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Author SHA1 Message Date
Dannon Baker 852773ed27 Fix let/const usage in components. 2019-04-30 16:45:24 -04:00
Dannon Baker d13e4bd902 Add prefer-const linting 2019-04-30 16:45:03 -04:00
Dannon Baker 78d0c1eb31 Prefer const when applicable 2019-04-30 16:41:42 -04:00
Nicola Soranzo ce85dbc906 Add ELIXIR OIDC backend, upgrade social-auth-core requirement version (#7852) 
Add ELIXIR OIDC backend, upgrade social-auth-core requirement version
 2019-04-30 15:10:32 +01:00
Nicola Soranzo fc84e97698 Merge branch 'release_19.05' into dev 2019-04-30 12:05:49 +01:00
Nicola Soranzo aa93448416 Merge branch 'release_19.01' into release_19.05 2019-04-30 12:03:14 +01:00
mvdbeek 9c53cb2076 Merge branch 'release_19.05' into dev 2019-04-30 11:53:19 +02:00
Kidane M. Tekle 79a5ade5cb updated documentation link 2019-04-30 10:40:51 +02:00
Marius van den Beek 7d8ec2b5fd Merge pull request #7850 from nsoranzo/release_19.01_backport_7696 
[19.01] Backport of #7696
 2019-04-30 10:03:58 +02:00
Aysam Guerler ea7f9c6326 Merge pull request #7749 from dannon/fix_user_reg 
Fix automatic user registration
 2019-04-30 02:07:23 -04:00
Nicola Soranzo 9822aba722 [19.05] Fix grouping1 with modern sort, fix test data (#7844) 
[19.05] Fix grouping1 with modern sort, fix test data
 2019-04-30 01:11:10 +01:00
Aysam Guerler ce6ee86dec Merge pull request #7845 from dannon/fix_trackster_overflow_issue 
[19.01] Fix trackster issue w/ constraining (overflow:non-visible) containers
 2019-04-29 17:39:16 -04:00
John Chilton 7512df35d2 Merge pull request #7847 from nsoranzo/release_19.01_backport_7696 
[19.01] Backport #7696
 2019-04-29 16:12:24 -04:00
Nicola Soranzo c9f63ac2f8 Simplify code 2019-04-29 19:22:11 +01:00
Bérénice Batut 3dc68dbe92 Add extra column metadata check for minimal biom1 file 2019-04-29 18:59:25 +01:00
Dannon 886a856674 Merge pull request #7827 from ic4f/dev 
Add option to wait for db to become available
 2019-04-29 13:38:11 -04:00
Martin Cech 6c50255a99 Merge pull request #7746 from guerler/add_data_dialog_lib_exec 
Enable the selection of library datasets in the tool form
 2019-04-29 13:18:58 -04:00
Aysam Guerler f6fc822ab2 Merge pull request #7843 from dannon/bs-mixin-deprecation 
Bootstrap style deprecation warning fix
 2019-04-29 12:47:40 -04:00
Dannon Baker f09bc22459 Fix trackster issue w/ constraining (overflow:non-visible) containers 2019-04-29 12:00:23 -04:00
mvdbeek 0c1334fea0 Fix grouping1 with modern sort, fix test data 
This tool currently fails with `sort: multi-character tab '$\\\\t'\n`
(https://jenkins.galaxyproject.org/view/All/job/docker-main-tools/lastCompletedBuild/testReport/test.functional/test_toolbox_pytest/test_tool_Grouping1_test_1_/).
This also removes test data that should be included in
galaxy-test-data instead (xref
https://github.com/galaxyproject/galaxy-test-data/pull/5),
and adds a test file that was missing from
https://github.com/galaxyproject/galaxy/pull/7205.
 2019-04-29 17:38:10 +02:00
Sergey Golitsynskiy b4f4a12fb2 Add break stmt in try block 
Break out of loop upon successfully connecting to db.
