Dave Bouvier
af815ee1bf
Merge bugfix from stable.
2014-06-09 11:15:45 -04:00
Dave Bouvier
d1d9f568ca
Fix step handling for setup of perl and ruby environments.
2014-06-09 11:11:24 -04:00
Dannon Baker
a6b6879f12
Reorder imports post-PR 403.
2014-06-09 10:53:00 -04:00
Dannon Baker
5f69ad21dc
Merged in saketkc/galaxy-fork (pull request #403 )
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PEP8 fixes, close find handles for 'convert delimiters to tab' tool
2014-06-09 10:52:03 -04:00
Dannon Baker
82ca2fcc77
Swap require_admin decorator and trans.user_is_amdin to use the newer correctly filtered admin_users_list in app.config
2014-06-09 10:42:33 -04:00
Dannon Baker
f2a711be12
Add correctly prefiltered admin_users_list to app.config and use it for remote auth.
2014-06-09 10:37:10 -04:00
John Chilton
530265d718
Merge.
2014-06-09 08:32:24 -05:00
John Chilton
069a9f61a1
Tools: MATCH (pair) multi-run datasets by default instead of doing ALL-V-ALL.
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Worried this might be responsible for problems on main. TODO is to make this an optional and explicit like with workflows.
2014-06-09 08:30:40 -05:00
Dannon Baker
18edb959ae
Merge.
2014-06-09 09:10:10 -04:00
Dannon Baker
5ff2875549
Wrap remote user conditional on multiple lines.
2014-06-09 09:09:45 -04:00
Aysam Guerler
2c2d63c477
Charts: Add custom d3-zooming and panning for nvd3, patch nvd3 transitions
2014-06-09 08:49:49 -04:00
Dannon Baker
eeb946cec9
Slightly simplify remote_user_header access logic.
2014-06-09 08:40:40 -04:00
Dannon Baker
480ea96d90
Cleanup/pep8 of remoteuser middleware.
2014-06-09 08:38:47 -04:00
Dannon Baker
6f9d687269
One more touchup in webframework -- correct raise form and use multiple lines.
2014-06-09 08:35:32 -04:00
Dannon Baker
23b488f7bb
pep8/cleanup. set NERD_tree_1noqa for impossible sqlalchemy lines.
2014-06-09 08:33:25 -04:00
Dannon Baker
5769ea88fa
Fix impersonation when using external authentication. Admins can now impersonate (and then log out of) users when using external auth.
2014-06-09 08:14:18 -04:00
Dannon Baker
a01ccc9f4a
Update user honeypot error message.
2014-06-09 07:58:18 -04:00
Saket Choudhary
769a1d4f49
PEP8 fixes, close find handles for 'convert delimiters to tab' tool
2014-06-09 11:56:06 +05:30
John Chilton
4db123b664
Merge latest stable.
2014-06-08 19:41:51 -05:00
Greg Von Kuster
5d56c27f9c
More fixes for handling 307 redirects not being handled nicely by urllib2.urlopen() when the urllib2.Request has data provided.
2014-06-08 08:45:16 -04:00
Aysam Guerler
e039de1ed9
Charts: Refactor nvd3 wrappers, remove excluded wrappers
2014-06-07 17:51:41 -04:00
John Chilton
550ad865d9
Pack scripts.
2014-06-07 12:31:44 -05:00
John Chilton
b90852c55d
Bugfix: Tool form logic for displaying allow_remap option was inverted.
2014-06-07 12:30:02 -05:00
Dannon Baker
5ccd70ebea
Clarify language in DeleteIntermediateDataset PJA.
2014-06-06 17:12:30 -04:00
Dannon Baker
54a6ebe355
Cleanup, pep8 for postjobactions.
2014-06-06 16:44:47 -04:00
Dannon Baker
4fb8b2d9f0
Initial version of delete intermediate output steps action for workflows.
2014-06-06 16:32:44 -04:00
Dannon Baker
82941fa9f8
Add Workflow.has_outputs_defined to the Workflow model.
