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July 2014
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- 146 discussions
commit/galaxy-central: dannon: Change behavior on creation of workflow to kick directly into the edit window, instead of going back to the workflow list from which you can click more times to go back to work on your new workflow.
by commits-noreply＠bitbucket.org 10 Jul '14
by commits-noreply＠bitbucket.org 10 Jul '14
10 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a129d77f8d20/
Changeset: a129d77f8d20
User: dannon
Date: 2014-07-10 21:33:33
Summary: Change behavior on creation of workflow to kick directly into the edit window, instead of going back to the workflow list from which you can click more times to go back to work on your new workflow.
Affected #: 1 file
diff -r 1d09105e1cade84ebacfe48ef4739266f3f073ca -r a129d77f8d203d4db7940dbd0b9fdc8c48436781 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -227,7 +227,7 @@
@web.expose
def display_by_username_and_slug( self, trans, username, slug, format='html' ):
- """
+ """
Display workflow based on a username and slug. Format can be html, json, or json-download.
"""
@@ -236,7 +236,7 @@
user = session.query( model.User ).filter_by( username=username ).first()
stored_workflow = trans.sa_session.query( model.StoredWorkflow ).filter_by( user=user, slug=slug, deleted=False ).first()
encoded_id = trans.security.encode_id( stored_workflow.id )
-
+
# Display workflow in requested format.
if format == 'html':
return self._display( trans, stored_workflow )
@@ -580,9 +580,7 @@
session = trans.sa_session
session.add( stored_workflow )
session.flush()
- # Display the management page
- trans.set_message( "Workflow '%s' created" % stored_workflow.name )
- return self.list( trans )
+ return self.editor( trans, id=trans.security.encode_id(stored_workflow.id ))
else:
return form( url_for(controller="workflow", action="create"), "Create New Workflow", submit_text="Create", use_panels=True ) \
.add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \
@@ -1224,7 +1222,7 @@
# Index page with message
workflow_id = trans.security.encode_id( stored_workflow.id )
return trans.show_message( 'Workflow "%s" created from current history. You can <a href="%s" target="_parent">edit</a> or <a href="%s">run</a> the workflow.' %
- ( workflow_name, url_for( controller='workflow', action='editor', id=workflow_id ),
+ ( workflow_name, url_for( controller='workflow', action='editor', id=workflow_id ),
url_for( controller='workflow', action='run', id=workflow_id ) ) )
@web.expose
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1
0
4 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6249e3b45f80/
Changeset: 6249e3b45f80
User: dannon
Date: 2014-07-10 20:31:35
Summary: Initial implementation adding tool input ids to rename action. Whole thing needs some prettification and refactoring, still, but this will at least make it usable for folks.
Affected #: 3 files
diff -r 06b64928f4a4da6384d0717fc9bb650aa5e307eb -r 6249e3b45f8039099fa696a35f237d898a7ab626 lib/galaxy/jobs/actions/post.py
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -215,6 +215,15 @@
p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label>\
<input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value=''/>";
}
+ inputlist = [];
+ $.each(node.input_terminals, function(i, v){
+ inputlist.push(v.name);
+ });
+ if (inputlist !== []){
+ p_str += "Available inputs are: <strong>" + inputlist.join(', ') + "</strong>";
+ }else{
+ p_str += "No inputs are available for templating into this action.";
+ }
"""
return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.")
diff -r 06b64928f4a4da6384d0717fc9bb650aa5e307eb -r 6249e3b45f8039099fa696a35f237d898a7ab626 static/scripts/galaxy.workflows.js
--- a/static/scripts/galaxy.workflows.js
+++ b/static/scripts/galaxy.workflows.js
@@ -361,7 +361,7 @@
// This function preloads how to display known pja's.
function display_pja(pja, node) {
// DBTODO SANITIZE INPUTS.
- $("#pja_container").append( get_pja_form(pja) );
+ $("#pja_container").append( get_pja_form(pja, node) );
$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){
action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
$(this).closest(".toolForm").remove();
diff -r 06b64928f4a4da6384d0717fc9bb650aa5e307eb -r 6249e3b45f8039099fa696a35f237d898a7ab626 templates/webapps/galaxy/workflow/editor.mako
--- a/templates/webapps/galaxy/workflow/editor.mako
+++ b/templates/webapps/galaxy/workflow/editor.mako
@@ -65,7 +65,7 @@
%>
// Post-job action vars.
var pja_list = "${ActionBox.get_add_list()}",
- get_pja_form = function(pja) {
+ get_pja_form = function(pja, node) {
var p_str = '';
// FIXME: this writes JS code; this logic should be codified in galaxy.workflows.js
${ActionBox.get_forms(trans)}
https://bitbucket.org/galaxy/galaxy-central/commits/c32e9cecb879/
Changeset: c32e9cecb879
User: dannon
Date: 2014-07-10 20:31:51
Summary: Merge.
Affected #: 142 files
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -9,4 +9,4 @@
9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14
68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14
7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02
-9b78595ec1142d75930dbfffd8baeaa689cb4c6c latest_2014.06.02
+8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -1,26 +1,26 @@
// dependencies
define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils',
- 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage',
+ 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage', 'plugin/library/deferred',
'plugin/views/viewer', 'plugin/views/editor',
'plugin/models/config', 'plugin/models/chart',
'plugin/charts/types'],
- function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage,
+ function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage, Deferred,
ViewerView, EditorView,
Config, Chart, Types
) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * Main application class.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(options)
- {
+ initialize: function(options){
// deactivate all debugs outputs
//window.console.debug = function() {};
// link options
this.options = options;
-
+
// link galaxy modal or create one
if (Galaxy && Galaxy.modal) {
this.modal = Galaxy.modal;
@@ -41,6 +41,7 @@
this.jobs = new Jobs(this);
this.datasets = new Datasets(this);
this.storage = new Storage(this);
+ this.deferred = new Deferred();
//
// views
@@ -62,7 +63,7 @@
// draw chart
var self = this;
- this.chart.deferred.execute(function() {
+ this.deferred.execute(function() {
self.chart.trigger('redraw');
});
}
@@ -100,19 +101,6 @@
console.debug('FAILED App:chartPath() - Invalid format: ' + chart_type);
}
return undefined;
- },
-
- // execute command
- execute: function(options) {
- },
-
- // unload
- onunload: function() {
- },
-
- // log
- log: function(location, message) {
- console.log(location + ' ' + message);
}
});
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf 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.
-define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$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.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn 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="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},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="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$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.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.chart.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<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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n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$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._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+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{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),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/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},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+")")}})});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/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],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/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}})}),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=this.app.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(){this.app.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=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$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.app.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.app.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)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_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({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new 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.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},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)},_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 fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(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 id="'+e.id+'" 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({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,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._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){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.$el)),f.append(r.wrap(this.types.$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.$el}),this.portlet.append(this.message.$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="Data label"),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});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_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()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],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 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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 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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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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.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,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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$.extend(!0,{},e,{title:"Heatmap",category:"Others",query_limit:1e3,library:"Custom",tag:"svg",keywords:"small",zoomable:!0,columns:{x:{title:"Column labels",is_label:!0,is_numeric:!0,is_unique:!0},y:{title:"Row labels",is_label:!0,is_numeric:!0,is_unique:!0},z:{title:"Observation",is_numeric:!0}},settings:{use_panels:{init:"true",hide:!0},color_set:{title:"Color scheme",info:"Select a color scheme for your heatmap",type:"select",init:"jet",data:[{label:"Cold-to-Hot",value:"hot"},{label:"Cool",value:"cool"},{label:"Copper",value:"copper"},{label:"Gray scale",value:"gray"},{label:"Jet",value:"jet"},{label:"No-Green",value:"no_green"},{label:"Ocean",value:"ocean"},{label:"Polar",value:"polar"},{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:"Wysiwyg",value:"wysiwyg"}]},url_template:{title:"Url template",info:"Enter a url to link the labels with external sources. Use __LABEL__ as placeholder.",type:"text",init:"",placeholder:"http://someurl.com?id=__LABEL__"}}})}),define("plugin/charts/others/heatmap_cluster/config",["plugin/charts/others/heatmap/config"],function(e){return $.extend(!0,{},e,{title:"Clustered Heatmap",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"heatmap",keywords:"small medium large"})}),define("plugin/charts/types",["plugin/charts/nvd3/bar/config","plugin/charts/nvd3/bar_stacked/config","plugin/charts/nvd3/bar_horizontal/config","plugin/charts/nvd3/bar_horizontal_stacked/config","plugin/charts/nvd3/line_focus/config","plugin/charts/nvd3/pie/config","plugin/charts/nvd3/stackedarea_full/config","plugin/charts/nvd3/stackedarea_stream/config","plugin/charts/nvd3/histogram/config","plugin/charts/nvd3/line/config","plugin/charts/nvd3/scatter/config","plugin/charts/nvd3/stackedarea/config","plugin/charts/jqplot/bar/config","plugin/charts/jqplot/line/config","plugin/charts/jqplot/scatter/config","plugin/charts/jqplot/boxplot/config","plugin/charts/jqplot/histogram_discrete/config","plugin/charts/others/heatmap/config","plugin/charts/others/heatmap_cluster/config"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p,d,v,m,g,y){return Backbone.Model.extend({defaults:{nvd3_bar:e,nvd3_bar_stacked:t,nvd3_bar_horizontal:n,nvd3_bar_horizontal_stacked:r,nvd3_line_focus:i,nvd3_stackedarea:c,nvd3_stackedarea_full:o,nvd3_stackedarea_stream:u,nvd3_pie:s,nvd3_line:f,nvd3_scatter:l,nvd3_histogram:a,jqplot_bar:h,jqplot_histogram_discrete:m,jqplot_line:p,jqplot_scatter:d,jqplot_boxplot:v,others_heatmap:g,others_heatmap_cluster:y}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/library/deferred","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new l,this.types=new h,this.chart=new c,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.deferred=new u,this.viewer_view=new a(this),this.editor_view=new f(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el);if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},chartPath:function(e){var t=e.split(/_(.+)/);return t.length>=2?t[0]+"/"+t[1]:(console.debug("FAILED App:chartPath() - Invalid format: "+e),undefined)}})});
\ No newline at end of file
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
@@ -1,9 +1,10 @@
// dependencies
define(['plugin/charts/jqplot/common/plot-config', 'plugin/charts/tools'], function(configmaker, Tools) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This is the common wrapper for jqplot based visualizations.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// get parameters
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
@@ -1,9 +1,10 @@
// dependencies
define(['plugin/charts/tools'], function(Tools) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This is the common wrapper for nvd3 based visualizations.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// get parameters
@@ -97,6 +98,7 @@
}
});
+ // return
return true;
},
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
--- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
+++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
@@ -28,7 +28,7 @@
chart.state('ok', 'Pie chart has been drawn.');
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
}
// request data
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/charts/tools.js
--- a/config/plugins/visualizations/charts/static/charts/tools.js
+++ b/config/plugins/visualizations/charts/static/charts/tools.js
@@ -2,8 +2,7 @@
define(['utils/utils'], function(Utils) {
// render
-function panelHelper (app, options)
-{
+function panelHelper (app, options) {
// link this
var self = this;
@@ -42,7 +41,7 @@
}
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
} catch (err) {
// log
console.debug('FAILED: Tools::panelHelper() - ' + err);
@@ -51,7 +50,7 @@
chart.state('failed', err);
// unregister process
- chart.deferred.done(process_id);
+ app.deferred.done(process_id);
}
};
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/datasets.js
--- a/config/plugins/visualizations/charts/static/library/datasets.js
+++ b/config/plugins/visualizations/charts/static/library/datasets.js
@@ -1,7 +1,9 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// widget
+/**
+ * This class handles, formats and caches datasets.
+ */
return Backbone.Collection.extend(
{
// list of datasets
@@ -11,8 +13,7 @@
cache: {},
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link app
this.app = app;
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/deferred.js
--- a/config/plugins/visualizations/charts/static/library/deferred.js
+++ b/config/plugins/visualizations/charts/static/library/deferred.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// deferred process handler
-return Backbone.Model.extend(
-{
+/**
+ * This class handles deferred processes. It makes it easy to handle multiple and overlapping sets of deferred processes.
+ */
+return Backbone.Model.extend({
// queue
queue: [],
@@ -14,8 +15,7 @@
counter: 0,
// initialize
- initialize: function()
- {
+ initialize: function(){
// loop through queue and check states
this.on('refresh', function() {
for (var index in this.queue) {
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// widget
-return Backbone.Model.extend(
-{
+/**
+ * This class handles job submissions to the charts tool.
+ */
+return Backbone.Model.extend({
// initialize
initialize: function(app, options) {
// link app
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/screenshot.js
--- a/config/plugins/visualizations/charts/static/library/screenshot.js
+++ b/config/plugins/visualizations/charts/static/library/screenshot.js
@@ -1,4 +1,6 @@
-// dependencies
+/**
+ * This class enables users to export/download a chart as PNG, SVG or PDF.
