Dannon Baker
56abf815d0
Merged in BjoernGruening/galaxy-central-1/obo-owl-datatype (pull request #542 )
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Add OWL & OBO datatype.
2014-11-10 08:14:49 -08:00
John Chilton
b391883060
Merged in nsoranzo/galaxy-central (pull request #551 )
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Small bugs, doc and pylint fixes.
2014-11-10 11:04:02 -05:00
Dannon Baker
0a1aa5dde6
Merged in kellrott/galaxy-farm/fix-tooltip (pull request #544 )
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Adding fake host_url to tooltip rendering
2014-11-07 19:53:38 -05:00
Dannon Baker
302953f6ac
Merged in kellrott/galaxy-farm/workflow-input-fix (pull request #552 )
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Fixing workflow import to correctly set the uuid
2014-11-07 19:48:15 -05:00
Kyle Ellrott
acda72d429
Putting in URL to current host for tooltip host_url variable
2014-11-07 14:18:32 -08:00
Aysam Guerler
113f90a91b
ToolForm: Integrate and optimize state population for tools api
2014-11-07 13:24:22 -05:00
Aysam Guerler
668cdc8309
ToolForm: Fix boolean handling
2014-11-07 10:39:19 -05:00
Kyle Ellrott
661b11cada
Removing whitespace fixes to avoid merge conflict
2014-11-06 14:18:03 -08:00
Martin Cech
70d0d2c970
fix for https://trello.com/c/pML6OsMl/249-html-escaping-error-in-toolshed-password-reset-message
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also removed bug with inproper redirecting when resetting password
2014-11-06 13:44:56 -05:00
Carl Eberhard
4825b9ed5c
History structure: incorporate tool data, refactor; HDA API: return create_time
2014-11-06 12:56:13 -05:00
Peter Cock
f9630ee81c
Fix typo nothting [sic] in test exception
2014-11-06 16:21:45 +00:00
Kyle Ellrott
0caeade5b9
Fixing workflow import to correctly set the uuid
2014-11-05 17:39:08 -05:00
Martin Cech
cadd51d097
initial commit of google analytics script
2014-11-04 11:14:31 -05:00
Nicola Soranzo
5cd46dc4dd
Bugs, doc and pylint fixes.
2014-11-04 16:48:33 +01:00
Nicola Soranzo
5d64d5d0b2
Add keys() and values() methods to Bunch.
2014-11-05 14:28:14 +01:00
Nicola Soranzo
0dc1fec519
Remove unused and buggy function.
2014-11-04 16:46:42 +01:00
Martin Cech
3d86007c7c
initial commit of google analytics tracking for toolshed
2014-11-04 10:31:15 -05:00
Martin Cech
20a20dffc1
gremmar
2014-11-04 10:26:53 -05:00
Björn Grüning
ee96638754
Remove set_meta() function. It's not used.
2014-11-04 11:01:42 +00:00
Björn Grüning
e1f299d626
Remove set_meta() function. It's not used.
2014-11-04 10:01:52 +00:00
Martin Cech
1b7b74e0bc
changes to account updates: added javascript valdiation of username and email changes; user account will be deactivated if you change an email address and you have to activate it once again
2014-11-03 15:16:36 -05:00
Dannon Baker
d1f0d323fe
Merge.
2014-11-03 15:04:17 -05:00
Dave Bouvier
5f68a5e303
Merge with upstream changes.
2014-11-03 14:59:16 -05:00
Dannon Baker
e5b624cf46
Patch from Eric Rasche, redacting a few things from sentry reports.
2014-11-03 14:52:21 -05:00
Nate Coraor
b483e64aec
Handle all submission failures in the drmaa runner.
2014-11-03 12:58:14 -06:00
Nicola Soranzo
d0b6aef8c5
API: Return also metrics for jobs when full=True and user is admin.
2014-10-31 17:16:20 +01:00
John Chilton
04dfe90d80
Another fix like PR 546.
2014-11-02 16:17:26 -05:00
John Chilton
4a415f8d53
Merged in ericenns/galaxy-central (pull request #546 )
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Update admin manage jobs time calculation
2014-11-02 16:16:01 -05:00
John Chilton
ad143cd535
Update and fix the version of node-http-proxy used by dynamic proxy.
