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25009 Commits
Author SHA1 Message Date
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
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
Sergey Golitsynskiy 86aa514ba3 Remove dataset search, update tests 
As per code review discussion
 2020-11-03 14:22:37 -05:00
Sergey GolitsynskiyandNicola Soranzo 8cbf292ea8 Do not look for datasets; use file_path value to decide 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-03 13:55:10 -05:00
Sergey Golitsynskiy 12c9833cb8 Rename iter > it 
In response to code review (iter is std lib function)
 2020-11-03 12:32:41 -05:00
Oleg Zharkov 493d37fb2b redirect to run page if version is specified 2020-11-03 18:11:13 +01:00
John Chilton 76cb40de64 Merge pull request #10560 from mvdbeek/fix_extracting_workflow_from_history_with_netsed_collection_input 
[20.05] Fix workflow extraction if nested collection in input step
 2020-11-03 10:58:10 -05:00
John Chilton 9985c85046 Merge pull request #10582 from mvdbeek/fix_ldda_circular_dependency 
[20.09] Resolve LDDA <-> Library Dataset circular dependency
 2020-11-03 10:57:27 -05:00
Sergey GolitsynskiyandNicola Soranzo 76a4cfce1c Do not use f-strings yet 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-03 10:49:52 -05:00
Sergey GolitsynskiyandNicola Soranzo 3fa5bc4754 Update comment: change effective as of 20.05 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-03 10:49:52 -05:00
mvdbeek 2f5742c7c0 Merge branch 'release_20.09' into dev 2020-11-03 16:04:22 +01:00
mvdbeek dda10fe8b9 Merge branch 'release_20.05' into release_20.09 2020-11-03 15:58:38 +01:00
mvdbeek cffa939e26 Merge branch 'release_20.01' into release_20.05 2020-11-03 15:57:02 +01:00
Matthias Bernt 1aa04e3ad9 revert parsing of metadata files 2020-11-03 15:48:39 +01:00
John Chilton b51f8471c4 Merge pull request #10569 from mvdbeek/allow_execution_of_tools_with_safe_updates 
[20.09] Allow execution of workflows for certain tool updates
 2020-11-03 09:26:10 -05:00
Sergey Golitsynskiy 518047b9ea Improve handling of uuid/id default configuration 2020-11-03 02:20:56 -05:00
Sergey Golitsynskiy 02d0b07165 Add functionality to check alt paths in config 
1. Add config._check_alt_path()
2. Add unit test
3. Fix file_path value: if new default path does not exist, check old default
 2020-11-02 14:17:00 -05:00
M BerntandMarius van den Beek 025c6db299 Apply suggestions from code review 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2020-11-02 17:42:17 +01:00
M Bernt 41b2872b29 fix import order 2020-11-02 17:42:17 +01:00
M Bernt e18dbb711b import order 2020-11-02 17:41:31 +01:00
M Bernt 41feef2d7c data_meta: linter fixes 2020-11-02 17:41:31 +01:00
M Bernt 7b4e2b54db data_meta: add separate test for paired collection 
otherwise the failing test can not be detected correctly
 2020-11-02 17:41:31 +01:00
M Bernt bbb412d516 dynamic options: from_dataset accept collections and multiple datasets 2020-11-02 17:41:31 +01:00
M Bernt ff625f8ae2 data_meta: simplify import and code 
code for getting ref_name from other_values and checking its type
has been simplified. to be reusable in the dynamic options it has been
moved to a function.
 2020-11-02 17:34:18 +01:00
M Bernt b14e998b96 data_meta: first test for metadata files 2020-11-02 17:34:18 +01:00