+ */
define(["libs/underscore"], function(_) {
//
// PNG export
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/storage.js
--- a/config/plugins/visualizations/charts/static/library/storage.js
+++ b/config/plugins/visualizations/charts/static/library/storage.js
@@ -1,9 +1,10 @@
// dependencies
-define(['utils/utils', 'plugin/models/chart', 'plugin/models/group'], function(Utils, Chart, Group) {
+define(['utils/utils', 'plugin/models/chart', 'plugin/models/group', 'mvc/visualization/visualization-model'], function(Utils, Chart, Group) {
-// collection
-return Backbone.Model.extend(
-{
+/**
+ * This class saves and loads a chart through the api.
+ */
+return Backbone.Model.extend({
// viz model
vis: null,
@@ -44,7 +45,6 @@
// pack and save nested chart model
save: function() {
-
// link chart
var chart = this.app.chart;
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/ui-button-menu.js
--- a/config/plugins/visualizations/charts/static/library/ui-button-menu.js
+++ b/config/plugins/visualizations/charts/static/library/ui-button-menu.js
@@ -1,8 +1,9 @@
// dependencies
-define(['utils/utils'],
- function(Utils) {
+define(['utils/utils'], function(Utils) {
-// return button menu
+/**
+ * This class creates a button with dropdown menu. It extends the functionality of the Ui.ButtonIcon class.
+ */
return Backbone.View.extend({
// main options
optionsDefault: {
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/ui-select.js
--- a/config/plugins/visualizations/charts/static/library/ui-select.js
+++ b/config/plugins/visualizations/charts/static/library/ui-select.js
@@ -1,9 +1,10 @@
// dependencies
define(['utils/utils'], function(Utils) {
-// plugin
-var View = Backbone.View.extend(
-{
+/**
+ * This class creates/wraps a default html select field as backbone class.
+ */
+var View = Backbone.View.extend({
// options
optionsDefault : {
id : '',
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/ui-table-form.js
--- a/config/plugins/visualizations/charts/static/library/ui-table-form.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js
@@ -2,9 +2,10 @@
define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
function(Table, Ui, Utils) {
-// widget
-var View = Backbone.View.extend(
-{
+/**
+ * This class takes a dictionary as input an creates an input form. It uses the Ui.Table element to organize and format the form elements.
+ */
+var View = Backbone.View.extend({
// options
optionsDefault: {
title : '',
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/ui-table.js
--- a/config/plugins/visualizations/charts/static/library/ui-table.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table.js
@@ -1,7 +1,10 @@
+// dependencies
define(['utils/utils'], function(Utils) {
-var View = Backbone.View.extend(
-{
+/**
+ * This class creates a ui table element.
+ */
+var View = Backbone.View.extend({
// current row
row: null,
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/library/ui.js
--- a/config/plugins/visualizations/charts/static/library/ui.js
+++ b/config/plugins/visualizations/charts/static/library/ui.js
@@ -2,9 +2,12 @@
define(['utils/utils', 'plugin/library/ui-select', 'plugin/library/ui-button-menu', 'mvc/ui/ui-modal'],
function(Utils, Select, ButtonMenu, Modal) {
+/**
+ * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.
+ */
+
// plugin
-var Image = Backbone.View.extend(
-{
+var Image = Backbone.View.extend({
// options
optionsDefault: {
url : '',
@@ -27,8 +30,7 @@
});
// plugin
-var Label = Backbone.View.extend(
-{
+var Label = Backbone.View.extend({
// options
optionsDefault: {
title : '',
@@ -61,8 +63,7 @@
});
// plugin
-var Icon = Backbone.View.extend(
-{
+var Icon = Backbone.View.extend({
// options
optionsDefault: {
float : 'right',
@@ -95,8 +96,7 @@
});
// plugin
-var Button = Backbone.View.extend(
-{
+var Button = Backbone.View.extend({
// options
optionsDefault: {
id : null,
@@ -134,8 +134,7 @@
});
// plugin
-var ButtonIcon = Backbone.View.extend(
-{
+var ButtonIcon = Backbone.View.extend({
// options
optionsDefault: {
id : null,
@@ -188,8 +187,7 @@
});
// plugin
-var Anchor = Backbone.View.extend(
-{
+var Anchor = Backbone.View.extend({
// options
optionsDefault: {
title : '',
@@ -215,8 +213,7 @@
});
// plugin
-var Message = Backbone.View.extend(
-{
+var Message = Backbone.View.extend({
// options
optionsDefault: {
message : '',
@@ -268,8 +265,7 @@
});
// plugin
-var Searchbox = Backbone.View.extend(
-{
+var Searchbox = Backbone.View.extend({
// options
optionsDefault: {
onclick : null,
@@ -308,8 +304,7 @@
});
// plugin
-var Input = Backbone.View.extend(
-{
+var Input = Backbone.View.extend({
// options
optionsDefault: {
value : '',
@@ -362,8 +357,7 @@
});
// plugin
-var Textarea = Backbone.View.extend(
-{
+var Textarea = Backbone.View.extend({
// options
optionsDefault: {
value : '',
@@ -416,8 +410,7 @@
});
// plugin
-var RadioButton = Backbone.View.extend(
-{
+var RadioButton = Backbone.View.extend({
// options
optionsDefault: {
value : '',
@@ -503,19 +496,19 @@
// return
return {
- Label : Label,
- Button : Button,
- Icon : Icon,
- ButtonIcon : ButtonIcon,
- Input : Input,
- Anchor : Anchor,
- Message : Message,
- Searchbox : Searchbox,
- Select : Select,
- ButtonMenu : ButtonMenu,
- Modal: Modal,
- Textarea: Textarea,
- Image: Image,
- RadioButton: RadioButton
+ Anchor : Anchor,
+ Button : Button,
+ ButtonIcon : ButtonIcon,
+ ButtonMenu : ButtonMenu,
+ Icon : Icon,
+ Image : Image,
+ Input : Input,
+ Label : Label,
+ Message : Message,
+ Modal : Modal,
+ RadioButton : RadioButton,
+ Searchbox : Searchbox,
+ Select : Select,
+ Textarea : Textarea
}
});
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/models/chart.js
--- a/config/plugins/visualizations/charts/static/models/chart.js
+++ b/config/plugins/visualizations/charts/static/models/chart.js
@@ -1,11 +1,8 @@
// dependencies
-define(['plugin/models/groups', 'plugin/library/deferred', 'mvc/visualization/visualization-model'],
- function(Groups, Deferred) {
-
+define(['plugin/models/groups'], function(Groups) {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// defaults
defaults : {
id : null,
@@ -23,7 +20,6 @@
initialize: function(options) {
this.groups = new Groups();
this.settings = new Backbone.Model();
- this.deferred = new Deferred();
},
// reset
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -2,8 +2,7 @@
define([], function() {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// options
defaults : {
query_limit : 500,
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/models/group.js
--- a/config/plugins/visualizations/charts/static/models/group.js
+++ b/config/plugins/visualizations/charts/static/models/group.js
@@ -2,8 +2,7 @@
define([], function() {
// model
-return Backbone.Model.extend(
-{
+return Backbone.Model.extend({
// options
defaults : {
key : 'Data label',
@@ -11,8 +10,7 @@
},
// reset
- reset: function()
- {
+ reset: function(){
this.clear({silent: true}).set(this.defaults);
this.trigger('reset', this);
}
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/models/groups.js
--- a/config/plugins/visualizations/charts/static/models/groups.js
+++ b/config/plugins/visualizations/charts/static/models/groups.js
@@ -2,8 +2,7 @@
define(['plugin/models/group'], function(Group) {
// collection
-return Backbone.Collection.extend(
-{
+return Backbone.Collection.extend({
model: Group
});
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/views/editor.js
--- a/config/plugins/visualizations/charts/static/views/editor.js
+++ b/config/plugins/visualizations/charts/static/views/editor.js
@@ -4,18 +4,13 @@
'plugin/views/group', 'plugin/views/settings', 'plugin/views/types'],
function(Tabs, Ui, Portlet, Utils, Chart, Group, GroupView, SettingsView, TypesView) {
-// widget
-return Backbone.View.extend(
-{
- // defaults options
- optionsDefault: {
- header : true,
- content : 'No content available.'
- },
-
+/**
+ * The charts editor holds the tabs for selecting chart types, chart configuration
+ * and data group selections.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link this
var self = this;
@@ -25,9 +20,6 @@
// get current chart object
this.chart = this.app.chart;
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
// message element
this.message = new Ui.Message();
@@ -49,7 +41,7 @@
tooltip : 'Return to Viewer',
title : 'Cancel',
onclick : function() {
- // show viewport
+ // show viewer/viewport
self.app.go('viewer');
// reset chart
@@ -200,7 +192,7 @@
this.title.value(title);
},
- // update
+ // refresh group
_refreshGroupKey: function() {
var self = this;
var counter = 0;
@@ -213,7 +205,7 @@
});
},
- // new group
+ // add group model
_addGroupModel: function() {
var group = new Group({
id : Utils.uuid()
@@ -222,7 +214,7 @@
return group;
},
- // add group
+ // add group tab
_addGroup: function(group) {
// link this
var self = this;
@@ -319,7 +311,7 @@
// wait until chart is ready
var self = this;
- this.chart.deferred.execute(function() {
+ this.app.deferred.execute(function() {
// save
self.app.storage.save();
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -2,9 +2,10 @@
define(['plugin/library/ui-table', 'plugin/library/ui', 'utils/utils'],
function(Table, Ui, Utils) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the data group selection fields.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// link app
@@ -59,7 +60,7 @@
this._refreshGroup();
},
- // update dataset
+ // update group selection table
_refreshTable: function() {
// identify datasets
var dataset_id = this.chart.get('dataset_id');
@@ -116,7 +117,7 @@
this.chart.state('wait', 'Loading metadata...');
// register process
- var process_id = this.chart.deferred.register();
+ var process_id = this.app.deferred.register();
// request dictionary
var request_dictionary = {
@@ -131,7 +132,7 @@
self.chart.state('ok', 'Metadata initialized...');
// unregister
- self.chart.deferred.done(process_id);
+ self.app.deferred.done(process_id);
}
};
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/views/settings.js
--- a/config/plugins/visualizations/charts/static/views/settings.js
+++ b/config/plugins/visualizations/charts/static/views/settings.js
@@ -2,9 +2,10 @@
define(['plugin/library/ui', 'plugin/library/ui-table-form', 'utils/utils'],
function(Ui, TableForm, Utils) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart configuration form.
+ */
+return Backbone.View.extend({
// initialize
initialize: function(app, options) {
// link app
@@ -36,7 +37,7 @@
// get settings
var chart_definition = this.chart.definition;
- // check if dataset is available
+ // check if chart definition is available
if (!chart_definition) {
return;
}
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/views/types.js
--- a/config/plugins/visualizations/charts/static/views/types.js
+++ b/config/plugins/visualizations/charts/static/views/types.js
@@ -1,7 +1,10 @@
+// dependencies
define(['utils/utils', 'plugin/library/ui'], function(Utils, Ui) {
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart type selection grid.
+ */
+return Backbone.View.extend({
// defaults options
optionsDefault: {
onchange : null,
@@ -16,7 +19,6 @@
// initialize
initialize : function(app, options) {
-
// link this
var self = this;
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/views/viewer.js
--- a/config/plugins/visualizations/charts/static/views/viewer.js
+++ b/config/plugins/visualizations/charts/static/views/viewer.js
@@ -1,14 +1,14 @@
// dependencies
define(['utils/utils', 'plugin/library/ui', 'mvc/ui/ui-portlet',
- 'plugin/models/group', 'plugin/views/viewport', 'plugin/library/screenshot'],
- function(Utils, Ui, Portlet, Group, ViewportView, Screenshot) {
+ 'plugin/views/viewport', 'plugin/library/screenshot'],
+ function(Utils, Ui, Portlet, ViewportView, Screenshot) {
-// widget
-return Backbone.View.extend(
-{
+/**
+ * This class renders the chart viewer which encapsulates the chart viewport.
+ */
+return Backbone.View.extend({
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options){
// link app
this.app = app;
@@ -152,7 +152,7 @@
// wait for chart to be ready
_wait: function(chart, callback) {
// get chart
- if (chart.deferred.ready()) {
+ if (this.app.deferred.ready()) {
callback();
} else {
this.message.update({message: 'Your chart is currently being processed. Please wait and try again.'});
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -2,7 +2,11 @@
define(['mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils'],
function(Portlet, Ui, Utils) {
-// widget
+/**
+ * The viewport creates and manages the dom elements used by the visualization plugins to draw the chart.