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Upgrade with:
% cd lib/galaxy/web/proxy/js
% npm install
Hoping to fix problems encountered by Bjoern or at least eliminate differences in our respective environments.
2014-10-31 14:41:30 -04:00
Eric Enns
b774d90f2c
Update job time output in admin manage jobs to prevent rollover when time surpasses 24 hours
2014-10-31 09:30:41 -05:00
Kyle Ellrott
4833f7e361
Adding fake host_url to tooltip rendering to stop certain tools from crashing the tool tip renderer
2014-10-30 21:14:05 -07:00
Dave Bouvier
1e661a7d90
Remove whitespace from the beginning and end of individual lines in a <command> tag before assembling it into a single line.
2014-10-30 11:30:46 -04:00
Aysam Guerler
99a7e0531c
ToolForm: Activate dynamic parameter handling
2014-10-30 11:27:26 -04:00
Bjoern Gruening
06107a9fa6
Add OWL & OBO datatype.
2014-10-27 16:13:14 +01:00
Eric Rasche
16416bb577
Enable configuration of dynamic external proxy
2014-10-24 11:48:54 -05:00
Björn Grüning
e2583b4d0b
Add -u $USER argument to the docker call.
2014-10-23 20:03:49 +00:00
Dave Bouvier
bb3c895e51
Add optional display of stdout/stderr to the jobs API return value, defaulting to not displayed. Rework the test API interactor to wait for jobs instead of histories and get the stdout and stderr from the API.
2014-10-23 10:34:17 -04:00
Aysam Guerler
6e3c1a9549
ToolForm: Add support for dynamic parameters, add tool version check
2014-10-23 09:50:31 -04:00
John Chilton
b31ce7c1de
Fix bug in tool watching.
2014-10-23 09:08:03 -04:00
Nate Coraor
828797a68b
Implement the "memory_limit_reached" runner state for slurm and allow resubmission on that state.
2014-10-22 22:05:07 -05:00
Nate Coraor
5a4990f2da
Merge stable.
2014-10-22 22:47:52 -04:00
Nate Coraor
271f91061c
Fix slurm job post-mortem for clusters functionality added to slurm-drmaa (and currently in use on usegalaxy.org).
2014-10-22 18:00:15 -04:00
Martin Cech
8b1a9e73f1
data libs API documentation
2014-10-22 14:08:57 -04:00
Martin Cech
190c0fb7f3
data libs: hide share button, render first page by default, fix admin imports from import_dir, fix height of folder item row changing on hover
2014-10-22 13:39:39 -04:00
John Chilton
ad391148c5
Require pyyaml egg before using.
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Thanks @natefoo.
2014-10-21 12:32:57 -04:00
John Chilton
9ad5e12e1c
Improvements to IPython configuration sample.
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Allow overiding galaxy_url directly (don't do this - use galaxy_infrastructure_url - but there will be deployments). Don't require setting older port range deployment options.
2014-10-18 18:38:04 -04:00
John Chilton
f0a7f1e2b6
Make dynamic proxy less noisy but add option dynamic_proxy_debug to re-enable for debugging.
2014-10-18 18:38:04 -04:00
John Chilton
5547bb7df5
Refactor interactive environment plugin framework out of IPython and into Galaxy.
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Rely on more Python and less on mako, setup a small shared common mako file in config/plugins/interactive_environments/common/ie.mako. Move ie.js into client/galaxy/scripts/galaxy.interactive_environments.js and extract IPython's require config out so it doesn't have to directly reference client/galaxy/scripts/galaxy.interactive_environments.js (I doubt it is where that file actually should be).
2014-10-18 18:38:04 -04:00
John Chilton
06175f83f9
Update plugin framework to distinguish between viz and IE frameworks.
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Update IPython accordingly.
2014-10-18 18:38:04 -04:00
John Chilton
a52f4c21ee
Split interactive_environments out into their own plugin directory.
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Pragmatically this allows visualizations to be enabled by default but not IPython stuff and provides a spot to put a warning about security issues. More abstractly I think it provides a nice separation (initially though superficial) between these plugin types.
2014-10-18 18:38:04 -04:00
Dannon Baker