James Taylor
2e86322d45
Backed out changeset bc87cbb31647
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Accidently overwrote 'twilltestcase.py' with and older version.
2009-01-12 20:42:37 -05:00
James Taylor
3950563374
Restore twill's buffer (nose captures this now so it is useful for debugging, perhaps a flag?)
2009-01-12 18:35:18 -05:00
James Taylor
5eed0e666d
History controller (missed in last commit)
2009-01-12 18:33:19 -05:00
James Taylor
c245b5b6ca
Changes to the 'list histories' interface. This incorporates the changes from Assaf Gordon to display datasets by state, as well as changing how switch / delete/ undelete work to make the interface less disruptive. Share and rename still work as before. There is now a history controller, and some fixes to tests to deal with that. New grid styles used here will eventually be propogated to other data grid tables.
2009-01-12 18:25:32 -05:00
Greg Von Kuster
f2c1abdd85
Fix unit_tests broken from my last commit.
2009-01-12 15:48:44 -05:00
Greg Von Kuster
41bedcfac3
Standardize the interface for creating new groups and roles and for associating users, groups, roles by eliminating the checkbox approach.
2009-01-12 15:40:05 -05:00
Nate Coraor
20f4b501c2
merging heads
2009-01-09 17:18:36 -05:00
Nate Coraor
9dbad8f623
galaxy.config.resolve_path is not absolute...
2009-01-09 17:18:18 -05:00
Nate Coraor
f89f96ff58
merging heads
2009-01-09 17:09:15 -05:00
Nate Coraor
2f0f2dfb9a
Make the PBS script/stdout/stderr directory configurable.
2009-01-09 17:08:49 -05:00
Nate Coraor
570b7387e4
merging heads
2009-01-09 16:01:10 -05:00
Nate Coraor
8330cbe472
merging heads, resolved conflicts
2009-01-09 16:00:59 -05:00
Nate Coraor
1423af2fd5
Add an option to override the output dataset(s) path, so they may be written to
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the working directory. This allows administrators to mount datasets read-only
on cluster nodes.
2009-01-09 15:59:29 -05:00
Nate Coraor
a0c99d0be5
merging heads
2009-01-09 14:08:38 -05:00
Nate Coraor
68d4d00997
Allow upstream proxy to set wsgi.url_scheme, so link generation is
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correct if the proxy uses a different transport with clients than it
does with Galaxy. This doesn't work automatically. In Apache, you'd
need to set the header yourself:
RequestHeader set X-URL-SCHEME https
For a discussion on how this affects links to the UCSC Genome Browser,
see:
http://mail.bx.psu.edu/pipermail/galaxy-user/2009-January/000430.html
2009-01-09 14:07:16 -05:00
Nate Coraor
df7be294d0
merging heads
2009-01-08 11:08:13 -05:00
Nate Coraor
76a02fcf76
Fix from James Casbon for a problem he has experienced when using remote_user (a new user creation seems to be attempted before a session exists).
2009-01-08 11:04:19 -05:00
Greg Von Kuster
ad33e0bc5a
Fix for my last commit.
2009-01-07 15:33:35 -05:00
Greg Von Kuster
81d3896fe6
merging from central
2009-01-07 15:32:39 -05:00
Greg Von Kuster
86c7a80c31
Add support for NCBI Blast XML data format.
2009-01-07 12:20:35 -05:00
Greg Von Kuster
b7c0bbc280
merging from central
2009-01-07 12:19:58 -05:00
Greg Von Kuster
fd25567658
log exceptions when removing temporary files when upload fails.
2009-01-06 13:29:03 -05:00
Greg Von Kuster
6bec493e04
merging from central
2009-01-06 13:28:44 -05:00
Greg Von Kuster
e508256568
merging from central
2009-01-06 11:38:37 -05:00
Greg Von Kuster
3ed821a39d
Better exception handling, messaging for upload utility.
2009-01-06 11:35:49 -05:00
Guruprasad Anada
8a7392aa7a
Pushing changes to security from central.
2009-01-06 11:12:53 -05:00
Guruprasad Anada
cc80d63745
Added a new option to the grouping tool to facilitate picking of random entries from columns not chosen for either grouping or aggregate operations.
2009-01-06 11:11:24 -05:00
Nate Coraor
d337613eeb
megablast fix from Anton
2009-01-05 15:26:17 -05:00
Nate Coraor
43a8e40b50
merge
2009-01-05 15:25:26 -05:00
Nate Coraor
6040c7b18a
merge
2009-01-05 15:25:17 -05:00
Greg Von Kuster
4216601beb
Fixes to enable multiple test runs that test security and libraries.
2009-01-05 11:36:57 -05:00
Nate Coraor
760f024584
New styles from Anton
2009-01-05 10:05:36 -05:00
Greg Von Kuster
7308a73429
Code cleanup, new functional tests for sharing histories with private datasets.
2008-12-23 16:06:01 -05:00
Nate Coraor
5506ec8d3b
merging heads
2008-12-23 13:28:43 -05:00
Nate Coraor
80f42e4199
Since tempfiles seem to occasionally be left behind, allow logging of
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open tempfiles, including a traceback (to determine callers) if
LOG_TEMPFILES is set in the environment when Galaxy starts. This
should be considered temporary and will be removed when it's determined
where/how this happens.
2008-12-23 13:28:27 -05:00
Nate Coraor
8fdd73aaed
merging heads
2008-12-23 13:28:24 -05:00
Greg Von Kuster
6a3f5a925e
Eagerload active_datasets for a history rather than activatable_datasets since it throws exceptions in the migration script.
2008-12-23 10:25:54 -05:00
Greg Von Kuster
61951c59e1
More optimization, code cleanup in migration script.
2008-12-23 09:29:58 -05:00
Greg Von Kuster
1cf912260d
Bug fixes for my last commit.
2008-12-22 17:12:20 -05:00
Greg Von Kuster
6d9db00839
Speed up script for migrating central to security.
2008-12-22 16:39:36 -05:00
Guruprasad Anada
0eb6e8d521
Pushing changes from central to security..
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G: Enter commit message. Lines beginning with 'HG:' are removed.
2008-12-22 13:38:00 -05:00
Guruprasad Anada
54dc919413
Script to enumerate GOPS JOIN jobs that could have returned an incorrect result before the issue with minimum overlap was fixed last week.
2008-12-22 13:35:01 -05:00
Guruprasad Anada
10d6090e81
Pushing changes from central to Security.
2008-12-22 12:16:14 -05:00
Guruprasad Anada
8c7c765480
Modified sort options in grouping tool to work correctly on older and newer versions of unix sort. Also included functional tests.
2008-12-22 12:15:02 -05:00
Nate Coraor
e853cc6f25
Make UCSC build update scripts find elementtree properly
2008-12-22 11:08:23 -05:00
Nate Coraor
aedc44b0d5
When require_login is set and an anonymous user accesses display_as, allow it through if it's the Genome Browser. Dataset actions still apply
2008-12-19 15:17:38 -05:00
Wen-Yu Chung
05513833f5
fix for short read score distribution tool. restore test data. passed functional tests in scofield
2008-12-19 14:28:09 -05:00
Wen-Yu Chung
b31191d4bd
fix for short read score distribution tool. restore test data.
2008-12-19 14:25:43 -05:00
Wen-Yu Chung
1da324ffb5
fixed for short read build distribution tool. remove unused arrays.
2008-12-19 12:28:02 -05:00
Wen-Yu Chung
170f9d2d77
fixed for short read build distribution tool. remove unused arrays. also update test data output.
2008-12-19 12:25:52 -05:00
James Taylor