+ * Additionally, this class creates default request strings and request dictionaries parsed to the visualization plugins.
+ * This is the last class of the charts core classes before handing control over to the visualization plugins.
+ */
return Backbone.View.extend({
// list of canvas elements
@@ -26,7 +30,7 @@
// use full screen for viewer
this._fullscreen(this.$el, 100);
- // create canvas element
+ // create container element
this._createContainer('div');
// events
@@ -126,7 +130,7 @@
var self = this;
// register process
- var process_id = chart.deferred.register();
+ var process_id = this.app.deferred.register();
// identify chart type
var chart_type = chart.get('type');
@@ -171,7 +175,7 @@
});
},
function() {
- chart.deferred.done(process_id);
+ this.app.deferred.done(process_id);
}
);
} else {
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -38,7 +38,7 @@
boto = 2.27.0
decorator = 3.1.2
docutils = 0.7
-drmaa = 0.6
+drmaa = 0.7.6
elementtree = 1.2.6_20050316
Fabric = 1.7.0
GeneTrack = 2.0.0_beta_1
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf 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
@@ -148,6 +154,11 @@
are available to all jobs and $job_directory is also available for
Pulsar jobs.
-->
+ <!-- One can run docker using volumes-from tag by setting the following
+ parameter. For more information on volumes-from check out the following
+ docker tutorial. https://docs.docker.com/userguide/dockervolumes/
+ -->
+ <!-- <param id="docker_volumes_from">parent_container_name</param> --><!-- Control memory allocatable by docker container with following option:
--><!-- <param id="docker_memory">24G</param> -->
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -12,7 +12,6 @@
from galaxy.visualization.data_providers.registry import DataProviderRegistry
from galaxy.visualization.registry import VisualizationsRegistry
from galaxy.tools.imp_exp import load_history_imp_exp_tools
-from galaxy.tools.genome_index import load_genome_index_tools
from galaxy.sample_tracking import external_service_types
from galaxy.openid.providers import OpenIDProviders
from galaxy.tools.data_manager.manager import DataManagers
@@ -93,8 +92,6 @@
self.datatypes_registry.load_external_metadata_tool( self.toolbox )
# Load history import/export tools.
load_history_imp_exp_tools( self.toolbox )
- # Load genome indexer tool.
- load_genome_index_tools( self.toolbox )
# visualizations registry: associates resources with visualizations, controls how to render
self.visualizations_registry = None
if self.config.visualization_plugins_directory:
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -126,10 +126,21 @@
rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy )
return rval
- def from_JSON_dict( self, filename, path_rewriter=None ):
+ def from_JSON_dict( self, filename=None, path_rewriter=None, json_dict=None ):
dataset = self.parent
- log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
- JSONified_dict = json.load( open( filename ) )
+ if filename is not None:
+ log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ JSONified_dict = json.load( open( filename ) )
+ elif json_dict is not None:
+ log.debug( 'loading metadata from dict for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ if isinstance( json_dict, basestring ):
+ JSONified_dict = json.loads( json_dict )
+ elif isinstance( json_dict, dict ):
+ JSONified_dict = json_dict
+ else:
+ raise ValueError( "json_dict must be either a dictionary or a string, got %s." % ( type( json_dict ) ) )
+ else:
+ raise ValueError( "You must provide either a filename or a json_dict" )
for name, spec in self.spec.items():
if name in JSONified_dict:
from_ext_kwds = {}
@@ -143,13 +154,15 @@
#metadata associated with our dataset, we'll delete it from our dataset's metadata dict
del dataset._metadata[ name ]
- def to_JSON_dict( self, filename ):
+ def to_JSON_dict( self, filename=None ):
#galaxy.model.customtypes.json_encoder.encode()
meta_dict = {}
dataset_meta_dict = self.parent._metadata
for name, spec in self.spec.items():
if name in dataset_meta_dict:
meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] )
+ if filename is None:
+ return json.dumps( meta_dict )
json.dump( meta_dict, open( filename, 'wb+' ) )
def __getstate__( self ):
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1181,17 +1181,21 @@
out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
out_data.update( [ ( da.name, da.dataset ) for da in job.output_library_datasets ] )
+ input_ext = 'data'
+ for _, data in inp_data.items():
+ # For loop odd, but sort simulating behavior in galaxy.tools.actions
+ if not data:
+ continue
+ input_ext = data.ext
+
param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows
param_dict = self.tool.params_from_strings( param_dict, self.app )
# Check for and move associated_files
self.tool.collect_associated_files(out_data, self.working_directory)
- gitd = self.sa_session.query( model.GenomeIndexToolData ).filter_by( job=job ).first()
- if gitd:
- self.tool.collect_associated_files({'': gitd}, self.working_directory)
# Create generated output children and primary datasets and add to param_dict
collected_datasets = {
'children': self.tool.collect_child_datasets(out_data, self.working_directory),
- 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory)
+ 'primary': self.tool.collect_primary_datasets(out_data, self.working_directory, input_ext)
}
param_dict.update({'__collected_datasets__': collected_datasets})
# Certain tools require tasks to be completed after job execution
@@ -1241,7 +1245,6 @@
self.external_output_metadata.cleanup_external_metadata( self.sa_session )
galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session )
galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.app, self.job_id ).cleanup_after_job()
- galaxy.tools.genome_index.GenomeIndexToolWrapper( self.job_id ).postprocessing( self.sa_session, self.app )
if delete_files:
self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id))
except:
@@ -1344,10 +1347,8 @@
dataset_path_rewriter = self.dataset_path_rewriter
job = self.get_job()
- # Job output datasets are combination of history, library, jeha and gitd datasets.
+ # Job output datasets are combination of history, library, and jeha datasets.
special = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first()
- if not special:
- special = self.sa_session.query( model.GenomeIndexToolData ).filter_by( job=job ).first()
false_path = None
results = []
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/jobs/deferred/genome_index.py
--- a/lib/galaxy/jobs/deferred/genome_index.py
+++ /dev/null
@@ -1,43 +0,0 @@
-"""
-Module for managing genome transfer jobs.
-"""
-from __future__ import with_statement
-
-import logging, shutil, gzip, bz2, zipfile, tempfile, tarfile, sys, os
-
-from galaxy import eggs
-from sqlalchemy import and_
-from data_transfer import *
-
-log = logging.getLogger( __name__ )
-
-__all__ = [ 'GenomeIndexPlugin' ]
-
-class GenomeIndexPlugin( DataTransfer ):
-
- def __init__( self, app ):
- super( GenomeIndexPlugin, self ).__init__( app )
- self.app = app
- self.tool = app.toolbox.tools_by_id['__GENOME_INDEX__']
- self.sa_session = app.model.context.current
-
- def create_job( self, trans, path, indexes, dbkey, intname ):
- params = dict( user=trans.user.id, path=path, indexes=indexes, dbkey=dbkey, intname=intname )
- deferred = trans.app.model.DeferredJob( state = self.app.model.DeferredJob.states.NEW, plugin = 'GenomeIndexPlugin', params = params )
- self.sa_session.add( deferred )
- self.sa_session.flush()
- log.debug( 'Job created, id %d' % deferred.id )
- return deferred.id
-
- def check_job( self, job ):
- log.debug( 'Job check' )
- return 'ready'
-
- def run_job( self, job ):
- incoming = dict( path=os.path.abspath( job.params[ 'path' ] ), indexer=job.params[ 'indexes' ][0], user=job.params[ 'user' ] )
- indexjob = self.tool.execute( self, set_output_hid=False, history=None, incoming=incoming, transfer=None, deferred=job )
- job.params[ 'indexjob' ] = indexjob[0].id
- job.state = self.app.model.DeferredJob.states.RUNNING
- self.sa_session.add( job )
- self.sa_session.flush()
- return self.app.model.DeferredJob.states.RUNNING
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/jobs/deferred/genome_transfer.py
--- a/lib/galaxy/jobs/deferred/genome_transfer.py
+++ /dev/null
@@ -1,250 +0,0 @@
-"""
-Module for managing genome transfer jobs.
-"""
-from __future__ import with_statement
-
-import logging, shutil, gzip, bz2, zipfile, tempfile, tarfile, sys
-
-from galaxy import eggs
-from sqlalchemy import and_
-
-from galaxy.util.odict import odict
-from galaxy.workflow.modules import module_factory
-from galaxy.jobs.actions.post import ActionBox
-
-from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter
-from galaxy.tools.data import ToolDataTableManager
-
-from galaxy.datatypes.checkers import *
-from galaxy.datatypes.sequence import Fasta
-from data_transfer import *
-
-log = logging.getLogger( __name__ )
-
-__all__ = [ 'GenomeTransferPlugin' ]
-
-class GenomeTransferPlugin( DataTransfer ):
-
- locations = {}
-
- def __init__( self, app ):
- super( GenomeTransferPlugin, self ).__init__( app )
- self.app = app
- self.tool = app.toolbox.tools_by_id['__GENOME_INDEX__']
- self.sa_session = app.model.context.current
- tdtman = ToolDataTableManager( app.config.tool_data_path )
- xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path )
- for node in xmltree:
- table = node.get('name')
- location = node.findall('file')[0].get('path')
- self.locations[table] = location
-
- def create_job( self, trans, url, dbkey, intname, indexes ):
- job = trans.app.transfer_manager.new( protocol='http', url=url )
- params = dict( user=trans.user.id, transfer_job_id=job.id, protocol='http', type='init_transfer', url=url, dbkey=dbkey, indexes=indexes, intname=intname, liftover=None )
- deferred = trans.app.model.DeferredJob( state = self.app.model.DeferredJob.states.NEW, plugin = 'GenomeTransferPlugin', params = params )
- self.sa_session.add( deferred )
- self.sa_session.flush()
- return deferred.id
-
- def check_job( self, job ):
- if job.params['type'] == 'init_transfer':
- if not hasattr(job, 'transfer_job'):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- if job.transfer_job.state == 'done':
- transfer = job.transfer_job
- transfer.state = 'downloaded'
- job.params['type'] = 'extract_transfer'
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- self.sa_session.flush()
- return self.job_states.READY
- elif job.transfer_job.state == 'running':
- return self.job_states.WAIT
- elif job.transfer_job.state == 'new':
- assert job.params[ 'protocol' ] in [ 'http', 'ftp', 'https' ], 'Unknown protocol %s' % job.params[ 'protocol' ]
- self.app.transfer_manager.run( job.transfer_job )
- self.sa_session.add( job.transfer_job )
- self.sa_session.flush()
- return self.job_states.WAIT
- else:
- log.error( "An error occurred while downloading from %s" % job.params[ 'url' ] )
- return self.job_states.INVALID
- elif job.params[ 'type' ] == 'extract_transfer':
- return self.job_states.READY
-
- def get_job_status( self, jobid ):
- job = self.sa_session.query( self.app.model.DeferredJob ).get( int( jobid ) )
- if 'transfer_job_id' in job.params:
- if not hasattr( job, 'transfer_job' ):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- return job
-
- def run_job( self, job ):
- params = job.params
- dbkey = params[ 'dbkey' ]
- if not hasattr( job, 'transfer_job' ):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- transfer = job.transfer_job
- if params[ 'type' ] == 'extract_transfer':
- CHUNK_SIZE = 2**20
- destpath = os.path.join( self.app.config.get( 'genome_data_path', 'tool-data/genome' ), job.params[ 'dbkey' ], 'seq' )
- destfile = '%s.fa' % job.params[ 'dbkey' ]
- destfilepath = os.path.join( destpath, destfile )
- tmpprefix = '%s_%s_download_unzip_' % ( job.params['dbkey'], job.params[ 'transfer_job_id' ] )
- tmppath = os.path.dirname( os.path.abspath( transfer.path ) )
- if not os.path.exists( destpath ):
- os.makedirs( destpath )
- protocol = job.params[ 'protocol' ]
- data_type = self._check_compress( transfer.path )
- if data_type is None:
- sniffer = Fasta()
- if sniffer.sniff( transfer.path ):
- data_type = 'fasta'
- fd, uncompressed = tempfile.mkstemp( prefix=tmpprefix, dir=tmppath, text=False )
- if data_type in [ 'tar.gzip', 'tar.bzip' ]:
- fp = open( transfer.path, 'r' )
- tar = tarfile.open( mode = 'r:*', bufsize = CHUNK_SIZE, fileobj = fp )
- files = tar.getmembers()
- for filename in files:
- z = tar.extractfile(filename)
- while 1:
- try:
- chunk = z.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.write( fd, '\n' )
- os.close( fd )
- tar.close()
- fp.close()
- elif data_type == 'gzip':
- compressed = gzip.open( transfer.path, mode = 'rb' )
- while 1:
- try:
- chunk = compressed.read( CHUNK_SIZE )
- except IOError:
- compressed.close()
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- compressed.close()
- elif data_type == 'bzip':
- compressed = bz2.BZ2File( transfer.path, mode = 'r' )
- while 1:
- try:
- chunk = compressed.read( CHUNK_SIZE )
- except IOError:
- compressed.close()
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- compressed.close()
- elif data_type == 'zip':
- uncompressed_name = None
- unzipped = False
- z = zipfile.ZipFile( transfer.path )
- z.debug = 3
- for name in z.namelist():
- if name.endswith('/'):
- continue
- zipped_file = z.open( name )
- while 1:
- try:
- chunk = zipped_file.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- log.error( 'Problem decompressing zipped data' )
- return self.app.model.DeferredJob.states.INVALID
- if not chunk:
- break
- os.write( fd, chunk )
- zipped_file.close()
- os.close( fd )
- z.close()
- elif data_type == 'fasta':
- uncompressed = transfer.path
- else:
- job.state = self.app.model.DeferredJob.states.INVALID
- log.error( "Unrecognized compression format for file %s." % transfer.path )
- self.sa_session.add( job )
- self.sa_session.flush()
- return
- shutil.move( uncompressed, destfilepath )
- if os.path.exists( transfer.path ):
- os.remove( transfer.path )
- os.chmod( destfilepath, 0644 )
- fastaline = '\t'.join( [ dbkey, dbkey, params[ 'intname' ], os.path.abspath( destfilepath ) ] )
- self._add_line( 'all_fasta', fastaline )
- if params[ 'indexes' ] is not None:
- job.state = self.app.model.DeferredJob.states.WAITING
- job.params[ 'indexjobs' ] = []
- else:
- job.state = self.app.model.DeferredJob.states.OK
- job.params[ 'type' ] = 'finish_transfer'
- transfer.path = os.path.abspath(destfilepath)
- transfer.state = 'done'
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- if transfer.state == 'done':
- if params[ 'indexes' ] is not None:
- for indexer in params[ 'indexes' ]:
- incoming = dict(indexer=indexer, dbkey=params[ 'dbkey' ], intname=params[ 'intname' ], path=transfer.path, user=params['user'] )
- deferred = self.tool.execute( self, set_output_hid=False, history=None, incoming=incoming, transfer=transfer, deferred=job )
- job.params[ 'indexjobs' ].append( deferred[0].id )
- else:
- job.state = self.app.model.DeferredJob.states.OK
- self.sa_session.add( job )
- self.sa_session.flush()
- return self.app.model.DeferredJob.states.OK
-
- def _check_compress( self, filepath ):
- retval = ''
- if tarfile.is_tarfile( filepath ):
- retval = 'tar.'
