commit/galaxy-central: natefoo: Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon).
by commits-noreplyï¼ bitbucket.org 25 Jun '14
by commits-noreplyï¼ bitbucket.org 25 Jun '14
25 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1802e93a4f18/
Changeset: 1802e93a4f18
User: natefoo
Date: 2014-06-26 02:07:58
Summary: Fix Ctrl+C (make the UpdateRepositoryManager's updater thread a daemon).
Affected #: 1 file
diff -r 6b672fb120994f308ce7914993418e67770aae14 -r 1802e93a4f1823f307de534d9b6ce73d911f6538 lib/tool_shed/galaxy_install/update_repository_manager.py
--- a/lib/tool_shed/galaxy_install/update_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/update_repository_manager.py
@@ -19,6 +19,7 @@
self.running = True
self.sleeper = Sleeper()
self.restarter = threading.Thread( target=self.__restarter )
+ self.restarter.daemon = True
self.restarter.start()
self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: Enhance the tool shed repository API controller to allow filtering by owner's username or repository name.
by commits-noreplyï¼ bitbucket.org 25 Jun '14
by commits-noreplyï¼ bitbucket.org 25 Jun '14
25 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6b672fb12099/
Changeset: 6b672fb12099
User: davebgx
Date: 2014-06-25 21:07:43
Summary: Enhance the tool shed repository API controller to allow filtering by owner's username or repository name.
Affected #: 1 file
diff -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b -r 6b672fb120994f308ce7914993418e67770aae14 lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -7,6 +7,7 @@
from galaxy import eggs
from galaxy import util
from galaxy import web
+from galaxy.model.orm import and_
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import HTTPBadRequest
from galaxy.web.framework.helpers import time_ago
@@ -297,16 +298,28 @@
return return_dict
@web.expose_api_anonymous
- def index( self, trans, deleted=False, **kwd ):
+ def index( self, trans, deleted=False, owner=None, name=None, **kwd ):
"""
GET /api/repositories
+
+ :param deleted: True/False, displays repositories that are or are not set to deleted.
+ :param owner: the owner's public username.
+ :param name: the repository name.
+
Displays a collection (list) of repositories.
"""
# Example URL: http://localhost:9009/api/repositories
repository_dicts = []
deleted = util.asbool( deleted )
+ clause_list = [ and_( trans.app.model.Repository.table.c.deprecated == False,
+ trans.app.model.Repository.table.c.deleted == deleted ) ]
+ if owner is not None:
+ clause_list.append( and_( trans.app.model.User.table.c.username == owner,
+ trans.app.model.Repository.table.c.user_id == trans.app.model.User.table.c.id ) )
+ if name is not None:
+ clause_list.append( trans.app.model.Repository.table.c.name == name )
for repository in trans.sa_session.query( trans.app.model.Repository ) \
- .filter( trans.app.model.Repository.table.c.deleted == deleted ) \
+ .filter( *clause_list ) \
.order_by( trans.app.model.Repository.table.c.name ):
repository_dict = repository.to_dict( view='collection',
value_mapper=self.__get_value_mapper( trans ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Another docfix for recent local job runner changes.
by commits-noreplyï¼ bitbucket.org 25 Jun '14
by commits-noreplyï¼ bitbucket.org 25 Jun '14
25 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8a161a3990b5/
Changeset: 8a161a3990b5
User: jmchilton
Date: 2014-06-25 16:11:26
Summary: Another docfix for recent local job runner changes.
Affected #: 1 file
diff -r 1c40abf8bc5b7555dd276e540f487f8c288da4b2 -r 8a161a3990b5e19dd2b324323ba934f8a5f37c8b universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -804,7 +804,7 @@
# the cluster that should be sourced by the user to set up the environment
# prior to running tools. This can be especially useful for running jobs as
# the actual user, to remove the need to configure each user's environment
-# individually. This only affects cluster jobs, not local jobs.
+# individually.
#environment_setup_file = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/75c63b579ccd/
Changeset: 75c63b579ccd
User: jmchilton
Date: 2014-06-25 15:01:52
Summary: Add documentation about local runner destination option embed_metadata_in_job.
Affected #: 1 file
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r 75c63b579ccdd63e0558dd9aefce7786677dbacd job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -102,6 +102,12 @@
<!-- Warning: Local slot count doesn't tie up additional worker threads, to prevent over
allocating machine define a second local runner with different name and fewer workers
to run this destination. -->
+ <param id="embed_metadata_in_job">True</param>
+ <!-- Above parameter will be default (with no option to set
+ to False) in an upcoming release of Galaxy, but you can
+ try it early - it will slightly speed up local jobs by
+ embedding metadata calculation in job script itself.
+ --><job_metrics /><!-- Above element demonstrates embedded job metrics definition - see
job_metrics_conf.xml.sample for full documentation on possible nested
https://bitbucket.org/galaxy/galaxy-central/commits/1c40abf8bc5b/
Changeset: 1c40abf8bc5b
User: jmchilton
Date: 2014-06-25 15:05:40
Summary: Merge.
Affected #: 1 file
diff -r 1fc71cb18c421f49be3c6629c0e53cca6b0caadb -r 1c40abf8bc5b7555dd276e540f487f8c288da4b2 job_conf.xml.sample_advanced
--- a/job_conf.xml.sample_advanced
+++ b/job_conf.xml.sample_advanced
@@ -102,6 +102,12 @@
<!-- Warning: Local slot count doesn't tie up additional worker threads, to prevent over
allocating machine define a second local runner with different name and fewer workers
to run this destination. -->
+ <param id="embed_metadata_in_job">True</param>
+ <!-- Above parameter will be default (with no option to set
+ to False) in an upcoming release of Galaxy, but you can
+ try it early - it will slightly speed up local jobs by
+ embedding metadata calculation in job script itself.
+ --><job_metrics /><!-- Above element demonstrates embedded job metrics definition - see
job_metrics_conf.xml.sample for full documentation on possible nested
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests
by commits-noreplyï¼ bitbucket.org 24 Jun '14
by commits-noreplyï¼ bitbucket.org 24 Jun '14
24 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/aff21e09778e/
Changeset: aff21e09778e
User: carlfeberhard
Date: 2014-06-24 23:02:23
Summary: Fix: phantomjs apparently lacks the bind fn on the Function prototype - correct failures in history-panel (line 252) by using underscore bind instead; up the standard upload timeout interval for api tests
Affected #: 2 files
diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -249,7 +249,7 @@
actions.push( {
// TODO: Only show quick pair if two things selected.
html: _l( 'Build List of Dataset Pairs (Experimental)' ),
- func: panel._showPairedCollectionModal.bind( panel )
+ func: _.bind( panel._showPairedCollectionModal, panel )
});
return new PopupMenu( $where.find( '.history-dataset-action-popup-btn' ), actions );
},
diff -r ae31e175f1cd836e89324a57d2c4276c5091f95f -r aff21e09778ece1bdbe987a4dad2adb6a26e5447 test/casperjs/modules/api.js
--- a/test/casperjs/modules/api.js
+++ b/test/casperjs/modules/api.js
@@ -555,7 +555,7 @@
};
/** amount of time allowed to upload a file (before erroring) */
-ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 12000;
+ToolsAPI.prototype.DEFAULT_UPLOAD_TIMEOUT = 30 * 1000;
/** add two casperjs steps - upload a file, wait for the job to complete, and run 'then' when they are */
ToolsAPI.prototype.thenUpload = function thenUpload( historyId, options, then ){
@@ -569,6 +569,9 @@
this.debug( 'uploadedId: ' + uploadedId );
});
+ spaceghost.debug( '---------------------------------------------------------- timeout: ' + ( options.timeout || spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT ) );
+ spaceghost.debug( 'timeout: ' + options.timeout );
+ spaceghost.debug( 'timeout: ' + spaceghost.api.tools.DEFAULT_UPLOAD_TIMEOUT );
spaceghost.then( function(){
this.waitFor(
function testHdaState(){
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Style fix: use MS/IE specific syntax for flexbox to correct layout of paired-collection-creator in IE10 (Note: IE9 has no flexbox and this interface can't be used with it)
by commits-noreplyï¼ bitbucket.org 24 Jun '14
by commits-noreplyï¼ bitbucket.org 24 Jun '14
24 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ae31e175f1cd/
Changeset: ae31e175f1cd
User: carlfeberhard
Date: 2014-06-24 22:11:57
Summary: Style fix: use MS/IE specific syntax for flexbox to correct layout of paired-collection-creator in IE10 (Note: IE9 has no flexbox and this interface can't be used with it)
Affected #: 2 files
diff -r 17fbd073d94df628997df9df5af7d1de077bf82a -r ae31e175f1cd836e89324a57d2c4276c5091f95f static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1367,13 +1367,13 @@
.collection-creator .scroll-container{overflow:auto}
.collection-creator .truncate{overflow:hidden;white-space:nowrap;text-overflow:ellipsis}
.collection-creator .empty-message{color:grey;font-style:italic}
-.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:flex;-webkit-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;align-content:stretch}
-.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;flex-direction:column}
-.collection-creator .flex-row{-webkit-flex:1 auto;flex:1 0 auto}
-.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;flex:0 0 auto}
-.collection-creator .flex-column-container{-webkit-flex-direction:row;flex-direction:row}
-.collection-creator .flex-column{-webkit-flex:1 auto;flex:1 1 auto}
-.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;flex:0 0 auto}
+.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:-ms-flexbox;display:flex;-webkit-align-items:stretch;-ms-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;-ms-align-content:stretch;align-content:stretch}
+.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;-ms-flex-direction:column;flex-direction:column}
+.collection-creator .flex-row{-webkit-flex:1 auto;-ms-flex:1 auto;flex:1 0 auto}
+.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;-ms-flex:0 auto;flex:0 0 auto}
+.collection-creator .flex-column-container{-webkit-flex-direction:row;-ms-flex-direction:row;flex-direction:row}
+.collection-creator .flex-column{-webkit-flex:1 auto;-ms-flex:1 auto;flex:1 1 auto}
+.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;-ms-flex:0 auto;flex:0 0 auto}
.collection-creator .choose-filters .help{margin-bottom:2px;font-size:90%;color:grey}
.collection-creator .choose-filters button{width:100%;margin-top:2px}
.collection-creator .header .alert{display:none}
diff -r 17fbd073d94df628997df9df5af7d1de077bf82a -r ae31e175f1cd836e89324a57d2c4276c5091f95f static/style/src/less/ui/paired-collection-creator.less
--- a/static/style/src/less/ui/paired-collection-creator.less
+++ b/static/style/src/less/ui/paired-collection-creator.less
@@ -44,11 +44,15 @@
.flex-column-container {
display: -webkit-box;
display: -webkit-flex;
+ display: -ms-flexbox;
display: flex;
-webkit-align-items: stretch;
+ -ms-align-items: stretch;
align-items: stretch;
+
-webkit-align-content: stretch;
+ -ms-align-content: stretch;
align-content: stretch;
}
@@ -56,28 +60,34 @@
&.flex-row-container,
.flex-row-container {
-webkit-flex-direction: column;
+ -ms-flex-direction: column;
flex-direction: column;
}
.flex-row {
-webkit-flex: 1 auto;
+ -ms-flex: 1 auto;
flex: 1 0 auto;
}
.flex-row.no-flex {
-webkit-flex: 0 auto;
+ -ms-flex: 0 auto;
flex: 0 0 auto;
}
// a series of horizontal elements that will expand to fill available space
.flex-column-container {
-webkit-flex-direction: row;
+ -ms-flex-direction: row;
flex-direction: row;
}
.flex-column {
-webkit-flex: 1 auto;
+ -ms-flex: 1 auto;
flex: 1 1 auto;
}
.flex-column.no-flex {
-webkit-flex: 0 auto;
+ -ms-flex: 0 auto;
flex: 0 0 auto;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Style fix: use Safari/webkit specific syntax for flexbox to correct layout of paired-collection-creator in Safari
by commits-noreplyï¼ bitbucket.org 24 Jun '14
by commits-noreplyï¼ bitbucket.org 24 Jun '14
24 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/17fbd073d94d/
Changeset: 17fbd073d94d
User: carlfeberhard
Date: 2014-06-24 21:46:12
Summary: Style fix: use Safari/webkit specific syntax for flexbox to correct layout of paired-collection-creator in Safari
Affected #: 5 files
diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/mvc/collection/dataset-collection-edit.js
--- a/static/scripts/mvc/collection/dataset-collection-edit.js
+++ b/static/scripts/mvc/collection/dataset-collection-edit.js
@@ -17,7 +17,7 @@
// ......................................................................... edit attr, delete
/** Render icon-button group for the common, most easily accessed actions.
- * Overrides _render_titleButtons to include editting related buttons.
+ * Overrides _render_titleButtons to include editing related buttons.
* @see DatasetCollectionBaseView#_render_titleButtons
* @returns {jQuery} rendered DOM
*/
diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/mvc/collection/paired-collection-creator.js
--- a/static/scripts/mvc/collection/paired-collection-creator.js
+++ b/static/scripts/mvc/collection/paired-collection-creator.js
@@ -7,6 +7,8 @@
*/
var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
+ className: 'collection-creator flex-row-container',
+
/** set up initial options, instance vars, behaviors, and autopair (if set to do so) */
initialize : function( attributes ){
//console.debug( '-- PairedCollectionCreator:', attributes );
@@ -541,7 +543,8 @@
/** render the entire interface */
render : function( speed, callback ){
//console.debug( '-- _render' );
- this.$el.empty().addClass( 'collection-creator' ).html( PairedCollectionCreator.templates.main() );
+ //this.$el.empty().html( PairedCollectionCreator.templates.main() );
+ this.$el.empty().html( PairedCollectionCreator.templates.main() );
this._renderHeader( speed );
this._renderMiddle( speed );
this._renderFooter( speed );
@@ -1191,9 +1194,9 @@
PairedCollectionCreator.templates = PairedCollectionCreator.templates || {
/** the skeleton */
main : _.template([
- '<div class="header"></div>',
- '<div class="middle"></div>',
- '<div class="footer">'
+ '<div class="header flex-row no-flex"></div>',
+ '<div class="middle flex-row flex-row-container"></div>',
+ '<div class="footer flex-row no-flex">'
].join('')),
/** the header (not including help text) */
@@ -1209,7 +1212,7 @@
'<span class="alert-message"></span>',
'</div>',
- '<div class="column-headers vertically-spaced row-flex-container">',
+ '<div class="column-headers vertically-spaced flex-column-container">',
'<div class="forward-column flex-column column">',
'<div class="column-header">',
'<div class="column-title">',
@@ -1221,7 +1224,7 @@
'</div>',
'</div>',
'</div>',
- '<div class="paired-column flex-column column">',
+ '<div class="paired-column flex-column no-flex column">',
'<div class="column-header">',
'<a class="choose-filters-link" href="javascript:void(0)">',
_l( 'Choose filters' ),
@@ -1250,11 +1253,12 @@
/** the middle: unpaired, divider, and paired */
middle : _.template([
- '<div class="unpaired-columns row-flex-container scroll-container">',
+ // contains two flex rows (rows that fill available space) and a divider btwn
+ '<div class="unpaired-columns flex-column-container scroll-container flex-row">',
'<div class="forward-column flex-column column">',
'<ol class="column-datasets"></ol>',
'</div>',
- '<div class="paired-column flex-column column">',
+ '<div class="paired-column flex-column no-flex column">',
'<ol class="column-datasets"></ol>',
'</div>',
'<div class="reverse-column flex-column column">',
@@ -1272,11 +1276,11 @@
'</a>',
'</div>',
'</div>',
- '<div class="paired-columns row-flex-container scroll-container">',
+ '<div class="paired-columns flex-column-container scroll-container flex-row">',
'<div class="forward-column flex-column column">',
'<ol class="column-datasets"></ol>',
'</div>',
- '<div class="paired-column flex-column column">',
+ '<div class="paired-column flex-column no-flex column">',
'<ol class="column-datasets"></ol>',
'</div>',
'<div class="reverse-column flex-column column">',
diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/scripts/packed/mvc/collection/paired-collection-creator.js
--- a/static/scripts/packed/mvc/collection/paired-collection-creator.js
+++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js
@@ -1,1 +1,1 @@
-define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.View.extend(a.LoggableMixin).extend({initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(g){return g.name.indexOf(this.filters[0])>=0},_filterRevFn:function(g){return g.name.indexOf(this.filters[1])>=0},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=d(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var 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','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",e(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>.',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};function d(h,g){if(h.length===0){return g.length}if(g.length===0){return h.length}var k=[];var m;for(m=0;m<=g.length;m++){k[m]=[m]}var l;for(l=0;l<=h.length;l++){k[0][l]=l}for(m=1;m<=g.length;m++){for(l=1;l<=h.length;l++){if(g.charAt(m-1)===h.charAt(l-1)){k[m][l]=k[m-1][l-1]}else{k[m][l]=Math.min(k[m-1][l-1]+1,Math.min(k[m][l-1]+1,k[m-1][l]+1))}}}return k[g.length][h.length]}(function(){jQuery.fn.extend({hoverhighlight:function g(i,h){i=i||"body";if(!this.size()){return this}$(this).each(function(){var k=$(this),j=k.data("target");if(j){k.mouseover(function(l){$(j,i).css({background:h})}).mouseout(function(l){$(j).css({background:""})})}});return this}})}());var b=function c(i,g){g=_.defaults(g||{},{datasets:i,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var h=new f(g).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:h.$el,width:"80%",height:"700px",closing_events:true});return h};return{PairedCollectionCreator:f,pairedCollectionCreatorModal:b}});
\ No newline at end of file
