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Author SHA1 Message Date
Dannon Baker 513fb016dc Sync client formatting. 2019-05-01 08:44:35 -04:00
guerler 89cf0a48fc Wait until workflow saving message disappears 2019-04-30 21:31:26 -04:00
guerler 2a0e0e1736 Remove close option from selenium tests 2019-04-30 19:14:25 -04:00
guerler 8527d0c5cf Remove close option from workflow settings menu 2019-04-30 15:17:48 -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
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
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
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 4e57b4eb9d Update version to 19.09.dev 2019-04-29 08:45:32 -04:00
John Chilton 7b4b6336ca Update version to 19.05.rc1 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
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 66ee598d99 Merge pull request #7829 from mvdbeek/fix_search_function 
Fix tool search function
 2019-04-26 09:34:09 -04:00
Helena Rasche 1b6b52ce10 swap to exception 2019-04-26 13:29:12 +02:00
Helena Rasche c54bddd3f3 it is pointless to load sample config 2019-04-26 13:27:59 +02:00
Helena Rasche cb7b26e25e Remove now-deprecated params + more defensive 2019-04-26 13:20:37 +02:00
Helena Rasche dcfff4d5de ensure a string is returned 
Very old values in EU db were missing this.
 2019-04-26 13:20:26 +02:00
mvdbeek e7b0406d26 Fix tool search function 
This broke in https://github.com/galaxyproject/galaxy/pull/7797
and was cuasing the Selenium test to fail (which weirdly enough it
didn't in that PR).
 2019-04-26 12:13:05 +02:00
mvdbeek 8886558e3d Allow specifying maxseconds in verify_tool 
And passing in tool_test_dicts, which shouold be helpful when
testing tools with many tests.
 2019-04-26 10:31:06 +02:00
Sergey Golitsynskiy 06f5cfa562 Add option to wait for db to become available 
Configurable option to wait for the database to become available instead
of failing immediately.

_configure_models() seems to be the earliest/reasonable place for it.
 2019-04-25 20:35:49 -04:00
mvdbeek 60d87107ee Fix InputValueWrapper gt/ge/lt/le comparisons 2019-04-25 21:32:47 +02:00
mvdbeek 77ae679746 Fix nested macro/token expansion on python 3 
I noticed that in multiqc @ESCAPE_IDENTIFIER@ wasn't being replaced.
It's surprising that this didn't cause any issues on python 2,
but might have to do with the iteration order changes.
 2019-04-25 19:51:25 +02:00
Martin Cech 6c460bab23 Merge pull request #7812 from nsoranzo/fix_7809 
Encode email messages using UTF-8
 2019-04-24 22:01:14 -04:00
Martin Cech a3c2829bbc Merge pull request #7815 from jmchilton/shorten_message 
More concise tool error warning message.
 2019-04-24 21:58:39 -04:00
John Chilton 616446e09f Merge pull request #7799 from mvdbeek/fix_parameter_workflow_outputs 
Don't let parameter_input steps be workflow outputs
 2019-04-24 17:16:42 -04:00
John Chilton 4e9b1478bf Merge pull request #7797 from mvdbeek/hide_expression_tools_in_main_analysis_app 
Hide ExpressionTools in main analysis app
 2019-04-24 17:16:00 -04:00
John Chilton d3f4294acc More concise tool error warning message. 
xref https://github.com/galaxyproject/galaxy/pull/7755#issuecomment-484621641
 2019-04-24 17:10:54 -04:00