- if check_zip( filepath ):
- return 'zip'
- is_bzipped, is_valid = check_bz2( filepath )
- if is_bzipped and is_valid:
- return retval + 'bzip'
- is_gzipped, is_valid = check_gzip( filepath )
- if is_gzipped and is_valid:
- return retval + 'gzip'
- return None
-
- def _add_line( self, locfile, newline ):
- filepath = self.locations[ locfile ]
- origlines = []
- output = []
- comments = []
- with open( filepath, 'r' ) as destfile:
- for line in destfile:
- if line.startswith( '#' ):
- comments.append( line.strip() )
- else:
- origlines.append( line.strip() )
- if newline not in origlines:
- origlines.append( newline )
- output.extend( comments )
- origlines.sort()
- output.extend( origlines )
- with open( filepath, 'w+' ) as destfile:
- destfile.write( '\n'.join( output ) )
-
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/jobs/deferred/liftover_transfer.py
--- a/lib/galaxy/jobs/deferred/liftover_transfer.py
+++ /dev/null
@@ -1,158 +0,0 @@
-"""
-Module for managing genome transfer jobs.
-"""
-from __future__ import with_statement
-
-import logging, shutil, gzip, tempfile, sys
-
-from galaxy import eggs
-from sqlalchemy import and_
-
-from galaxy.util.odict import odict
-from galaxy.workflow.modules import module_factory
-from galaxy.jobs.actions.post import ActionBox
-
-from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter
-
-from galaxy.datatypes.checkers import *
-
-from data_transfer import *
-
-log = logging.getLogger( __name__ )
-
-__all__ = [ 'LiftOverTransferPlugin' ]
-
-class LiftOverTransferPlugin( DataTransfer ):
-
- locations = {}
-
- def __init__( self, app ):
- super( LiftOverTransferPlugin, self ).__init__( app )
- self.app = app
- self.sa_session = app.model.context.current
-
- def create_job( self, trans, url, dbkey, from_genome, to_genome, destfile, parentjob ):
- job = trans.app.transfer_manager.new( protocol='http', url=url )
- params = dict( user=trans.user.id, transfer_job_id=job.id, protocol='http',
- type='init_transfer', dbkey=dbkey, from_genome=from_genome,
- to_genome=to_genome, destfile=destfile, parentjob=parentjob )
- deferred = trans.app.model.DeferredJob( state = self.app.model.DeferredJob.states.NEW, plugin = 'LiftOverTransferPlugin', params = params )
- self.sa_session.add( deferred )
- self.sa_session.flush()
- return deferred.id
-
- def check_job( self, job ):
- if job.params['type'] == 'init_transfer':
- if not hasattr(job, 'transfer_job'):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- if job.transfer_job.state == 'done':
- transfer = job.transfer_job
- transfer.state = 'downloaded'
- job.params['type'] = 'extract_transfer'
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- self.sa_session.flush()
- return self.job_states.READY
- elif job.transfer_job.state == 'running':
- return self.job_states.WAIT
- elif job.transfer_job.state == 'new':
- assert job.params[ 'protocol' ] in [ 'http', 'ftp', 'https' ], 'Unknown protocol %s' % job.params[ 'protocol' ]
- ready = True
- parent = self.sa_session.query( self.app.model.DeferredJob ).get( int( job.params[ 'parentjob' ] ) )
- if not hasattr( parent, 'transfer_job' ):
- parent.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( parent.params[ 'transfer_job_id' ] ) )
- if parent.transfer_job.state not in [ 'ok', 'error', 'done' ]:
- ready = False
- for lo_job in parent.params[ 'liftover' ]:
- liftoverjob = self.sa_session.query( self.app.model.TransferJob ).get( int( lo_job ) )
- if liftoverjob:
- if liftoverjob.state not in [ 'ok', 'error', 'new', 'done' ]:
- ready = False
- if ready:
- self.app.transfer_manager.run( job.transfer_job )
- self.sa_session.add( job.transfer_job )
- self.sa_session.flush()
- return self.job_states.WAIT
- else:
- log.error( "An error occurred while downloading from %s" % job.transfer_job.params[ 'url' ] )
- return self.job_states.INVALID
- elif job.params[ 'type' ] == 'extract_transfer':
- return self.job_states.READY
-
- def get_job_status( self, jobid ):
- job = self.sa_session.query( self.app.model.DeferredJob ).get( int( jobid ) )
- return job
-
- def run_job( self, job ):
- params = job.params
- dbkey = params[ 'dbkey' ]
- source = params[ 'from_genome' ]
- target = params[ 'to_genome' ]
- if not hasattr( job, 'transfer_job' ):
- job.transfer_job = self.sa_session.query( self.app.model.TransferJob ).get( int( job.params[ 'transfer_job_id' ] ) )
- else:
- self.sa_session.refresh( job.transfer_job )
- transfer = job.transfer_job
- if params[ 'type' ] == 'extract_transfer':
- CHUNK_SIZE = 2**20
- destpath = os.path.join( self.app.config.get( 'genome_data_path', 'tool-data/genome' ), source, 'liftOver' )
- if not os.path.exists( destpath ):
- os.makedirs( destpath )
- destfile = job.params[ 'destfile' ]
- destfilepath = os.path.join( destpath, destfile )
- tmpprefix = '%s_%s_download_unzip_' % ( job.params['dbkey'], job.params[ 'transfer_job_id' ] )
- tmppath = os.path.dirname( os.path.abspath( transfer.path ) )
- if not os.path.exists( destpath ):
- os.makedirs( destpath )
- fd, uncompressed = tempfile.mkstemp( prefix=tmpprefix, dir=tmppath, text=False )
- chain = gzip.open( transfer.path, 'rb' )
- while 1:
- try:
- chunk = chain.read( CHUNK_SIZE )
- except IOError:
- os.close( fd )
- log.error( 'Problem decompressing compressed data' )
- exit()
- if not chunk:
- break
- os.write( fd, chunk )
- os.close( fd )
- chain.close()
- # Replace the gzipped file with the decompressed file if it's safe to do so
- shutil.move( uncompressed, destfilepath )
- os.remove( transfer.path )
- os.chmod( destfilepath, 0644 )
- locline = '\t'.join( [ source, target, os.path.abspath( destfilepath ) ] )
- self._add_line( locline )
- job.state = self.app.model.DeferredJob.states.OK
- job.params[ 'type' ] = 'finish_transfer'
- transfer.path = os.path.abspath(destfilepath)
- transfer.state = 'done'
- parentjob = self.sa_session.query( self.app.model.DeferredJob ).get( int( job.params[ 'parentjob' ] ) )
- finished = True
- for i in parentjob.params[ 'liftover' ]:
- sibling = self.sa_session.query( self.app.model.DeferredJob ).get( int( i ) )
- if sibling.state not in [ 'done', 'ok', 'error' ]:
- finished = False
- if finished:
- parentjob.state = self.app.model.DeferredJob.states.OK
- self.sa_session.add( parentjob )
- self.sa_session.add( job )
- self.sa_session.add( transfer )
- self.sa_session.flush()
- return self.app.model.DeferredJob.states.OK
-
- def _add_line( self, newline ):
- filepath = 'tool-data/liftOver.loc'
- origlines = []
- with open( filepath, 'r' ) as destfile:
- for line in destfile:
- origlines.append( line.strip() )
- if newline not in origlines:
- origlines.append( newline )
- with open( filepath, 'w+' ) as destfile:
- destfile.write( '\n'.join( origlines ) )
-
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/jobs/mapper.py
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -83,7 +83,7 @@
if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names or "resource_params" in function_arg_names:
job = self.job_wrapper.get_job()
history = job.history
- user = history and history.user
+ user = job.user
user_email = user and str(user.email)
if "job" in function_arg_names:
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/jobs/metrics/formatting.py
--- a/lib/galaxy/jobs/metrics/formatting.py
+++ b/lib/galaxy/jobs/metrics/formatting.py
@@ -15,4 +15,4 @@
elif value < 3600:
return "%s minutes" % ( value / 60 )
else:
- return "%s days and %s minutes" % ( value / 3600, ( value % 3600 ) / 60 )
+ return "%s hours and %s minutes" % ( value / 3600, ( value % 3600 ) / 60 )
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/managers/__init__.py
--- a/lib/galaxy/managers/__init__.py
+++ b/lib/galaxy/managers/__init__.py
@@ -1,4 +1,33 @@
-""" 'Business logic' independent of web transactions/user context (trans)
-should be pushed into models - but logic that requires the context trans
-should be placed under this module.
"""
+Classes that manage resources (models, tools, etc.) by using the current
+Transaction.
+
+Encapsulates the intersection of trans (or trans.sa_session), models,
+and Controllers.
+
+Responsibilities:
+ model operations that involve the trans/sa_session (CRUD)
+ security:
+ ownership, accessibility
+ common aspect-oriented operations via new mixins:
+ sharable, annotatable, tagable, ratable
+
+Not responsible for:
+ encoding/decoding ids
+ any http gobblygook
+ formatting of returned data (always python structures)
+ formatting of raised errors
+
+The goal is to have Controllers only handle:
+ query-string/payload parsing and encoding/decoding ids
+ http
+ return formatting
+
+and:
+ control, improve namespacing in Controllers
+ DRY for Controller ops (define here - use in both UI/API Controllers)
+
+In other words, 'Business logic' independent of web transactions/user context
+(trans) should be pushed into models - but logic that requires the context
+trans should be placed under this module.
+"""
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/managers/base.py
--- /dev/null
+++ b/lib/galaxy/managers/base.py
@@ -0,0 +1,7 @@
+
+
+class ModelManager( object ):
+ pass
+
+class ModelSerializer( object ):
+ pass
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/managers/hdas.py
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -1,16 +1,35 @@
+"""
+Manager and Serializer for HDAs.
+
+HistoryDatasetAssociations (HDAs) are datasets contained or created in a
+history.
+"""
+
from galaxy import exceptions
-from ..managers import histories
+from galaxy.managers import base as manager_base
+from galaxy.managers import histories as history_manager
-class HDAManager( object ):
+import galaxy.web
+import galaxy.datatypes.metadata
+from galaxy import objectstore
+
+class HDAManager( manager_base.ModelManager ):
+ """
+ Interface/service object for interacting with HDAs.
