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9001 Commits
Author SHA1 Message Date
Carl Eberhard 83cc4361b7 Fix to safari flexbox and merge 2015-03-03 13:32:10 -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
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 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 48b37efaff Merge branch 'sentry_shed_debug_fix' into dev 2015-03-02 15:19:59 -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
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 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
Nicola Soranzo 7cec9d2d5a WIP: Initial work on yapsy removal from galaxy.auth . 2015-03-01 22:23:54 -05:00
Nicola Soranzo bfcdff0f8b Rename CustomAuth to Auth. 2015-03-01 22:23:54 -05:00
Nicola Soranzo 832514bf6e Make customauth always active. 
Added a config/customauth_conf.xml.sample file containing only the normal
Galaxy database authentication method.
Removed enable_customauth config option.
 2015-03-01 22:23:54 -05:00
Nicola Soranzo ba4acdd1f9 PEP-8, doc and other fixes suggested in PR #555 review. 2015-03-01 22:23:54 -05:00
Nicola Soranzo 3c0221ee5e Remove AlwaysAccept customauth plugin. 2015-03-01 22:23:54 -05:00
Nicola Soranzo 7951d0ced5 Rename enable_customauth_echo config option to customauth_debug. 2015-03-01 22:23:54 -05:00
Andrew Robinson 357a23b290 Added Custom Authentication module support (CustomAuth) 
Initial modules:
- ActiveDirectory (ldap)
- LocalDB (fall back to galaxy users)
- AlwaysAccept (whitelist)
- AlwaysReject (blacklist)
Sysadmin documentation at: https://docs.google.com/document/d/1CJp_m3vW7QKtAyBTMbE1MLgV6FAMuG3VO4HR-wHPkGk
Testing documentation at: https://docs.google.com/document/d/1Cocx6Rt3eqPdm8IjOKYAR4RaY-9P2iFNXCt3AYg3PlA
 2015-03-01 22:23:53 -05:00
guerler d4fbd581b9 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev 
Conflicts:
	static/scripts/packed/mvc/tools/tools-form-base.js
 2015-02-28 05:15:02 -05:00
guerler 28a4e6c354 Parameters: Remove unused uncoded id from data parameter dictionaries 2015-02-28 05:01:55 -05:00
Daniel Blankenberg 86f66bc1c4 Allow External display applications to use Tool Data Tables. 
Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).

Merge branch 'release_15.03' into dev
 2015-02-27 15:53:58 -05:00
Daniel Blankenberg 9f68fe0792 Allow External display applications to use Tool Data Tables. 2015-02-27 15:50:13 -05:00
John Chilton aa83a87d8a Move integrated tool panel logic into its own module/mixin. 2015-02-27 15:35:07 -05:00
John Chilton 6c2fc68476 PEP-8 in toolbox/base.py. 2015-02-27 15:35:07 -05:00
John Chilton c2378c197a Use append_section abstraction. 2015-02-27 15:35:07 -05:00
John Chilton 7488039b88 Eliminate duplication between ts installing from API and web controller. 
Favoring the web controller variant slightly - it is known to work better and has test coverage.
 2015-02-27 15:35:06 -05:00
John Chilton 5bac3dafce Refactor __install_repositories so it looks more like newer install_web. 2015-02-27 15:35:06 -05:00