Daniel Blankenberg
4d88ce03de
Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool.
2014-04-09 17:24:56 -04:00
Carl Eberhard
86da018f62
Metrics API: allow posting of metrics sending to app.trace_logger.log if available
2014-04-09 16:15:00 -04:00
Jeremy Goecks
be37a0846c
Automated merge of next-stable to default.
2014-04-09 12:53:57 -04:00
Jeremy Goecks
38452da57a
SAM/BAM data provider: fix bug and streamline code to support both genomes with reference data and those without.
2014-04-09 12:53:34 -04:00
Jeremy Goecks
c892a67f13
Genome data provider: (a) handle regions with no mapped reads and (b) clean up trailing whitespace.
2014-04-09 10:47:22 -04:00
Greg Von Kuster
27e60943bf
The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.
2014-04-09 10:11:48 -04:00
Daniel Blankenberg
dc6aba0497
merge next-stable
2014-04-08 17:05:21 -04:00
Daniel Blankenberg
6c704a4e7f
fix tab spaces in javascript
2014-04-08 17:05:09 -04:00
Daniel Blankenberg
d9a8d92695
merge next-stable
2014-04-08 17:03:38 -04:00
Daniel Blankenberg
cee2ac4485
When submiting bug reports disable submit buttons while form is being submitted. When submiting bug report to Biostar, have user confirm that they are posting to a public forum.
2014-04-08 17:03:19 -04:00
Carl Eberhard
8207cb0043
merge next-stable
2014-04-08 14:14:58 -04:00
Carl Eberhard
d7dda26c58
Remove debugging statements
2014-04-08 14:14:17 -04:00
Carl Eberhard
5120673dbd
Metrics: allow time to be passed into fluent_log.py, log
2014-04-08 12:55:30 -04:00
Jeremy Goecks
6366ef405e
Automated merge of next-stable to default
2014-04-08 12:08:20 -04:00
Jeremy Goecks
9d64557de5
Trackster: update jQuery selector so that all tool inputs are updated on change rather only <input> elements. Pack script.
2014-04-08 12:07:50 -04:00
Aysam Guerler
09d1f2811f
Charts: Add libraries
2014-04-07 19:19:42 -04:00
Aysam Guerler
fb48f9889f
Charts: Add boxplots
2014-04-07 19:18:25 -04:00
hillrunner2008
148dcc474c
Merged galaxy/galaxy-central into default
2014-04-07 16:31:01 -04:00
dcnorris
3049d6e5d0
removed dataset hash from the bookmark generated urls since they are not needed and make for ugly track names
2014-04-07 16:29:17 -04:00
Aysam Guerler
595f3253bb
Merge
2014-04-07 13:54:37 -04:00
Aysam Guerler
04b2d95d65
Charts: Fix api call
2014-04-07 13:53:14 -04:00
Carl Eberhard
2187795562
QA: upgrade browser testing framework and tests to use casperjs 1.1-beta3 and phantomjs 1.9.2
2014-04-07 13:27:55 -04:00
Jeremy Goecks
15aeb3f49c
Automated merge of next-stable to default
2014-04-07 12:22:25 -04:00
Jeremy Goecks
910fc94c94
Pack script.
2014-04-07 12:22:01 -04:00
Jeremy Goecks
5edebad3e6
Visualization client-side framework: use simpler/faster/boundary-condition insensitive calculation for extracting subsets of reference sequence data.
2014-04-07 12:21:43 -04:00
Carl Eberhard
5245708a2f
merge next-stable
2014-04-07 10:11:07 -04:00
Carl Eberhard
b5b2635b0a
Fix encoding/serialization of returned data from HDA create API
2014-04-07 10:10:26 -04:00
Jeremy Goecks
99d94c5220
Merge next-stable --> default
2014-04-04 16:33:32 -04:00
Jeremy Goecks
086e37c557
Trackster: only draw incomplete features when displaying features, not coverage data. Pack script.
