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Author SHA1 Message Date
Martin Cech a2f0bdbded disable conda_auto_init 2016-08-22 13:34:18 -04:00
Nicola Soranzo f4806e9dd4 Merge branch 'release_16.04' into release_16.07 2016-08-18 15:49:30 +01:00
Martin Cech 3492e96574 Merge pull request #2811 from nsoranzo/release_16.04_backports 
[16.04] Two backports
 2016-08-18 10:08:48 -04:00
Dave Bouvier a134587c89 Correctly check set_environment declarations when updating repository. 2016-08-18 14:08:40 +01:00
Nicola Soranzo 1f69bf32e8 Fix run.sh --daemon 
Broken in commit d5c52cadfd .
Partial backport from #2765 .
Close #2724.
 2016-08-18 14:07:26 +01:00
Martin Cech 6c2468832b Merge pull request #2809 from carlfeberhard/fix.hdca-dnd 
[16.07] API, history contents: allow 'source' in payload
 2016-08-17 16:08:14 -04:00
Dannon Baker 30d5b45d43 Merge pull request #2810 from natefoo/split-kwargs 
[16.07] Revert str.split() syntax for Python 2 compatibility
 2016-08-17 15:40:39 -04:00
Nate Coraor c3d7ca8eef Revert str.split() syntax for Python 2 compatibility 2016-08-17 14:02:15 -04:00
carlfeberhard bf9a15389e API, history contents: allow 'source' in payload 
In create, checks both kwd and payload for 'source' parameter when
creating a new hdca. This allows source to be passed in the body and
not query string.

This fixes the copy call in history-contents when copying an hdca
by drag and drop in the multi history view.
 2016-08-17 13:08:27 -04:00
Marius van den Beek d1c58f7ab0 Merge pull request #2800 from jmchilton/dbkey_output_without_cond 
[16.04] Fix dbkey problem discovered by @hrhotz
 2016-08-17 09:12:17 +02:00
Dannon Baker 8d512c98e2 Merge branch 'release_16.04' into release_16.07 2016-08-16 16:45:11 -04:00
Björn Grüning 752df7f82b Merge pull request #2788 from dannon/backport_condainstall 
[16.04] Conda explicitly checks for .sh in the command as a part of it's logi…
 2016-08-16 20:41:49 +02:00
John Chilton e06cf9a978 Add None check to fill_template... 
... as requested by @nsoranzo.
 2016-08-16 14:12:17 -04:00
John Chilton 0110d5a05a Add a test case to dbkey_output_action.xml. 
Per @nsoranzo's template and suggestion.
 2016-08-16 14:08:38 -04:00
John Chilton 88d02dba6e Don't fill in a cheetah default if unavailable. 
... in metadata hack from #961.
 2016-08-16 12:55:56 -04:00
Dannon Baker a13117fdf5 Merge pull request #2792 from natefoo/uwsgi-fork-raven 
[16.07] Do not instantiate the raven (sentry) client or tool conf watchdog threads until uWSGI postfork
 2016-08-16 12:41:42 -04:00
John Chilton 510290feea Add example of regressed 16.04 behavior related to dbkey output actions. 2016-08-16 10:34:57 -04:00
Nate Coraor c431d8c06c Fix import linting error 2016-08-15 17:12:16 -04:00
Nate Coraor 59e88fa6f7 Do not instantiate the raven (sentry) client until uWSGI postfork 2016-08-15 16:18:44 -04:00
Nate Coraor c3c97cef1e Do not start tool conf watchdog threads until postfork 2016-08-15 16:17:45 -04:00
Björn Grüning 40f8589c38 Merge pull request #2789 from mvdbeek/is_conda_installed 
Make conda install and resolver status more robust
 2016-08-15 20:48:05 +02:00
Marius van den Beek 30a14e3c39 Raise a more specific exception 2016-08-15 19:38:32 +02:00
Marius van den Beek 0cc10d184d Move can_install_conda and is_conda_installed into CondaContext 2016-08-15 19:36:04 +02:00
Marius van den Beek fdc43a1448 Rephrase conda options and explain conda_prefix, add current length limitation 2016-08-15 18:34:06 +02:00
Marius van den Beek 85aaa23785 Make conda install and resolver status more robust 
We disable the conda resolver if conda_exec is not found and we are
unable to install conda. Skip installing conda if it won't be used
(because conda exec is outside of conda_prefix).