 2019-04-29 11:02:40 -04:00
Sergey Golitsynskiy 2170c2326c Merge branch 'dev' of github.com:galaxyproject/galaxy into dev 2019-04-29 10:59:58 -04:00
Nicola Soranzo 65cdb6f0d9 Merge pull request #7840 from jmchilton/version-19.09.dev 
Version 19.09.dev
 2019-04-29 15:53:45 +01:00
Nicola Soranzo 43fbe6a289 Merge pull request #7839 from jmchilton/version-19.05 
[19.05] Update version to 19.05.rc1
 2019-04-29 15:53:13 +01:00
Dannon Baker 0e7e68cebd Swap to extend instead of relying on (recently deprecated) bootstrap float mixin 2019-04-29 10:44:23 -04:00
Nicola Soranzo fc4e883c32 Use markupsafe.escape instead of cgi.escape (#7837) 
Use markupsafe.escape instead of cgi.escape
 2019-04-29 13:51:05 +01:00
Nicola Soranzo ed18d34f08 Merge pull request #7838 from mvdbeek/use_getfullargspec_on_python3 
Use getfullargspec on python3
 2019-04-29 13:50:45 +01:00
John Chilton 5a6e4f0849 Merge branch 'version-19.05' into version-19.09.dev 2019-04-29 08:45:33 -04:00
John Chilton 7b4b6336ca Update version to 19.05.rc1 2019-04-29 08:45:32 -04:00
John Chilton 4e57b4eb9d Update version to 19.09.dev 2019-04-29 08:45:32 -04:00
John Chilton d008e47303 Merge remote-tracking branch 'upstream/release_19.01' into dev 2019-04-29 08:43:11 -04:00
mvdbeek 75c15b4666 Use markupsafe.escape instead of cgi.escape 
This silences some deprecation warnings on python 3.
 2019-04-29 12:24:52 +02:00
mvdbeek b68dcb4507 Use getfullargspec on python3 
`getargspec` is marked for deprecation.
 2019-04-29 11:52:33 +02:00
Marius van den Beek 2d0a68429d Merge pull request #7832 from pcm32/patch-3 
Fix failure in resubmitting job more than once
 2019-04-29 10:48:50 +02:00
Kidane M. Tekle 5723e15cce added elixir oidc backend, python soical auth version upgraded 2019-04-29 08:25:18 +02:00
Marius van den Beek e23c9466c9 Merge pull request #7834 from nsoranzo/followup_on_7823 
Remove recursion from ``expand_nested_tokens()``
 2019-04-27 12:07:45 +02:00
Sergey Golitsynskiy 158fb6b454 Update config_schema + run make config-rebuild 2019-04-27 01:19:57 -04:00
Sergey Golitsynskiy f8bfd16d5a Remove inline import; call time.sleep instead 
time module already imported.
 2019-04-26 20:37:05 -04:00
Nicola Soranzoandic4f cf6ab64a89 Update config/galaxy.yml.sample 
Co-Authored-By: ic4f <sgolitsynskiy@gmail.com>
 2019-04-26 19:51:06 -04:00
Sergey Golitsynskiy 5cab87947a Add Exception to except statement 
Fixing lint error
 2019-04-26 19:34:32 -04:00
Nicola Soranzo 084296c92a Remove recursion from `expand_nested_tokens()` 
Also add test for recursive nested token.
 2019-04-27 00:09:31 +01:00
Sergey Golitsynskiy 7ead1cedd4 Delete test file 
This test file contained 2 basic unit tests that tested the proposed new
config values. Instantiating a Configuration object without passing the
required arguments seems to have caused other tests to fail. Trying same
PR without additional unit tests.
 2019-04-26 18:03:57 -04:00
Sergey Golitsynskiy 4604bac4d6 Merge remote-tracking branch 'upstream/dev' into dev 2019-04-26 18:03:46 -04:00
Pablo Moreno 96256b21f0 Fix failure in resubmitting job more than once 2019-04-26 18:42:38 +01:00
John Chilton 003cdb83fd Merge pull request #7823 from mvdbeek/fix_token_replacement_py3 
Fix nested macro/token expansion on python 3
 2019-04-26 10:59:38 -04:00
John Chilton c0291c4267 Merge pull request #7826 from mvdbeek/fix_value_wrapper_comparison 
Fix InputValueWrapper gt/ge/lt/le comparisons
 2019-04-26 10:58:13 -04:00
John Chilton a13e9cbc12 Merge pull request #7828 from mvdbeek/maxseconds_interactor 
Allow specifying maxseconds in verify_tool
 2019-04-26 10:56:52 -04:00
John Chilton b09f48978e Merge pull request #7830 from erasche/grt-tiny-fix 
grt small bugfix for ancient data, deprecated params table
 2019-04-26 10:56:21 -04:00
Dannon Baker c20a6d139d Drop autoregistration flag; we'll use create instead. 2019-04-26 09:42:13 -04:00
Dannon 66ee598d99 Merge pull request #7829 from mvdbeek/fix_search_function 
Fix tool search function
 2019-04-26 09:34:09 -04:00