+define(["mvc/base-mvc","utils/localization"],function(a,e){var f=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(g){g=_.defaults(g,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=g.datasets;this.historyId=g.historyId;this.filters=this.commonFilters[g.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(g.filters)){this.filters=g.filters}this.automaticallyPair=g.automaticallyPair;this.matchPercentage=g.matchPercentage;this.strategy=this.strategies[g.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(g.strategy)){this.strategy=g.strategy}this.oncancel=g.oncancel;this.oncreate=g.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(g){g.sort(function(i,h){return naturalSort(i.name,h.name)});return g},_ensureIds:function(){this.initialList.forEach(function(g){if(!g.hasOwnProperty("id")){g.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(i){var h=[],g=[];this.unpaired.forEach(function(j){if(this._filterFwdFn(j)){h.push(j)}if(this._filterRevFn(j)){g.push(j)}}.bind(this));return[h,g]},_filterFwdFn:function(g){return g.name.indexOf(this.filters[0])>=0},_filterRevFn:function(g){return g.name.indexOf(this.filters[1])>=0},_addToUnpaired:function(h){var g=function(i,k){if(i===k){return i}var j=Math.floor((k-i)/2)+i,l=naturalSort(h.name,this.unpaired[j].name);if(l<0){return g(i,j)}else{if(l>0){return g(j+1,k)}}while(this.unpaired[j]&&this.unpaired[j].name===h.name){j++}return j}.bind(this);this.unpaired.splice(g(0,this.unpaired.length),0,h)},autoPair:function(g){g=g||this.strategy;this.simpleAutoPair();return this[g].call(this)},simpleAutoPair:function(){var m=0,k,q=this._splitByFilters(),g=q[0],p=q[1],o,r,h=false;while(m<g.length){var l=g[m];o=l.name.replace(this.filters[0],"");h=false;for(k=0;k<p.length;k++){var n=p[k];r=n.name.replace(this.filters[1],"");if(l!==n&&o===r){h=true;this._pair(g.splice(m,1)[0],p.splice(k,1)[0],{silent:true});break}}if(!h){m+=1}}},autoPairLevenshtein:function(){var n=0,l,s=this._splitByFilters(),g=s[0],q=s[1],p,u,h,r,k;while(n<g.length){var m=g[n];p=m.name.replace(this.filters[0],"");k=Number.MAX_VALUE;for(l=0;l<q.length;l++){var o=q[l];u=o.name.replace(this.filters[1],"");if(m!==o){if(p===u){r=l;k=0;break}h=d(p,u);if(h<k){r=l;k=h}}}var t=1-(k/(Math.max(p.length,u.length)));if(t>=this.matchPercentage){this._pair(g.splice(n,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{n+=1}}},autoPairLCSs:function(){var l=0,h,s=this._splitByFilters(),g=s[0],q=s[1],p,v,u,r,n;if(!g.length||!q.length){return}while(l<g.length){var k=g[l];p=k.name.replace(this.filters[0],"");n=0;for(h=0;h<q.length;h++){var o=q[h];v=o.name.replace(this.filters[1],"");if(k!==o){if(p===v){r=h;n=p.length;break}var m=this._naiveStartingAndEndingLCS(p,v);u=m.length;if(u>n){r=h;n=u}}}var t=n/(Math.min(p.length,v.length));if(t>=this.matchPercentage){this._pair(g.splice(l,1)[0],q.splice(r,1)[0],{silent:true});if(g.length<=0||q.length<=0){return}}else{l+=1}}},_naiveStartingAndEndingLCS:function(l,h){var m="",n="",k=0,g=0;while(k<l.length&&k<h.length){if(l[k]!==h[k]){break}m+=l[k];k+=1}if(k===l.length){return l}if(k===h.length){return h}k=(l.length-1);g=(h.length-1);while(k>=0&&g>=0){if(l[k]!==h[g]){break}n=[l[k],n].join("");k-=1;g-=1}return m+n},_pair:function(i,g,h){h=h||{};var j=this._createPair(i,g,h.name);this.paired.push(j);this.unpaired=_.without(this.unpaired,i,g);if(!h.silent){this.trigger("pair:new",j)}return j},_createPair:function(i,g,h){if(!(i&&g)||(i===g)){throw new Error("Bad pairing: "+[JSON.stringify(i),JSON.stringify(g)])}h=h||this._guessNameForPair(i,g);return{forward:i,name:h,reverse:g}},_guessNameForPair:function(i,g){var h=this._naiveStartingAndEndingLCS(i.name.replace(this.filters[0],""),g.name.replace(this.filters[1],""));return h||(i.name+" & "+g.name)},_unpair:function(h,g){g=g||{};if(!h){throw new Error("Bad pair: "+JSON.stringify(h))}this.paired=_.without(this.paired,h);this._addToUnpaired(h.forward);this._addToUnpaired(h.reverse);if(!g.silent){this.trigger("pair:unpair",[h])}return h},unpairAll:function(){var g=[];while(this.paired.length){g.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",g)},_pairToJSON:function(g){return{collection_type:"paired",src:"new_collection",name:g.name,element_identifiers:[{name:"forward",id:g.forward.id,src:"hda"},{name:"reverse",id:g.reverse.id,src:"hda"}]}},createList:function(){var i=this,h;if(i.historyId){h="/api/histories/"+this.historyId+"/contents/dataset_collections"}var g={type:"dataset_collection",collection_type:"list:paired",name:_.escape(i.$(".collection-name").val()),element_identifiers:i.paired.map(function(j){return i._pairToJSON(j)})};return jQuery.ajax(h,{type:"POST",contentType:"application/json",data:JSON.stringify(g)}).fail(function(m,j,l){console.error(m,j,l);var k=e("An error occurred while creating this collection");if(m){if(m.readyState===0&&m.status===0){k+=": "+e("Galaxy could not be reached and may be updating.")+e(" Try again in a few minutes.")}else{if(m.responseJSON){k+="<br /><pre>"+JSON.stringify(m.responseJSON)+"</pre>"}else{k+=": "+l}}}i._showAlert(k,"alert-danger")}).done(function(j,k,l){i.trigger("collection:created",j,k,l);if(typeof i.oncreate==="function"){i.oncreate.call(this,j,k,l)}})},render:function(g,h){this.$el.empty().html(f.templates.main());this._renderHeader(g);this._renderMiddle(g);this._renderFooter(g);this._addPluginComponents();return this},_renderHeader:function(h,i){var g=this.$(".header").empty().html(f.templates.header()).find(".help-content").prepend($(f.templates.helpContent()));this._renderFilters();return g},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(h,i){var g=this.$(".middle").empty().html(f.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return g},_renderUnpaired:function(l,m){var j=this,k,h,g=[],i=this._splitByFilters();this.$(".forward-column .title").text([i[0].length,e("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[0].length));this.$(".reverse-column .title").text([i[1].length,e("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-i[1].length));this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty()}h=i[1].map(function(o,n){if((i[0][n]!==undefined)&&(i[0][n]!==o)){g.push(j._renderPairButton())}return j._renderUnpairedDataset(o)});k=i[0].map(function(n){return j._renderUnpairedDataset(n)});this.$(".unpaired-columns .column-datasets").empty();return this.$(".unpaired-columns .forward-column .column-datasets").append(k).add(this.$(".unpaired-columns .paired-column .column-datasets").append(g)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(h))},_renderUnpairedDisplayStr:function(g){return["(",g," ",e("filtered out"),")"].join("")},_renderUnpairedDataset:function(g){return $("<li/>").attr("id","dataset-"+g.id).addClass("dataset 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g},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 192, 255, 255, 1.0 )")},_chooseFiltersPopover:function(g){function h(k,j){return['<button class="filter-choice btn" ','data-forward="',k,'" data-reverse="',j,'">',e("Forward"),": ",k,", ",e("Reverse"),": ",j,"</button>"].join("")}var i=$(_.template(['<div class="choose-filters">','<div class="help">',e("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",h("_1","_2"),h("_R1","_R2"),"</div>"].join(""),{}));return this.$(g).popover({container:".collection-creator",placement:"bottom",html:true,content:i})},_validationWarning:function(h,g){var i="validation-warning";if(h==="name"){h=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(g){h=h||this.$("."+i);h.removeClass(i)}else{h.addClass(i)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(g){this._renderUnpaired();this._renderPaired()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired()});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click 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g=this;_.each(h,function(i){if(h===g.paired){g._printPair(i)}else{}})},_printPair:function(g){console.debug(g.forward.name,g.reverse.name,": ->",g.name)},toString:function(){return"PairedCollectionCreator"}});f.templates=f.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',e("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',e("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',e("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',e("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',e("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',e("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',e("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',e("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',e("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>",'<div class="flexible-partition">','<div class="flexible-partition-drag"></div>','<div class="column-header">','<div class="column-title paired-column-title">','<span class="title"></span>',"</div>",'<a class="unpair-all-link" href="javascript:void(0);">',e("Unpair all"),"</a>","</div>","</div>",'<div class="paired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>"].join("")),footer:_.template(['<div class="attributes clear">','<input class="collection-name form-control pull-right" ','placeholder="',e("Enter a name for your new list"),'" />','<div class="collection-name-prompt pull-right">',e("Name"),":</div>","</div>",'<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',e("Cancel"),"</button>",'<div class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',e("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',e("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',e("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',e("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",e(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse ","reads) that can be passed to tools and workflows in order to have analyses done on the entire ","group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",e(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",e(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",e(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",e(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>.',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};function d(h,g){if(h.length===0){return g.length}if(g.length===0){return h.length}var k=[];var m;for(m=0;m<=g.length;m++){k[m]=[m]}var l;for(l=0;l<=h.length;l++){k[0][l]=l}for(m=1;m<=g.length;m++){for(l=1;l<=h.length;l++){if(g.charAt(m-1)===h.charAt(l-1)){k[m][l]=k[m-1][l-1]}else{k[m][l]=Math.min(k[m-1][l-1]+1,Math.min(k[m][l-1]+1,k[m-1][l]+1))}}}return k[g.length][h.length]}(function(){jQuery.fn.extend({hoverhighlight:function g(i,h){i=i||"body";if(!this.size()){return this}$(this).each(function(){var k=$(this),j=k.data("target");if(j){k.mouseover(function(l){$(j,i).css({background:h})}).mouseout(function(l){$(j).css({background:""})})}});return this}})}());var b=function c(i,g){g=_.defaults(g||{},{datasets:i,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var h=new f(g).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:h.$el,width:"80%",height:"700px",closing_events:true});return h};return{PairedCollectionCreator:f,pairedCollectionCreatorModal:b}});
\ No newline at end of file
diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1360,13 +1360,20 @@
.toast-error{background-color:#bd362f}
.toast-info{background-color:#2f96b4}
.toast-warning{background-color:#f89406}
-@media all and (max-width:240px){#toast-container>div{padding:8px 8px 8px 50px;width:11em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:241px) and (max-width:480px){#toast-container>div{padding:8px 8px 8px 50px;width:18em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:481px) and (max-width:768px){#toast-container>div{padding:15px 15px 15px 50px;width:25em}}.collection-creator{height:100%;display:flex;flex-direction:column;align-items:stretch;align-content:stretch;overflow:hidden;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none}.collection-creator ol,.collection-creator li{list-style:none;padding:0;margin:0}
+@media all and (max-width:240px){#toast-container>div{padding:8px 8px 8px 50px;width:11em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:241px) and (max-width:480px){#toast-container>div{padding:8px 8px 8px 50px;width:18em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:481px) and (max-width:768px){#toast-container>div{padding:15px 15px 15px 50px;width:25em}}.collection-creator{height:100%;overflow:hidden;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none}.collection-creator ol,.collection-creator li{list-style:none;padding:0;margin:0}
.collection-creator>*:not(.popover){padding:0px 8px 0px 8px}
.collection-creator .btn{border-color:#BFBFBF}
.collection-creator .vertically-spaced{margin-top:8px}
.collection-creator .scroll-container{overflow:auto}
.collection-creator .truncate{overflow:hidden;white-space:nowrap;text-overflow:ellipsis}
.collection-creator .empty-message{color:grey;font-style:italic}
+.collection-creator.flex-row-container,.collection-creator .flex-row-container,.collection-creator .flex-column-container{display:-webkit-box;display:-webkit-flex;display:flex;-webkit-align-items:stretch;align-items:stretch;-webkit-align-content:stretch;align-content:stretch}
+.collection-creator.flex-row-container,.collection-creator .flex-row-container{-webkit-flex-direction:column;flex-direction:column}
+.collection-creator .flex-row{-webkit-flex:1 auto;flex:1 0 auto}
+.collection-creator .flex-row.no-flex{-webkit-flex:0 auto;flex:0 0 auto}
+.collection-creator .flex-column-container{-webkit-flex-direction:row;flex-direction:row}
+.collection-creator .flex-column{-webkit-flex:1 auto;flex:1 1 auto}
+.collection-creator .flex-column.no-flex{-webkit-flex:0 auto;flex:0 0 auto}
.collection-creator .choose-filters .help{margin-bottom:2px;font-size:90%;color:grey}
.collection-creator .choose-filters button{width:100%;margin-top:2px}
.collection-creator .header .alert{display:none}
@@ -1374,8 +1381,8 @@
.collection-creator .column-title{height:22px;line-height:22px;overflow:hidden}.collection-creator .column-title:hover{text-decoration:underline;cursor:pointer}
.collection-creator .column-title .title{font-weight:bold}
.collection-creator .column-title .title-info{color:grey}.collection-creator .column-title .title-info:before{content:' - '}
-.collection-creator .paired-column{text-align:center;width:22%;flex:0 1 auto}
-.collection-creator .header{flex:0 0 auto;padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal}
+.collection-creator .paired-column{text-align:center;width:22%}
+.collection-creator .header{padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal}
.collection-creator .header .main-help .help-content ul,.collection-creator .header .main-help .help-content li{list-style:circle;margin-left:16px}
.collection-creator .header .main-help .help-content p:first-child{overflow:hidden;white-space:nowrap;text-overflow:ellipsis}
.collection-creator .header .main-help .help-content .less-help{display:inline-block;width:100%;text-align:right}
@@ -1383,11 +1390,7 @@
.collection-creator .header .column-headers .column-header .unpaired-filter{width:100%}.collection-creator .header .column-headers .column-header .unpaired-filter .search-query{width:100%;height:22px}
.collection-creator .header .paired-column a:not(:last-child){margin-right:8px}
.collection-creator .header .reverse-column .column-title{text-align:right}
-.collection-creator .row-flex-container{display:flex;flex-direction:row;align-items:stretch;align-content:stretch}
-.collection-creator .flex-column{flex:1 1 auto}
-.collection-creator .middle{flex:1 0 auto;display:flex;flex-direction:column;align-items:stretch;align-content:stretch}
-.collection-creator .unpaired-columns,.collection-creator .paired-columns{flex:1 0 auto;height:0;border:1px solid lightgrey;border-radius:3px;border-width:1px 0 1px 0;overflow-y:auto;padding:4px}
-.collection-creator .unpaired-columns{flex:1 0 auto}
+.collection-creator .unpaired-columns,.collection-creator .paired-columns{height:0;border:1px solid lightgrey;border-width:1px 0 1px 0;padding:4px}
.collection-creator .paired-columns{margin-bottom:8px}
.collection-creator .column-datasets{list-style:none;overflow:hidden}.collection-creator .column-datasets .dataset{height:32px;margin-bottom:2px;border:1px solid lightgrey;border-radius:3px;padding:0 8px 0 8px;line-height:28px;cursor:pointer;overflow:hidden}.collection-creator .column-datasets .dataset:last-child{margin-bottom:4px}
.collection-creator .unpaired-columns .dataset.unpaired{border-color:grey}.collection-creator .unpaired-columns .dataset.unpaired:hover{border-color:black}
@@ -1402,7 +1405,7 @@
.collection-creator .paired-columns .paired-column .dataset.paired{border-radius:0;border-width:2px 0 2px 0}.collection-creator .paired-columns .paired-column .dataset.paired .dataset-name:hover{text-decoration:underline}
.collection-creator .paired-columns .reverse-column .dataset.paired{margin-right:32px;border-radius:0 3px 3px 0;border-left-color:grey;border-left-width:1px}.collection-creator .paired-columns .reverse-column .dataset.paired:before{margin-right:8px;font-family:FontAwesome;content:'\f060'}
.collection-creator .paired-columns .reverse-column .unpair-btn{float:right;margin-top:-34px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator .paired-columns .reverse-column .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE}
-.collection-creator .footer{flex:0 0 auto;padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red}
+.collection-creator .footer{padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red}
.collection-creator .footer .collection-name{width:50%}.collection-creator .footer .collection-name.validation-warning{border-color:red}
.collection-creator .footer .other-options>*{display:none;margin-left:4px}
.collection-creator .footer .collection-name-prompt{margin:5px 4px 0 0}
diff -r 476aa78a1b1a48bc15d983bf2694959cbbf6d45c -r 17fbd073d94df628997df9df5af7d1de077bf82a static/style/src/less/ui/paired-collection-creator.less
--- a/static/style/src/less/ui/paired-collection-creator.less
+++ b/static/style/src/less/ui/paired-collection-creator.less
@@ -2,11 +2,6 @@
.collection-creator {
height: 100%;
- display: flex;
- flex-direction: column;
- align-items: stretch;
- align-content: stretch;
-
overflow: hidden;
-webkit-user-select: none;
@@ -43,6 +38,49 @@
font-style: italic;
}
+ // ------------------------------------------------------------------------ flex
+ &.flex-row-container,
+ .flex-row-container,
+ .flex-column-container {
+ display: -webkit-box;
+ display: -webkit-flex;
+ display: flex;
+
+ -webkit-align-items: stretch;
+ align-items: stretch;
+ -webkit-align-content: stretch;
+ align-content: stretch;
+ }
+
+ // a series of vertical elements that will expand to fill available space
+ &.flex-row-container,
+ .flex-row-container {
+ -webkit-flex-direction: column;
+ flex-direction: column;
+ }
+ .flex-row {
+ -webkit-flex: 1 auto;
+ flex: 1 0 auto;
+ }
+ .flex-row.no-flex {
+ -webkit-flex: 0 auto;
+ flex: 0 0 auto;
+ }
+
+ // a series of horizontal elements that will expand to fill available space
+ .flex-column-container {
+ -webkit-flex-direction: row;
+ flex-direction: row;
+ }
+ .flex-column {
+ -webkit-flex: 1 auto;
+ flex: 1 1 auto;
+ }
+ .flex-column.no-flex {
+ -webkit-flex: 0 auto;
+ flex: 0 0 auto;
+ }
+
// ------------------------------------------------------------------------ sub-components
.choose-filters {
.help {
@@ -87,12 +125,10 @@
text-align: center;
// mess with these two to make center more/less priority
width: 22%;
- flex: 0 1 auto;
}
// ------------------------------------------------------------------------ header
.header {
- flex: 0 0 auto;
padding-bottom: 8px;
.main-help {
@@ -151,45 +187,21 @@
}
- // ------------------------------------------------------------------------ flex
- .row-flex-container {
- display: flex;
- flex-direction: row;
- align-items: stretch;
- align-content: stretch;
- }
- .flex-column {
- flex: 1 1 auto;
- }
-
// ------------------------------------------------------------------------ middle
.middle {
- // highest flex count - will priority fill with this
- flex: 1 0 auto;
-
- display: flex;
- flex-direction: column;
- align-items: stretch;
- align-content: stretch;
}
.unpaired-columns,
.paired-columns {
- flex: 1 0 auto;
// huh! - giving these any static height will pull them in
height: 0;
