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Author SHA1 Message Date
Carl Eberhard 34725e8a84 Fix to 7ac8631 to use proper registrationForm id 2015-03-03 16:35:00 -05:00
Carl Eberhard 7ac86312e4 Fix user registration to respect use_panels when in the Galaxy app 2015-03-03 16:11:44 -05:00
Carl Eberhard 83cc4361b7 Fix to safari flexbox and merge 2015-03-03 13:32:10 -05:00
Martin Cech 5f67895a00 compile AND pack handlebar templates 2015-03-03 13:17:29 -05:00
Carl Eberhard d390ef2955 Fix to safari that still uses prefixed flexbox attributes 2015-03-03 13:13:26 -05:00
Daniel Blankenberg 2e3bebbfe2 Fix for reports app not running mysql. 2015-03-03 11:55:47 -05:00
Daniel Blankenberg 30d7549538 When loading Dynamic Display application links, allow the application to load even if one set of links does not. 2015-03-03 10:57:54 -05:00
Daniel Blankenberg 853f5156c0 When loading Dynamic Display application links, allow the application to load even if one set of links does not. 2015-03-03 10:49:12 -05:00
Daniel Blankenberg 05ff2aa6ce Add a 10 second timeout to loading data URLs for Tool Data Tables. 2015-03-03 10:24:58 -05:00
John Chilton f823278efd Fix bug in workflows test for implicit connections between steps. 
It would fail when being run with the rest of the suite and not on its own - because it was using the same id for the workflow id and invocation id - which is obviously wrong unless it is a completely fresh database :).
 2015-03-03 09:37:30 -05:00
John Chilton fc0a6d8764 Fix intermittently failing test test_workflow_run_dynamic_output_collections. 
Love it when the bugs correspond to actual TODOs I left in the code.
 2015-03-03 09:30:55 -05:00
John Chilton 391abd5fd6 Remove assert False from test/api/test_workflows_from_yaml.py. 
These aren't ideal tests - but it is some indication that things are working that the API will import the workflow and produce a representation. Should follow up at some point and verify the representation is in fact the correct one.
 2015-03-02 22:39:58 -05:00
John Chilton f8bfe89c42 Clarify failing test test_tools.py. 2015-03-02 22:39:58 -05:00
John Chilton a20938fc48 Attempt to fix intermittently failing jobs API test. 
Retry check several times in case there is some sort of timing problem where a history turns okay - before a job. Improve assertion error message.
 2015-03-02 22:39:50 -05:00
John Chilton b1f3654208 Tool data API testing fixes. 
- Add files I didn't commit previously in test/functional/tool-data/.
 - Comment out test for tool data table deletion since Dan fixed the problem of regular users running data managers through the API (https://github.com/galaxyproject/galaxy/commit/48f77dc742acf01ddbafafcc4634e69378f1f020) that I previously exploited to write the test.
 2015-03-02 22:36:24 -05:00
dannon 3e11f96a6e One more bugfix in admin_toolshed / undefined var. 2015-03-02 20:51:40 -05:00
dannon 7670184006 Remove cruft and unused vars, cleanup/pep8 in admin_toolshed controller. 2015-03-02 20:43:37 -05:00
dannon 3961a8f3f9 Fix another bug in admin_toolshed controller encountered if tool_dependency_dir not set but deps are defined 2015-03-02 20:10:28 -05:00
dannon ce42cbf489 Fix bug in toolshed set_tool_versions during error case 2015-03-02 19:51:46 -05:00
guerler 0d62ee6960 Parameters: Fix collection selection for multiple dataset input field 2015-03-02 18:25:46 -05:00
guerler 434aa056a2 Parameters: Cover additional case for multiple hdas 2015-03-02 18:12:34 -05:00
dannon c01c3e9f4f Swap logging in auth exception handling to use log.exception 2015-03-02 17:35:14 -05:00
dannon 8fe7eb116a Change auth_debug behavior -- simply use an appropriate loglevel 2015-03-02 17:26:11 -05:00
Martin Cech 28863fefd1 compile handlebar templates 
I wanted only one but the compilation alg probably changed so
am adding all
 2015-03-02 17:19:11 -05:00
Martin Cech 2bf52fe2f9 increase toolbox search delay 
log search terms
 2015-03-02 16:39:48 -05:00
Martin Cech 86db9034e5 Merge branch 'release_15.03' into dev 2015-03-02 16:37:45 -05:00
Martin Cech 8e6fbe34ca tweak toolbox search to provide better (and more) results 
with the inclusion of toolhelp in index and with more versions
of the same tools being massively installed the search results were
inconsistent and inaccurate and incomplete.