2014-04-04 16:33:06 -04:00
John Chilton
38f1cba0c9
Merged in jmchilton/galaxy-central-fork-1 (pull request #357 )
...
Unit testing framework for client code.
2014-04-04 14:24:47 -05:00
Greg Von Kuster
2ba8e40654
Merged next-stable
2014-04-04 11:55:45 -04:00
Greg Von Kuster
a5161f2c7d
Enhance error message displayed when installing a repository into Galaxy that has an invalid repository dependency definiton.
2014-04-04 11:55:24 -04:00
Daniel Blankenberg
9694783037
merge next stable
2014-04-04 11:46:24 -04:00
Daniel Blankenberg
5845ca36a3
Provide a full URL including protocol in activation emails.
2014-04-04 11:46:03 -04:00
Greg Von Kuster
4096595808
merged next-stable
2014-04-04 11:40:16 -04:00
Greg Von Kuster
5015dbcc87
Render tool shed features based on a combination of the webapp and a rendor_for value. Things get tricky when visiting the tool shed from galaxy to install repositories.
2014-04-04 11:39:48 -04:00
Dave Bouvier
a828eedead
Merge in fix from next-stable.
2014-04-04 10:38:40 -04:00
Dave Bouvier
db12448003
Fixed JAVA_JAR_PATH for realigner_target_creator.
2014-04-04 10:37:52 -04:00
Daniel Blankenberg
3b1bd98bd2
Merged in hillrunner2008/galaxy-central (pull request #354 )
...
modified igb display xml files
2014-04-04 10:00:59 -04:00
Greg Von Kuster
399f5508f6
Merged next-stable
2014-04-03 17:41:18 -04:00
Greg Von Kuster
2abe24b292
Better fix than ea1fbe9 and handle first discovered unhandled secure / insecure protocol issue when messing with the tool shed url for installed repositories.
2014-04-03 17:40:44 -04:00
John Chilton
bb9634e7ee
Unit testing framework for client code.
...
This work is based on QUnit and tests are runnable in-browser without any external dependencies or via command-line using grunt and PhantomJS. See README.txt in `test/qunit` directory for more information on how to run tests.
A test case is defined by an HTML and JavaScript source file. The file `test-common.js` will bootstrap most of the minimal HTML needed for qunit and configure require so nearly all testing logic is isolated into test js file. An example test is included that demonstrates how to build tests using requirejs's `define` and target backbone components. Tests can target non-backbone code as well.
Sinon is included for stubbing out server interactions, etc... when testing backbone components. This seems to be a popular fallback for backbone projects not using Jasmine.
2014-04-03 16:20:59 -05:00
Jeremy Goecks
e630fb10c8
Automated merge of next-stable to default
2014-04-03 14:34:17 -04:00
Jeremy Goecks
18c2e3fc71
Trackster: fixes for creating and resizing composite line tracks.
2014-04-03 14:33:48 -04:00
Nate Coraor
dfb34ae108
Open next-stable branch.
2014-04-03 12:02:24 -04:00
Greg Von Kuster
9f5f3a93e1
Add exception handling when updating an installed repository to a revision that include newly defined dependency definitions.
2014-04-03 12:00:25 -04:00
Daniel Blankenberg
a5b23557bf
Change Biostar 'submit' parameter to be called 'action'. Resolves needing to use workaround of 'click()' on submit button instead of submit() on form.
2014-04-03 11:17:47 -04:00
hillrunner2008
9e4683e74e
Changed the link text to match other file formats
2014-04-03 15:05:36 +00:00
Greg Von Kuster
8f031dfd7b
Upon import, handle problematic prior_installation_required attribute incorrectly added (and set to "False") to the <repository> tag when a repository was exported.
2014-04-03 10:19:46 -04:00
Dave Bouvier
463b50bb1d
Use correct revisions of best_regression_subsets and weightedaverage.
2014-04-03 09:45:51 -04:00
Daniel Blankenberg