// NOT setting the above will give a full-height page
border: 1px solid lightgrey;
- border-radius: 3px;
border-width: 1px 0 1px 0;
- overflow-y: auto;
+ //overflow-y: auto;
padding: 4px;
}
// ------------------------------------------------------------------------ unpaired
- .unpaired-columns {
- flex: 1 0 auto;
- }
-
.paired-columns {
margin-bottom: 8px;
}
@@ -337,9 +349,6 @@
// ------------------------------------------------------------------------ footer
.footer {
- flex: 0 0 auto;
- padding-bottom: 8px;
-
.collection-name-prompt.validation-warning:before {
//TODO: localize (somehow)
content: '(required)';
@@ -361,5 +370,6 @@
.collection-name-prompt {
margin: 5px 4px 0 0;
}
+ padding-bottom: 8px;
}
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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0
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/476aa78a1b1a/
Changeset: 476aa78a1b1a
User: guerler
Date: 2014-06-24 21:00:13
Summary: Merge
Affected #: 76 files
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a15c52999493/
Changeset: a15c52999493
Branch: stable
User: guerler
Date: 2014-06-24 19:38:13
Summary: Charts plugin update
Affected #: 164 files
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/app.css
--- a/config/plugins/visualizations/charts/static/app.css
+++ b/config/plugins/visualizations/charts/static/app.css
@@ -1,3 +1,20 @@
+.charts-tooltip {
+ position: absolute;
+ text-align: center;
+ padding: 3px 5px 3px 5px;
+ font: 12px sans-serif;
+ background: white;
+ border: 1px solid gray;
+ border-radius: 4px;
+ pointer-events: none;
+}
+
+.charts-tooltip-first {
+ font-weight: bold;
+ text-align: left;
+ padding-right: 5px;
+}
+
.charts-grid .item {
padding: 5px;
margin: 5px;
@@ -17,6 +34,7 @@
.charts-grid .image {
padding: 10px;
width: 100px;
+ height: 86px;
}
.charts-grid .title {
@@ -47,6 +65,7 @@
margin-left: 5px;
top: -1px;
font-size: 1.0em;
+ display: inline;
}
.charts-viewport .icon {
@@ -63,5 +82,6 @@
.charts-viewport .charts-viewport-canvas {
display: block;
width:100%;
+ min-height: 100px;
height: inherit;
}
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -86,6 +86,22 @@
}
},
+ // get root path
+ chartPath: function(chart_type) {
+ // create path from id
+ var path = chart_type.split(/_(.+)/);
+
+ // check path
+ if (path.length >= 2) {
+ // return path
+ return path[0] + '/' + path[1];
+ } else {
+ // log status
+ console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type);
+ }
+ return undefined;
+ },
+
// execute command
execute: function(options) {
},
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
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t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var 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"+t+":"+n;return r}return{cssLoadFile:i,cssGetAttribute:r,get:t,merge:s,bytesToString:o,uuid:u,time:f,wrap:a,request:n}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{url:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img src="'+e.url+'"/>'}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return'<label class="'+e.cls+'"><b>'+e.title+"</b></label>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),s=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),a=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),f=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),l=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:r,Image:n,Button:s,Icon:u,ButtonIcon:o,Input:p,Anchor:a,Message:f,Searchbox:l,Title:c,Text:i,Select:t,ButtonMenu:h}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._get(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.end+"_"+t},_get:function(e,t){e.start||(e.start=0),e.end||(e.end=this.app.config.get("query_limit"));var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f])continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,end:e.end,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){console.debug("Datasets::_fill_from_cache() - Filling request from cache.");for(var t in e.groups){var n=e.groups[t];n.values=[];for(var r in n.columns){var i=n.columns[r],s=this._block_id(e,i.index),o=this.cache[s];for(k in o){var u=n.values[k];u===undefined&&(u={x:parseInt(k)+e.start},n.values[k]=u);var a=o[k];isNaN(a)&&!i.is_label&&(a=0),u[r]=a}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o=0;t.columns&&(o=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+o+" column(s)")),o==0&&console.debug("Datasets::_fetch() - No columns requested");var u="";for(var a in t.columns)u+=t.columns[a]+",";u=u.substring(0,u.length-1);var f=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:u},function(e){var t=new Array(o);for(var r=0;r<o;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var s in i){var u=i[s];u!==undefined&&u!=2147483647&&t[s].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find("container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info")),t.hide();var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning");break;default:n.addClass("icon fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,e=="svg"?this.canvas_list[n]=d3.select(r.find("#canvas")[0]):this.canvas_list[n]=r.find("#canvas")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r);var i=this.chart_settings.use_panels,s=1;i&&(s=e.groups.length),this._createContainer(this.chart_settings.tag,s),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/wrapper"],function(r){var i=new r(t.app,{canvas:t.canvas_list});t.chart_settings.execute?t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_settings.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns){var o=r.chart_settings.columns[s];i[s]={index:e.get(s),is_label:o.is_label}}t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon" /><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="canvas" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){for(var t in s){var n=i.columns[t].is_label,o=[],u=e.metadata_column_types;for(var a in u)(!n&&(u[a]=="int"||u[a]=="float")||n)&&o.push({label:"Column: "+(parseInt(a)+1)+" ["+u[a]+"]",value:a});s[t].update(o),s[t].show()}r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.category+" - "+t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault);var r=$('<div class="charts-grid"/>');this.setElement(r);var i={},s=t.types.attributes;for(var o in s){var u=s[o],a=u.category;i[a]||(i[a]={}),i[a][o]=u}for(var a in i){var r=$('<div style="clear: both;"/>');r.append(e.wrap(this._template_header({title:a})));for(var o in i[a]){var u=i[a][o];r.append(e.wrap(this._template_item({id:o,title:u.title,url:config.app_root+"charts/"+o+"/logo.png"})))}this.$el.append(e.wrap(r))}},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div class="header">• '+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("viewer"),o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0)},ondblclick:function(e){o.app.go("viewer"),o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap((new t.Label({title:"Select a chart type:"})).$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:5e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",category:"",library:"nvd3.js",tag:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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'+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Label:s,Button:u,Icon:o,ButtonIcon:a,Input:h,Anchor:f,Message:l,Searchbox:c,Select:t,ButtonMenu:n,Modal:r,Textarea:p,Image:i,RadioButton:d}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){e.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){s.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){s.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com).",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){s.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){e.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" 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t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - 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n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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S=e.filter(function(e){return!e.disabled});e=d3.layout.stack().order(l).offset(f).values(function(e){return e.values}).x(o).y(u).out(function(e,t,n){var r=u(e)===0?0:n;e.display={y:r,y0:t}})(S);var T=w.selectAll("g.nv-wrap.nv-stackedarea").data([e]),N=T.enter().append("g").attr("class","nvd3 nv-wrap nv-stackedarea"),C=N.append("defs"),k=N.append("g"),L=T.select("g");k.append("g").attr("class","nv-areaWrap"),k.append("g").attr("class","nv-scatterWrap"),T.attr("transform","translate("+t.left+","+t.top+")"),v.width(a).height(b).x(o).y(function(e){return e.display.y+e.display.y0}).forceY([0]).color(e.map(function(e,t){return e.color||i(e,e.seriesIndex)}));var A=L.select(".nv-scatterWrap").datum(e);A.call(v),C.append("clipPath").attr("id","nv-edge-clip-"+s).append("rect"),T.select("#nv-edge-clip-"+s+" rect").attr("width",a).attr("height",b),L.attr("clip-path",h?"url(#nv-edge-clip-"+s+")":"");var O=d3.svg.area().x(function(e,t){return p(o(e,t))}).y0(function(e){return 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v.size(2.2).sizeDomain([2.2,2.2]),v.dispatch.on("elementClick.area",function(e){m.areaClick(e)}),v.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+t.left,e.pos[1]+t.top],m.tooltipShow(e)}),v.dispatch.on("elementMouseout.tooltip",function(e){m.tooltipHide(e)}),g.dispatch=m,g.scatter=v,d3.rebind(g,v,"interactive","size","xScale","yScale","zScale","xDomain","yDomain","xRange","yRange","sizeDomain","forceX","forceY","forceSize","clipVoronoi","useVoronoi","clipRadius","highlightPoint","clearHighlights"),g.options=e.utils.optionsFunc.bind(g),g.x=function(e){return arguments.length?(o=d3.functor(e),g):o},g.y=function(e){return arguments.length?(u=d3.functor(e),g):u},g.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,g):t},g.width=function(e){return 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diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/forms/default.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/forms/default.js
@@ -0,0 +1,252 @@
+define([], function() {
+
+return {
+ title : '',
+ category : '',
+ library : '',
+ tag : '',
+ keywords : '',
+ query_limit : 0,
+ settings : {
+ separator_x : {
+ title : 'X axis',
+ type : 'separator'
+ },
+ x_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'X-axis',
+ placeholder : 'Axis label'
+ },
+ x_axis_type : {
+ title : 'Axis value type',
+ info : 'Select the value type of the axis.',
+ type : 'select',
+ init : 'auto',
+ data : [
+ {
+ label : '-- Do not show values --',
+ value : 'hide',
+ operations : {
+ hide : ['x_axis_precision']
+ }
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ operations : {
+ hide : ['x_axis_precision']
+ }
+ },
+ {
+ label : 'Float',
+ value : 'f',
+ operations : {
+ show : ['x_axis_precision']
+ }
+ },
+ {
+ label : 'Exponent',
+ value : 'e',
+ operations : {
+ show : ['x_axis_precision']
+ }
+ },
+ {
+ label : 'Integer',
+ value : 'd',
+ operations : {
+ hide : ['x_axis_precision']
+ }
+ },
+ {
+ label : 'Percentage',
+ value : 'p',
+ operations : {
+ show : ['x_axis_precision']
+ }
+ },
+ {
+ label : 'SI-prefix',
+ value : 's',
+ operations : {
+ hide : ['x_axis_precision']
+ }
+ }
+ ]
+ },
+ x_axis_precision : {
+ title : 'Axis tick format',
+ info : 'Select the tick format for the axis.',
+ type : 'select',
+ init : '1',
+ data : [
+ {
+ label : '0.00001',
+ value : '5'
+ },
+ {
+ label : '0.0001',
+ value : '4'
+ },
+ {
+ label : '0.001',
+ value : '3'
+ },
+ {
+ label : '0.01',
+ value : '2'
+ },
+ {
+ label : '0.1',
+ value : '1'
+ },
+ {
+ label : '1',
+ value : '0'
+ }
+ ]
+
+ },
+ separator_y : {
+ title : 'Y axis',
+ type : 'separator'
+ },
+ y_axis_label : {
+ title : 'Axis label',
+ info : 'Provide a label for the axis.',
+ type : 'text',
+ init : 'Y-axis',
+ placeholder : 'Axis label'
+ },
+ y_axis_type : {
+ title : 'Axis value type',
+ info : 'Select the value type of the axis.',
+ type : 'select',
+ init : 'auto',
+ data : [
+ {
+ label : '-- Do not show values --',
+ value : 'hide',
+ operations : {
+ hide : ['y_axis_precision']
+ }
+ },
+ {
+ label : 'Auto',
+ value : 'auto',
+ operations : {
+ hide : ['y_axis_precision']
+ }
+ },
+ {
+ label : 'Float',
+ value : 'f',
+ operations : {
+ show : ['y_axis_precision']
+ }
+ },
+ {
+ label : 'Exponent',
+ value : 'e',
+ operations : {
+ show : ['y_axis_precision']
+ }
+ },
+ {
+ label : 'Integer',
+ value : 'd',
+ operations : {
+ hide : ['y_axis_precision']
+ }
+ },
+ {
+ label : 'Percentage',
+ value : 'p',
+ operations : {
+ show : ['y_axis_precision']
+ }
+ },
+ {
+ label : 'SI-prefix',
+ value : 's',
+ operations : {
+ hide : ['y_axis_precision']
+ }
+ }
+ ]
+ },
+ y_axis_precision : {
+ title : 'Axis tick format',
+ info : 'Select the tick format for the axis.',
+ type : 'select',
+ init : '1',
+ data : [
+ {
+ label : '0.00001',
+ value : '5'
+ },
+ {
+ label : '0.0001',
+ value : '4'
+ },
+ {
+ label : '0.001',
+ value : '3'
+ },
+ {
+ label : '0.01',
+ value : '2'
+ },
+ {
+ label : '0.1',
+ value : '1'
+ },
+ {
+ label : '1',
+ value : '0'
+ }
+ ]
+
+ },
+ separator_legend : {
+ title : 'Others',
+ type : 'separator'
+ },
+ show_legend : {
+ title : 'Show legend',
+ info : 'Would you like to add a legend?',
+ type : 'radiobutton',
+ init : 'true',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ },
+ use_panels : {
+ title : 'Use multi-panels',
+ info : 'Would you like to separate your data into individual panels?',
+ type : 'radiobutton',
+ init : 'false',
+ data : [
+ {
+ label : 'Yes',
+ value : 'true'
+ },
+ {
+ label : 'No',
+ value : 'false'
+ }
+ ]
+ }
+ }
+};
+
+});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/config.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/config.js
+++ /dev/null
@@ -1,195 +0,0 @@
-define([], function() {
-
-return {
- title : 'Heatmap',
- category : 'Data processing (requires \'charts\' tool from Toolshed)',
- library : '',
- tag : 'div',
- use_panels : true,
- execute : 'heatmap',
-
- // columns
- columns : {
- row_label : {
- title : 'Row labels',
- is_label : true
- },
- col_label : {
- title : 'Column labels',
- is_label : true
- },
- value : {
- title : 'Observations'
- },
- },
-
- // settings
- settings: {
- /*limit : {
- title : 'Limit',
- info : 'Which to ranked clusters would you like to visualize',
- type : 'select',
- init : '20',
- data : [
- {
- label : '20',
- value : '20'
- },
- {
- label : '30',
- value : '30'
- },
- {
- label : '40',
- value : '40'
- },
- {
- label : '50',
- value : '50'
- },
- {
- label : '60',
- value : '60'
- },
- {
- label : '70',
- value : '70'
- },
- {
- label : '80',
- value : '80'
- },
- {
- label : '90',
- value : '90'
- },
- {
- label : '100',
- value : '100'
- }
- ]
- },*/
- color_set : {
- title : 'Color scheme',
- info : 'Select a color scheme for your heatmap',
- type : 'select',
- init : 'ocean',
- data : [
- {
- label : 'Cold-to-Hot',
- value : 'hot'
- },
- {
- label : 'Cool',
- value : 'cool'
- },
- {
- label : 'Copper',
- value : 'copper'
- },
- {
- label : 'Gebco',
- value : 'gebco'
- },
- {
- label : 'Globe',
- value : 'globe'
- },
- {
- label : 'Gray scale',
- value : 'gray'
- },
- {
- label : 'Haxby',
- value : 'haxby'
- },
- {
- label : 'Jet',
- value : 'jet'
- },
- {
- label : 'No-Green',
- value : 'no_green'
- },
- {
- label : 'Ocean',
- value : 'ocean'
- },
- {
- label : 'Polar',
- value : 'polar'
- },
- {
- label : 'Rainbow',
- value : 'rainbow'
- },
- {
- label : 'Red-to-Green',
- value : 'redgreen'
- },
- {
- label : 'Red-to-green (saturated)',
- value : 'red2green'
- },
- {
- label : 'Relief',
- value : 'relief'
- },
- {
- label : 'Seismograph',
- value : 'seis'
- },
- {
- label : 'Sealand',
- value : 'sealand'
- },
- {
- label : 'Split',
- value : 'split'
- },
- {
- label : 'Topo',
- value : 'topo'
- },
- {
- label : 'Wysiwyg',
- value : 'wysiwyg'
- }
- ]
- },
-
- sorting : {
- title : 'Sorting',
- info : 'How should the columns be clustered?',
- type : 'select',
- init : 'hclust',
- data : [
- {
- label : 'Read from dataset',
- value : 'hclust'
- },
- {
- label : 'Sort column and row labels',
- value : 'byboth'
- },
- {
- label : 'Sort column labels',
- value : 'bycolumns'
- },
- {
- label : 'Sort by rows',
- value : 'byrow'
- }
- ]
- }
- },
-
- // menu definition
- menu : function() {
- return {
- color_set : this.settings.color_set
- }
- }
-};
-
-});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-parameters.js
+++ /dev/null
@@ -1,52 +0,0 @@
-// dependencies
-define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin'], function(Utils, HeatmapPlugin) {
-
-// color palettes
-var colorSets = {
- seis: ['#AA0000', '#D00000', '#F70000', '#FF1D00', '#FF4400', '#FF6A00', '#FF9000', '#FFB700', '#FFDD00', '#FFFF00', '#FFFF00', '#FFFF00', '#BDFF0C', '#73FF1A', '#3FFA36', '#16F45A', '#00D08B', '#0087CD', '#0048FA', '#0024E3'],
-
- sealand: ['#8C66FF', '#6A66FF', '#6684FF', '#66A7FF', '#66CAFF', '#66ECFF', '#66FFF0', '#66FFCE', '#66FFAB', '#66FF88', '#66FF66', '#88FF66', '#ABFF66', '#CEFF66', '#FFEEA6', '#FFD3A6', '#FFB8A6', '#FFAAB0', '#FFB5CB', '#FFC0E1'],
-
- redgreen: ['#005824', '#1A693B', '#347B53', '#4F8D6B', '#699F83', '#83B09B', '#9EC2B3', '#B8D4CB', '#D2E6E3', '#EDF8FB', '#FFFFFF', '#F1EEF6', '#E6D3E1','#DBB9CD', '#D19EB9', '#C684A4', '#BB6990', '#B14F7C', '#A63467', '#9B1A53', '#91003F'],
-
- ocean: ['#000000', '#000209', '#000413', '#00061E', '#000728', '#000932', '#002650', '#00426E', '#005E8C', '#007AAA', '#0096C8', '#22A9C2', '#45BCBB', '#67CFB5', '#8AE2AE', '#ACF6A8', '#BCF8B9', '#CBF9CA', '#DBFBDC', '#EBFDED'],
-
- cool: ['#00FFFF', '#0DF2FF', '#19E6FF', '#26D9FF', '#33CCFF', '#3FBFFF', '#4CB3FF', '#59A6FF', '#6699FF', '#738CFF', '#7F7FFF', '#8C73FF', '#9966FF', '#A659FF', '#B24DFF', '#BF3FFF', '#CC33FF', '#D926FF', '#E619FF', '#F20DFF'],
-
- copper: ['#000000', '#100906', '#1F130D', '#301E13', '#40281A', '#50321F', '#603C26', '#70462D', '#805033', '#905A3A', '#A06440', '#B06E46', '#C0784D', '#D08253', '#E08C5A', '#F09660', '#FFA066', '#FFAA6D', '#FFB473', '#FFBE7A'],
-
- gebco: ['#00F0FF', '#00F0FF', '#00F0FF', '#23FFFF', '#23FFFF', '#23FFFF', '#5AFFFF', '#5AFFFF', '#5AFFFF', '#8CFFE6', '#8CFFE6', '#8CFFE6', '#A5FFD7', '#A5FFD7', '#A5FFD7', '#C3FFD7', '#C3FFD7', '#C3FFD7', '#D2FFD7', '#E6FFF0'],
-
- globe: ['#9900FF', '#9900FF', '#7722FF', '#5544FF', '#3366FF', '#1188FF', '#1BA4FF', '#51BAFF', '#86D0FF', '#BCE6FF', '#336600', '#F3CA89', '#D9A627', '#A49019', '#9F7B0D', '#996600', '#B27676', '#C2B0B0', '#E5E5E5', '#FFFFFF'],
-
- gray: ['#000000', '#0D0D0D', '#191919', '#262626', '#333333', '#3F3F3F', '#4C4C4C', '#595959', '#666666', '#737373', '#7F7F7F', '#8C8C8C', '#999999', '#A6A6A6', '#B2B2B2', '#BFBFBF', '#CCCCCC', '#D9D9D9', '#E6E6E6', '#F2F2F2'],
-
- haxby: ['#090079', '#280096', '#0009C8', '#0019D4', '#1A66F0', '#19AFFF', '#32BEFF', '#61E1F0', '#6AECE1', '#8AECAE', '#CDFFA2', '#DFF68D', '#F8D768', '#FFBD57', '#F4754B', '#FF5A5A', '#FF7C7C', '#F6B3AE', '#FFC4C4', '#FFECEC'],
-
- hot: ['#000000', '#220000', '#440000', '#660000', '#880000', '#AA0000', '#CC0000', '#EE0000', '#FF1100', '#FF3300', '#FF5500', '#FF7700', '#FF9900', '#FFBB00', '#FFDD00', '#FFFF00', '#FFFF33', '#FFFF66', '#FFFF99', '#FFFFCC'],
-