Install conda if conda_prefix is an empty directory.
 2016-08-15 18:34:06 +02:00
Dannon Baker 43320aa8d1 Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. 2016-08-15 12:25:17 -04:00
Dannon Baker d87fbdd5b8 Merge pull request #2774 from natefoo/uwsgi-fork 
[16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork
 2016-08-15 12:15:18 -04:00
Nate Coraor 6ca6f9019e Merge pull request #5 from dannon/uwsgi-fork 
Add a warning when it is detected that a process is uwsgi based but u…
 2016-08-15 12:12:54 -04:00
Dannon Baker be7c5bce1d Words. 2016-08-15 12:08:25 -04:00
Dannon Baker 699e955d7f Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available. 2016-08-15 12:00:05 -04:00
Nate Coraor 2f0c4562ae Merge pull request #4 from dannon/uwsgi-fork 
Force update repository manager to launch postfork.
 2016-08-15 11:56:26 -04:00
Dannon Baker efbd8f2d9f Separates the decorator from the injected uwsgi package to fix 
'process_is_uwsgi' logic.
 2016-08-15 11:29:39 -04:00
Carl Eberhard 0719d83837 Merge pull request #2780 from martenson/lib-style-fix 
[16.07] separate styles of new and old libraries fixing various ui bugs
 2016-08-12 15:24:48 -04:00
Dannon Baker 66e725b6e3 Merge branch 'release_16.04' into release_16.07 2016-08-12 13:34:41 -04:00
Dannon Baker ceeef39edb Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 
[16.04] Backport #2734
 2016-08-12 13:33:36 -04:00
Martin Cech fb6f3c9c69 separate styles of new and old libs fixing various ui bugs 2016-08-12 13:04:42 -04:00
guerler d24ce8b0a4 Add implicit conversions target extension to hda name when listed as selection option 2016-08-12 18:01:45 +01:00
Dannon Baker 7c5cadbe7d Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future. 2016-08-12 08:12:19 -04:00
Dannon Baker 7ebf7e5706 Force update repository manager to launch postfork. 2016-08-12 07:55:57 -04:00
Nate Coraor af533a7a6f Create a uWSGI postfork function registry. Also, start the tool conf 
watcher thread post-fork.
 2016-08-11 12:28:09 -04:00
John Chilton 4b86f6137f Merge pull request #2773 from nsoranzo/release_16.07_followup_for_2759 
[16.07] Small followup for #2759
 2016-08-11 11:43:22 -04:00
Nicola Soranzo a9e04331de Ensure EXIT_CODE is set. Kill Galaxy for local testing 
Also properly initialise $i and use POSIX syntax
 2016-08-11 15:05:44 +01:00
Nicola Soranzo 89304762a2 Rephrase comment 2016-08-11 15:00:14 +01:00
Björn Grüning a7be24e111 Merge pull request #2759 from martenson/conda_config 
[16.07] install Conda at startup; enable conda_auto_init in sample conf
 2016-08-11 10:11:13 +02:00
Martin Cech 702891e3ef Merge pull request #16 from mvdbeek/fix_string_substitution 
Extend startup time
 2016-08-10 13:59:09 -04:00
Marius van den Beek e35c629569 Extend startup time 2016-08-10 19:23:17 +02:00
Nicola Soranzo 9c03d4c16f Merge branch 'release_16.04' into release_16.07 
flake8 pinned also for py27-lint-imports-include-list testenv
 2016-08-10 16:31:51 +01:00
Nicola Soranzo f2f62f340e Merge branch 'release_16.01' into release_16.04 
Conflicts:
	.ci/flake8_blacklist.txt
	tox.ini
 2016-08-10 16:19:19 +01:00
Martin Cech 68f718d53b Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package 
[16.01] Fix misplaced parenthesis
 2016-08-10 11:05:05 -04:00
Nicola Soranzo f4cb63d6f2 Pin flake8 version 
Do not pin when forward-merging to dev branch.
Also ignore .tox/ and eggs/ as in #2650 .
 2016-08-10 15:17:21 +01:00