+ """
def __init__( self ):
- self.histories_mgr = histories.HistoryManager()
+ """
+ Set up and initialize other managers needed by hdas.
+ """
+ self.histories_mgr = history_manager.HistoryManager()
def get( self, trans, unencoded_id, check_ownership=True, check_accessible=True ):
"""
+ Get an HDA by its unencoded db id, checking ownership (via its history)
+ or accessibility (via dataset shares/permissions).
"""
- # this is a replacement for UsesHistoryDatasetAssociationMixin because mixins are a bad soln/structure
hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( unencoded_id )
if hda is None:
raise exceptions.ObjectNotFound()
@@ -19,7 +38,8 @@
def secure( self, trans, hda, check_ownership=True, check_accessible=True ):
"""
- checks if (a) user owns item or (b) item is accessible to user.
+ check ownership (via its history) or accessibility (via dataset
+ shares/permissions).
"""
# all items are accessible to an admin
if trans.user and trans.user_is_admin():
@@ -31,12 +51,18 @@
return hda
def can_access_dataset( self, trans, hda ):
+ """
+ Use security agent to see if current user has access to dataset.
+ """
current_user_roles = trans.get_current_user_roles()
return trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset )
#TODO: is_owner, is_accessible
def check_ownership( self, trans, hda ):
+ """
+ Use history to see if current user owns HDA.
+ """
if not trans.user:
#if hda.history == trans.history:
# return hda
@@ -51,6 +77,9 @@
"HistoryDatasetAssociation is not owned by the current user", type='error' )
def check_accessible( self, trans, hda ):
+ """
+ Raise error if HDA is not accessible.
+ """
if trans.user and trans.user_is_admin():
return hda
# check for access of the containing history...
@@ -62,6 +91,151 @@
"HistoryDatasetAssociation is not accessible to the current user", type='error' )
def err_if_uploading( self, trans, hda ):
+ """
+ Raise error if HDA is still uploading.
+ """
if hda.state == trans.model.Dataset.states.UPLOAD:
raise exceptions.Conflict( "Please wait until this dataset finishes uploading" )
return hda
+
+ def get_hda_dict( self, trans, hda ):
+ """
+ Return full details of this HDA in dictionary form.
+ """
+ #precondition: the user's access to this hda has already been checked
+ #TODO:?? postcondition: all ids are encoded (is this really what we want at this level?)
+ expose_dataset_path = trans.user_is_admin() or trans.app.config.expose_dataset_path
+ hda_dict = hda.to_dict( view='element', expose_dataset_path=expose_dataset_path )
+ hda_dict[ 'api_type' ] = "file"
+
+ # Add additional attributes that depend on trans must be added here rather than at the model level.
+ can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+ can_access_hda = ( trans.user_is_admin() or can_access_hda )
+ if not can_access_hda:
+ return self.get_inaccessible_hda_dict( trans, hda )
+ hda_dict[ 'accessible' ] = True
+
+ #TODO: I'm unclear as to which access pattern is right
+ hda_dict[ 'annotation' ] = hda.get_item_annotation_str( trans.sa_session, hda.history.user, hda )
+ #annotation = getattr( hda, 'annotation', hda.get_item_annotation_str( trans.sa_session, trans.user, hda ) )
+
+ # ---- return here if deleted AND purged OR can't access
+ purged = ( hda.purged or hda.dataset.purged )
+ if ( hda.deleted and purged ):
+ #TODO: to_dict should really go AFTER this - only summary data
+ return trans.security.encode_dict_ids( hda_dict )
+
+ if expose_dataset_path:
+ try:
+ hda_dict[ 'file_name' ] = hda.file_name
+ except objectstore.ObjectNotFound:
+ log.exception( 'objectstore.ObjectNotFound, HDA %s.', hda.id )
+
+ hda_dict[ 'download_url' ] = galaxy.web.url_for( 'history_contents_display',
+ history_id = trans.security.encode_id( hda.history.id ),
+ history_content_id = trans.security.encode_id( hda.id ) )
+
+ # indeces, assoc. metadata files, etc.
+ meta_files = []
+ for meta_type in hda.metadata.spec.keys():
+ if isinstance( hda.metadata.spec[ meta_type ].param, galaxy.datatypes.metadata.FileParameter ):
+ meta_files.append( dict( file_type=meta_type ) )
+ if meta_files:
+ hda_dict[ 'meta_files' ] = meta_files
+
+ # currently, the viz reg is optional - handle on/off
+ if trans.app.visualizations_registry:
+ hda_dict[ 'visualizations' ] = trans.app.visualizations_registry.get_visualizations( trans, hda )
+ else:
+ hda_dict[ 'visualizations' ] = hda.get_visualizations()
+ #TODO: it may also be wiser to remove from here and add as API call that loads the visualizations
+ # when the visualizations button is clicked (instead of preloading/pre-checking)
+
+ # ---- return here if deleted
+ if hda.deleted and not purged:
+ return trans.security.encode_dict_ids( hda_dict )
+
+ return trans.security.encode_dict_ids( hda_dict )
+
+ def get_inaccessible_hda_dict( self, trans, hda ):
+ """
+ Return truncated serialization of HDA when inaccessible to user.
+ """
+ return trans.security.encode_dict_ids({
+ 'id' : hda.id,
+ 'history_id': hda.history.id,
+ 'hid' : hda.hid,
+ 'name' : hda.name,
+ 'state' : hda.state,
+ 'deleted' : hda.deleted,
+ 'visible' : hda.visible,
+ 'accessible': False
+ })
+
+ def get_hda_dict_with_error( self, trans, hda=None, history_id=None, id=None, error_msg='Error' ):
+ """
+ Return truncated serialization of HDA when error raised getting
+ details.
+ """
+ return trans.security.encode_dict_ids({
+ 'id' : hda.id if hda else id,
+ 'history_id': hda.history.id if hda else history_id,
+ 'hid' : hda.hid if hda else '(unknown)',
+ 'name' : hda.name if hda else '(unknown)',
+ 'error' : error_msg,
+ 'state' : trans.model.Dataset.states.NEW
+ })
+
+ def get_display_apps( self, trans, hda ):
+ """
+ Return dictionary containing new-style display app urls.
+ """
+ display_apps = []
+ for display_app in hda.get_display_applications( trans ).itervalues():
+
+ app_links = []
+ for link_app in display_app.links.itervalues():
+ app_links.append({
+ 'target': link_app.url.get( 'target_frame', '_blank' ),
+ 'href' : link_app.get_display_url( hda, trans ),
+ 'text' : gettext( link_app.name )
+ })
+ if app_links:
+ display_apps.append( dict( label=display_app.name, links=app_links ) )
+
+ return display_apps
+
+ def get_old_display_applications( self, trans, hda ):
+ """
+ Return dictionary containing old-style display app urls.
+ """
+ display_apps = []
+ if not trans.app.config.enable_old_display_applications:
+ return display_apps
+
+ for display_app in hda.datatype.get_display_types():
+ target_frame, display_links = hda.datatype.get_display_links( hda,
+ display_app, trans.app, trans.request.base )
+
+ if len( display_links ) > 0:
+ display_label = hda.datatype.get_display_label( display_app )
+
+ app_links = []
+ for display_name, display_link in display_links:
+ app_links.append({
+ 'target': target_frame,
+ 'href' : display_link,
+ 'text' : gettext( display_name )
+ })
+ if app_links:
+ display_apps.append( dict( label=display_label, links=app_links ) )
+
+ return display_apps
+
+
+# =============================================================================
+class HistorySerializer( manager_base.ModelSerializer ):
+ """
+ Interface/service object for serializing HDAs into dictionaries.
+ """
+ pass
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/managers/histories.py
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -1,9 +1,32 @@
+"""
+Manager and Serializer for histories.
+
+Histories are containers for datasets or dataset collections
+created (or copied) by users over the course of an analysis.
+"""
+
from galaxy import exceptions
from galaxy.model import orm
+from galaxy.managers import base as manager_base
+import galaxy.managers.hdas
-class HistoryManager( object ):
+import galaxy.web
+import galaxy.dataset_collections.util
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+# =============================================================================
+class HistoryManager( manager_base.ModelManager ):
+ """
+ Interface/service object for interacting with HDAs.
+ """
+
#TODO: all the following would be more useful if passed the user instead of defaulting to trans.user
+ def __init__( self, *args, **kwargs ):
+ super( HistoryManager, self ).__init__( *args, **kwargs )
def get( self, trans, unencoded_id, check_ownership=True, check_accessible=True, deleted=None ):
"""
@@ -44,7 +67,7 @@
def secure( self, trans, history, check_ownership=True, check_accessible=True ):
"""
- checks if (a) user owns item or (b) item is accessible to user.
+ Checks if (a) user owns item or (b) item is accessible to user.
"""
# all items are accessible to an admin
if trans.user and trans.user_is_admin():
@@ -56,15 +79,28 @@
return history
def is_current( self, trans, history ):
+ """
+ True if the given history is the user's current history.
+
+ Returns False if the session has no current history.
+ """
+ if trans.history is None:
+ return False
return trans.history == history
def is_owner( self, trans, history ):
+ """
+ True if the current user is the owner of the given history.
+ """
# anon users are only allowed to view their current history
if not trans.user:
return self.is_current( trans, history )
return trans.user == history.user
def check_ownership( self, trans, history ):
+ """
+ Raises error if the current user is not the owner of the history.
+ """
if trans.user and trans.user_is_admin():
return history
if not trans.user and not self.is_current( trans, history ):
@@ -74,6 +110,9 @@
raise exceptions.ItemOwnershipException( "History is not owned by the current user", type='error' )
def is_accessible( self, trans, history ):
+ """
+ True if the user can access (read) the current history.
+ """
# admin always have access
if trans.user and trans.user_is_admin():
return True
@@ -88,6 +127,103 @@
return False
def check_accessible( self, trans, history ):
+ """
+ Raises error if the current user can't access the history.
+ """
if self.is_accessible( trans, history ):
return history
raise exceptions.ItemAccessibilityException( "History is not accessible to the current user", type='error' )
+
+ #TODO: bleh...
+ def _get_history_data( self, trans, history ):
+ """
+ Returns a dictionary containing ``history`` and ``contents``, serialized
+ history and an array of serialized history contents respectively.
+ """
+ hda_mgr = galaxy.managers.hdas.HDAManager()
+ collection_dictifier = galaxy.dataset_collections.util.dictify_dataset_collection_instance
+
+ history_dictionary = {}
+ contents_dictionaries = []
+ try:
+ #for content in history.contents_iter( **contents_kwds ):
+ for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
+ hda_dict = {}
+
+ if isinstance( content, trans.app.model.HistoryDatasetAssociation ):
+ try:
+ hda_dict = hda_mgr.get_hda_dict( trans, content )
+ except Exception, exc:
+ # don't fail entire list if hda err's, record and move on
+ log.exception( 'Error bootstrapping hda: %s', exc )
+ hda_dict = hda_mgr.get_hda_dict_with_error( trans, content, str( exc ) )
+
+ elif isinstance( content, trans.app.model.HistoryDatasetCollectionAssociation ):
+ try:
+ service = trans.app.dataset_collections_service
+ dataset_collection_instance = service.get_dataset_collection_instance(
+ trans=trans,
+ instance_type='history',
+ id=trans.security.encode_id( content.id ),
+ )
+ hda_dict = collection_dictifier( dataset_collection_instance,
+ security=trans.security, parent=dataset_collection_instance.history, view="element" )
+
+ except Exception, exc:
+ log.exception( "Error in history API at listing dataset collection: %s", exc )
+ #TODO: return some dict with the error
+
+ contents_dictionaries.append( hda_dict )
+
+ # re-use the hdas above to get the history data...
+ history_dictionary = self.get_history_dict( trans, history, contents_dictionaries=contents_dictionaries )
+
+ except Exception, exc:
+ user_id = str( trans.user.id ) if trans.user else '(anonymous)'
+ log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) )
+ message = ( 'An error occurred getting the history data from the server. '
+ + 'Please contact a Galaxy administrator if the problem persists.' )
+ history_dictionary[ 'error' ] = message
+
+ return {
+ 'history' : history_dictionary,
+ 'contents' : contents_dictionaries
+ }
+
+ def get_history_dict( self, trans, history, contents_dictionaries=None ):
+ """
+ Returns history data in the form of a dictionary.