- jet: ['#00007F', '#0000B2', '#0000E5', '#0019FF', '#004DFF', '#007FFF', '#00B2FF', '#00E5FF', '#FFFFF2', '#FFFFD9', '#FFFFBF', '#FFFFA5', '#FFFF8C', '#FFE500', '#FFB300', '#FF7F00', '#FF4C00', '#FF1900', '#E50000', '#B20000'],
-
- no_green: ['#1F60FF', '#1F60FF', '#1F9FFF', '#1FBFFF', '#00CFFF', '#2AFFFF', '#2AFFFF', '#55FFFF', '#7FFFFF', '#AAFFFF', '#FFFF54', '#FFFF54', '#FFF000', '#FFBF00', '#FFA800', '#FF8A00', '#FF8A00', '#FF7000', '#FF4D00', '#FF0000'],
-
- polar: ['#0000FF', '#1919FF', '#3333FF', '#4C4CFF', '#6666FF', '#7F7FFF', '#9999FF', '#B2B2FF', '#CCCCFF', '#E6E6FF', '#FFFFFF', '#FFE5E5', '#FFCCCC', '#FFB2B2', '#FF9999', '#FF7F7F', '#FF6666', '#FF4C4C', '#FF3333', '#FF1A1A'],
-
- rainbow: ['#FF00FF', '#BF00FF', '#7F00FF', '#3F00FF', '#0000FF', '#003FFF', '#007FFF', '#00BFFF', '#00FFFF', '#00FFBF', '#00FF7F', '#00FF3F', '#00FF00', '#3FFF00', '#7FFF00', '#BFFF00', '#FFFF00', '#FFBF00', '#FF7F00', '#FF3F00'],
-
- red2green: ['#FF0000', '#FF1919', '#FF3333', '#FF4C4C', '#FF6666', '#FF7F7F', '#FF9999', '#FFB2B2', '#FFCCCC', '#FFE6E6', '#FFFFFF', '#E5FFE5', '#CCFFCC', '#B2FFB2', '#99FF99', '#7FFF7F', '#66FF66', '#4CFF4C', '#33FF33', '#1AFF1A'],
-
- relief: ['#000000', '#000413', '#000728', '#002650', '#005E8C', '#0096C8', '#45BCBB', '#8AE2AE', '#BCF8B9', '#DBFBDC', '#467832', '#887438', '#B19D48', '#DBC758', '#FAE769', '#FAEB7E', '#FCED93', '#FCF1A7', '#FCF6C1', '#FDFAE0'],
-
- split: ['#7F7FFF', '#6666E6', '#4D4DCC', '#3333B3', '#1A1A99', '#00007F', '#000066', '#00004D', '#000033', '#00001A', '#000000', '#1A0000', '#330000', '#4D0000', '#660000', '#7F0000', '#991A1A', '#B33333', '#CC4D4D', '#E66666'],
-
- topo: ['#C977D9', '#A18AE6', '#8AA2E6', '#8BD1E7', '#8AF3CF', '#85F38E', '#BDF385', '#EDE485', '#F0B086', '#DE9F8B', '#74A3B3', '#99CC70', '#DCD68E', '#EDDFAD', '#F7E8CA', '#FFF9F3', '#FFF9F6', '#FFFBF9', '#FFFCFA', '#FFFEFD'],
-
- wysiwyg: ['#3F003F', '#3F003F', '#3F00BF', '#003FFF', '#00A0FF', '#3FBFFF', '#3FBFFF', '#40E0FF', '#3FFFBF', '#3FFF3F', '#7FFF3F', '#BFFF3F', '#BFFF3F', '#FFE040', '#FFE040', '#FF6040', '#FF1F40', '#FF60C0', '#FFA0FF', '#FFA0FF']
-}
-
-// return
-return {
- colorSets: colorSets
-}
-
-});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/heatmap-plugin.js
+++ /dev/null
@@ -1,739 +0,0 @@
-// dependencies
-define(['utils/utils'],
-function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // number of columns and rows
- colNumber: 0,
- rowNumber: 0,
-
- // indices
- rowIndex: [],
- colIndex: [],
-
- // labels
- rowLabel: [],
- colLabel: [],
-
- // cell size
- cellSize: 0,
-
- // font size
- fontSize: 0,
-
- // color buckets
- nColors: 0,
-
- // margins as cells
- margin : {
- top : 5,
- right : 5,
- bottom : 5,
- left : 5
- },
-
- // default settings
- optionsDefault: {
- title : '',
- pace : 1000,
- },
-
- // initialize
- initialize: function(options) {
- // link this
- var self = this;
-
- // load options
- this.options = Utils.merge(options, this.optionsDefault)
-
- // check requirements
- if (!this.options.data || !this.options.div || !this.options.colors) {
- console.debug('FAILED - HeatMapPlugin::initialize() - Parameters (container and/or data and/or colors) missing.');
- return;
- }
-
- // link data
- this.data = this.options.data;
-
- // set element
- this.setElement(this.options.div);
-
- //
- // data indexing
- //
-
- // labels (in alphabetical order)
- this.rowLabel = [];
- this.colLabel = [];
-
- // index (order from original dataset)
- this.rowIndex = [];
- this.colIndex = [];
-
- // unique keys (key indices are unique per label and indicate the labels rank in the alphabetical sorting)
- this.colRank = {};
- this.rowRank = {};
-
- //
- // identify and parse labels
- //
- for (var i in this.data) {
- var cell = this.data[i];
-
- // add label to index list
- var col_label = cell.col_label;
- if (this.colRank[col_label] === undefined) {
- this.colRank[col_label] = true;
- this.colLabel.push(col_label);
- this.colIndex.push(col_label);
- }
- var row_label = cell.row_label;
- if (this.rowRank[row_label] === undefined) {
- this.rowRank[row_label] = true;
- this.rowLabel.push(row_label);
- this.rowIndex.push(row_label);
- }
- }
-
- //
- // sort labels and update rank dictionary
- //
-
- // set sizes
- this.rowNumber = this.rowLabel.length
- this.colNumber = this.colLabel.length
-
- // sort labels alphabetical
- this.rowLabel.sort();
- this.colLabel.sort();
-
- // generate sorted key list for rows
- for (var i in this.rowLabel) {
- var row_label = this.rowLabel[i];
- var row = parseInt(i);
- this.rowRank[row_label] = row;
- }
-
- // generate sorted key list for columns
- for (var i in this.colLabel) {
- var col_label = this.colLabel[i];
- var col = parseInt(i);
- this.colRank[col_label] = col;
- }
-
- //
- // parse indexing from rank dictionary to cells
- //
-
- // min/max
- this.max = undefined;
- this.min = undefined
-
- // add indices to data
- for (var i in this.data) {
- // get cell data
- var cell = this.data[i];
-
- // add rank
- cell.col = this.colRank[cell.col_label];
- cell.row = this.rowRank[cell.row_label];
-
- // identify max/min values
- if (this.min == undefined || this.min > cell.value) {
- this.min = cell.value;
- }
- if (this.max == undefined || this.max < cell.value) {
- this.max = cell.value;
- }
- }
-
- //
- // translate original create cluster from order in original data
- //
-
- // generate sorted key list for columns
- for (var i in this.colIndex) {
- this.colIndex[i] = this.colRank[this.colIndex[i]];
- }
- // generate sorted key list for columns
- for (var i in this.rowIndex) {
- this.rowIndex[i] = this.rowRank[this.rowIndex[i]];
- }
-
- // middle
- this.mid = (this.max + this.min) / 2;
-
- //
- // set colors
- //
-
- // identify buckets
- this.nColors = this.options.colors.length;
-
- // color scale
- this.colorScale = d3.scale.quantile()
- .domain([this.min, this.mid, this.max])
- .range(this.options.colors);
-
- //
- // add ui elements
- //
- // create tooltip
- this.$tooltip = $(this._templateTooltip());
- this.$el.append(this.$tooltip);
-
- //
- // finally draw the heatmap
- //
- this._build();
-
- // catch window resize event
- $(window).resize(function () {
- self._build();
- });
- },
-
- _build: function() {
- // link this
- var self = this;
-
- // container (full draw area)
- this.widthContainer = this.$el.width();
- this.heightContainer = this.$el.height();
-
- // get grid dimensions
- this.width = this.widthContainer;
- this.height = this.heightContainer;
-
- // calculate cell size
- this.cellSize = Math.min(((this.height) / (this.rowNumber + this.margin.top + this.margin.bottom)),
- (this.width / (this.colNumber + this.margin.left + this.margin.right)));
-
- // set font size
- this.fontSize = Math.min(this.cellSize, 16);
-
- // set width/height for plugin
- this.width = this.cellSize * this.colNumber;
- this.height = this.cellSize * this.rowNumber;
-
- // get dimensions
- var margin = this.options.margin;
- var width = this.width;
- var height = this.height;
-
- // reset svg
- if (this.svg !== undefined) {
- this.$el.find('svg').remove();
- }
-
- // add main group and translate
- this.svg = d3.select(this.$el[0]).append('svg')
- .append('g')
- .attr('transform', 'translate(' + (this.widthContainer - width) / 2 + ',' +
- (this.heightContainer - height) / 2 + ')');
-
- // reset sorting
- this.rowSortOrder = false;
- this.colSortOrder = false;
-
- // build
- this.d3RowLabels = this._buildRowLabels();
- this.d3ColLabels = this._buildColLabels();
- this.d3HeatMap = this._buildHeatMap();
- this.d3Legend = this._buildLegend();
- this.d3Title = this._buildTitle();
- },
-
- // build title
- _buildTitle: function() {
- // link this
- var self = this;
-
- // gather data
- var height = this.height;
- var width = this.width;
- var cellSize = this.cellSize;
- var fontSize = this.fontSize;
- var title = this.options.title;
-
- // add title
- return this.svg.append('g')
- .append('text')
- .attr('x', width / 2)
- .attr('y', height + 3 * cellSize + fontSize + 3)
- .attr('text-anchor', 'middle')
- .text(title);
- },
-
- // build legend
- _buildLegend: function() {
- // link this
- var self = this;
-
- // gather data
- var cellSize = this.cellSize;
- var fontSize = this.fontSize;
- var height = this.height;
- var legendCellWidth = this.width / this.nColors;
-
- // create range labels
- var dataRange = [];
- for(var i = 0; i < this.nColors; i++) {
- dataRange.push('');
- }
-
- // prepare indices
- var dataRangeMin = 0;
- var dataRangeMid = parseInt((dataRange.length - 1) / 2);
- var dataRangeMax = dataRange.length - 1;
-
- // add labels
- dataRange[dataRangeMin] = this.min;
- dataRange[dataRangeMid] = this.mid;
- dataRange[dataRangeMax] = this.max;
-
- // create legend
- var legend = this.svg.selectAll('.legend')
- .data(dataRange)
- .enter().append('g')
- .attr('class', 'legend');
-
- // add boxes
- legend.append('rect')
- .attr('x', function(d, i) {
- return legendCellWidth * i;
- })
- .attr('y', height + cellSize)
- .attr('width', legendCellWidth)
- .attr('height', cellSize)
- .style('fill', function(d, i) {
- return self.options.colors[i];
- });
-
- // add text
- legend.append('text')
- .attr('class', 'mono')
- .text(function(d) {
- return d;
- })
- .attr('width', legendCellWidth)
- .attr('x', function(d, i) {
- return legendCellWidth * i;
- })
- .attr('y', height + cellSize - 3)
- .style('font-size', fontSize + 'px');
-
- // return
- return legend;
- },
-
- // build column labels
- _buildColLabels: function() {
- // link this
- var self = this;
-
- // gather data
- var cellSize = this.cellSize;
- var fontSize = this.fontSize;
- var colIndex = this.colIndex;
- var colLabel = this.colLabel;
-
- // column labels
- var colLabels = this.svg.append('g')
- .selectAll('.colLabelg')
- .data(colLabel)
- .enter()
- .append('text')
- .text(function (d) {
- return d;
- })
- .attr('x', 0)
- .attr('y', function (d, i) {
- return colIndex.indexOf(i) * cellSize;
- })
- .style('font-size', fontSize + 'px')
- .style('text-anchor', 'left')
- .attr('transform', 'translate(' + cellSize / 2 + ', -17) rotate (-90)')
- .attr('class', function (d, i) {
- return 'colLabel mono c' + i;
- })
- .on('mouseover', function(d) {
- d3.select(this).classed('text-hover',true);
- })
- .on('mouseout' , function(d) {
- d3.select(this).classed('text-hover',false);
- })
- .on('click', function(d, i) {
- self.colSortOrder=!self.colSortOrder;
- self._sortByLabel('c', 'row', self.rowNumber, i, self.colSortOrder);
- d3.select('#order').property('selectedIndex', 4).node().focus();
- });
-
- // return
- return colLabels;
- },
-
- // build row labels
- _buildRowLabels: function() {
- // link this
- var self = this;
-
- // gather data
- var cellSize = this.cellSize;
- var fontSize = this.fontSize;
- var rowIndex = this.rowIndex;
- var rowLabel = this.rowLabel;
-
- // draw labels
- var rowLabels = this.svg.append('g')
- .selectAll('.rowLabelg')
- .data(rowLabel)
- .enter()
- .append('text')
- .text(function (d) {
- return d;
- })
- .attr('x', 0)
- .attr('y', function (d, i) {
- return rowIndex.indexOf(i) * cellSize;
- })
- .style('font-size', fontSize + 'px')
- .style('text-anchor', 'end')
- .attr('transform', 'translate(-10,' + cellSize / 1.5 + ')')
- .attr('class', function (d, i) {
- return 'rowLabel mono r' + i;
- } )
- .on('mouseover', function(d) {
- d3.select(this).classed('text-hover',true);
- })
- .on('mouseout' , function(d) {
- d3.select(this).classed('text-hover',false);
- })
- .on('click', function(d, i) {
- self.rowSortOrder=!self.rowSortOrder;
- self._sortByLabel('r', 'col', self.colNumber, i, self.rowSortOrder);
- d3.select('#order').property('selectedIndex', 4).node().focus();
- });
-
- // return
- return rowLabels;
- },
-
- // build heat map
- _buildHeatMap: function() {
- // link this
- var self = this;
-
- // gather data
- var cellSize = this.cellSize;
- var rowIndex = this.rowIndex;
- var rowLabel = this.rowLabel;
- var colIndex = this.colIndex;
- var colLabel = this.colLabel;
-
- // heat map
- var heatmap = this.svg.append('g').attr('class','g3')
- .selectAll('.cellg')
- .data(self.data, function(d) {
- return d.row + ':' + d.col;
- })
- .enter()
- .append('rect')
- .attr('x', function(d) {
- return colIndex.indexOf(d.col) * cellSize;
- })
- .attr('y', function(d) {
- return rowIndex.indexOf(d.row) * cellSize;
- })
- .attr('class', function(d){
- return 'cell cell-border cr' + d.row + ' cc' + d.col;
- })
- .attr('width', cellSize)
- .attr('height', cellSize)
- .style('fill', function(d) {
- return self.colorScale(d.value);
- })
- .on('mouseover', function(d){
- // highlight text
- d3.select(this).classed('cell-hover',true);
- d3.selectAll('.rowLabel').classed('text-highlight',function(r,ri){ return ri==(d.row);});
- d3.selectAll('.colLabel').classed('text-highlight',function(c,ci){ return ci==(d.col);});
-
- // update the tooltip position and value
- d3.select('#heatmap-tooltip')
- .style('left', (d3.event.pageX+10) + 'px')
- .style('top', (d3.event.pageY-10) + 'px')
- .select('#value')
- .text('Label: ' + rowLabel[d.row] + ' | ' + colLabel[d.col] + ', Value: ' + d.value);
- // show the tooltip
- d3.select('#heatmap-tooltip').classed('hidden', false);
- })
- .on('mouseout', function(){
- d3.select(this).classed('cell-hover',false);
- d3.selectAll('.rowLabel').classed('text-highlight',false);
- d3.selectAll('.colLabel').classed('text-highlight',false);
- d3.select('#heatmap-tooltip').classed('hidden', true);
- });
-
- // return
- return heatmap;
- },
-
- // change ordering of cells
- _sortByLabel: function(rORc, rowORcol, n, index, sortOrder) {
- // get cell size
- var cellSize = this.cellSize;
-
- // define transition / prepare element
- var t = this.svg.transition().duration(this.options.pace);
-
- // create cells
- var cells=[];
- for (var i = 0; i < n; i++) {
- cells[i] = {
- value: this.min - 1
- }
- cells[i][rowORcol] = i;
- }
-
- // collect cells
- t.selectAll('.c' + rORc + index).filter(function(ce) {
- cells[ce[rowORcol]].value = ce.value;
- });
-
- // sort cells
- cells.sort(function(a, b) {
- if (sortOrder) {
- return b.value - a.value;
- } else {
- return a.value - b.value;
- }
- });
-
- // get sorted key list
- var sorted = [];
- for (var i in cells) {
- sorted.push(cells[i][rowORcol]);
- }
-
- // rows or columns
- if(rORc == 'r') {
- // sort cells
- t.selectAll('.cell')
- .attr('x', function(d) {
- return sorted.indexOf(d.col) * cellSize;
- });
-
- // sort labels
- t.selectAll('.colLabel')
- .attr('y', function (d, i) {
- return sorted.indexOf(i) * cellSize;
- });
- } else {
- // sort cells
- t.selectAll('.cell')
- .attr('y', function(d) {
- return sorted.indexOf(d.row) * cellSize;
- });
-
- // sort labels
- t.selectAll('.rowLabel')
- .attr('y', function (d, i) {
- return sorted.indexOf(i) * cellSize;
- });
- }
- },
-
- // sort function
- _sortByOrder: function (value) {
- // link this
- var self = this;
-
- // gather data
- var cellSize = this.cellSize;
- var rowIndex = this.rowIndex;
- var rowLabel = this.rowLabel;
- var colIndex = this.colIndex;
- var colLabel = this.colLabel;
-
- // set duration / select element
- var t = this.svg.transition().duration(this.options.pace);
- if(value=='hclust'){
- t.selectAll('.cell')
- .attr('x', function(d) {
- return colIndex.indexOf(d.col) * cellSize;
- })
- .attr('y', function(d) {
- return rowIndex.indexOf(d.row) * cellSize;
- });
-
- t.selectAll('.rowLabel')
- .attr('y', function(d, i) {
- return rowIndex.indexOf(i) * cellSize;
- });
-
- t.selectAll('.colLabel')
- .attr('y', function(d, i) {
- return colIndex.indexOf(i) * cellSize;
- });
-
- } else if (value=='byboth') {
- t.selectAll('.cell')
- .attr('x', function(d) {
- return d.col * cellSize;
- })
- .attr('y', function(d) {
- return d.row * cellSize;
- });
-
- t.selectAll('.rowLabel')
- .attr('y', function (d, i) {
- return i * cellSize;
- });
-
- t.selectAll('.colLabel')
- .attr('y', function (d, i) {
- return i * cellSize;
- });
- } else if (value=='byrow') {
- t.selectAll('.cell')
- .attr('y', function(d) {
- return d.row * cellSize;
- });
-
- t.selectAll('.rowLabel')
- .attr('y', function (d, i) {
- return i * cellSize;
- });
- } else if (value=='bycol'){
- t.selectAll('.cell')
- .attr('x', function(d) {
- return d.col * cellSize;
- });
- t.selectAll('.colLabel')
- .attr('y', function (d, i) {
- return i * cellSize;
- });
- }
- },
-
- // selection of cells
- _addSelectionTool: function() {
- //
- // selection
- //
- var sa=d3.select('.g3')
- .on('mousedown', function() {
- if( !d3.event.altKey) {
- d3.selectAll('.cell-selected').classed('cell-selected', false);
- d3.selectAll('.rowLabel').classed('text-selected', false);
- d3.selectAll('.colLabel').classed('text-selected', false);
- }
- var p = d3.mouse(this);
- sa.append('rect')
- .attr({
- rx : 0,
- ry : 0,
- class : 'selection',
- x : p[0],
- y : p[1],
- width : 1,
- height : 1
- })
- })
- .on('mousemove', function() {
- var s = sa.select('rect.selection');
-
- if(!s.empty()) {
- var p = d3.mouse(this),
- d = {
- x : parseInt(s.attr('x'), 10),
- y : parseInt(s.attr('y'), 10),
- width : parseInt(s.attr('width'), 10),
- height : parseInt(s.attr('height'), 10)
- },
- move = {
- x : p[0] - d.x,
- y : p[1] - d.y
- };
-
- if(move.x < 1 || (move.x*2<d.width)) {
- d.x = p[0];
- d.width -= move.x;
- } else {
- d.width = move.x;
- }
-
- if(move.y < 1 || (move.y*2<d.height)) {
- d.y = p[1];
- d.height -= move.y;
- } else {
- d.height = move.y;
- }
- s.attr(d);
-
- // deselect all temporary selected state objects
- d3.selectAll('.cell-selection.cell-selected').classed('cell-selected', false);
- d3.selectAll('.text-selection.text-selected').classed('text-selected',false);
- d3.selectAll('.cell').filter(function(cell_d, i) {
- if(!d3.select(this).classed('cell-selected') &&
- // inner circle inside selection frame
- (this.x.baseVal.value)+cellSize >= d.x && (this.x.baseVal.value)<=d.x+d.width &&
- (this.y.baseVal.value)+cellSize >= d.y && (this.y.baseVal.value)<=d.y+d.height)
- {
- d3.select(this)
- .classed('cell-selection', true)
- .classed('cell-selected', true);
-
- d3.select('.r' + cell_d.row)
- .classed('text-selection',true)
- .classed('text-selected',true);
-
- d3.select('.c' + cell_d.col)
- .classed('text-selection',true)
- .classed('text-selected',true);
- }
- });
- }
- })
- .on('mouseup', function() {
- // remove selection frame
- sa.selectAll('rect.selection').remove();
-
- // remove temporary selection marker class
- d3.selectAll('.cell-selection').classed('cell-selection', false);
- d3.selectAll('.text-selection').classed('text-selection', false);
- })
- .on('mouseout', function() {
- if(d3.event.relatedTarget.tagName=='html') {
- // remove selection frame
- sa.selectAll('rect.selection').remove();
-
- // remove temporary selection marker class
- d3.selectAll('.cell-selection').classed('cell-selection', false);
- d3.selectAll('.rowLabel').classed('text-selected',false);
- d3.selectAll('.colLabel').classed('text-selected',false);
- }
- });
- },
-
- // template
- _templateSelect: function() {
- return '<select id="order">' +
- '<option value="hclust">Cluster</option>' +
- '<option value="byboth">Sort by row and column</option>' +
- '<option value="byrow">Sort by row label</option>' +
- '<option value="bycol">Sort by column label</option>' +
- '</select>';
- },
-