2014-06-06 15:36:07 -04:00
Aysam Guerler
bb6fae5928
Charts: Reduce number of available chart types
2014-06-06 15:34:40 -04:00
Dannon Baker
1bd292973d
Update amqp_internal_connection sqlite default in universe_sample to be correct.
2014-06-06 12:08:16 -04:00
Greg Von Kuster
9580a076d5
Fix for getting updates to an installed repository that has a dependency on a Tool dependency definition repository that also has available updates.
2014-06-06 09:45:37 -04:00
John Chilton
2a90811ea3
Another fix for remotely populated metadata FileParameters.
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Requires update to remote LWR as well.
2014-06-05 17:08:24 -05:00
Nate Coraor
41a7637a76
Allow hiding tools from the toolbox config.
2014-06-05 14:46:56 -04:00
John Chilton
036168bdad
Fix working directory used for remote metadata command generation.
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In short - should fix bam outputs for LWR jobs when setting metadata on remote resource. Thanks to @natefoo for tracking down problem.
2014-06-05 11:54:58 -05:00
Nate Coraor
fecfff16ee
Merge stable
2014-06-05 10:14:36 -04:00
Nate Coraor
bd78b3eb80
Updated tag latest_2014.06.02 for changeset fb68af9a775a
2014-06-05 10:13:29 -04:00
Nate Coraor
5a460288df
Upgrade kombu/amqp to fix ssl disconnect on consumer timeout bug: https://github.com/celery/py-amqp/pull/38
2014-06-05 10:07:39 -04:00
Aysam Guerler
439feed3e6
Charts: Add zoomable heatmaps, add chart type definition to charts model
2014-06-04 18:57:27 -04:00
Dave Bouvier
67718f9d52
Merge bugfix from stable.
2014-06-04 15:15:23 -04:00
Dave Bouvier
d206339d2b
Fix resetting all metadata based on issue found by Nicola Soranzo.
2014-06-04 15:04:33 -04:00
John Chilton
51762ac859
Update LWR client throught LWR changeset 860ba9c.
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Allows asynchornous submission of LWR jobs to remote servers without a remote LWR service running. LWR still needs to be configured there and job updates are should be configured to be sent back to Galaxy through AMQP.
A long running process will be executed on the remote server to monitor the job - while this will always be needed in some cases - for others it would be great to be able to embedded the update steps into the job to be submitted to the DRM itself so that this long running process can be just a submission.
This is one more potential step down the road toward allowing remote execution of Galaxy jobs with ever fewer remote constraints. Extensions to this would include allowing Galaxy job updates via the jobs API (along with staging) so MQ becomes optional, allowing auto-configuration of remote LWR application if unavailable or unconfigured, more transfer options (scp), more CLI shell options (fabric, ansible, etc...).
2014-06-04 12:16:38 -05:00
Daniel Blankenberg
42d9136147
Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
2014-06-04 11:05:36 -04:00
Daniel Blankenberg
104d36a187
Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.
2014-06-04 11:05:36 -04:00
Greg Von Kuster
0285192a4c
Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string.
2014-06-04 09:21:18 -04:00
Aysam Guerler
0e4a71f580
Charts: Improve notifications and error handling
2014-06-04 03:54:54 -04:00
Aysam Guerler
ba1bd64c13
Charts: Extend boxplot options
2014-06-04 02:10:32 -04:00
Aysam Guerler
0559eed63e
Charts: Remove helper function
2014-06-04 01:52:58 -04:00
Aysam Guerler
f259ac94bd
Charts: Adding chart subset selection filter, setting zoomable charts as default
2014-06-04 01:49:43 -04:00
Dannon Baker
1db9a64b79
Pack scripts.
2014-06-03 17:42:17 -04:00
Dannon Baker
c43d604f4f
Stop loading indicator at the end of get_next_chunk regardless of result.
2014-06-03 17:40:00 -04:00
Dave Bouvier
57440965e7
Merge fix from stable.
2014-06-03 17:04:13 -04:00
Dave Bouvier