+ """
+ #TODO: to serializer
+ history_dict = history.to_dict( view='element', value_mapper={ 'id':trans.security.encode_id })
+ history_dict[ 'user_id' ] = None
+ if history.user_id:
+ history_dict[ 'user_id' ] = trans.security.encode_id( history.user_id )
+
+ history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True )
+ history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, history.user, history )
+ if not history_dict[ 'annotation' ]:
+ history_dict[ 'annotation' ] = ''
+
+ #TODO: item_slug url
+ if history_dict[ 'importable' ] and history_dict[ 'slug' ]:
+ username_and_slug = ( '/' ).join(( 'u', history.user.username, 'h', history_dict[ 'slug' ] ))
+ history_dict[ 'username_and_slug' ] = username_and_slug
+
+#TODO: re-add
+ #hda_summaries = hda_dictionaries if hda_dictionaries else self.get_hda_summary_dicts( trans, history )
+ ##TODO remove the following in v2
+ #( state_counts, state_ids ) = self._get_hda_state_summaries( trans, hda_summaries )
+ #history_dict[ 'state_details' ] = state_counts
+ #history_dict[ 'state_ids' ] = state_ids
+ #history_dict[ 'state' ] = self._get_history_state_from_hdas( trans, history, state_counts )
+
+ return history_dict
+
+
+# =============================================================================
+class HistorySerializer( manager_base.ModelSerializer ):
+ """
+ Interface/service object for serializing histories into dictionaries.
+ """
+ pass
diff -r 6249e3b45f8039099fa696a35f237d898a7ab626 -r c32e9cecb879d613b25fe270f6c2a86562d23cdf lib/galaxy/model/tool_shed_install/__init__.py
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -68,7 +68,9 @@
@property
def can_deactivate( self ):
- return self.status not in [ self.installation_status.DEACTIVATED, self.installation_status.UNINSTALLED ]
+ return self.status not in [ self.installation_status.DEACTIVATED,
+ self.installation_status.ERROR,
+ self.installation_status.UNINSTALLED ]
@property
def can_reinstall_or_activate( self ):
This diff is so big that we needed to truncate the remainder.
https://bitbucket.org/galaxy/galaxy-central/commits/21fed77e18f8/
Changeset: 21fed77e18f8
User: dannon
Date: 2014-07-10 20:33:26
Summary: Pack scripts.
Affected #: 1 file
diff -r c32e9cecb879d613b25fe270f6c2a86562d23cdf -r 21fed77e18f88ae64023afe5c64fc9866270bde8 static/scripts/packed/galaxy.workflows.js
--- a/static/scripts/packed/galaxy.workflows.js
+++ b/static/scripts/packed/galaxy.workflows.js
@@ -1,1 +1,1 @@
-$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal})}else{hide_modal()}show_workflow_parameters()},beforeSubmit:function(h){show_message("Loading workflow","progress")}})}});$(document).ajaxStart(function(){active_ajax_call=true;$(document).bind("ajaxStop.global",function(){active_ajax_call=false})});$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});make_popupmenu($("#workflow-options-button"),{Save:save_current_workflow,Run:function(){window.location=run_workflow_url},"Edit Attributes":c,"Auto Re-layout":f,Close:close_editor});function b(){workflow.clear_active_node();$(".right-content").hide();var j="";for(var h in workflow.nodes){var i=workflow.nodes[h];if(i.type=="tool"){j+="<div class='toolForm' style='margin-bottom:5px;'><div class='toolFormTitle'>Step "+i.id+" - "+i.name+"</div>";for(var k in i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes 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d=this;$(this).find("select[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find("input[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find(".popupmenu").each(function(){var g=$(this).parents("div.form-row").attr("id");var e=$('<a class="popup-arrow" id="popup-arrow-for-'+g+'">▼</a>');var f={};$(this).find("button").each(function(){var h=$(this).attr("name");var i=$(this).attr("value");f[$(this).text()]=function(){$(d).append("<input type='hidden' name='"+h+"' value='"+i+"' />").submit()}});e.insertAfter(this);$(this).remove();make_popupmenu(e,f)});$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=true})})})}var close_editor=function(){workflow.check_changes_in_active_form();if(workflow&&workflow.has_changes){do_close=function(){window.onbeforeunload=undefined;window.document.location=workflow_index_url};show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})}else{window.document.location=workflow_index_url}};var save_current_workflow=function(b,c){show_message("Saving workflow","progress");workflow.check_changes_in_active_form();if(!workflow.has_changes){hide_modal();if(c){c()}return}workflow.rectify_workflow_outputs();var a=function(d){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(g){var e=$("<div></div>").text(g.message);if(g.errors){e.addClass("warningmark");var f=$("<ul/>");$.each(g.errors,function(j,h){$("<li></li>").text(h).appendTo(f)});e.append(f)}else{e.addClass("donemark")}workflow.name=g.name;workflow.has_changes=false;workflow.stored=true;show_workflow_parameters();if(g.errors){show_modal("Saving workflow",e,{Ok:hide_modal})}else{if(d){d()}hide_modal()}}})};if(active_ajax_call){$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow");a();$(document).unbind("ajaxStop.save_workflow");active_ajax_call=false})}else{a(c)}};
\ No newline at end of file
+$(function(){if(window.lt_ie_7){show_modal("Browser not supported","Sorry, the workflow editor is not supported for IE6 and below.");return}$("#tool-search-query").click(function(){$(this).focus();$(this).select()}).keyup(function(){$(this).css("font-style","normal");if(this.value.length<3){reset_tool_search(false)}else{if(this.value!=this.lastValue){$(this).addClass("search_active");var g=this.value+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();this.timer=setTimeout(function(){$.get(tool_search_url,{query:g},function(i){$("#search-no-results").hide();$(".toolSectionWrapper").hide();$(".toolSectionWrapper").find(".toolTitle").hide();if(i.length!=0){var h=$.map(i,function(k,j){return"link-"+k});$(h).each(function(j,k){$("[id='"+k+"']").parent().addClass("search_match");$("[id='"+k+"']").parent().show().parent().parent().show().parent().show()});$(".toolPanelLabel").each(function(){var l=$(this);var k=l.next();var j=true;while(k.length!==0&&k.hasClass("toolTitle")){if(k.is(":visible")){j=false;break}else{k=k.next()}}if(j){l.hide()}})}else{$("#search-no-results").show()}$("#search-spinner").hide()},"json")},200)}}this.lastValue=this.value});canvas_manager=new CanvasManager($("#canvas-viewport"),$("#overview"));reset();$.ajax({url:get_datatypes_url,dataType:"json",cache:false,success:function(g){populate_datatype_info(g);$.ajax({url:load_workflow_url,data:{id:workflow_id,_:"true"},dataType:"json",cache:false,success:function(h){reset();workflow.from_simple(h);workflow.has_changes=false;workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview();upgrade_message="";$.each(h.upgrade_messages,function(j,i){upgrade_message+=("<li>Step "+(parseInt(j,10)+1)+": "+workflow.nodes[j].name+"<ul>");$.each(i,function(k,l){upgrade_message+="<li>"+l+"</li>"});upgrade_message+="</ul></li>"});if(upgrade_message){show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). 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i.output_terminals){var g=i.output_terminals[k];if($.inArray(g.name,i.workflow_outputs)!=-1){j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' checked /></p>"}else{j+="<p>"+g.name+"<input type='checkbox' name='"+i.id+"|"+g.name+"' /></p>"}}j+="</div>"}}$("#output-fill-area").html(j);$("#output-fill-area input").bind("click",function(){var n=this.name.split("|")[0];var l=this.name.split("|")[1];if(this.checked){if($.inArray(l,workflow.nodes[n].workflow_outputs)==-1){workflow.nodes[n].workflow_outputs.push(l)}}else{while($.inArray(l,workflow.nodes[n].workflow_outputs)!=-1){var m=$.inArray(l,workflow.nodes[n].workflow_outputs);workflow.nodes[n].workflow_outputs=workflow.nodes[n].workflow_outputs.slice(0,m).concat(workflow.nodes[n].workflow_outputs.slice(m+1))}}workflow.has_changes=true});$("#workflow-output-area").show()}function f(){workflow.layout();workflow.fit_canvas_to_nodes();scroll_to_nodes();canvas_manager.draw_overview()}function c(){workflow.clear_active_node();$(".right-content").hide();$("#edit-attributes").show()}overview_size=$.jStorage.get("overview-size");if(overview_size!==undefined){$("#overview-border").css({width:overview_size,height:overview_size})}if($.jStorage.get("overview-off")){d()}else{e()}$("#overview-border").bind("dragend",function(h,j){var k=$(this).offsetParent();var i=k.offset();var g=Math.max(k.width()-(j.offsetX-i.left),k.height()-(j.offsetY-i.top));$.jStorage.set("overview-size",g+"px")});function e(){$.jStorage.set("overview-off",false);$("#overview-border").css("right","0px");$("#close-viewport").css("background-position","0px 0px")}function d(){$.jStorage.set("overview-off",true);$("#overview-border").css("right","20000px");$("#close-viewport").css("background-position","12px 0px")}$("#close-viewport").click(function(){if($("#overview-border").css("right")==="0px"){d()}else{e()}});window.onbeforeunload=function(){if(workflow&&workflow.has_changes){return"There are unsaved changes 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add_node_for_tool(b,a){node=add_node("tool",a,b);$.ajax({url:get_new_module_info_url,data:{type:"tool",tool_id:b,_:"true"},global:false,dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status===0){c+=", server unavailable"}node.error(c)}})}function add_node_for_module(a,b){node=add_node(a,b);$.ajax({url:get_new_module_info_url,data:{type:a,_:"true"},dataType:"json",success:function(c){node.init_field_data(c)},error:function(d,f){var c="error loading field data";if(d.status==0){c+=", server unavailable"}node.error(c)}})}function display_pja(b,a){$("#pja_container").append(get_pja_form(b,a));$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text();$(this).closest(".toolForm").remove();delete workflow.active_node.post_job_actions[action_to_rem];workflow.active_form_has_changes=true})}function display_pja_list(){return pja_list}function display_file_list(b){addlist="<select id='node_data_list' name='node_data_list'>";for(var a in b.output_terminals){addlist+="<option value='"+a+"'>"+a+"</option>"}addlist+="</select>";return addlist}function new_pja(d,b,a){if(a.post_job_actions===undefined){a.post_job_actions={}}if(a.post_job_actions[d+b]===undefined){var c={};c.action_type=d;c.output_name=b;a.post_job_actions[d+b]=null;a.post_job_actions[d+b]=c;display_pja(c,a);workflow.active_form_has_changes=true;return true}else{return false}}function show_workflow_parameters(){var c=/\$\{.+?\}/g;var b=[];var f=$("#workflow-parameters-container");var e=$("#workflow-parameters-box");var a="";var d=[];$.each(workflow.nodes,function(g,h){var i=h.form_html.match(c);if(i){d=d.concat(i)}if(h.post_job_actions){$.each(h.post_job_actions,function(j,l){if(l.action_arguments){$.each(l.action_arguments,function(m,n){var o=n.match(c);if(o){d=d.concat(o)}})}});if(d){$.each(d,function(j,l){if($.inArray(l,b)===-1){b.push(l)}})}}});if(b&&b.length!==0){$.each(b,function(g,h){a+="<div>"+h.substring(2,h.length-1)+"</div>"});f.html(a);e.show()}else{f.html(a);e.hide()}}function show_form_for_tool(c,b){$(".right-content").hide();$("#right-content").show().html(c);if(b){$("#right-content").find(".toolForm:first").after("<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Attributes</div><div class='form-row'><label>Annotation / Notes:</label><div style='margin-right: 10px;'><textarea name='annotation' rows='3' style='width: 100%'>"+b.annotation+"</textarea><div class='toolParamHelp'>Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div></div>")}if(b&&b.type=="tool"){pjastr="<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'> "+display_pja_list()+" <br/> "+display_file_list(b)+" <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div></div><div class='form-row'><div style='margin-right: 10px;'><span id='pja_container'></span>";pjastr+="<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";$("#right-content").find(".toolForm").after(pjastr);for(var a in b.post_job_actions){if(a!="undefined"){display_pja(b.post_job_actions[a],b)}}$("#add_pja").click(function(){new_pja($("#new_pja_list").val(),$("#node_data_list").val(),b)})}$("#right-content").find("form").ajaxForm({type:"POST",dataType:"json",success:function(d){workflow.active_form_has_changes=false;b.update_field_data(d);show_workflow_parameters()},beforeSubmit:function(d){d.push({name:"tool_state",value:b.tool_state});d.push({name:"_",value:"true"})}}).each(function(){var d=this;$(this).find("select[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find("input[refresh_on_change='true']").change(function(){$(d).submit()});$(this).find(".popupmenu").each(function(){var g=$(this).parents("div.form-row").attr("id");var e=$('<a class="popup-arrow" id="popup-arrow-for-'+g+'">▼</a>');var f={};$(this).find("button").each(function(){var h=$(this).attr("name");var i=$(this).attr("value");f[$(this).text()]=function(){$(d).append("<input type='hidden' name='"+h+"' value='"+i+"' />").submit()}});e.insertAfter(this);$(this).remove();make_popupmenu(e,f)});$(this).find("input,textarea,select").each(function(){$(this).bind("focus click",function(){workflow.active_form_has_changes=true})})})}var close_editor=function(){workflow.check_changes_in_active_form();if(workflow&&workflow.has_changes){do_close=function(){window.onbeforeunload=undefined;window.document.location=workflow_index_url};show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){save_current_workflow(null,do_close)}},{"Don't Save":do_close})}else{window.document.location=workflow_index_url}};var save_current_workflow=function(b,c){show_message("Saving workflow","progress");workflow.check_changes_in_active_form();if(!workflow.has_changes){hide_modal();if(c){c()}return}workflow.rectify_workflow_outputs();var a=function(d){$.ajax({url:save_workflow_url,type:"POST",data:{id:workflow_id,workflow_data:function(){return JSON.stringify(workflow.to_simple())},_:"true"},dataType:"json",success:function(g){var e=$("<div></div>").text(g.message);if(g.errors){e.addClass("warningmark");var f=$("<ul/>");$.each(g.errors,function(j,h){$("<li></li>").text(h).appendTo(f)});e.append(f)}else{e.addClass("donemark")}workflow.name=g.name;workflow.has_changes=false;workflow.stored=true;show_workflow_parameters();if(g.errors){show_modal("Saving workflow",e,{Ok:hide_modal})}else{if(d){d()}hide_modal()}}})};if(active_ajax_call){$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow");a();$(document).unbind("ajaxStop.save_workflow");active_ajax_call=false})}else{a(c)}};
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/1d09105e1cad/
Changeset: 1d09105e1cad
User: dannon
Date: 2014-07-10 20:36:15
Summary: Include link to wiki explaining rename syntax.