- // template
- _templateTooltip: function() {
- return '<div id="heatmap-tooltip" class="hidden">' +
- '<p><span id="value"></p>'
- '</div>';
- }
-});
-});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/logo.png
Binary file config/plugins/visualizations/charts/static/charts/heatmap/logo.png has changed
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/heatmap/wrapper.js
+++ /dev/null
@@ -1,86 +0,0 @@
-// dependencies
-define(['utils/utils', 'plugin/charts/heatmap/heatmap-plugin', 'plugin/charts/heatmap/heatmap-parameters'],
-function(Utils, HeatmapPlugin, HeatmapParameters) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // link this
- var self = this;
-
- // loop through data groups
- var index = 0;
- for (var group_index in request_dictionary.groups) {
-
- // configure request
- var tmp_dict = {
- id : request_dictionary.id,
- groups : [{
- key : request_dictionary.groups[group_index].key,
- columns : {
- row_label: {
- index : index++,
- is_label : true
- },
- col_label: {
- index : index++,
- is_label : true
- },
- value: {
- index : index++
- }
- }
- }]
- };
-
- // target div
- var group_div = self.options.canvas[group_index];
-
- // draw group
- this._draw_group(group_index, group_div, chart, tmp_dict, function(group_index) {
- if (group_index == request_dictionary.groups.length - 1) {
- // set chart state
- chart.state('ok', 'Heat map drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- }
- });
- }
- },
-
- // draw group
- _draw_group: function(group_index, div, chart, request_dictionary, callback) {
- // link this
- var self = this;
-
- // request data
- this.app.datasets.request(request_dictionary, function() {
-
- // get group
- var group = request_dictionary.groups[0];
-
- // draw plot
- var heatmap = new HeatmapPlugin({
- 'title' : group.key,
- 'colors' : HeatmapParameters.colorSets[chart.settings.get('color_set')],
- 'data' : group.values,
- 'div' : div
- });
-
- // callback on completion
- callback (group_index);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
--- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/config.js
+++ /dev/null
@@ -1,40 +0,0 @@
-define([], function() {
-
-return {
- title : 'Box plot',
- category : 'Data processing (requires \'charts\' tool from Toolshed)',
- library : 'highcharts.js',
- tag : 'div',
- execute : 'boxplot',
- columns : {
- y : {
- title : 'Observations'
- }
- },
- settings : {
- separator_label : {
- title : 'X axis',
- type : 'separator'
- },
- x_axis_label : {
- title : 'Axis label',
- info : 'Provide a label for the axis.',
- type : 'text',
- init : 'X-axis',
- placeholder : 'Axis label'
- },
- separator_tick : {
- title : 'Y axis',
- type : 'separator'
- },
- y_axis_label : {
- title : 'Axis label',
- info : 'Provide a label for the axis.',
- type : 'text',
- init : 'Y-axis',
- placeholder : 'Axis label'
- }
- }
-};
-
-});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png
Binary file config/plugins/visualizations/charts/static/charts/highcharts_boxplot/logo.png has changed
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/wrapper.js
+++ /dev/null
@@ -1,122 +0,0 @@
-// dependencies
-define(['utils/utils'], function(Utils) {
-
-// widget
-return Backbone.View.extend(
-{
- // highcharts configuration
- hc_config : {
- chart: {
- type: 'boxplot'
- },
-
- title: {
- text: ''
- },
-
- legend: {
- enabled: false
- },
-
- credits: {
- enabled: false
- },
-
- plotOptions: {
- series: {
- animation: false
- }
- },
-
- xAxis: {
- categories: [],
- title: {
- text: ''
- }
- },
-
- yAxis: {
- title: {
- text: ''
- }
- },
-
- series: [{
- name: 'Details:',
- data: [],
- tooltip: {
- headerFormat: '<em>{point.key}</em><br/>'
- }
- }]
- },
-
- // initialize
- initialize: function(app, options) {
- this.app = app;
- this.options = options;
- },
-
- // render
- draw : function(process_id, chart, request_dictionary)
- {
- // configure request
- var index = 0;
- for (var i in request_dictionary.groups) {
- var group = request_dictionary.groups[i];
- group.columns = null;
- group.columns = {
- x: {
- index: index++
- }
- }
- }
-
- // set axis labels
- this.hc_config.xAxis.title.text = chart.settings.get('x_axis_label');
- this.hc_config.yAxis.title.text = chart.settings.get('y_axis_label');
-
- // request data
- var self = this;
- this.app.datasets.request(request_dictionary, function() {
-
- // reset data/categories
- var data = [];
- var categories = [];
-
- // loop through data groups
- for (var key in request_dictionary.groups) {
- // get group
- var group = request_dictionary.groups[key];
-
- // add category
- categories.push(group.key);
-
- // format chart data
- var point = [];
- for (var key in group.values) {
- point.push(group.values[key].x);
- }
-
- // add to data
- data.push (point);
- }
-
- // categories
- self.hc_config.xAxis.categories = categories;
-
- // update data
- self.hc_config.series[0].data = data;
-
- // draw plot
- self.options.canvas[0].highcharts(self.hc_config);
-
- // set chart state
- chart.state('ok', 'Box plot drawn.');
-
- // unregister process
- chart.deferred.done(process_id);
- });
- }
-});
-
-});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
@@ -0,0 +1,20 @@
+define(['plugin/charts/jqplot/common/config'], function(plot_config) {
+
+return $.extend(true, {}, plot_config, {
+ title : 'Regular',
+ category : 'Bar diagrams',
+ columns : {
+ x : {
+ title : 'Values for x-axis',
+ is_label : true,
+ is_auto : true,
+ is_unique : true
+ },
+ y : {
+ title : 'Values for y-axis',
+ is_numeric : true
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
Binary file config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png has changed
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
@@ -0,0 +1,26 @@
+// dependencies
+define(['plugin/charts/jqplot/common/wrapper'], function(Plot) {
+
+// widget
+return Backbone.Model.extend({
+ initialize: function(app, options) {
+ options.makeConfig = function(groups, plot_config){
+ $.extend(true, plot_config, {
+ seriesDefaults: {
+ renderer : $.jqplot.BarRenderer
+ },
+ axes: {
+ xaxis: {
+ min : -1
+ },
+ yaxis: {
+ pad : 1.2
+ }
+ }
+ });
+ };
+ new Plot(app, options);
+ }
+});
+
+});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
@@ -0,0 +1,23 @@
+define(['plugin/charts/jqplot/common/config'], function(plot_config) {
+
+return $.extend(true, {}, plot_config, {
+ title : 'Box plot',
+ category : 'Data processing (requires \'charts\' tool from Toolshed)',
+ library : 'jqPlot',
+ tag : 'div',
+ execute : 'boxplot',
+ keywords : 'small medium large',
+ columns : {
+ y : {
+ title : 'Observations',
+ is_numeric : true
+ }
+ },
+ settings : {
+ show_legend : {
+ init : 'false'
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
Binary file config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png has changed
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
@@ -0,0 +1,127 @@
+// dependencies
+define(['plugin/charts/jqplot/common/wrapper', 'plugin/charts/tools'], function(Plot, Tools) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options) {
+ // get request dictionary
+ var request_dictionary = options.request_dictionary;
+ var chart = options.chart;
+
+ // modify request
+ var index = 0;
+ for (var i in request_dictionary.groups) {
+ var group = request_dictionary.groups[i];
+ group.columns = null;
+ group.columns = {
+ x: {
+ index: index++
+ }
+ }
+ }
+
+ // create plot
+ var plot = new Plot(app, {
+ process_id : options.process_id,
+ chart : options.chart,
+ request_dictionary : options.request_dictionary,
+ canvas_list : options.canvas_list,
+ makeConfig : function(groups, plot_config){
+ var boundary = Tools.getDomains(groups, 'x');
+ $.extend(true, plot_config, {
+ seriesDefaults: {
+ renderer: $.jqplot.OHLCRenderer,
+ rendererOptions : {
+ candleStick : true,
+ fillUpBody : true,
+ fillDownBody : true
+ }
+ },
+ axes : {
+ xaxis: {
+ min: -1,
+ max: groups.length + 0.01
+ },
+ yaxis: {
+ min: boundary.x.min,
+ max: boundary.x.max
+ }
+ }
+ });
+ },
+ makeCategories: function(groups) {
+ // define custom category labels
+ var x_labels = [];
+ for (var group_index in groups) {
+ x_labels.push(groups[group_index].key);
+ }
+
+ // use default mapping
+ Tools.mapCategories (groups, x_labels);
+
+ // return labels array for x axis
+ return {
+ array: {
+ x : x_labels
+ }
+ }
+ },
+ makeSeriesLabels : function (groups, plot_config) {
+ return [{
+ label: 'Boxplot values'
+ }];
+ },
+ makeSeries: function (groups) {
+ /*/ example data
+ var catOHLC = [
+ [0, 138.7, 139.68, 135.18, 135.4],
+ [1, 143.46, 144.66, 139.79, 140.02],
+ [2, 140.67, 143.56, 132.88, 142.44],
+ [3, 136.01, 139.5, 134.53, 139.48]
+ ];
+ return [catOHLC];*/
+
+ // plot data
+ var plot_data = [];
+
+ // check group length
+ if (groups.length == 0 || groups[0].values.length < 5) {
+ chart.state('failed', 'Boxplot data could not be found.');
+ return [plot_data];
+ }
+
+ // loop through data groups
+ var indeces = [2, 4, 0, 1];
+ for (var group_index in groups) {
+ // get group
+ var group = groups[group_index];
+
+ // format chart data
+ var point = [];
+ point.push(parseInt(group_index));
+ for (var key in indeces) {
+ point.push(group.values[indeces[key]].x);
+ }
+
+ // add to data
+ plot_data.push (point);
+ }
+
+ // HACK: the boxplot renderer has an issue with single elements
+ var point = [];
+ point[0] = plot_data.length;
+ for (var key in indeces) {
+ point.push(0);
+ }
+ plot_data.push (point);
+
+ // return
+ return [plot_data];
+ }
+ });
+ }
+});
+
+});
\ No newline at end of file
diff -r 803567ccb30e01477a96d47cd39f6354337c5c5d -r a15c52999493cd723c114899d4224912b2c28ffc config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
@@ -0,0 +1,51 @@
+define(['plugin/charts/forms/default'], function(config_default) {
+
+return $.extend(true, {}, config_default, {
+ title : '',
+ category : '',
+ library : 'jqPlot',
+ tag : 'div',
+ zoomable : true,
+ keywords : 'medium',
+ query_limit : 10000,
+ settings : {
+ separator_grid : {
+ title : 'Grids',
+ type : 'separator'
+ },
+ x_axis_grid : {
+ title : 'Axis grid',
+ info : 'Would you like to show grid lines for the X axis?',
+ type : 'radiobutton',
+ init : 'false',
+ data : [
+ {
+ label : 'On',
+ value : 'true'
+ },
+ {
+ label : 'Off',
+ value : 'false'
+ }
+ ]
+ },
+ y_axis_grid : {
+ title : 'Axis grid',
+ info : 'Would you like to show grid lines for the Y axis?',
+ type : 'radiobutton',
+ init : 'true',
+ data : [
+ {
+ label : 'On',
+ value : 'true'
+ },
+ {
+ label : 'Off',
+ value : 'false'
+ }
+ ]
+ }
+ }
+});
+
+});
\ No newline at end of file
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/8bf883f2638e/
Changeset: 8bf883f2638e
Branch: stable
User: guerler
Date: 2014-06-24 19:50:03
Summary: Charts style update
Affected #: 2 files
diff -r a15c52999493cd723c114899d4224912b2c28ffc -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -148,7 +148,7 @@
.form-control::-moz-placeholder{color:#999}
.form-control:-ms-input-placeholder{color:#999}
.form-control::-webkit-input-placeholder{color:#999}
-.form-control{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
+.form-control,.ui-input{display:block;width:100%;height:27px;padding:4px 10px;font-size:12px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #aaa;border-radius:3px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s, box-shadow ease-in-out .15s}.form-control:focus{border-color:#66afe9;outline:0;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,.075), 0 0 8px rgba(102, 175, 233, 0.6)}
.form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee}
textarea.form-control{height:auto}
.form-group{margin-bottom:15px}
@@ -1278,17 +1278,25 @@
.upload-ftp .upload-ftp-help{margin-bottom:10px}
.upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px}
.upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop}
+.ui-radiobutton label{height:23px;line-height:1em}
+.ui-table-form-separator{font-weight:bold;font-size:0.9em}
+.ui-label{font-weight:bold}
+.ui-message{padding:2px 2px 2px 10px}
+.ui-icon{font-size:1.2em}
+.ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px}
+.ui-button-icon .button{margin-right:5px;margin-left:5px}
+.ui-button-icon .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px}
+.ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px}
+.ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer}
.no-highlight{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;}
-.portlet-view{min-width:300px}.portlet-view .portlet-title-icon{float:left;font-size:1.2em;padding-top:4px}
-.portlet-view .portlet-title{overflow:hidden;padding:2px 5px 2px 10px}
-.portlet-view .portlet-title-text{float:left;padding-top:2px}
-.portlet-view .portlet-operations{float:right;cursor:pointer}
-.portlet-view .portlet-buttons{height:50px;padding:10px}
-.portlet-view .portlet-content{height:inherit;padding:10px}
-.popover-view{max-width:700px;display:none}.popover-view .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
-.popover-view .popover-title{padding:4px 10px}
-.styled-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.styled-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2}
-.styled-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none}
+.ui-portlet{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{padding:5px 10px;background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header h1,.ui-portlet .portlet-header h2,.ui-portlet .portlet-header h3,.ui-portlet .portlet-header h4,.ui-portlet .portlet-header h5,.ui-portlet .portlet-header h6{float:left;font-weight:normal;display:inline-block;vertical-align:middle;font-size:1em;margin:3px}.ui-portlet .portlet-header h1 .icon,.ui-portlet .portlet-header h2 .icon,.ui-portlet .portlet-header h3 .icon,.ui-portlet .portlet-header h4 .icon,.ui-portlet .portlet-header h5 .icon,.ui-portlet .portlet-header h6 .icon{font-size:1.2em}
+.ui-portlet .portlet-buttons{height:50px;padding:10px}
+.ui-portlet .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons{height:50px;padding:10px}
+.ui-portlet .no-scroll{height:calc(100% - 80px)}
+.ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
+.ui-popover .popover-title{padding:4px 10px}
+.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2}
+.ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none}
.libraryRow{background-color:#ebd9b2}
.datasetHighlighted{background-color:#f9f9f9}
.libraryItemDeleted-True{font-style:italic}
@@ -1453,7 +1461,7 @@
div.form-row-input{width:90%;float:left}
div.form-row-input label{font-weight:normal;display:inline}
div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0}
-.form-row .help,.toolParamHelp{color:#666}.form-row .help a,.toolParamHelp a{color:#666}
+.form-row .help,.toolParamHelp,.ui-table-form-info{color:#666}.form-row .help a,.toolParamHelp a{color:#666}
.form-row.form-actions{background:whiteSmoke;border-top:solid #ddd 1px;padding-top:10px;padding-bottom:10px;margin-top:5px}
select{padding:2px;font-size:12px;line-height:1.428571429}
select,input,textarea{font:inherit}
@@ -1519,13 +1527,13 @@
.grid-header{padding-bottom:1em}
.grid-header h2{margin:0;margin-bottom:0.5em}
.grid-header .title{font-weight:bold}
-.grid{padding-top:1em;border-collapse:collapse;width:100%}
-.grid tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px}
+.grid,.ui-table{padding-top:1em;border-collapse:collapse;width:100%}
+.grid tbody td,.ui-table tbody td{line-height:1.428571429;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px}
.grid tbody td:empty{padding:0}
.grid thead tr{height:2em}
.grid thead th{line-height:1.428571429;background:#ebd9b2;color:#000;border-top:solid #d6b161 1px;border-bottom:solid #d6b161 1px;padding:5px;text-align:left;white-space:nowrap}
.grid tfoot td{background-color:#F8F8F8;border-top:solid #DDDDDD 1px;border-bottom:solid #DDDDDD 1px;padding:5px}
-.grid .current{background-color:#EEEEFF}
+.grid .current,.ui-table .current{background-color:#EEEEFF}
.count-box{min-width:1.1em;padding:5px;border-width:1px;border-style:solid;text-align:center;display:inline-block}
.text-filter-val{border:solid 1px #AAAAAA;padding:1px 2px 1px 3px;margin-right:5px;-moz-border-radius:.5em;-webkit-border-radius:.5em;font-style:italic}
.page-link a,.inactive-link{padding:0px 7px 0px 7px;color:#555}
diff -r a15c52999493cd723c114899d4224912b2c28ffc -r 8bf883f2638e1bae7a1761a0fab98a981d6fa315 static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -1,3 +1,80 @@
+.ui-radiobutton {
+ label {
+ height: 23px;
+ line-height: 1em;
+ }
+}
+
+.ui-table {
+ &:extend(.grid);
+
+ tbody td {
+ &:extend(.grid tbody td);
+ }
+ .current {
+ &:extend(.grid .current);
+ }
+}
+
+.ui-table-form-info {
+ &:extend(.toolParamHelp);
+}
+
+.ui-table-form-separator {
+ font-weight: bold;
+ font-size: 0.9em;
+}
+
+.ui-label {
+ font-weight: bold;
+}
+
+.ui-message {
+ padding: 2px 2px 2px 10px;
+}
+
+.ui-icon {
+ font-size: 1.2em;
+}
+
+.ui-button-icon {
+ margin-right: 5px;
+ ul {
+ i {
+ font-size: 1.2em; margin-right: 5px; position: relative; top: 1px;
+ }
+ }
+}
+
+.ui-button-icon .button {
+ margin-right: 5px;
+ margin-left: 5px;
+}
+
+.ui-button-icon .title {
+ position: relative;
+ font-size: 0.8em;
+ font-weight: normal;
+ top: -1px;
+}
+
+.ui-input {
+ &:extend(.form-control);
+}
+
+.ui-tabs {
+ .ui-tabs-add {
+ font-size : 0.8em;
+ margin-right : 5px;
+ }
+
+ .ui-tabs-delete {
+ font-size : 0.8em;
+ margin-left : 5px;
+ cursor : pointer;
+ }
+}
+
.no-highlight {
-webkit-user-select: none; /* webkit (safari, chrome) browsers */
-moz-user-select: none; /* mozilla browsers */
@@ -5,30 +82,38 @@
-ms-user-select: none; /* IE10+ */
}
-.portlet-view {
- min-width: 300px;
+.ui-portlet {
+ border: solid @form-border 1px;
+ .border-radius(@panel-border-radius);
- .portlet-title-icon {
- float: left;
- font-size: 1.2em;
- padding-top: 4px;
- }
-
- .portlet-title {
- overflow: hidden;
- padding: 2px 5px 2px 10px;
+ position: relative;
+ clear: both;
+ width: auto;
+ height: 100%;
+
+ .portlet-header {
+ padding: 5px 10px;
+ background: @form-heading-bg;
+ border-bottom: solid @form-border 1px;
+ padding: 2px 8px;
+ overflow: visible;
+ float: right;
+ width:100%;
+
+ h1, h2, h3, h4, h5, h6 {
+ float: left;
+ font-weight: normal;
+ display: inline-block;
+ vertical-align: middle;
+ font-size: 1em;
+ margin: 3px;
+
+ .icon {
+ font-size: 1.2em;
+ }
+ }
}
- .portlet-title-text {
- float: left;
- padding-top: 2px;
- }
-
- .portlet-operations {
- float: right;
- cursor: pointer;
- }
-
.portlet-buttons {
height: 50px;
padding: 10px;
@@ -37,10 +122,26 @@
.portlet-content {
height: inherit;
padding: 10px;
+ clear: both;
+
+ .content {
+ padding : 10px;
+ height : 100%;
+ width : 100%;
+
+ .buttons {
+ height: 50px;
+ padding: 10px;
+ }
+ }
+ }
+
+ .no-scroll {
+ height: ~'calc(100% - 80px)';
}
}
-.popover-view {
+.ui-popover {
max-width: 700px;
display: none;
@@ -57,7 +158,7 @@
}
}
-.styled-select {
+.ui-select {
position: relative;
height: 27px;
overflow: hidden;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.
by commits-noreplyï¼ bitbucket.org 24 Jun '14
by commits-noreplyï¼ bitbucket.org 24 Jun '14
24 Jun '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fdaad2cad392/
Changeset: fdaad2cad392
User: greg
Date: 2014-06-24 19:11:24
Summary: Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.