addresses https://trello.com/c/6Bvbduci/2486-toolbox-search-is-behaving-wrongly-differently
 2015-03-02 16:33:43 -05:00
Dannon Baker 671e91bc5e Merge branch 'dev' of github.com:galaxyproject/galaxy into dev 2015-03-02 15:20:15 -05:00
Dannon Baker 48b37efaff Merge branch 'sentry_shed_debug_fix' into dev 2015-03-02 15:19:59 -05:00
Nate Coraor e4e5df04de Make the UCSC Browser to pull new builds from (in the cron script) a 
command line argument. Default is UCSC Main, but for Galaxy Test and
Main we use UCSC Test.
 2015-03-02 14:56:01 -05:00
Dannon Baker 1b23706b8f Rearranging the layers of middleware to allow sentry and debug to coexist without exploding (but you probably don't want to use both at once anyway) 2015-03-02 14:54:29 -05:00
Carl Eberhard e3f3c3599e Merge branch 'fix.validate-genome' into dev 2015-03-02 14:25:41 -05:00
Carl Eberhard ebda6ac03d Fix to remove validation of genome builds since some data source tools will assign invalid genome builds and later validation makes these hdas un-updatable 2015-03-02 14:22:00 -05:00
John Chilton 589b3fb226 Update basic.py to allow collection reduction with new tool form. 2015-03-02 13:53:17 -05:00
John Chilton dbb9dd78ab Update basic.py to allow collection reduction with new tool form. 2015-03-02 13:45:12 -05:00
Dannon Baker b6cc9d5fc5 Fix for auth when user doesn't exist. 2015-03-02 12:29:54 -05:00
Daniel Blankenberg 6e17bf4e40 Add a 10 second timeout to loading data URLs for Tool Data Tables. 2015-03-02 11:34:55 -05:00
Carl Eberhard 0c94f04c5c Fix to sessionStorage Model to surpress QUOTA DOMExceptions when Safari users are in private browsing mode 2015-03-02 11:20:37 -05:00
Dannon Baker 6224e2226b Remove unnecessary complexity of _get_child_element 2015-03-02 10:15:27 -05:00
Dannon Baker daa663e8bd Fix customauth to be python2.6 compatible. 2015-03-02 10:12:21 -05:00
John Chilton aaa5ea5f7a PEP-8 variable names in galaxy.auth and submodules. 2015-03-01 22:23:56 -05:00
John Chilton 4044a66aa9 PEP-8 method names in galaxy.auth and submodules. 2015-03-01 22:23:55 -05:00
John Chilton 00ee2ab29c Replace print statements with log statements in auth providers. 
This is more galactic.
 2015-03-01 22:23:55 -05:00
John Chilton 9fd6685f4b Auth fixes for switch from YAPSY to plugin_config. 2015-03-01 22:23:55 -05:00
John Chilton 9787ce8c63 Default auth provider should allow password change. 2015-03-01 22:23:55 -05:00
John Chilton 538487d465 Rearrange auth to use a Galaxy manager object pattern. 
On the positive-side this feels much more like a traditional Galaxy style access pattern and each operation is likely much more efficient since the plugins aren't be reloaded and XML re-parsed for each action. The downside is a Galaxy restart is required to update the authentication providers for Galaxy - while this is less than ideal in some ways - it is what Galaxy admins would expect for the other configuration files anyway so it is arguably better to not be more clever here.
 2015-03-01 22:23:55 -05:00
John Chilton 25d72de62b Finish replacing YAPSY with galaxy.util.plugin_config. 2015-03-01 22:23:55 -05:00
John Chilton 441c8fe1af PEP-8 fixes for auth code. 2015-03-01 22:23:55 -05:00
John Chilton b3174efa8e Reuse galaxy.util bool checking in galaxy.auth. 2015-03-01 22:23:55 -05:00
John Chilton 2d7d97d343 Use galaxy-style logging instead of print in galaxy.auth. 2015-03-01 22:23:54 -05:00