Affected #: 1 file
diff -r 21fed77e18f88ae64023afe5c64fc9866270bde8 -r 1d09105e1cade84ebacfe48ef4739266f3f073ca lib/galaxy/jobs/actions/post.py
--- a/lib/galaxy/jobs/actions/post.py
+++ b/lib/galaxy/jobs/actions/post.py
@@ -225,7 +225,7 @@
p_str += "No inputs are available for templating into this action.";
}
"""
- return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset.")
+ return get_form_template(cls.name, cls.verbose_name, form, "This action will rename the result dataset. See <a href='https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables'>the wiki</a> for usage information.")
@classmethod
def get_short_str(cls, pja):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: 1.) Enhance set_metadata scripts to be able to handle metadata declared by tools for both regular declared outputs and new primary output datasets using JSON.
by commits-noreply＠bitbucket.org 10 Jul '14
by commits-noreply＠bitbucket.org 10 Jul '14
10 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c713d035edff/
Changeset: c713d035edff
User: dan
Date: 2014-07-10 18:09:50
Summary: 1.) Enhance set_metadata scripts to be able to handle metadata declared by tools for both regular declared outputs and new primary output datasets using JSON.
2.) Enhance collect_primary_datasets to allow tools to provide extra_files.
Affected #: 3 files
diff -r cef33a0617405e7b3f25c79955890c72e69dc14b -r c713d035edff866476384a47ab25410d9a271b54 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -126,10 +126,21 @@
rval[key] = self.spec[key].param.make_copy( value, target_context=self, source_context=to_copy )
return rval
- def from_JSON_dict( self, filename, path_rewriter=None ):
+ def from_JSON_dict( self, filename=None, path_rewriter=None, json_dict=None ):
dataset = self.parent
- log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
- JSONified_dict = json.load( open( filename ) )
+ if filename is not None:
+ log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ JSONified_dict = json.load( open( filename ) )
+ elif json_dict is not None:
+ log.debug( 'loading metadata from dict for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
+ if isinstance( json_dict, basestring ):
+ JSONified_dict = json.loads( json_dict )
+ elif isinstance( json_dict, dict ):
+ JSONified_dict = json_dict
+ else:
+ raise ValueError( "json_dict must be either a dictionary or a string, got %s." % ( type( json_dict ) ) )
+ else:
+ raise ValueError( "You must provide either a filename or a json_dict" )
for name, spec in self.spec.items():
if name in JSONified_dict:
from_ext_kwds = {}
@@ -143,13 +154,15 @@
#metadata associated with our dataset, we'll delete it from our dataset's metadata dict
del dataset._metadata[ name ]
- def to_JSON_dict( self, filename ):
+ def to_JSON_dict( self, filename=None ):
#galaxy.model.customtypes.json_encoder.encode()
meta_dict = {}
dataset_meta_dict = self.parent._metadata
for name, spec in self.spec.items():
if name in dataset_meta_dict:
meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] )
+ if filename is None:
+ return json.dumps( meta_dict )
json.dump( meta_dict, open( filename, 'wb+' ) )
def __getstate__( self ):
diff -r cef33a0617405e7b3f25c79955890c72e69dc14b -r c713d035edff866476384a47ab25410d9a271b54 lib/galaxy/tools/parameters/output_collect.py
--- a/lib/galaxy/tools/parameters/output_collect.py
+++ b/lib/galaxy/tools/parameters/output_collect.py
@@ -100,13 +100,36 @@
sa_session.flush()
primary_data.state = outdata.state
#add tool/metadata provided information
- new_primary_datasets_attributes = new_primary_datasets.get( os.path.split( filename )[-1] )
+ new_primary_datasets_attributes = new_primary_datasets.get( os.path.split( filename )[-1], {} )
if new_primary_datasets_attributes:
dataset_att_by_name = dict( ext='extension' )
for att_set in [ 'name', 'info', 'ext', 'dbkey' ]:
dataset_att_name = dataset_att_by_name.get( att_set, att_set )
setattr( primary_data, dataset_att_name, new_primary_datasets_attributes.get( att_set, getattr( primary_data, dataset_att_name ) ) )
- primary_data.set_meta()
+ extra_files_path = new_primary_datasets_attributes.get( 'extra_files', None )
+ if extra_files_path:
+ extra_files_path_joined = os.path.join( job_working_directory, extra_files_path )
+ for root, dirs, files in os.walk( extra_files_path_joined ):
+ extra_dir = os.path.join( primary_data.extra_files_path, root.replace( extra_files_path_joined, '', 1 ).lstrip( os.path.sep ) )
+ for f in files:
+ app.object_store.update_from_file( primary_data.dataset,
+ extra_dir=extra_dir,
+ alt_name=f,
+ file_name=os.path.join( root, f ),
+ create=True,
+ dir_only=True,
+ preserve_symlinks=True
+ )
+ # FIXME:
+ # since these are placed into the job working dir, let the standard
+ # Galaxy cleanup methods handle this (for now?)
+ # there was an extra_files_path dir, attempt to remove it
+ #shutil.rmtree( extra_files_path_joined )
+ metadata_dict = new_primary_datasets_attributes.get( 'metadata', None )
+ if metadata_dict:
+ primary_data.metadata.from_JSON_dict( json_dict=metadata_dict )
+ else:
+ primary_data.set_meta()
primary_data.set_peek()
sa_session.add( primary_data )
sa_session.flush()
diff -r cef33a0617405e7b3f25c79955890c72e69dc14b -r c713d035edff866476384a47ab25410d9a271b54 scripts/set_metadata.py
--- a/scripts/set_metadata.py
+++ b/scripts/set_metadata.py
@@ -31,16 +31,27 @@
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
galaxy.model.Job() # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
from galaxy.util import stringify_dictionary_keys
-from galaxy.util.json import from_json_string
from sqlalchemy.orm import clear_mappers
from galaxy.objectstore import build_object_store_from_config
from galaxy import config
import ConfigParser
+def set_meta_with_tool_provided( dataset_instance, file_dict, set_meta_kwds ):
+ # This method is somewhat odd, in that we set the metadata attributes from tool,
+ # then call set_meta, then set metadata attributes from tool again.
+ # This is intentional due to interplay of overwrite kwd, the fact that some metadata
+ # parameters may rely on the values of others, and that we are accepting the
+ # values provided by the tool as Truth.
+ for metadata_name, metadata_value in file_dict.get( 'metadata', {} ).iteritems():
+ setattr( dataset_instance.metadata, metadata_name, metadata_value )
+ dataset_instance.datatype.set_meta( dataset_instance, **set_meta_kwds )
+ for metadata_name, metadata_value in file_dict.get( 'metadata', {} ).iteritems():
+ setattr( dataset_instance.metadata, metadata_name, metadata_value )
+
def __main__():
file_path = sys.argv.pop( 1 )
- tmp_dir = sys.argv.pop( 1 )
+ tool_job_working_directory = tmp_dir = sys.argv.pop( 1 ) #this is also the job_working_directory now
galaxy.model.Dataset.file_path = file_path
galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir
@@ -77,15 +88,19 @@
galaxy.model.set_datatypes_registry( datatypes_registry )
job_metadata = sys.argv.pop( 1 )
- ext_override = dict()
+ existing_job_metadata_dict = {}
+ new_job_metadata_dict = {}
if job_metadata != "None" and os.path.exists( job_metadata ):
for line in open( job_metadata, 'r' ):
try:
- line = stringify_dictionary_keys( from_json_string( line ) )
- assert line['type'] == 'dataset'
- ext_override[line['dataset_id']] = line['ext']
+ line = stringify_dictionary_keys( json.loads( line ) )
+ if line['type'] == 'dataset':
+ existing_job_metadata_dict[ line['dataset_id'] ] = line
+ elif line['type'] == 'new_primary_dataset':
+ new_job_metadata_dict[ line[ 'filename' ] ] = line
except:
continue
+
for filenames in sys.argv[1:]:
fields = filenames.split( ',' )
filename_in = fields.pop( 0 )
@@ -100,12 +115,13 @@
override_metadata = fields.pop( 0 )
else:
override_metadata = None
+ set_meta_kwds = stringify_dictionary_keys( json.load( open( filename_kwds ) ) ) # load kwds; need to ensure our keywords are not unicode
try:
dataset = cPickle.load( open( filename_in ) ) # load DatasetInstance
if dataset_filename_override:
dataset.dataset.external_filename = dataset_filename_override
- if ext_override.get( dataset.dataset.id, None ):
- dataset.extension = ext_override[ dataset.dataset.id ]
+ if dataset.dataset.id in existing_job_metadata_dict:
+ dataset.extension = existing_job_metadata_dict[ dataset.dataset.id ].get( 'ext', dataset.extension )
# Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
if override_metadata:
override_metadata = json.load( open( override_metadata ) )
@@ -113,12 +129,27 @@
if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
setattr( dataset.metadata, metadata_name, metadata_file_override )
- kwds = stringify_dictionary_keys( json.load( open( filename_kwds ) ) ) # load kwds; need to ensure our keywords are not unicode
- dataset.datatype.set_meta( dataset, **kwds )
+ file_dict = existing_job_metadata_dict.get( dataset.dataset.id, {} )
+ set_meta_with_tool_provided( dataset, file_dict, set_meta_kwds )
dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta
json.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) # setting metadata has succeeded
except Exception, e:
json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) # setting metadata has failed somehow
+
+ for i, ( filename, file_dict ) in enumerate( new_job_metadata_dict.iteritems(), start=1 ):
+ new_dataset = galaxy.model.Dataset( id=-i, external_filename=os.path.join( tool_job_working_directory, file_dict[ 'filename' ] ) )
+ extra_files = file_dict.get( 'extra_files', None )
+ if extra_files is not None:
+ new_dataset._extra_files_path = os.path.join( tool_job_working_directory, extra_files )
+ new_dataset.state = new_dataset.states.OK
+ new_dataset_instance = galaxy.model.HistoryDatasetAssociation( id=-i, dataset=new_dataset, extension=file_dict.get( 'ext', 'data' ) )
+ set_meta_with_tool_provided( new_dataset_instance, file_dict, set_meta_kwds )
+ file_dict[ 'metadata' ] = json.loads( new_dataset_instance.metadata.to_JSON_dict() ) #storing metadata in external form, need to turn back into dict, then later jsonify
+ if existing_job_metadata_dict or new_job_metadata_dict:
+ with open( job_metadata, 'wb' ) as job_metadata_fh:
+ for value in existing_job_metadata_dict.values() + new_job_metadata_dict.values():
+ job_metadata_fh.write( "%s\n" % ( json.dumps( value ) ) )
+
clear_mappers()
# Shut down any additional threads that might have been created via the ObjectStore
object_store.shutdown()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: History panel: refactor hda/collection views; pack scripts
by commits-noreply＠bitbucket.org 10 Jul '14
by commits-noreply＠bitbucket.org 10 Jul '14
10 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/cef33a061740/
Changeset: cef33a061740
User: carlfeberhard
Date: 2014-07-10 17:15:30
Summary: History panel: refactor hda/collection views; pack scripts
Affected #: 13 files
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/mvc/collection/dataset-collection-base.js
--- a/static/scripts/mvc/collection/dataset-collection-base.js
+++ b/static/scripts/mvc/collection/dataset-collection-base.js
@@ -1,7 +1,7 @@
define([
- "mvc/dataset/hda-model",
- "mvc/dataset/hda-base"
-], function( hdaModel, hdaBase ){
+ "mvc/history/history-content-base-view",
+ "utils/localization"
+], function( historyContentBaseView, _l ){
/* global Backbone, LoggableMixin */
//==============================================================================
/** @class Read only view for HistoryDatasetCollectionAssociation.
