00
John Chilton b387139837 Prep a development release of 21.1.0 for galaxy-tool-util. 2020-11-16 09:28:41 -05:00
Marius van den Beek f25bd49804 Merge pull request #10716 from jmchilton/tool-util-cwl-sync 
Re-sync galaxy.tool_util.cwl with CWL branch of Galaxy.
 2020-11-16 10:36:27 +01:00
John Chilton a1505cb8da Merge pull request #10718 from mvdbeek/fix_ready_check_for_empty_collections 
Fix state check for empty collections
 2020-11-15 18:34:10 -05:00
John Chilton a3fe5092cb Merge pull request #10722 from mvdbeek/recover_step_outputs 
Recover step output value
 2020-11-15 18:32:48 -05:00
John Chilton 3338a9966e Merge pull request #10476 from jmchilton/dataset_info 
Fix report's library function call in dataset_info.mako.
 2020-11-15 14:22:48 -05:00
mvdbeek f43188d9a2 Add test for input parameter in nested workflow 2020-11-15 18:59:29 +01:00
mvdbeek 6b3d13e427 Recover step output value 
in WorkflowProgress instance. Fixes running subworkflows with
parameter_input steps.
Fixes https://github.com/galaxyproject/galaxy/issues/8390 and
allows us to get rid of one FIXME I added when working around
https://github.com/galaxyproject/galaxy/issues/8248.
 2020-11-15 13:23:12 +01:00
mvdbeek 1233da0544 Fix state check for empty collections 2020-11-14 18:13:22 +01:00
mvdbeek a2c83ee722 Fix state check for empty collections 2020-11-14 17:54:22 +01:00
Dannon 82458cccf1 Merge pull request #10717 from blankenberg/typo1 
of --> or
 2020-11-13 12:35:56 -05:00
John Chiltonandmvdbeek db34db1b76 Re-sync galaxy.tool_util.cwl with CWL branch of Galaxy. 
Co-authored-by: mvdbeek <m.vandenbeek@gmail.com>
 2020-11-13 12:03:11 -05:00
Daniel Blankenberg ebbf76a55e of --> or 2020-11-13 11:56:04 -05:00
Marius van den Beek f7bba746b1 Merge pull request #10703 from jmchilton/null_handling_2 
Null handling and optional values for integers, floats, and text params.
 2020-11-13 11:24:32 +01:00
Dannon 768fbf6b13 Merge pull request #10713 from jmchilton/fix_toolbox_filter 
Fix toolbox filters integration tests.
 2020-11-12 22:52:54 -05:00
John Chilton c81ffcff82 Merge pull request #10696 from guerler/improve_visibility_upload 
Improve visibility of upload button
 2020-11-12 20:55:15 -05:00
John Chilton b97155add3 Fix toolbox filters integration tests. 2020-11-12 20:48:29 -05:00
John Chilton 75bcdf6b2d Null handling and optional values for integers, floats, and text parameters. 2020-11-12 15:08:35 -05:00
Marius van den Beek 24432c3e5f Merge pull request #10700 from jmchilton/expression_tool_hdas 
Allow expression tools to output copies of input HDAs.
 2020-11-12 16:36:22 +01:00
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
John Chilton 9e8530c074 Allow expression tools to output copies of input HDAs. 
Important for conditional logic, etc... Also tests null file handling in expression tools and tool test plumbing.
 2020-11-12 08:42:31 -05:00
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
guerler 5b40dcbbc3 Improve visibility of upload button 2020-11-11 13:18:54 -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