opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 10:24:38 +08:00
Code Issues Packages Projects Releases Wiki Activity
19,781 Commits 62 Branches 243 Tags
a3034ab6d99d5087a7dcc1de0360fe2ebafde40f
Commit Graph
10392 Commits
Author SHA1 Message Date
Dannon Baker 6953bdf704 Merge pull request #1059 from guerler/fix_message_000 
[15.10] Fix parsing of message configuration
 2015-11-11 10:03:24 -05:00
Dannon Baker 4f72178a95 Merge pull request #1038 from guerler/fix_imported_rerun_000 
[15.10] Fix job rerun for imported histories
 2015-11-11 09:52:58 -05:00
guerler 6580701395 Fix parsing of message configuration 
Fix default value

Add root to Galaxy object
 2015-11-10 23:51:29 -05:00
guerler b2723e7467 Disable invalid test case. Add validation criteria. 
Fix comments

Fix comment
 2015-11-10 15:36:55 -05:00
guerler b88864586c Fix warning statement 2015-11-10 13:45:20 -05:00
guerler a8147327af Derive permission from job outputs 
Remove history manager

Use dataset manager
 2015-11-09 23:58:08 -05:00
guerler fef1e548bb Fix job permission handling 
Catch unavailable history

Fix test
 2015-11-06 23:10:08 -05:00
Dannon Baker d20677bb64 Fix Remote User failures due to apache null headers. 2015-10-29 12:09:45 -04:00
Vimalkumar Velayudhan dfb59002ba Use object store for imported history datasets and included files 
(cherry picked from commit ea89dd8f14)
 2015-10-22 12:51:48 -04:00
Vimalkumar Velayudhan 57d0620292 Fix for missing included files on history export and import. 
Notes:

If a history was exported previously, galaxy would just serve the cached version.
In that case, it is better to make some changes to the history for example, by re-running
the last job and then exporting it.

Export of histories that haven't been exported previously should work without problems.

(cherry picked from commit 9ea0fee48a)
 2015-10-22 12:51:42 -04:00
guerler 8a0a445ec3 Fix workflow extraction from history 2015-10-21 17:36:44 -04:00
guerler 9d3893ed63 Undo commit, wrong branch 2015-10-21 17:26:33 -04:00
guerler ee327702d7 Fix workflow extraction from history 
Fix history extraction by returning value dictionary

Remove previous fix
 2015-10-21 17:20:42 -04:00
Dannon Baker 6f5aafe627 For require_login=True, redirect directly to login without showing empty (and broken) looking panels, and potentially hitting an endless reload cycle. 2015-10-21 12:19:00 -04:00
Dannon Baker a742198a36 Fixes for switching history (standard as well as multiview) when using IE11. Intentionally minimal fix for 15.10, more comprehensive refactoring+solution forthcoming for dev. 2015-10-14 21:57:23 -04:00
Eric Rasche 4705409d38 Expose all API keys to admins under REMOTE_USER 
This is the default setting for non-remote-user setups, this commit
adjusts the middleware to behave as expected.

Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authentication-disabled-td4668052.html
 2015-10-08 10:22:41 -05:00
Daniel Blankenberg 092fc17ec0 Merge pull request #846 from jmchilton/ucsc_cleanup 
UCSC Tool Cleanup
 2015-10-05 17:05:56 -04:00
Martin Cech 753bb9de0f Merge pull request #839 from jmchilton/text_file_busy 
Attempt to fix "Text file busy" errors (testing and production)
 2015-10-05 14:57:16 -04:00
John Chilton 1aebbc3f68 Remove likely broken UCSC proxy and associated tools. 
Unused for many, many years and likely no longer works.
 2015-10-05 15:55:21 +01:00
Nicola Soranzo 54410d7d70 Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ . 
Fix https://github.com/galaxyproject/galaxy/issues/809#issuecomment-145107037 .
 2015-10-05 12:03:36 +01:00
John Chilton b75175f18d Centralize logic for writing job scripts. 
Runners were using various permissions, some didn't close file handles, etc....

