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 )
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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
Greg Von Kuster
971e9d6f88
Don't add unnecessary (and problematic) prior_installation_required attributes to repository dependency definitions when exporting a repository and its dependencies into a capsule.
2014-04-03 09:31:43 -04:00
Martin Cech
1758f3d63a
libraries: removed unused and deprecated function
2014-04-02 17:21:06 -04:00
Martin Cech
5f928cd92d
libraries: more refactoring fun; full UI for permissions handling; repainting from cache
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should be ready for stable
2014-04-02 17:18:51 -04:00
Dave Bouvier
b6af887925
Corrected an error in the analyze_covariates tool shed repository.
2014-04-02 16:05:57 -04:00
Greg Von Kuster
ffa19b77a5
Add a new RepositoryGridFilterManager to the Tool Shed framework to support filtering the repositories displayed in the many Tool Shed grids. The current filters are CERTIFIED_LEVEL_ONE, CERTIFIED_LEVEL_ONE_SUITE and CERTIFIED_LEVEL_TWO, CERTIFIED_LEVEL_TWO_SUITE. The "level one" filters display repositories or suites that have been certified by the Tool Shed's install and test framework. The "level two" filters are not yet supported (the query enhancements are trivial, but not yet done) since no repositories in the test or main Tool Shed have been certified at this level (this level requires reviews and approvals by IUC members). When set, filters are stored in session cookies. Filters are easy to set. The Javascript event handler (e.g. checking a filter checkbox) would make a call something like: trans.app.repository_grid_filter_manager.set_filter( trans.app.repository_grid_filter_manager.filters.CERTIFIED_LEVEL_ONE ).
2014-04-02 15:18:40 -04:00
Daniel Blankenberg
ba7a5c7b08
When a tool dependency has failed to install, display the error message as pretty escaped html.
2014-04-02 15:15:00 -04:00
Martin Cech
8d2a8f9b7b
libraries: more refactoring; basic UI based on role handling; attaching to global Galaxy object; persistent lib preferences
2014-04-02 11:07:04 -04:00
Jeremy Goecks
579ebf5157
Circster fixes: (a) make compatible with new config object; (b) fix formatting issue with negative values; and (c) clean up debugging statements. Pack scripts.
2014-04-02 10:15:54 -04:00
Dave Bouvier
0994d4c2bd
Fix issue in migrations where the same complex repository would be installed once for each repository that depends on it.
2014-04-02 09:13:33 -04:00
Jeremy Goecks
867df48180
Automated merge
2014-04-02 09:12:22 -04:00
Jeremy Goecks
fee4cb7333
Trackster: CompositeTrack fixes for recent refactoring. Pack script.
2014-04-02 09:12:07 -04:00
Greg Von Kuster
7e9f07c9d3
Don't require categories and status attributes to be associated with a repository being imported from a capsule, although they should always exist.
2014-04-02 07:22:01 -04:00
Jeremy Goecks
573456d475
Trackster: show drawn reads across all tiles by pooling incompletely drawn reads and drawing them at the end.
2014-04-01 16:21:32 -04:00
Jeremy Goecks
2ebd82519e
Automated merge.
2014-04-01 15:09:45 -04:00
Jeremy Goecks
e2f56b50f2
Trackster: drawing performance improvement. Packed scripts.
2014-04-01 15:09:30 -04:00
Dave Bouvier
f807d8f406
Remove escaped double quotes from setup_virtualenv action.
2014-04-01 14:48:48 -04:00
Jeremy Goecks
67288cb54f
Fix for 615d504: do not use downsampling when all reads can be returned.
2014-04-01 14:45:34 -04:00
Daniel Blankenberg
01a77cc319
Update Biostar question posting to use POST. Have biostar bug reports automatically post.
2014-04-01 14:11:56 -04:00
Dave Bouvier
10cda06773
Pass shell=True to subprocess.Popen, which eliminates the need to escape double quotes and prepend /bin/sh -c to a tool dependency shell command.
2014-04-01 13:08:02 -04:00
Dave Bouvier
2f2e163df7
Remove migrated tools from main's tool conf.
2014-04-01 11:05:31 -04:00
Dave Bouvier
83af05b1f2
Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
2014-04-01 11:04:32 -04:00
Carl Eberhard