Bjoern Gruening
cef67fb4f1
Add command_inject to IE config files. This makes it possible to modify the executed "docker run" command from the config file.
2015-04-18 16:54:34 +02:00
yhoogstrate
b29ea767d9
Update scatterplot-display.js
2015-04-07 15:51:55 +02:00
yhoogstrate
fc51b85d2c
Update scatterplot-edit.js
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automatically generated by grunt
2015-04-07 15:50:30 +02:00
yhoogstrate
af8ddb14a3
ScatterPlot No API connection for nested www_root
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ScatterPlot makes use of a hardcoded API url which is incorrect for certain server configuratoins. Currently these servers need to be manually configured to link to the correct API URL. This patch creates the correct URL from the parental variable parent.galaxy_config.root and returns "/" if this variable can not be found. More visualisations suffer from this bug and have to be patched as well.
2015-04-07 14:59:29 +02:00
John Chilton
543eb5b489
Provide convenience attribute for logging in IE mako.
2015-04-02 08:54:56 -04:00
Carl Eberhard
4e5218f4dc
Charts: fix script tag order to prevent new version of Backbone loading as AMD; UI, Histories: remove debug statement
2015-03-16 10:48:52 -04:00
guerler
5bee11df4c
Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful)
2015-02-28 12:12:10 -05:00
guerler
e6399874e8
Charts: Fix missing data message
2015-02-24 19:41:30 -05:00
guerler
e2f5e9e326
Charts: Rebuild and update charts
2015-02-24 19:08:36 -05:00
Carl Eberhard
8a79dfe99e
UI, multi-history: minor fixes, tabindeces, cleanup; Scatterplot: refactor mako and fix missing figure tag; Client build, styles: add jstree to cleaned files
2015-02-16 11:43:22 -05:00
Aysam Guerler
3ffcc2448c
Charts: Fix error message
2015-02-11 20:56:10 -05:00
Aysam Guerler
7eec63204d
Charts: Repack scripts
2015-02-11 20:26:46 -05:00
Carl Eberhard
2b8fca4a03
Visualizations, scatterplot: update handlebars since server runtime was updated
2015-02-09 11:02:31 -05:00
Aysam Guerler
68d9ea0fad
Ui: Fix class name
2015-02-06 11:23:19 -05:00
Aysam Guerler
836b3bb913
Ui: Revise portlet margins
2015-02-06 11:05:23 -05:00
Aysam Guerler
c8aece99eb
Workflow: Add style for workflow tool form
2015-02-05 22:25:22 -05:00
Carl Eberhard
ed8b7bd9ec
Plugins, Scatterplot: fix library imports to use proper path after ui.js breakup
2015-01-23 12:50:21 -05:00
Aysam Guerler
b709d7c061
Update to_html function for text tool, generalize text fields, remove trailing tabs
2015-01-21 11:20:02 -05:00
Aysam Guerler
0057365b06
Charts: Update scroll handler
2015-01-15 01:52:17 -05:00
Aysam Guerler
25100850c8
Charts: Prevent scrolling while zooming, add info text, fix styles
2015-01-15 01:40:39 -05:00
Aysam Guerler
c8f123fa2f
Charts: Avoid cursor replacement in label field
2015-01-14 11:08:14 -05:00
Aysam Guerler
adc2d60bed
ToolForm/Workflow: Add post job action forms, enable custom tool form sections
2015-01-13 01:09:03 -05:00
Aysam Guerler
0795557583
Ui: Minor style fix, Charts: Repack scripts
2014-12-10 10:51:37 -05:00
Carl Eberhard
612f3be1cc
Client build: modularize pagination plugin from ui.js
2014-12-08 15:04:47 -05:00
Carl Eberhard
3274d882bc
Client build: begin modularizing ui.js by extracting peekControl/peek-column-selector plugin, use UMD pattern, rename to peek-column-selector, extract less rules to their own file; Plugins, scatterplot: remove require and rework to use the new module
2014-12-08 14:47:48 -05:00
Aysam Guerler
bdff562a51
Charts: Use most recent select field style
2014-12-02 11:47:59 -05:00
Aysam Guerler
80c6aeaf93
Charts: Repack scripts
2014-11-13 16:40:59 -05:00
Aysam Guerler
a946ebf66f
Ui: Resize select fields
2014-11-13 16:38:49 -05:00
Aysam Guerler
e02ae27ab2
ToolForm: Prevent redundant ajax requests
2014-11-04 15:28:58 -05:00
Aysam Guerler
8ef50622cc
Charts: Fix storage call
2014-10-31 12:15:26 -04:00
Aysam Guerler
5d29c29cad
Charts: Update query limits
2014-10-29 13:37:33 -04:00
Aysam Guerler
916c7b4cc1
ToolForm: Fix citations
2014-10-29 11:37:04 -04:00
John Chilton
e8b4f8085f
Remove files indicated by Bjoern.
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No need to LICENSE this differently, INSTALL.md probably should be rewritten, and .gitignore is now pointless.
https://bitbucket.org/galaxy/galaxy-central/pull-request/533 .
2014-10-19 17:38:30 -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
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
c58742e55b
Use newer-style Galaxy configuration of interactive environments.
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Setup a sample file and fallback on it if a materialized .ini isn't present. Use .ini instead of .conf for consistency with the rest of the config directory.
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
John Chilton
9969e10829
Update ie.mako to use galaxy_infrastructure_url if available...
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Also use the method guess_galaxy_port on Galaxy's config object that was moved there from ie.mako in a previous Galaxy commit.
2014-10-18 18:38:04 -04:00
John Chilton
eb5fb10726
Updated more correct discovery of Galaxy config file.
2014-10-18 18:38:04 -04:00
John Chilton
8ec1b636cd
Adapt IPython/IE framework for dynamic Galaxy proxy.
2014-10-18 18:38:04 -04:00
John Chilton
07c2be2bae
Fix conf -> config hack in IPython for history rewrite.
2014-10-18 18:38:04 -04:00
Eric Rasche
5f8e6a5397
Set timeout lower than time between requests
2014-10-18 18:38:04 -04:00
Eric Rasche
30cbb35f72
Fixes #27
2014-10-18 18:38:04 -04:00
Eric Rasche
73b9f8740c
Missing URL on ajax request
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This was causing serious havock with the RStudio version, not sure why the problems weren't
presenting as badly here. Without a URL, the ajax request requests the page you're on, spawning
dozens and dozens of docker containers.
2014-10-18 18:38:04 -04:00
Eric Rasche
6afc29358f
Removed unused imports
2014-10-18 18:38:04 -04:00
Eric Rasche
0cf7450f0a
Patch requested by Bjoern
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Tested, works.
2014-10-18 18:38:04 -04:00
Bjoern Gruening
e98a4479c7
Migrate from <object> to <iframe>. Objects seems to have some bugs in FF32.
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Conflicts:
static/js/ipython.js
2014-10-18 18:38:04 -04:00
Eric Rasche
87640a7166
Moved JS files to subdirectory
2014-10-18 18:38:04 -04:00
Eric Rasche
61062bc569
Fixes #25
2014-10-18 18:38:04 -04:00
Bjoern Gruening