Affected #: 10 files
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/api/repositories.py
--- a/lib/galaxy/webapps/tool_shed/api/repositories.py
+++ b/lib/galaxy/webapps/tool_shed/api/repositories.py
@@ -10,14 +10,14 @@
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.base.controller import HTTPBadRequest
from galaxy.web.framework.helpers import time_ago
+from tool_shed.capsule import capsule_manager
import tool_shed.repository_types.util as rt_util
-import tool_shed.util.shed_util_common as suc
from tool_shed.util import basic_util
from tool_shed.util import encoding_util
from tool_shed.util import hg_util
-from tool_shed.util import import_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_maintenance_util
+from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_util
log = logging.getLogger( __name__ )
@@ -248,10 +248,14 @@
except tarfile.ReadError, e:
log.debug( 'Error opening capsule file %s: %s' % ( str( capsule_file_name ), str( e ) ) )
return {}
+ irm = capsule_manager.ImportRepositoryManager( trans.app,
+ trans.request.host,
+ trans.user,
+ trans.user_is_admin() )
capsule_dict[ 'tar_archive' ] = tar_archive
capsule_dict[ 'capsule_file_name' ] = capsule_file_name
- capsule_dict = import_util.extract_capsule_files( **capsule_dict )
- capsule_dict = import_util.validate_capsule( **capsule_dict )
+ capsule_dict = irm.extract_capsule_files( **capsule_dict )
+ capsule_dict = irm.validate_capsule( **capsule_dict )
status = capsule_dict.get( 'status', 'error' )
if status == 'error':
log.debug( 'The capsule contents are invalid and cannot be imported:<br/>%s' % \
@@ -263,15 +267,12 @@
return {}
file_path = encoding_util.tool_shed_decode( encoded_file_path )
export_info_file_path = os.path.join( file_path, 'export_info.xml' )
- export_info_dict = import_util.get_export_info_dict( export_info_file_path )
+ export_info_dict = irm.get_export_info_dict( export_info_file_path )
manifest_file_path = os.path.join( file_path, 'manifest.xml' )
# The manifest.xml file has already been validated, so no error_message should be returned here.
- repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path )
+ repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path )
# Determine the status for each exported repository archive contained within the capsule.
- repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app,
- trans.user,
- trans.user_is_admin(),
- repository_info_dicts )
+ repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts )
# Generate a list of repository name / import results message tuples for display after the capsule is imported.
import_results_tups = []
# Only create repositories that do not yet exist and that the current user is authorized to create. The
@@ -280,12 +281,9 @@
# Add the capsule_file_name and encoded_file_path to the repository_status_info_dict.
repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name
repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path
- import_results_tups = import_util.create_repository_and_import_archive( trans.app,
- trans.request.host,
- trans.user,
- repository_status_info_dict,
- import_results_tups )
- import_util.check_status_and_reset_downloadable( trans.app, import_results_tups )
+ import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict,
+ import_results_tups )
+ irm.check_status_and_reset_downloadable( import_results_tups )
basic_util.remove_dir( file_path )
# NOTE: the order of installation is defined in import_results_tups, but order will be lost
# when transferred to return_dict.
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/api/repository_revisions.py
--- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
+++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py
@@ -5,7 +5,7 @@
from galaxy import util
from galaxy.model.orm import and_, not_, select
from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest
-from tool_shed.util import export_util
+from tool_shed.capsule import capsule_manager
from tool_shed.util import hg_util
import tool_shed.util.shed_util_common as suc
@@ -53,15 +53,14 @@
log.debug( error_message )
return None, error_message
repository_id = trans.security.encode_id( repository.id )
- return export_util.export_repository( trans.app,
- trans.user,
- tool_shed_url,
- repository_id,
- str( repository.name ),
- changeset_revision,
- file_type,
- export_repository_dependencies,
- api=True )
+ erm = capsule_manager.ExportRepositoryManager( app=trans.app,
+ user=trans.user,
+ tool_shed_url=tool_shed_url,
+ repository=repository,
+ changeset_revision=changeset_revision,
+ export_repository_dependencies=export_repository_dependencies,
+ using_api=True )
+ return erm.export_repository()
def __get_value_mapper( self, trans ):
value_mapper = { 'id' : trans.security.encode_id,
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -14,20 +14,19 @@
from galaxy.web.framework.helpers import grids
from galaxy.util import json
from galaxy.model.orm import and_
-import tool_shed.util.shed_util_common as suc
+from tool_shed.capsule import capsule_manager
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import encoding_util
-from tool_shed.util import export_util
from tool_shed.util import hg_util
-from tool_shed.util import import_util
from tool_shed.util import metadata_util
from tool_shed.util import readme_util
from tool_shed.util import repository_dependency_util
from tool_shed.util import repository_maintenance_util
from tool_shed.util import review_util
from tool_shed.util import search_util
+from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
from tool_shed.util import workflow_util
@@ -1149,7 +1148,7 @@
# server account's .hgrc file to include the following setting:
# [web]
# allow_archive = bz2, gz, zip
- file_type_str = export_util.get_file_type_str( changeset_revision, file_type )
+ file_type_str = basic_util.get_file_type_str( changeset_revision, file_type )
repository.times_downloaded += 1
trans.sa_session.add( repository )
trans.sa_session.flush()
@@ -1172,15 +1171,14 @@
file_type = 'gz'
export_repository_dependencies = CheckboxField.is_checked( export_repository_dependencies )
tool_shed_url = web.url_for( '/', qualified=True )
- repositories_archive, error_message = export_util.export_repository( trans.app,
- trans.user,
- tool_shed_url,
- repository_id,
- str( repository.name ),
- changeset_revision,
- file_type,
- export_repository_dependencies,
- api=False )
+ erm = capsule_manager.ExportRepositoryManager( app=trans.app,
+ user=trans.user,
+ tool_shed_url=tool_shed_url,
+ repository=repository,
+ changeset_revision=changeset_revision,
+ export_repository_dependencies=export_repository_dependencies,
+ using_api=False )
+ repositories_archive, error_message = erm.export_repository()
repositories_archive_filename = os.path.basename( repositories_archive.name )
if error_message:
message = error_message
@@ -1969,15 +1967,16 @@
encoded_file_path = kwd.get( 'encoded_file_path', None )
file_path = encoding_util.tool_shed_decode( encoded_file_path )
export_info_file_path = os.path.join( file_path, 'export_info.xml' )
- export_info_dict = import_util.get_export_info_dict( export_info_file_path )
+ irm = capsule_manager.ImportRepositoryManager( trans.app,
+ trans.request.host,
+ trans.user,
+ trans.user_is_admin() )
+ export_info_dict = irm.get_export_info_dict( export_info_file_path )
manifest_file_path = os.path.join( file_path, 'manifest.xml' )
# The manifest.xml file has already been validated, so no error_message should be returned here.
- repository_info_dicts, error_message = import_util.get_repository_info_from_manifest( manifest_file_path )
+ repository_info_dicts, error_message = irm.get_repository_info_from_manifest( manifest_file_path )
# Determine the status for each exported repository archive contained within the capsule.
- repository_status_info_dicts = import_util.get_repository_status_from_tool_shed( trans.app,
- trans.user,
- trans.user_is_admin(),
- repository_info_dicts )
+ repository_status_info_dicts = irm.get_repository_status_from_tool_shed( repository_info_dicts )
if 'import_capsule_button' in kwd:
# Generate a list of repository name / import results message tuples for display after the capsule is imported.
import_results_tups = []
@@ -1987,12 +1986,9 @@
# Add the capsule_file_name and encoded_file_path to the repository_status_info_dict.
repository_status_info_dict[ 'capsule_file_name' ] = capsule_file_name
repository_status_info_dict[ 'encoded_file_path' ] = encoded_file_path
- import_results_tups = import_util.create_repository_and_import_archive( trans.app,
- trans.request.host,
- trans.user,
- repository_status_info_dict,
- import_results_tups )
- import_util.check_status_and_reset_downloadable( trans.app, import_results_tups )
+ import_results_tups = irm.create_repository_and_import_archive( repository_status_info_dict,
+ import_results_tups )
+ irm.check_status_and_reset_downloadable( import_results_tups )
basic_util.remove_dir( file_path )
return trans.fill_template( '/webapps/tool_shed/repository/import_capsule_results.mako',
export_info_dict=export_info_dict,
@@ -3081,13 +3077,17 @@
status = kwd.get( 'status', 'done' )
url = kwd.get( 'url', '' )
if 'upload_capsule_button' in kwd:
- capsule_dict = import_util.upload_capsule( **kwd )
+ irm = capsule_manager.ImportRepositoryManager( trans.app,
+ trans.request.host,
+ trans.user,
+ trans.user_is_admin() )
+ capsule_dict = irm.upload_capsule( **kwd )
status = capsule_dict.get( 'status', 'error' )
if status == 'error':
message = capsule_dict.get( 'error_message', '' )
else:
- capsule_dict = import_util.extract_capsule_files( **capsule_dict )
- capsule_dict = import_util.validate_capsule( **capsule_dict )
+ capsule_dict = irm.extract_capsule_files( **capsule_dict )
+ capsule_dict = irm.validate_capsule( **capsule_dict )
status = capsule_dict.get( 'status', 'error' )
if status == 'ok':
return trans.response.send_redirect( web.url_for( controller='repository',
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/capsule/capsule_manager.py
--- /dev/null
+++ b/lib/tool_shed/capsule/capsule_manager.py
@@ -0,0 +1,867 @@
+import logging
+import os
+import shutil
+import tarfile
+import tempfile
+import threading
+import urllib
+from time import gmtime
+from time import strftime
+import tool_shed.repository_types.util as rt_util
+from galaxy import web
+from galaxy.util import asbool
+from galaxy.util import CHUNK_SIZE
+from galaxy.util.odict import odict
+from tool_shed.dependencies import dependency_manager
+from tool_shed.util import basic_util
+from tool_shed.util import commit_util
+from tool_shed.util import common_util
+from tool_shed.util import encoding_util
+from tool_shed.util import hg_util
+from tool_shed.util import metadata_util
+from tool_shed.util import repository_dependency_util
+from tool_shed.util import repository_maintenance_util
+from tool_shed.util import shed_util_common as suc
+from tool_shed.util import xml_util
+from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager
+
+log = logging.getLogger( __name__ )
+
+
+class ExportedRepositoryRegistry( object ):
+
+ def __init__( self ):
+ self.exported_repository_elems = []
+
+class ExportRepositoryManager( object ):
+
+ def __init__( self, app, user, tool_shed_url, repository, changeset_revision, export_repository_dependencies, using_api ):
+ self.app = app
+ self.capsule_filename = 'capsule'
+ self.capsule_with_dependencies_filename = 'capsule_with_dependencies'
+ self.changeset_revision = changeset_revision
+ self.export_repository_dependencies = asbool( export_repository_dependencies )
+ self.file_type = 'gz'
+ self.repository = repository
+ self.repository_id = self.app.security.encode_id( repository.id )
+ self.tool_shed_url = tool_shed_url
+ self.user = user
+ self.using_api = using_api
+
+ def export_repository( self ):
+ repositories_archive_filename = self.generate_repository_archive_filename( use_tmp_archive_dir=True )
+ if self.export_repository_dependencies:
+ repo_info_dicts = self.get_repo_info_dicts()
+ repository_ids = self.get_repository_ids( repo_info_dicts )
+ ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \
+ self.order_components_for_import( repository_ids, repo_info_dicts )
+ else:
+ ordered_repository_ids = []
+ ordered_repositories = []
+ ordered_changeset_revisions = []
+ if self.repository:
+ repository_metadata = \
+ suc.get_current_repository_metadata_for_changeset_revision( self.app,
+ self.repository,
+ self.changeset_revision )
+ if repository_metadata:
+ ordered_repository_ids = [ self.repository_id ]
+ ordered_repositories = [ self.repository ]
+ ordered_changeset_revisions = [ repository_metadata.changeset_revision ]
+ repositories_archive = None
+ error_messages = ''
+ lock = threading.Lock()
+ lock.acquire( True )
+ try:
+ repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % self.file_type )
+ exported_repository_registry = ExportedRepositoryRegistry()
+ for index, repository_id in enumerate( ordered_repository_ids ):
+ work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" )
+ ordered_repository = ordered_repositories[ index ]
+ ordered_changeset_revision = ordered_changeset_revisions[ index ]
+ repository_archive, error_message = self.generate_repository_archive( ordered_repository,
+ ordered_changeset_revision,
+ work_dir )
+ if error_message:
+ error_messages = '%s %s' % ( error_messages, error_message )
+ else:
+ archive_name = str( os.path.basename( repository_archive.name ) )
+ repositories_archive.add( repository_archive.name, arcname=archive_name )
+ attributes, sub_elements = self.get_repository_attributes_and_sub_elements( ordered_repository,
+ archive_name )
+ elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements )
+ exported_repository_registry.exported_repository_elems.append( elem )
+ basic_util.remove_dir( work_dir )
+ # Keep information about the export in a file named export_info.xml in the archive.
+ sub_elements = self.generate_export_elem()
+ export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements )
+ tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True )
+ repositories_archive.add( tmp_export_info, arcname='export_info.xml' )
+ # Write the manifest, which must preserve the order in which the repositories should be imported.
+ exported_repository_root = xml_util.create_element( 'repositories' )
+ for exported_repository_elem in exported_repository_registry.exported_repository_elems:
+ exported_repository_root.append( exported_repository_elem )
+ tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True )
+ repositories_archive.add( tmp_manifest, arcname='manifest.xml' )
+ except Exception, e:
+ log.exception( str( e ) )
+ finally:
+ lock.release()
+ if repositories_archive is not None:
+ repositories_archive.close()
+ if self.using_api:
+ encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename )
+ params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name
+ download_url = common_util.url_join( web.url_for( '/', qualified=True ),
+ 'repository/export_via_api%s' % params )
+ return dict( download_url=download_url, error_messages=error_messages )
+ return repositories_archive, error_messages
+
+ def generate_export_elem( self ):
+ sub_elements = odict()
+ sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() )
+ sub_elements[ 'tool_shed' ] = str( self.tool_shed_url.rstrip( '/' ) )
+ sub_elements[ 'repository_name' ] = str( self.repository.name )
+ sub_elements[ 'repository_owner' ] = str( self.repository.user.username )
+ sub_elements[ 'changeset_revision' ] = str( self.changeset_revision )
+ sub_elements[ 'export_repository_dependencies' ] = str( self.export_repository_dependencies )
+ sub_elements[ 'exported_via_api' ] = str( self.using_api )
+ return sub_elements
+
+ def generate_repository_archive( self, repository, changeset_revision, work_dir ):
+ rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=True )
+ tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=True )
+ file_type_str = basic_util.get_file_type_str( changeset_revision, self.file_type )
+ file_name = '%s-%s' % ( repository.name, file_type_str )
+ return_code, error_message = hg_util.archive_repository_revision( self.app,
+ repository,
+ work_dir,
+ changeset_revision )
+ if return_code:
+ return None, error_message
+ repository_archive_name = os.path.join( work_dir, file_name )
+ # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files.
+ repository_archive = tarfile.open( repository_archive_name, "w:%s" % self.file_type )
+ for root, dirs, files in os.walk( work_dir ):
+ if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
+ for dir in dirs:
+ if dir in commit_util.UNDESIRABLE_DIRS:
+ dirs.remove( dir )
+ for name in files:
+ name = str( name )
+ if str( name ) in commit_util.UNDESIRABLE_FILES:
+ continue
+ full_path = os.path.join( root, name )
+ relative_path = full_path.replace( work_dir, '' ).lstrip( '/' )
+ # See if we have a repository dependencies defined.
+ if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
+ # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags.
+ altered, root_elem, error_message = rdah.handle_tag_attributes( full_path )
+ if error_message:
+ return None, error_message
+ if altered:
+ tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True )
+ shutil.move( tmp_filename, full_path )
+ elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
+ # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags.
+ altered, root_elem, error_message = tdah.handle_tag_attributes( full_path )
+ if error_message:
+ return None, error_message
+ if altered:
+ tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True )
+ shutil.move( tmp_filename, full_path )
+ repository_archive.add( full_path, arcname=relative_path )
+ repository_archive.close()
+ return repository_archive, error_message
+
+ def generate_repository_archive_filename( self, use_tmp_archive_dir=False ):
+ tool_shed = self.remove_protocol_from_tool_shed_url()
+ file_type_str = basic_util.get_file_type_str( self.changeset_revision, self.file_type )
+ if self.export_repository_dependencies:
+ repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_with_dependencies_filename,
+ tool_shed,
+ str( self.repository.name ),
+ str( self.repository.user.username ),
+ file_type_str )
+ else:
+ repositories_archive_filename = '%s_%s_%s_%s_%s' % ( self.capsule_filename,
+ tool_shed,
+ str( self.repository.name ),
+ str( self.repository.user.username ),
+ file_type_str )
+ if use_tmp_archive_dir:
+ tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" )
+ repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename )
+ return repositories_archive_filename
+
+ def get_components_from_repo_info_dict( self, repo_info_dict ):
+ """
+ Return the repository and the associated latest installable changeset_revision (including
+ # updates) for the repository defined by the received repo_info_dict.
+ """
+ for repository_name, repo_info_tup in repo_info_dict.items():
+ # There should only be one entry in the received repo_info_dict.
+ description, \
+ repository_clone_url, \
+ changeset_revision, \
+ ctx_rev, \
+ repository_owner, \
+ repository_dependencies, \
+ tool_dependencies = \
+ suc.get_repo_info_tuple_contents( repo_info_tup )
+ repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner )
+ repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( self.app,
+ repository,
+ changeset_revision )
+ if repository_metadata:
+ return repository, repository_metadata.changeset_revision
+ return None, None
+
+ def get_repo_info_dict_for_import( self, encoded_repository_id, encoded_repository_ids, repo_info_dicts ):
+ """
+ The received encoded_repository_ids and repo_info_dicts are lists that contain associated
+ elements at each location in the list. This method will return the element from repo_info_dicts
+ associated with the received encoded_repository_id by determining its location in the received
+ encoded_repository_ids list.
+ """
+ for index, repository_id in enumerate( encoded_repository_ids ):
+ if repository_id == encoded_repository_id:
+ repo_info_dict = repo_info_dicts[ index ]
+ return repo_info_dict
+ return None
+
+ def get_repo_info_dicts( self ):
+ """
+ Return a list of dictionaries defining repositories that are required by the repository
+ associated with self.repository_id.
+ """
+ rdm = RepositoryDependencyManager( self.app )
+ repository = suc.get_repository_in_tool_shed( self.app, self.repository_id )
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
+ self.repository_id,
+ self.changeset_revision )
+ # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
+ toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
+ repository_dependencies = \
+ repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=self.app,
+ repository=self.repository,
+ repository_metadata=repository_metadata,
+ toolshed_base_url=toolshed_base_url,
+ key_rd_dicts_to_be_processed=None,
+ all_repository_dependencies=None,
+ handled_key_rd_dicts=None )
+ repo = hg_util.get_repo_for_repository( self.app,
+ repository=self.repository,
+ repo_path=None,
+ create=False )
+ ctx = hg_util.get_changectx_for_changeset( repo, self.changeset_revision )
+ repo_info_dict = {}
+ # Cast unicode to string.
+ repo_info_dict[ str( repository.name ) ] = ( str( self.repository.description ),
+ common_util.generate_clone_url_for_repository_in_tool_shed( self.user,
+ self.repository ),
+ str( self.changeset_revision ),
+ str( ctx.rev() ),
+ str( self.repository.user.username ),
+ repository_dependencies,
+ None )
+ all_required_repo_info_dict = rdm.get_required_repo_info_dicts( self.tool_shed_url, [ repo_info_dict ] )
+ all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] )
+ return all_repo_info_dicts
+
+ def get_repository_attributes_and_sub_elements( self, repository, archive_name ):
+ """
+ Get the information about a repository to create and populate an XML tag set. The
+ generated attributes will be contained within the <repository> tag, while the sub_elements
+ will be tag sets contained within the <repository> tag set.
+ """
+ attributes = odict()
+ sub_elements = odict()
+ attributes[ 'name' ] = str( repository.name )
+ attributes[ 'type' ] = str( repository.type )
+ # We have to associate the public username since the user_id will be different between tool sheds.
+ attributes[ 'username' ] = str( repository.user.username )
+ # Don't coerce description or long description from unicode to string because the fields are free text.
+ sub_elements[ 'description' ] = repository.description
+ sub_elements[ 'long_description' ] = repository.long_description
+ sub_elements[ 'archive' ] = archive_name
+ # Keep track of Category associations.
+ categories = []
+ for rca in repository.categories:
+ category = rca.category
+ categories.append( ( 'category', str( category.name ) ) )
+ sub_elements[ 'categories' ] = categories
+ return attributes, sub_elements
+
+ def get_repository_ids( self, repo_info_dicts ):
+ """Return a list of repository ids associated with each dictionary in the received repo_info_dicts."""
+ repository_ids = []
+ for repo_info_dict in repo_info_dicts:
+ for repository_name, repo_info_tup in repo_info_dict.items():
+ description, \
+ repository_clone_url, \
+ changeset_revision, \
+ ctx_rev, \
+ repository_owner, \
+ repository_dependencies, \
+ tool_dependencies = \
+ suc.get_repo_info_tuple_contents( repo_info_tup )
+ repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner )
+ repository_ids.append( self.app.security.encode_id( repository.id ) )
+ return repository_ids
+
+ def order_components_for_import( self, repository_ids, repo_info_dicts ):
+ """
+ Some repositories may have repository dependencies that must be imported and have metadata set on
+ them before the dependent repository is imported. This method will inspect the list of repositories
+ about to be exported and make sure to order them appropriately for proper import. For each repository
+ about to be exported, if required repositories are not contained in the list of repositories about to
+ be exported, then they are not considered. Repository dependency definitions that contain circular
+ dependencies should not result in an infinite loop, but obviously ordering the list will not be handled
+ for one or more of the repositories that require prior import.
+ """
+ # The received list of repository_ids are the ids of all of the primary exported repository's
+ # repository dependencies. The primary repository will always be last in the returned lists.
+ ordered_repository_ids = []
+ ordered_repositories = []
+ ordered_changeset_revisions = []
+ # Create a dictionary whose keys are the received repository_ids and whose values are a list of
+ # repository_ids, each of which is contained in the received list of repository_ids and whose associated
+ # repository must be imported prior to the repository associated with the repository_id key.
+ prior_import_required_dict = suc.get_prior_import_or_install_required_dict( self.app,
+ repository_ids,
+ repo_info_dicts )
+ processed_repository_ids = []
+ # Process the list of repository dependencies defined for the primary exported repository.
+ while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ):
+ repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict,
+ processed_repository_ids )
+ if repository_id == self.repository_id:
+ # Append self.repository_id without processing it since it must be returned last in the order.
+ # It will be processed below after all dependencies are processed.
+ processed_repository_ids.append( self.repository_id )
+ continue
+ processed_repository_ids.append( repository_id )
+ if repository_id not in ordered_repository_ids:
+ prior_import_required_ids = prior_import_required_dict[ repository_id ]
+ for prior_import_required_id in prior_import_required_ids:
+ if prior_import_required_id not in ordered_repository_ids:
+ # Import the associated repository dependency first.
