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Author SHA1 Message Date
Helena Rasche 2837fa985b Add user facing release notes 2020-11-05 19:18:05 +01:00
mvdbeek 8cc1a34b35 Make a couple of enhancements major-ish 2020-11-05 19:18:05 +01:00
mvdbeek 5fcf60a02f Release notes for 20.09 2020-11-05 19:18:05 +01:00
mvdbeek 1095e8ac2e Merge branch 'release_20.05' into release_20.09 2020-11-05 18:58:07 +01:00
Aysam Guerler 844c4e50f4 Merge pull request #10626 from mvdbeek/workflow_editor_fixes 
[20.09] Fix Workflow node input terminal not updating
 2020-11-05 12:46:33 -05:00
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
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
mvdbeek 6e3e91b6a2 Fix updating workflow node input terminal 
This fixes a silent error when hitting
`this.outputTerminals[name].$el.remove();`

This seems to not be necessary, but it is super weird that there is no
error logged. I just found it by stepping through this line by line in
the debugger.

This fixes https://github.com/galaxyproject/galaxy/issues/10622
 2020-11-04 21:35:25 +01:00
Nicola Soranzo 5ce152b279 Improve testing of _configure_dataset_storage() 2020-11-04 19:13:17 +00:00
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 GolitsynskiyandNicola Soranzo a9d4418161 Use NamedTemporaryFile, context manager 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-03 13:40:02 -05:00
Sergey GolitsynskiyandNicola Soranzo c31dcb8f52 Use context manager; fix test logic 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-03 13:30:43 -05:00
Sergey GolitsynskiyandNicola Soranzo b231fedfef Rename test 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-03 12:34:21 -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
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 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
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
Marius van den Beek 956020ce00 Merge pull request #10355 from dannon/mvpcleanup 
[20.09] Viz - mvpapp fixes and refinement
 2020-11-03 15:00:37 +01:00
Martin Cech a44c9ec4a7 Merge pull request #10611 from mvdbeek/backport_10511 
[20.09] Backport Properly scale workflow node coordinates before saving workflow
 2020-11-03 14:52:53 +01:00
Martin Cech 45b0a5d504 Merge pull request #10612 from mvdbeek/backport_10494 
[20.09] Backport Fix drag and drop highlighting in tool form for data inputs
 2020-11-03 14:48:50 +01:00
John Chilton 5d58c79c08 Merge pull request #10616 from OlegZharkov/20.09-trs-query-str 
[20.09] fix  trs_id and trs_server query strings
 2020-11-03 08:12:23 -05:00
Sergey Golitsynskiy 518047b9ea Improve handling of uuid/id default configuration 2020-11-03 02:20:56 -05:00
Sergey Golitsynskiy c825498aa9 Merge pull request #10610 from mvdbeek/backport_10518 
[20.09] Backport Fix trailing commas
 2020-11-02 14:36:09 -05:00
Nicola Soranzo 1e393a0506 Merge pull request #10609 from mvdbeek/response_body_fix 
[20.01] Change response body from str to bytes
 2020-11-02 19:26:35 +00:00
Nicola Soranzo 47a7951712 Merge pull request #10613 from mvdbeek/backport_10588 2020-11-02 19:22:51 +00:00
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
Sergey Golitsynskiy 7846d13dea Merge pull request #10615 from mvdbeek/move_linting_to_github_action 
[20.09] Move linting to GitHub action, fix linting
 2020-11-02 14:15:36 -05:00
mvdbeek 724139e0f9 Fix linting in markdown unit test 2020-11-02 18:08:14 +01:00
mvdbeek 00657532e2 Move linting to github workflow 2020-11-02 18:08:14 +01:00
Oleg Zharkov 8e21ff351f fix query string 2020-11-02 17:20:59 +01:00
Mehmet TekmanandNicola Soranzo cff9921d42 Update lib/galaxy/datatypes/interval.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-02 16:41:19 +01:00
Mehmet TekmanandNicola Soranzo 64c4a657a9 Update lib/galaxy/datatypes/interval.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-02 16:41:19 +01:00
Mehmet TekmanandNicola Soranzo db3530b4e0 Update lib/galaxy/datatypes/interval.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-11-02 16:41:19 +01:00
Mehmet Tekman d1eea98a21 Update lib/galaxy/datatypes/interval.py 2020-11-02 16:41:18 +01:00
Mehmet Tekman 103ec6360e GTF test fail for GFF class 2020-11-02 16:41:18 +01:00
Mehmet Tekman cdbda850d2 GTF rejection method 
if neither 'gene_id' nor 'transcript_id' are present in the file
    then reject it as a GTF, but pseudogenes and pseudotranscripts can
    exist without having to declare both a 'gene_id' and 'transcript_id'
 2020-11-02 16:41:18 +01:00
Mehmet Tekman 5ce70fc340 add gtf test dataset 2020-11-02 16:41:17 +01:00
guerler 8ecf77925e Fix drag and drop highlighting in tool form for data inputs 2020-11-02 16:38:58 +01:00
guerler 5dacaefbd8 Properly scale workflow node coordinates before saving workflow 2020-11-02 16:37:03 +01:00
cat-bro 3bca3c7ff1 fix trailing commas 2020-11-02 16:31:30 +01:00
Qiang Gu 33df9c17b4 Change response body from str to bytes 2020-11-02 16:27:02 +01:00
mvdbeek ba5ee3017e Refresh folder content once import is complete 
The way we did this previously we'd request new folder contents before
the folder item had been added. We can instead request the folder
contents once at the end of the chained import.
 2020-11-02 16:23:16 +01:00