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25035 Commits
Author SHA1 Message Date
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
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
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
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
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 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
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
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
Nicola Soranzo 9f4dcc924f Update cwltool 3.0.20201109103151 requirements 2020-11-09 13:40:17 +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
John Chilton 177bd9f7fe Fix ObjectUploadTarget handling in tool util staging code. 
With test cases.
 2020-11-07 08:44:46 -05:00
mvdbeek 7df17504bf Merge branch 'release_20.09' into dev 2020-11-05 19:03:01 +01:00
mvdbeek 1095e8ac2e Merge branch 'release_20.05' into release_20.09 2020-11-05 18:58:07 +01:00
Marius van den Beek 5a10667554 Merge pull request #10623 from mvdbeek/fix_static_welcome_html_link 
[20.09] Restore welcome html link for non-uwsgi setups
 2020-11-05 17:57:07 +01:00
John Chilton 97305501bd Merge pull request #10625 from bernt-matthias/topic/singularity-bind-spec 
Don't specify default bind type for singularity
 2020-11-05 09:24:03 -05:00
Sergey Golitsynskiy 017c7ee344 Merge pull request #10617 from ic4f/20.09_filepath_fix 
[20.09] Fix file_path bug; change default assignment of file_path and id/uuid
 2020-11-04 17:57:08 -05:00
Matthias Bernt f35d06eef0 omit default bind type for singularity 2020-11-04 21:31:05 +01:00
mvdbeek a87781fe09 Restore welcome html link for non-uwsgi setups 
by restoring the symlink from lib/galaxy/webapps/base/static to static.

This is the default location for `/static/welcome.html` as set in https://github.com/galaxyproject/galaxy/blob/release_20.09/lib/galaxy/webapps/base/webapp.py#L1032).
This fixes the `Not Found` in the center panel for Selenium tests and
planemo.
I am not sure if this is the right fix w.r.t packaging.

Alternatively we could sett a default of `static/welcome.html` for `static_welcome_html`
(and putting this in the schema, I have the impression that some users think this is what
`welcome_url` does).
 2020-11-04 12:10:04 +01:00
Sergey Golitsynskiy 4890ba17d5 Update docs to reflect uuid/id, file_path updates 
Run `make config-rebuild`
 2020-11-03 16:07:30 -05:00
Sergey Golitsynskiy 592eec1059 Check alt path before using default 
As per code review discussion
 2020-11-03 14:41:14 -05:00