+ prior_repo_info_dict = \
+ self.get_repo_info_dict_for_import( prior_import_required_id,
+ repository_ids,
+ repo_info_dicts )
+ prior_repository, prior_import_changeset_revision = \
+ self.get_components_from_repo_info_dict( prior_repo_info_dict )
+ if prior_repository and prior_import_changeset_revision:
+ ordered_repository_ids.append( prior_import_required_id )
+ ordered_repositories.append( prior_repository )
+ ordered_changeset_revisions.append( prior_import_changeset_revision )
+ repo_info_dict = self.get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts )
+ repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict )
+ if repository and changeset_revision:
+ ordered_repository_ids.append( repository_id )
+ ordered_repositories.append( repository )
+ ordered_changeset_revisions.append( changeset_revision )
+ # Process the repository associated with self.repository_id last.
+ repo_info_dict = self.get_repo_info_dict_for_import( self.repository_id, repository_ids, repo_info_dicts )
+ repository, changeset_revision = self.get_components_from_repo_info_dict( repo_info_dict )
+ if repository and changeset_revision:
+ ordered_repository_ids.append( repository_id )
+ ordered_repositories.append( repository )
+ ordered_changeset_revisions.append( changeset_revision )
+ return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions
+
+ def remove_protocol_from_tool_shed_url( self ):
+ protocol, base = self.tool_shed_url.split( '://' )
+ base = base.replace( ':', '_colon_' )
+ base = base.rstrip( '/' )
+ return base
+
+
+class ImportRepositoryManager( object ):
+
+ def __init__( self, app, host, user, user_is_admin ):
+ self.app = app
+ self.host = host
+ self.user = user
+ self.user_is_admin = user_is_admin
+
+ def check_status_and_reset_downloadable( self, import_results_tups ):
+ """Check the status of each imported repository and set downloadable to False if errors."""
+ sa_session = self.app.model.context.current
+ flush = False
+ for import_results_tup in import_results_tups:
+ ok, name_owner, message = import_results_tup
+ name, owner = name_owner
+ if not ok:
+ repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
+ if repository is not None:
+ # Do not allow the repository to be automatically installed if population resulted in errors.
+ tip_changeset_revision = repository.tip( self.app )
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
+ self.app.security.encode_id( repository.id ),
+ tip_changeset_revision )
+ if repository_metadata:
+ if repository_metadata.downloadable:
+ repository_metadata.downloadable = False
+ sa_session.add( repository_metadata )
+ if not flush:
+ flush = True
+ # Do not allow dependent repository revisions to be automatically installed if population
+ # resulted in errors.
+ dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( self.app, repository_metadata )
+ for dependent_downloadable_revision in dependent_downloadable_revisions:
+ if dependent_downloadable_revision.downloadable:
+ dependent_downloadable_revision.downloadable = False
+ sa_session.add( dependent_downloadable_revision )
+ if not flush:
+ flush = True
+ if flush:
+ sa_session.flush()
+
+ def create_repository_and_import_archive( self, repository_archive_dict, import_results_tups ):
+ """
+ Create a new repository in the tool shed and populate it with the contents of a gzip compressed
+ tar archive that was exported as part or all of the contents of a capsule.
+ """
+ results_message = ''
+ name = repository_archive_dict.get( 'name', None )
+ username = repository_archive_dict.get( 'owner', None )
+ if name is None or username is None:
+ ok = False
+ results_message += 'Import failed: required repository name <b>%s</b> or owner <b>%s</b> is missing.' % \
+ ( str( name ), str( username ))
+ import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) )
+ else:
+ status = repository_archive_dict.get( 'status', None )
+ if status is None:
+ # The repository does not yet exist in this Tool Shed and the current user is authorized to import
+ # the current archive file.
+ type = repository_archive_dict.get( 'type', 'unrestricted' )
+ description = repository_archive_dict.get( 'description', '' )
+ long_description = repository_archive_dict.get( 'long_description', '' )
+ # The owner entry in the repository_archive_dict is the public username of the user associated with
+ # the exported repository archive.
+ user = suc.get_user_by_username( self.app, username )
+ if user is None:
+ ok = False
+ results_message += 'Import failed: repository owner <b>%s</b> does not have an account in this Tool Shed.' % \
+ str( username )
+ import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) )
+ else:
+ user_id = user.id
+ # The categories entry in the repository_archive_dict is a list of category names. If a name does not
+ # exist in the current Tool Shed, the category will not be created, so it will not be associated with
+ # the repository.
+ category_ids = []
+ category_names = repository_archive_dict.get( 'category_names', [] )
+ for category_name in category_names:
+ category = suc.get_category_by_name( self.app, category_name )
+ if category is None:
+ results_message += 'This Tool Shed does not have the category <b>%s</b> so it ' % str( category_name )
+ results_message += 'will not be associated with this repository.'
+ else:
+ category_ids.append( self.app.security.encode_id( category.id ) )
+ # Create the repository record in the database.
+ repository, create_message = repository_maintenance_util.create_repository( self.app,
+ name,
+ type,
+ description,
+ long_description,
+ user_id=user_id,
+ category_ids=category_ids )
+ if create_message:
+ results_message += create_message
+ # Populate the new repository with the contents of exported repository archive.
+ results_dict = self.import_repository_archive( repository, repository_archive_dict )
+ ok = results_dict.get( 'ok', False )
+ error_message = results_dict.get( 'error_message', '' )
+ if error_message:
+ results_message += error_message
+ import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) )
+ else:
+ # The repository either already exists in this Tool Shed or the current user is not authorized to create it.
+ ok = True
+ results_message += 'Import not necessary: repository status for this Tool Shed is: %s.' % str( status )
+ import_results_tups.append( ( ok, ( str( name ), str( username ) ), results_message ) )
+ return import_results_tups
+
+ def extract_capsule_files( self, **kwd ):
+ """
+ Extract the uploaded capsule archive into a temporary location for inspection, validation
+ and potential import.
+ """
+ return_dict = {}
+ tar_archive = kwd.get( 'tar_archive', None )
+ capsule_file_name = kwd.get( 'capsule_file_name', None )
+ if tar_archive is not None and capsule_file_name is not None:
+ return_dict.update( kwd )
+ extract_directory_path = tempfile.mkdtemp( prefix="tmp-capsule-ecf" )
+ if capsule_file_name.endswith( '.tar.gz' ):
+ extract_directory_name = capsule_file_name.replace( '.tar.gz', '' )
+ elif capsule_file_name.endswith( '.tar' ):
+ extract_directory_name = capsule_file_name.replace( '.tar', '' )
+ else:
+ extract_directory_name = capsule_file_name
+ file_path = os.path.join( extract_directory_path, extract_directory_name )
+ return_dict[ 'encoded_file_path' ] = encoding_util.tool_shed_encode( file_path )
+ tar_archive.extractall( path=file_path )
+ try:
+ tar_archive.close()
+ except Exception, e:
+ log.exception( "Cannot close tar_archive: %s" % str( e ) )
+ del return_dict[ 'tar_archive' ]
+ return return_dict
+
+ def get_archives_from_manifest( self, manifest_file_path ):
+ """
+ Return the list of archive names defined in the capsule manifest. This method will validate
+ the manifest by ensuring all <repository> tag sets contain a valid <archive> sub-element.
+ """
+ archives = []
+ error_message = ''
+ manifest_tree, error_message = xml_util.parse_xml( manifest_file_path )
+ if error_message:
+ return archives, error_message
+ manifest_root = manifest_tree.getroot()
+ for elem in manifest_root:
+ # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test">
+ if elem.tag != 'repository':
+ error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. '
+ error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag )
+ return [], error_message
+ archive_file_name = None
+ for repository_elem in elem:
+ if repository_elem.tag == 'archive':
+ # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive>
+ archive_file_name = repository_elem.text
+ break
+ if archive_file_name is None:
+ error_message = 'The %s tag set is missing a required <archive> sub-element.' % str( elem.tag )
+ return [], error_message
+ archives.append( archive_file_name )
+ return archives, error_message
+
+ def get_export_info_dict( self, export_info_file_path ):
+ """
+ Parse the export_info.xml file contained within the capsule and return a dictionary
+ containing its entries.
+ """
+ export_info_tree, error_message = xml_util.parse_xml( export_info_file_path )
+ export_info_root = export_info_tree.getroot()
+ export_info_dict = {}
+ for elem in export_info_root:
+ if elem.tag == 'export_time':
+ export_info_dict[ 'export_time' ] = elem.text
+ elif elem.tag == 'tool_shed':
+ export_info_dict[ 'tool_shed' ] = elem.text
+ elif elem.tag == 'repository_name':
+ export_info_dict[ 'repository_name' ] = elem.text
+ elif elem.tag == 'repository_owner':
+ export_info_dict[ 'repository_owner' ] = elem.text
+ elif elem.tag == 'changeset_revision':
+ export_info_dict[ 'changeset_revision' ] = elem.text
+ elif elem.tag == 'export_repository_dependencies':
+ if asbool( elem.text ):
+ export_info_dict[ 'export_repository_dependencies' ] = 'Yes'
+ else:
+ export_info_dict[ 'export_repository_dependencies' ] = 'No'
+ return export_info_dict
+
+ def get_repository_info_from_manifest( self, manifest_file_path ):
+ """
+ Parse the capsule manifest and return a list of dictionaries containing information about
+ each exported repository archive contained within the capsule.
+ """
+ repository_info_dicts = []
+ manifest_tree, error_message = xml_util.parse_xml( manifest_file_path )
+ if error_message:
+ return repository_info_dicts, error_message
+ manifest_root = manifest_tree.getroot()
+ for elem in manifest_root:
+ # <repository name="package_lapack_3_4" type="tool_dependency_definition" username="test">
+ if elem.tag != 'repository':
+ error_message = 'All level one sub-elements in the manifest.xml file must be <repository> tag sets. '
+ error_message += 'The tag <b><%s></b> is invalid.' % str( elem.tag )
+ return [], error_message
+ name = elem.get( 'name', None )
+ owner = elem.get( 'username', None )
+ type = elem.get( 'type', None )
+ if name is None or owner is None or type is None:
+ error_message = 'Missing required name, type, owner attributes from the tag %s' % str( elem.tag )
+ return [], error_message
+ repository_info_dict = dict( name=name, owner=owner, type=type )
+ for repository_elem in elem:
+ if repository_elem.tag == 'archive':
+ # <archive>package_lapack_3_4-9e7a45ad3522.tar.gz</archive>
+ archive_file_name = repository_elem.text
+ repository_info_dict[ 'archive_file_name' ] = archive_file_name
+ items = archive_file_name.split( '-' )
+ changeset_revision = items[ 1 ].rstrip( '.tar.gz' )
+ repository_info_dict [ 'changeset_revision' ] = changeset_revision
+ elif repository_elem.tag == 'categories':
+ category_names = []
+ for category_elem in repository_elem:
+ if category_elem.tag == 'category':
+ category_names.append( category_elem.text )
+ repository_info_dict[ 'category_names' ] = category_names
+ elif repository_elem.tag == 'description':
+ repository_info_dict[ 'description' ] = repository_elem.text
+ elif repository_elem.tag == 'long_description':
+ repository_info_dict[ 'long_description' ] = repository_elem.text
+ repository_info_dicts.append( repository_info_dict )
+ return repository_info_dicts, error_message
+
+ def get_repository_status_from_tool_shed( self, repository_info_dicts ):
+ """
+ For each exported repository archive contained in the capsule, inspect the Tool Shed to
+ see if that repository already exists or if the current user is authorized to create the
+ repository and set a status appropriately. If repository dependencies are included in the
+ capsule, repositories may have various owners. We will keep repositories associated with
+ owners, so we need to restrict created repositories to those the current user can create.
+ If the current user is an admin or a member of the IUC, all repositories will be created
+ no matter the owner. Otherwise only repositories whose associated owner is the current
+ user will be created.
+ """
+ repository_status_info_dicts = []
+ for repository_info_dict in repository_info_dicts:
+ repository = suc.get_repository_by_name_and_owner( self.app,
+ repository_info_dict[ 'name' ],
+ repository_info_dict[ 'owner' ] )
+ if repository:
+ if repository.deleted:
+ repository_info_dict[ 'status' ] = 'Exists, deleted'
+ elif repository.deprecated:
+ repository_info_dict[ 'status' ] = 'Exists, deprecated'
+ else:
+ repository_info_dict[ 'status' ] = 'Exists'
+ else:
+ # No repository with the specified name and owner currently exists, so make sure
+ # the current user can create one.
+ if self.user_is_admin:
+ repository_info_dict[ 'status' ] = None
+ elif self.app.security_agent.user_can_import_repository_archive( self.user,
+ repository_info_dict[ 'owner' ] ):
+ repository_info_dict[ 'status' ] = None
+ else:
+ repository_info_dict[ 'status' ] = 'Not authorized to import'
+ repository_status_info_dicts.append( repository_info_dict )
+ return repository_status_info_dicts
+
+ def import_repository_archive( self, repository, repository_archive_dict ):
+ """Import a repository archive contained within a repository capsule."""
+ rdah = dependency_manager.RepositoryDependencyAttributeHandler( self.app, unpopulate=False )
+ tdah = dependency_manager.ToolDependencyAttributeHandler( self.app, unpopulate=False )
+ archive_file_name = repository_archive_dict.get( 'archive_file_name', None )
+ capsule_file_name = repository_archive_dict[ 'capsule_file_name' ]
+ encoded_file_path = repository_archive_dict[ 'encoded_file_path' ]
+ file_path = encoding_util.tool_shed_decode( encoded_file_path )
+ results_dict = dict( ok=True, error_message='' )
+ archive_file_path = os.path.join( file_path, archive_file_name )
+ archive = tarfile.open( archive_file_path, 'r:*' )
+ repo_dir = repository.repo_path( self.app )
+ repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False )
+ undesirable_dirs_removed = 0
+ undesirable_files_removed = 0
+ ok, error_message = commit_util.check_archive( repository, archive )
+ if ok:
+ full_path = os.path.abspath( repo_dir )
+ filenames_in_archive = []
+ for tarinfo_obj in archive.getmembers():
+ # Check files and directories in the archive.
+ ok = os.path.basename( tarinfo_obj.name ) not in commit_util.UNDESIRABLE_FILES
+ if ok:
+ for file_path_item in tarinfo_obj.name.split( '/' ):
+ if file_path_item in commit_util.UNDESIRABLE_DIRS:
+ undesirable_dirs_removed += 1
+ error_message = 'Import failed: invalid file path <b>%s</b> in archive <b>%s</b>' % \
+ ( str( file_path_item ), str( archive_file_name ) )
+ results_dict[ 'ok' ] = False
+ results_dict[ 'error_message' ] += error_message
+ return results_dict
+ filenames_in_archive.append( tarinfo_obj.name )
+ else:
+ undesirable_files_removed += 1
+ # Extract the uploaded archive to the repository root.
+ archive.extractall( path=full_path )
+ archive.close()
+ for filename in filenames_in_archive:
+ uploaded_file_name = os.path.join( full_path, filename )
+ if os.path.split( uploaded_file_name )[ -1 ] == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
+ # Inspect the contents of the file to see if toolshed or changeset_revision attributes
+ # are missing and if so, set them appropriately.
+ altered, root_elem, error_message = rdah.handle_tag_attributes( uploaded_file_name )
+ if error_message:
+ results_dict[ 'ok' ] = False
+ results_dict[ 'error_message' ] += error_message
+ if altered:
+ tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
+ shutil.move( tmp_filename, uploaded_file_name )
+ elif os.path.split( uploaded_file_name )[ -1 ] == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
+ # Inspect the contents of the file to see if toolshed or changeset_revision
+ # attributes are missing and if so, set them appropriately.
+ altered, root_elem, error_message = tdah.handle_tag_attributes( uploaded_file_name )
+ if error_message:
+ results_dict[ 'ok' ] = False
+ results_dict[ 'error_message' ] += error_message
+ if altered:
+ tmp_filename = xml_util.create_and_write_tmp_file( root_elem )
+ shutil.move( tmp_filename, uploaded_file_name )
+ commit_message = 'Imported from capsule %s' % str( capsule_file_name )
+ # Send email notification to those that have registered to receive alerts for new repositories in this Tool Shed.
+ new_repo_alert = True
+ # Since the repository is new, the following must be False.
+ remove_repo_files_not_in_tar = False
+ ok, error_message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = \
+ commit_util.handle_directory_changes( self.app,
+ self.host,
+ self.user.username,
+ repository,
+ full_path,
+ filenames_in_archive,
+ remove_repo_files_not_in_tar,
+ new_repo_alert,
+ commit_message,
+ undesirable_dirs_removed,
+ undesirable_files_removed )
+ if error_message:
+ results_dict[ 'ok' ] = False
+ results_dict[ 'error_message' ] += error_message
+ try:
+ status, error_message = metadata_util.set_repository_metadata_due_to_new_tip( self.app,
+ self.host,
+ self.user,
+ repository,
+ content_alert_str=content_alert_str )
+ if error_message:
+ results_dict[ 'ok' ] = False
+ results_dict[ 'error_message' ] += error_message
+ except Exception, e:
+ log.debug( "Error setting metadata on repository %s created from imported archive %s: %s" % \
+ ( str( repository.name ), str( archive_file_name ), str( e ) ) )
+ else:
+ archive.close()
+ results_dict[ 'ok' ] = False
+ results_dict[ 'error_message' ] += error_message
+ return results_dict
+
+ def upload_capsule( self, **kwd ):
+ """Upload and prepare an exported repository capsule for validation."""
+ file_data = kwd.get( 'file_data', '' )
+ url = kwd.get( 'url', '' )
+ uploaded_file = None
+ return_dict = dict( error_message='',
+ encoded_file_path=None,
+ status='ok',
+ tar_archive=None,
+ uploaded_file=None,
+ capsule_file_name=None )
+ if file_data == '' and url == '':
+ message = 'No files were entered on the import form.'
+ status = 'error'
+ elif url:
+ valid_url = True
+ try:
+ stream = urllib.urlopen( url )
+ except Exception, e:
+ valid_url = False
+ message = 'Error importing file via http: %s' % str( e )
+ status = 'error'
+ if valid_url:
+ fd, uploaded_file_name = tempfile.mkstemp()
+ uploaded_file = open( uploaded_file_name, 'wb' )
+ while 1:
+ chunk = stream.read( CHUNK_SIZE )
+ if not chunk:
+ break
+ uploaded_file.write( chunk )
+ uploaded_file.flush()
+ uploaded_file_filename = url.split( '/' )[ -1 ]
+ isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
+ elif file_data not in ( '', None ):
+ uploaded_file = file_data.file
+ uploaded_file_name = uploaded_file.name
+ uploaded_file_filename = os.path.split( file_data.filename )[ -1 ]
+ isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0
+ if uploaded_file is not None:
+ if isempty:
+ uploaded_file.close()
+ return_dict[ 'error_message' ] = 'Your uploaded capsule file is empty.'
+ return_dict[ 'status' ] = 'error'
+ return return_dict
+ try:
+ # Open for reading with transparent compression.
+ tar_archive = tarfile.open( uploaded_file_name, 'r:*' )
+ except tarfile.ReadError, e:
+ error_message = 'Error opening file %s: %s' % ( str( uploaded_file_name ), str( e ) )
+ log.exception( error_message )
+ return_dict[ 'error_message' ] = error_message
+ return_dict[ 'status' ] = 'error'
+ uploaded_file.close()
+ return return_dict
+ return_dict[ 'tar_archive' ] = tar_archive
+ return_dict[ 'capsule_file_name' ] = uploaded_file_filename
+ uploaded_file.close()
+ else:
+ return_dict[ 'error_message' ] = 'No files were entered on the import form.'
+ return_dict[ 'status' ] = 'error'
+ return return_dict
+ return return_dict
+
+ def validate_capsule( self, **kwd ):
+ """
+ Inspect the uploaded capsule's manifest and its contained files to ensure it is a valid
+ repository capsule.
+ """
+ capsule_dict = {}
+ capsule_dict.update( kwd )
+ encoded_file_path = capsule_dict.get( 'encoded_file_path', '' )
+ file_path = encoding_util.tool_shed_decode( encoded_file_path )
+ # The capsule must contain a valid XML file named export_info.xml.
+ export_info_file_path = os.path.join( file_path, 'export_info.xml' )
+ export_info_tree, error_message = xml_util.parse_xml( export_info_file_path )
+ if error_message:
+ capsule_dict[ 'error_message' ] = error_message
+ capsule_dict[ 'status' ] = 'error'
+ return capsule_dict
+ # The capsule must contain a valid XML file named manifest.xml.
+ manifest_file_path = os.path.join( file_path, 'manifest.xml' )
+ # Validate the capsule manifest by inspecting name, owner, changeset_revision and type
+ # information contained within each <repository> tag set.