In addition, run sync after script is written to avoid "Text file busy" problems in all job script scenerios.
 2015-10-05 11:02:14 +01:00
John Chilton 4e35ff04a1 More improved file handling for job code. 
Another stab in the dark that won't actually fix the testing issues with Docker.
 2015-10-05 09:44:26 +01:00
Dannon Baker 02962ae646 Merge pull request #830 from jmchilton/local_close 
Improved file handling in local runner.
 2015-10-02 11:08:29 -04:00
John Chilton b3a3756424 Merge pull request #821 from dannon/statsd 
Request timing middleware via statsd
 2015-10-02 15:57:37 +01:00
John Chilton 8af833cb34 Fix a potentially problematic file operation. 
It might be causing intermittent test failures when running this code in Docker containers, we are unsure.
 2015-10-02 11:05:55 +01:00
Dannon Baker 5592422d01 Merge pull request #826 from guerler/fix_select_000 
Fix default value for optional select fields
 2015-10-01 16:08:02 -04:00
guerler 8cc27b45d0 Fix default value for optional select fields 2015-10-01 15:23:06 -04:00
Dannon Baker de82b1236d Merge branch 'master' into dev 2015-10-01 12:38:44 -04:00
Martin Cech c133078b60 Merge pull request #822 from jmchilton/db_test_fix 
Fix db initialization when galaxy.ini doesn't exist.
 2015-10-01 12:03:08 -04:00
Dannon Baker 3fa7844956 Opt for failing instead of continuing to run Galaxy if statsd middleware is configured but module is not available. 2015-10-01 11:44:23 -04:00
Dannon Baker 72330cc316 'Fix' for unit tests. 2015-10-01 11:32:55 -04:00
Dannon Baker c6794e62c5 In lieu of rolling an egg, just test for statsd when middleware is wrapped. 2015-10-01 11:19:44 -04:00
Dannon Baker fc69247d50 Fix default statsd port. 2015-10-01 10:50:48 -04:00
John Chilton 6592a14089 Fix db initialization when galaxy.ini doesn't exist. 2015-10-01 12:02:13 +01:00
Dannon Baker 52a51af4ed Fix middleware application message. 2015-09-30 16:01:18 -04:00
Dannon Baker 6ee9a08cf2 Merge pull request #786 from guerler/tool_form_003 
Remove tool form mako, reduce tool runner, fix job resubmission options
 2015-09-30 13:57:25 -04:00
Dannon Baker 1b841a9aa4 Tweak docstring 2015-09-30 13:25:09 -04:00
Dannon Baker e710c46f24 Fix namespacing of events 2015-09-30 13:16:25 -04:00
carlfeberhard 1a13efe488 API, Datasets: fix returned tuple from creating_job; normalize id encoding, parens, naming; move both rerunnable and creating_job into datasets.py to allow (future?) use by lddas and ldas 2015-09-30 11:57:40 -04:00
Dannon Baker 9aee212225 Merge pull request #770 from nsoranzo/dev 
flake8 lib/galaxy/webapps/tool_shed/model/migrate/versions/ .
 2015-09-30 10:28:00 -04:00
Dannon Baker 56734878e7 Statsd middleware for request timing. 2015-09-30 10:23:26 -04:00
guerler 6d00f38f0a Merge branch 'dev' of https://github.com/galaxyproject/galaxy into tool_form_003 
Conflicts:
	client/galaxy/scripts/mvc/tools/tools-form.js
	static/maps/mvc/tools/tools-form.js.map
	static/scripts/mvc/tools/tools-form.js
 2015-09-29 15:55:59 -04:00
Martin Cech 76fcde3274 Merge pull request #811 from dannon/prt_fix 
[15.07] Fix change_password (destination for password reset link) to work w/ …
 2015-09-29 14:54:02 -04:00
Daniel Blankenberg 6406276146 Merge pull request #806 from martenson/data-lib-work 
UI and API for data library folders management
 2015-09-29 14:15:11 -04:00
Daniel Blankenberg 531875753d Merge pull request #812 from dannon/prt_email_tweak 
Tweak password reset email template to truly be plain text.
 2015-09-29 14:04:09 -04:00
Daniel Blankenberg 75cc56793c Merge pull request #813 from jmchilton/tool_loading 
Small tweaks to tool loading.
 2015-09-29 14:03:37 -04:00
Nate Coraor 90dc2b1093 Merge branch 'release_15.07' into dev 2015-09-29 13:55:22 -04:00
Dannon Baker 90f63a401b Tweak password reset email template to truly be plain text. 2015-09-29 11:37:20 -04:00
Dannon Baker 8a30d3add4 Fix change_password (destination for password reset link) to work w/ require_login 2015-09-29 11:27:38 -04:00
John Chilton de2bb5771b Remove unused code. 2015-09-29 13:57:15 +01:00