+ repository_info_dicts, error_message = self.get_repository_info_from_manifest( manifest_file_path )
+ if error_message:
+ capsule_dict[ 'error_message' ] = error_message
+ capsule_dict[ 'status' ] = 'error'
+ return capsule_dict
+ # Validate the capsule manifest by ensuring all <repository> tag sets contain a valid
+ # <archive> sub-element.
+ archives, error_message = self.get_archives_from_manifest( manifest_file_path )
+ if error_message:
+ capsule_dict[ 'error_message' ] = error_message
+ capsule_dict[ 'status' ] = 'error'
+ return capsule_dict
+ # Validate the capsule manifest by ensuring each defined archive file name exists within
+ # the capsule.
+ error_message = self.verify_archives_in_capsule( file_path, archives )
+ if error_message:
+ capsule_dict[ 'error_message' ] = error_message
+ capsule_dict[ 'status' ] = 'error'
+ return capsule_dict
+ capsule_dict[ 'status' ] = 'ok'
+ return capsule_dict
+
+ def verify_archives_in_capsule( self, file_path, archives ):
+ """
+ Inspect the files contained within the capsule and make sure each is defined correctly
+ in the capsule manifest.
+ """
+ error_message = ''
+ for archive_file_name in archives:
+ full_path = os.path.join( file_path, archive_file_name )
+ if not os.path.exists( full_path ):
+ error_message = 'The uploaded capsule is invalid because the contained manifest.xml '
+ error_message += 'file defines an archive file named <b>%s</b> which ' % str( archive_file_name )
+ error_message += 'is not contained within the capsule.'
+ break
+ return error_message
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/scripts/api/export.py
--- a/lib/tool_shed/scripts/api/export.py
+++ b/lib/tool_shed/scripts/api/export.py
@@ -1,6 +1,7 @@
#!/usr/bin/env python
"""
-Export a specified repository revision and optionally all of its defined repository dependencies from the tool shed into a compressed archive.
+Export a specified repository revision and optionally all of its defined repository
+dependencies from the tool shed into a compressed archive.
Here is a working example of how to use this script to export a repository from the tool shed.
./export.py --url http://testtoolshed.g2.bx.psu.edu --name chemicaltoolbox --owner bgruening --revision 4133dbf7ff4d --export_repository_dependencies True --download_dir /tmp
@@ -8,15 +9,45 @@
import os
import sys
+import tempfile
import argparse
import urllib2
sys.path.insert( 0, os.path.dirname( __file__ ) )
from common import display
from common import submit
-from tool_shed.util import export_util
+from tool_shed.util import basic_util
+CAPSULE_FILENAME = 'capsule'
+CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies'
CHUNK_SIZE = 2**20 # 1Mb
+def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type,
+ export_repository_dependencies, use_tmp_archive_dir=False ):
+ tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url )
+ file_type_str = basic_util.get_file_type_str( changeset_revision, file_type )
+ if self.export_repository_dependencies:
+ repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME,
+ tool_shed,
+ name,
+ owner,
+ file_type_str )
+ else:
+ repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME,
+ tool_shed,
+ name,
+ owner,
+ file_type_str )
+ if use_tmp_archive_dir:
+ tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" )
+ repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename )
+ return repositories_archive_filename
+
+def remove_protocol_from_tool_shed_url( tool_shed_url ):
+ protocol, base = tool_shed_url.split( '://' )
+ base = base.replace( ':', '_colon_' )
+ base = base.rstrip( '/' )
+ return base
+
def string_as_bool( string ):
if str( string ).lower() in ( 'true', 'yes', 'on' ):
return True
@@ -50,14 +81,15 @@
if error_messages:
print "Error attempting to export revision ", options.changeset_revision, " of repository ", options.name, " owned by ", options.owner, ":\n", error_messages
else:
+ export_repository_dependencies = string_as_bool( options.export_repository_dependencies )
repositories_archive_filename = \
- export_util.generate_repository_archive_filename( base_tool_shed_url,
- options.name,
- options.owner,
- options.changeset_revision,
- file_type,
- export_repository_dependencies=string_as_bool( options.export_repository_dependencies ),
- use_tmp_archive_dir=False )
+ generate_repository_archive_filename( base_tool_shed_url,
+ options.name,
+ options.owner,
+ options.changeset_revision,
+ file_type,
+ export_repository_dependencies=export_repository_dependencies,
+ use_tmp_archive_dir=False )
download_url = export_dict[ 'download_url' ]
download_dir = os.path.abspath( options.download_dir )
file_path = os.path.join( download_dir, repositories_archive_filename )
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/basic_util.py
--- a/lib/tool_shed/util/basic_util.py
+++ b/lib/tool_shed/util/basic_util.py
@@ -45,6 +45,17 @@
env_var_dict[ '__is64bit__' ] = sys.maxsize > 2**32
return env_var_dict
+def get_file_type_str( changeset_revision, file_type ):
+ if file_type == 'zip':
+ file_type_str = '%s.zip' % changeset_revision
+ elif file_type == 'bz2':
+ file_type_str = '%s.tar.bz2' % changeset_revision
+ elif file_type == 'gz':
+ file_type_str = '%s.tar.gz' % changeset_revision
+ else:
+ file_type_str = ''
+ return file_type_str
+
def move_file( current_dir, source, destination, rename_to=None ):
source_path = os.path.abspath( os.path.join( current_dir, source ) )
source_file = os.path.basename( source_path )
diff -r fbf4b5ab17a90ec7b0deac658ead6a99b9a6ca76 -r fdaad2cad3926f1266bb534d998cdf24a5969578 lib/tool_shed/util/export_util.py
--- a/lib/tool_shed/util/export_util.py
+++ /dev/null
@@ -1,355 +0,0 @@
-import logging
-import os
-import shutil
-import tarfile
-import tempfile
-import threading
-from time import gmtime
-from time import strftime
-import tool_shed.repository_types.util as rt_util
-from galaxy import web
-from galaxy.util.odict import odict
-from tool_shed.dependencies import dependency_manager
-from tool_shed.util import basic_util
-from tool_shed.util import commit_util
-from tool_shed.util import common_util
-from tool_shed.util import encoding_util
-from tool_shed.util import hg_util
-from tool_shed.util import repository_dependency_util
-from tool_shed.util import shed_util_common as suc
-from tool_shed.util import xml_util
-from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyManager
-
-log = logging.getLogger( __name__ )
-
-CAPSULE_FILENAME = 'capsule'
-CAPSULE_WITH_DEPENDENCIES_FILENAME = 'capsule_with_dependencies'
-
-class ExportedRepositoryRegistry( object ):
-
- def __init__( self ):
- self.exported_repository_elems = []
-
-def export_repository( app, user, tool_shed_url, repository_id, repository_name, changeset_revision, file_type,
- export_repository_dependencies, api=False ):
- repository = suc.get_repository_in_tool_shed( app, repository_id )
- repositories_archive_filename = generate_repository_archive_filename( tool_shed_url,
- str( repository.name ),
- str( repository.user.username ),
- changeset_revision,
- file_type,
- export_repository_dependencies=export_repository_dependencies,
- use_tmp_archive_dir=True )
- if export_repository_dependencies:
- repo_info_dicts = get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision )
- repository_ids = get_repository_ids( app, repo_info_dicts )
- ordered_repository_ids, ordered_repositories, ordered_changeset_revisions = \
- order_components_for_import( app, repository_id, repository_ids, repo_info_dicts )
- else:
- ordered_repository_ids = []
- ordered_repositories = []
- ordered_changeset_revisions = []
- if repository:
- repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app,
- repository,
- changeset_revision )
- if repository_metadata:
- ordered_repository_ids = [ repository_id ]
- ordered_repositories = [ repository ]
- ordered_changeset_revisions = [ repository_metadata.changeset_revision ]
- repositories_archive = None
- error_messages = ''
- lock = threading.Lock()
- lock.acquire( True )
- try:
- repositories_archive = tarfile.open( repositories_archive_filename, "w:%s" % file_type )
- exported_repository_registry = ExportedRepositoryRegistry()
- for index, repository_id in enumerate( ordered_repository_ids ):
- work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-export-er" )
- ordered_repository = ordered_repositories[ index ]
- ordered_changeset_revision = ordered_changeset_revisions[ index ]
- repository_archive, error_message = generate_repository_archive( app,
- work_dir,
- tool_shed_url,
- ordered_repository,
- ordered_changeset_revision,
- file_type )
- if error_message:
- error_messages = '%s %s' % ( error_messages, error_message )
- else:
- archive_name = str( os.path.basename( repository_archive.name ) )
- repositories_archive.add( repository_archive.name, arcname=archive_name )
- attributes, sub_elements = get_repository_attributes_and_sub_elements( ordered_repository, archive_name )
- elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements )
- exported_repository_registry.exported_repository_elems.append( elem )
- basic_util.remove_dir( work_dir )
- # Keep information about the export in a file name export_info.xml in the archive.
- sub_elements = generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api )
- export_elem = xml_util.create_element( 'export_info', attributes=None, sub_elements=sub_elements )
- tmp_export_info = xml_util.create_and_write_tmp_file( export_elem, use_indent=True )
- repositories_archive.add( tmp_export_info, arcname='export_info.xml' )
- # Write the manifest, which must preserve the order in which the repositories should be imported.
- exported_repository_root = xml_util.create_element( 'repositories' )
- for exported_repository_elem in exported_repository_registry.exported_repository_elems:
- exported_repository_root.append( exported_repository_elem )
- tmp_manifest = xml_util.create_and_write_tmp_file( exported_repository_root, use_indent=True )
- repositories_archive.add( tmp_manifest, arcname='manifest.xml' )
- except Exception, e:
- log.exception( str( e ) )
- finally:
- lock.release()
- repositories_archive.close()
- if api:
- encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename )
- params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name
- download_url = common_util.url_join( web.url_for( '/', qualified=True ),
- 'repository/export_via_api%s' % params )
- return dict( download_url=download_url, error_messages=error_messages )
- return repositories_archive, error_messages
-
-def generate_repository_archive( app, work_dir, tool_shed_url, repository, changeset_revision, file_type ):
- rdah = dependency_manager.RepositoryDependencyAttributeHandler( app, unpopulate=True )
- tdah = dependency_manager.ToolDependencyAttributeHandler( app, unpopulate=True )
- file_type_str = get_file_type_str( changeset_revision, file_type )
- file_name = '%s-%s' % ( repository.name, file_type_str )
- return_code, error_message = hg_util.archive_repository_revision( app,
- repository,
- work_dir,
- changeset_revision )
- if return_code:
- return None, error_message
- repository_archive_name = os.path.join( work_dir, file_name )
- # Create a compressed tar archive that will contain only valid files and possibly altered dependency definition files.
- repository_archive = tarfile.open( repository_archive_name, "w:%s" % file_type )
- for root, dirs, files in os.walk( work_dir ):
- if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0:
- for dir in dirs:
- if dir in commit_util.UNDESIRABLE_DIRS:
- dirs.remove( dir )
- for name in files:
- name = str( name )
- if str( name ) in commit_util.UNDESIRABLE_FILES:
- continue
- full_path = os.path.join( root, name )
- relative_path = full_path.replace( work_dir, '' ).lstrip( '/' )
- # See if we have a repository dependencies defined.
- if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
- # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags.
- altered, root_elem, error_message = rdah.handle_tag_attributes( full_path )
- if error_message:
- return None, error_message
- if altered:
- tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True )
- shutil.move( tmp_filename, full_path )
- elif name == rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME:
- # Eliminate the toolshed, and changeset_revision attributes from all <repository> tags.
- altered, root_elem, error_message = tdah.handle_tag_attributes( full_path )
- if error_message:
- return None, error_message
- if altered:
- tmp_filename = xml_util.create_and_write_tmp_file( root_elem, use_indent=True )
- shutil.move( tmp_filename, full_path )
- repository_archive.add( full_path, arcname=relative_path )
- repository_archive.close()
- return repository_archive, error_message
-
-def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type,
- export_repository_dependencies=False, use_tmp_archive_dir=False ):
- tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url )
- file_type_str = get_file_type_str( changeset_revision, file_type )
- if export_repository_dependencies:
- repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, tool_shed, name, owner, file_type_str )
- else:
- repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_FILENAME, tool_shed, name, owner, file_type_str )
- if use_tmp_archive_dir:
- tmp_archive_dir = tempfile.mkdtemp( prefix="tmp-toolshed-arcdir" )
- repositories_archive_filename = os.path.join( tmp_archive_dir, repositories_archive_filename )
- return repositories_archive_filename
-
-def generate_export_elem( tool_shed_url, repository, changeset_revision, export_repository_dependencies, api ):
- sub_elements = odict()
- sub_elements[ 'export_time' ] = strftime( '%a, %d %b %Y %H:%M:%S +0000', gmtime() )
- sub_elements[ 'tool_shed' ] = str( tool_shed_url.rstrip( '/' ) )
- sub_elements[ 'repository_name' ] = str( repository.name )
- sub_elements[ 'repository_owner' ] = str( repository.user.username )
- sub_elements[ 'changeset_revision' ] = str( changeset_revision )
- sub_elements[ 'export_repository_dependencies' ] = str( export_repository_dependencies )
- sub_elements[ 'exported_via_api' ] = str( api )
- return sub_elements
-
-def get_components_from_repo_info_dict( app, repo_info_dict ):
- """
- Return the repository and the associated latest installable changeset_revision (including updates) for the
- repository defined by the received repo_info_dict.
- """
- for repository_name, repo_info_tup in repo_info_dict.items():
- # There should only be one entry in the received repo_info_dict.
- description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
- suc.get_repo_info_tuple_contents( repo_info_tup )
- repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner )
- repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app,
- repository,
- changeset_revision )
- if repository_metadata:
- return repository, repository_metadata.changeset_revision
- return None, None
-
-def get_file_type_str( changeset_revision, file_type ):
- if file_type == 'zip':
- file_type_str = '%s.zip' % changeset_revision
- elif file_type == 'bz2':
- file_type_str = '%s.tar.bz2' % changeset_revision
- elif file_type == 'gz':
- file_type_str = '%s.tar.gz' % changeset_revision
- else:
- file_type_str = ''
- return file_type_str
-
-def get_repo_info_dict_for_import( encoded_repository_id, encoded_repository_ids, repo_info_dicts ):
- """
- The received encoded_repository_ids and repo_info_dicts are lists that contain associated elements at each
- location in the list. This method will return the element from repo_info_dicts associated with the received
- encoded_repository_id by determining its location in the received encoded_repository_ids list.
- """
- for index, repository_id in enumerate( encoded_repository_ids ):
- if repository_id == encoded_repository_id:
- repo_info_dict = repo_info_dicts[ index ]
- return repo_info_dict
- return None
-
-def get_repo_info_dicts( app, user, tool_shed_url, repository_id, changeset_revision ):
- """
- Return a list of dictionaries defining repositories that are required by the repository associated with the
- received repository_id.
- """
- rdm = RepositoryDependencyManager( app )
- repository = suc.get_repository_in_tool_shed( app, repository_id )
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, repository_id, changeset_revision )
- # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
- toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
- repository_dependencies = \
- repository_dependency_util.get_repository_dependencies_for_changeset_revision( app=app,
- repository=repository,
- repository_metadata=repository_metadata,
- toolshed_base_url=toolshed_base_url,
- key_rd_dicts_to_be_processed=None,
- all_repository_dependencies=None,
- handled_key_rd_dicts=None )
- repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
- ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
- repo_info_dict = {}
- # Cast unicode to string.
- repo_info_dict[ str( repository.name ) ] = ( str( repository.description ),
- common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ),
- str( changeset_revision ),
- str( ctx.rev() ),
- str( repository.user.username ),
- repository_dependencies,
- None )
- all_required_repo_info_dict = rdm.get_required_repo_info_dicts( tool_shed_url, [ repo_info_dict ] )
- all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] )
- return all_repo_info_dicts
-
-def get_repository_attributes_and_sub_elements( repository, archive_name ):
- """
- Get the information about a repository to create and populate an XML tag set. The generated attributes will
- be contained within the <repository> tag, while the sub_elements will be tag sets contained within the <repository>
- tag set.
- """
- attributes = odict()
- sub_elements = odict()
- attributes[ 'name' ] = str( repository.name )
- attributes[ 'type' ] = str( repository.type )
- # We have to associate the public username since the user_id will be different between tool sheds.
- attributes[ 'username' ] = str( repository.user.username )
- # Don't coerce description or long description from unicode to string because the fields are free text.
- sub_elements[ 'description' ] = repository.description
- sub_elements[ 'long_description' ] = repository.long_description
- sub_elements[ 'archive' ] = archive_name
- # Keep track of Category associations.
- categories = []
- for rca in repository.categories:
- category = rca.category
- categories.append( ( 'category', str( category.name ) ) )
- sub_elements[ 'categories' ] = categories
- return attributes, sub_elements
-
-def get_repository_ids( app, repo_info_dicts ):
- """Return a list of repository ids associated with each dictionary in the received repo_info_dicts."""
- repository_ids = []
- for repo_info_dict in repo_info_dicts:
- for repository_name, repo_info_tup in repo_info_dict.items():
- description, \
- repository_clone_url, \
- changeset_revision, \
- ctx_rev, \
- repository_owner, \
- repository_dependencies, \
- tool_dependencies = \
- suc.get_repo_info_tuple_contents( repo_info_tup )
- repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner )
- repository_ids.append( app.security.encode_id( repository.id ) )
- return repository_ids
-
-def order_components_for_import( app, primary_repository_id, repository_ids, repo_info_dicts ):
- """
- Some repositories may have repository dependencies that must be imported and have metadata set on
- them before the dependent repository is imported. This method will inspect the list of repositories
- about to be exported and make sure to order them appropriately for proper import. For each repository
- about to be exported, if required repositories are not contained in the list of repositories about to
- be exported, then they are not considered. Repository dependency definitions that contain circular
- dependencies should not result in an infinite loop, but obviously ordering the list will not be handled
- for one or more of the repositories that require prior import.
- """
- # The received primary_repository_id is the id of the repository being exported, with the received list
- # of repository_ids being only the ids of all of its repository dependencies. The primary repository will
- # always be last in the returned lists.
- ordered_repository_ids = []
- ordered_repositories = []
- ordered_changeset_revisions = []
- # Create a dictionary whose keys are the received repository_ids and whose values are a list of
- # repository_ids, each of which is contained in the received list of repository_ids and whose associated
- # repository must be imported prior to the repository associated with the repository_id key.
- prior_import_required_dict = suc.get_prior_import_or_install_required_dict( app, repository_ids, repo_info_dicts )
- processed_repository_ids = []
- # Process the list of repository dependencies defined for the repository associated with the received
- # primary_repository_id.
- while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ):
- repository_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_import_required_dict, processed_repository_ids )
- if repository_id == primary_repository_id:
- # Append the primary_repository_id without processing it since it must be returned last in the order.
- # It will be processed below after all dependencies are processed.
- processed_repository_ids.append( primary_repository_id )
- continue
- processed_repository_ids.append( repository_id )
- if repository_id not in ordered_repository_ids:
- prior_import_required_ids = prior_import_required_dict[ repository_id ]
- for prior_import_required_id in prior_import_required_ids:
- if prior_import_required_id not in ordered_repository_ids:
- # Import the associated repository dependency first.
- prior_repo_info_dict = get_repo_info_dict_for_import( prior_import_required_id, repository_ids, repo_info_dicts )
- prior_repository, prior_import_changeset_revision = get_components_from_repo_info_dict( app, prior_repo_info_dict )
- if prior_repository and prior_import_changeset_revision:
- ordered_repository_ids.append( prior_import_required_id )
- ordered_repositories.append( prior_repository )
- ordered_changeset_revisions.append( prior_import_changeset_revision )
- repo_info_dict = get_repo_info_dict_for_import( repository_id, repository_ids, repo_info_dicts )
- repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict )
- if repository and changeset_revision:
- ordered_repository_ids.append( repository_id )
- ordered_repositories.append( repository )
- ordered_changeset_revisions.append( changeset_revision )
- # Process the repository associated with the received primary_repository_id last.
- repo_info_dict = get_repo_info_dict_for_import( primary_repository_id, repository_ids, repo_info_dicts )
- repository, changeset_revision = get_components_from_repo_info_dict( app, repo_info_dict )
- if repository and changeset_revision:
- ordered_repository_ids.append( repository_id )
- ordered_repositories.append( repository )
- ordered_changeset_revisions.append( changeset_revision )
- return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions
-
-def remove_protocol_from_tool_shed_url( base_url ):
- protocol, base = base_url.split( '://' )
- base = base.replace( ':', '_colon_' )
- base = base.rstrip( '/' )
- return base
This diff is so big that we needed to truncate the remainder.
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