@@ -12,10 +12,11 @@
* @borrows LoggableMixin#log as #log
* @constructs
*/
-var DatasetCollectionBaseView = hdaBase.HistoryContentBaseView.extend({
+var DatasetCollectionBaseView = historyContentBaseView.HistoryContentBaseView.extend({
className : "dataset hda history-panel-hda",
id : function(){ return 'hdca-' + this.model.get( 'id' ); },
+ /** */
initialize : function( attributes ){
if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }
this.log( this + '.initialize:', attributes );
@@ -28,6 +29,7 @@
this.expanded = attributes.expanded || false;
},
+ /** */
render : function( fade ){
var $newRender = this._buildNewRender();
@@ -35,53 +37,47 @@
return this;
},
- // main template for folder browsing
- templateSkeleton : function (){
- return [
- '<div class="dataset hda">',
- '<div class="dataset-warnings">',
- '<% if ( deleted ) { %>',
- '<div class="dataset-deleted-msg warningmessagesmall"><strong>',
- _l( 'This dataset has been deleted.' ),
- '</div>',
- '<% } %>',
- '<% if ( ! visible ) { %>',
- '<div class="dataset-hidden-msg warningmessagesmall"><strong>',
- _l( 'This dataset has been hidden.' ),
- '</div>',
- '<% } %>',
- '</div>',
- '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>',
- '<div class="dataset-primary-actions"></div>',
- '<div class="dataset-title-bar clear" tabindex="0">',
- '<span class="dataset-state-icon state-icon"></span>',
- '<div class="dataset-title">',
- '<span class="hda-hid"><%= hid %></span> ',
- '<span class="dataset-name"><%= name %></span>',
- '</div>',
- '</div>',
- '<div class="dataset-body"></div>',
- '</div>'
- ].join( '' );
- },
-
- templateBody : function() {
- return [
- '<div class="dataset-body">',
- '<div class="dataset-summary">',
- 'A dataset collection.',
- '</div>'
- ].join( '' );
- },
-
+ /** */
_buildNewRender : function(){
- var $newRender = $( _.template(this.templateSkeleton(), this.model.toJSON() ) );
+ var $newRender = $( DatasetCollectionBaseView.templates.skeleton( this.model.toJSON() ) );
$newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() );
$newRender.children( '.dataset-body' ).replaceWith( this._render_body() );
this._setUpBehaviors( $newRender );
return $newRender;
},
+ /** */
+ _queueNewRender : function( $newRender, fade ) {
+ fade = ( fade === undefined )?( true ):( fade );
+ var view = this;
+
+ // fade the old render out (if desired)
+ if( fade ){
+ $( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); });
+ }
+ // empty the old render, update to any new HDA state, swap in the new render contents, handle multi-select
+ $( view ).queue( function( next ){
+ this.$el.empty()
+ .attr( 'class', view.className ).addClass( 'state-' + view.model.get( 'state' ) )
+ .append( $newRender.children() );
+ if( this.selectable ){ this.showSelector( 0 ); }
+ next();
+ });
+ // fade the new in
+ if( fade ){
+ $( view ).queue( function( next ){ this.$el.fadeIn( view.fxSpeed, next ); });
+ }
+ // trigger an event to know we're ready
+ $( view ).queue( function( next ){
+ this.trigger( 'rendered', view );
+ if( this.model.inReadyState() ){
+ this.trigger( 'rendered:ready', view );
+ }
+ if( this.draggable ){ this.draggableOn(); }
+ next();
+ });
+ },
+
// ................................................................................ titlebar buttons
/** Render icon-button group for the common, most easily accessed actions.
* @returns {jQuery} rendered DOM
@@ -134,6 +130,31 @@
'click .dataset-selector' : 'toggleSelect'
},
+ /** Show or hide the body/details of history content.
+ * note: if the model does not have detailed data, fetch that data before showing the body
+ * @param {Event} event the event that triggered this (@link HDABaseView#events)
+ * @param {Boolean} expanded if true, expand; if false, collapse
+ * @fires body-expanded when a body has been expanded
+ * @fires body-collapsed when a body has been collapsed
+ */
+ toggleBodyVisibility : function( event, expand ){
+ // bail (with propagation) if keydown and not space or enter
+ var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13;
+ if( event && ( event.type === 'keydown' )
+ && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){
+ return true;
+ }
+
+ var $body = this.$el.find( '.dataset-body' );
+ expand = ( expand === undefined )?( !$body.is( ':visible' ) ):( expand );
+ if( expand ){
+ this.expandBody();
+ } else {
+ this.collapseBody();
+ }
+ return false;
+ },
+
/** Render and show the full, detailed body of this view including extra data and controls.
* @fires body-expanded when a body has been expanded
*/
@@ -162,13 +183,12 @@
});
},
-
/** Render an 'ok' collection.
* @param {jQuery} parent DOM to which to append this body
*/
_render_body_ok : function(){
// most common state renderer and the most complicated
- var $body = $( _.template( this.templateBody(), this.model.toJSON() ) );
+ var $body = $( DatasetCollectionBaseView.templates.body( this.model.toJSON() ) );
// return shortened form if del'd (no display apps or peek?)
if( this.model.get( 'deleted' ) ){
@@ -176,13 +196,133 @@
}
return $body;
+ },
+
+ // ......................................................................... selection
+ /** display a (fa-icon) checkbox on the left of the hda that fires events when checked
+ * Note: this also hides the primary actions
+ */
+ showSelector : function(){
+ // make sure selected state is represented properly
+ if( this.selected ){
+ this.select( null, true );
+ }
+
+ this.selectable = true;
+ this.trigger( 'selectable', true, this );
+
+ this.$( '.dataset-primary-actions' ).hide();
+ this.$( '.dataset-selector' ).show();
+ },
+
+ /** remove the selection checkbox */
+ hideSelector : function(){
+ // reverse the process from showSelect
+ this.selectable = false;
+ this.trigger( 'selectable', false, this );
+
+ this.$( '.dataset-selector' ).hide();
+ this.$( '.dataset-primary-actions' ).show();
+ },
+
+ toggleSelector : function(){
+ if( !this.$el.find( '.dataset-selector' ).is( ':visible' ) ){
+ this.showSelector();
+ } else {
+ this.hideSelector();
+ }
+ },
+
+ /** event handler for selection (also programmatic selection)
+ */
+ select : function( event ){
+ // switch icon, set selected, and trigger event
+ this.$el.find( '.dataset-selector span' )
+ .removeClass( 'fa-square-o' ).addClass( 'fa-check-square-o' );
+ if( !this.selected ){
+ this.trigger( 'selected', this, event );
+ this.selected = true;
+ }
+ return false;
+ },
+
+ /** event handler for clearing selection (also programmatic deselection)
+ */
+ deselect : function( event ){
+ // switch icon, set selected, and trigger event
+ this.$el.find( '.dataset-selector span' )
+ .removeClass( 'fa-check-square-o' ).addClass( 'fa-square-o' );
+ if( this.selected ){
+ this.trigger( 'de-selected', this, event );
+ this.selected = false;
+ }
+ return false;
+ },
+
+ toggleSelect : function( event ){
+ if( this.selected ){
+ this.deselect( event );
+ } else {
+ this.select( event );
+ }
+ },
+
+ // ......................................................................... misc
+ /** String representation */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'HDCABaseView(' + modelString + ')';
}
-
});
-//==============================================================================
-return {
- DatasetCollectionBaseView : DatasetCollectionBaseView
+//------------------------------------------------------------------------------ TEMPLATES
+//TODO: possibly break these out into a sep. module
+var skeletonTemplate = _.template([
+ '<div class="dataset hda">',
+ '<div class="dataset-warnings">',
+ '<% if ( collection.deleted ) { %>',
+ '<div class="dataset-deleted-msg warningmessagesmall"><strong>',
+ _l( 'This collection has been deleted.' ),
+ '</div>',
+ '<% } %>',
+ '<% if ( !collection.visible ) { %>',
+ '<div class="dataset-hidden-msg warningmessagesmall"><strong>',
+ _l( 'This collection has been hidden.' ),
+ '</div>',
+ '<% } %>',
+ '</div>',
+ '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>',
+ '<div class="dataset-primary-actions"></div>',
+ '<div class="dataset-title-bar clear" tabindex="0">',
+ '<span class="dataset-state-icon state-icon"></span>',
+ '<div class="dataset-title">',
+ '<span class="hda-hid"><%= collection.hid %></span> ',
+ '<span class="dataset-name"><%= collection.name %></span>',
+ '</div>',
+ '</div>',
+ '<div class="dataset-body"></div>',
+ '</div>'
+].join( '' ));
+
+var bodyTemplate = _.template([
+ '<div class="dataset-body">',
+ '<div class="dataset-summary">',
+ _l( 'A dataset collection.' ),
+ '</div>'
+].join( '' ));
+
+DatasetCollectionBaseView.templates = {
+ // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within
+ skeleton : function( collectionJSON ){
+ return skeletonTemplate({ _l: _l, collection: collectionJSON });
+ },
+ body : function( collectionJSON ){
+ return bodyTemplate({ _l: _l, collection: collectionJSON });
+ }
};
+//==============================================================================
+ return {
+ DatasetCollectionBaseView : DatasetCollectionBaseView
+ };
});
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b 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
@@ -1,7 +1,8 @@
define([
"mvc/dataset/hda-model",
"mvc/collection/dataset-collection-base",
-], function( hdaModel, datasetCollectionBase ){
+ "utils/localization"
+], function( hdaModel, datasetCollectionBase, _l ){
//==============================================================================
/** @class Editing view for HistoryDatasetCollectionAssociation.
* @name DatasetCollectionEditView
@@ -57,13 +58,18 @@
}
deleteBtnData.faIcon = 'fa-times';
return faIconButton( deleteBtnData );
+ },
+
+ // ......................................................................... misc
+ /** string rep */
+ toString : function(){
+ var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
+ return 'HDCAEditView(' + modelString + ')';
}
-
});
//==============================================================================
-return {
- DatasetCollectionEditView : DatasetCollectionEditView
-};
-
+ return {
+ DatasetCollectionEditView : DatasetCollectionEditView
+ };
});
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -1,152 +1,10 @@
define([
"mvc/dataset/hda-model",
- "mvc/base-mvc",
+ "mvc/history/history-content-base-view",
"mvc/data",
"utils/localization"
-], function( hdaModel, baseMVC, dataset, _l ){
+], function( hdaModel, historyContentBaseView, dataset, _l ){
/* global Backbone */
-
-/** @class Read only view for history content views to extend.
- * @name HistoryContentBaseView
- *
- * @augments Backbone.View
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
- */
-var HistoryContentBaseView = Backbone.View.extend( baseMVC.LoggableMixin ).extend(
-/** @lends HistoryContentBaseView.prototype */{
- tagName : "div",
- fxSpeed : 'fast',
-
- _queueNewRender : function( $newRender, fade ) {
- fade = ( fade === undefined )?( true ):( fade );
- var view = this;
-
- // fade the old render out (if desired)
- if( fade ){
- $( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); });
- }
- // empty the old render, update to any new HDA state, swap in the new render contents, handle multi-select
- $( view ).queue( function( next ){
- this.$el.empty()
- .attr( 'class', view.className ).addClass( 'state-' + view.model.get( 'state' ) )
- .append( $newRender.children() );
- if( this.selectable ){ this.showSelector( 0 ); }
- next();
- });
- // fade the new in
- if( fade ){
- $( view ).queue( function( next ){ this.$el.fadeIn( view.fxSpeed, next ); });
- }
- // trigger an event to know we're ready
- $( view ).queue( function( next ){
- this.trigger( 'rendered', view );
- if( this.model.inReadyState() ){
- this.trigger( 'rendered:ready', view );
- }
- if( this.draggable ){ this.draggableOn(); }
- next();
- });
- },
-
- /** Show or hide the body/details of history content.
- * note: if the model does not have detailed data, fetch that data before showing the body
- * @param {Event} event the event that triggered this (@link HDABaseView#events)
- * @param {Boolean} expanded if true, expand; if false, collapse
- * @fires body-expanded when a body has been expanded
- * @fires body-collapsed when a body has been collapsed
- */
- toggleBodyVisibility : function( event, expand ){
- // bail (with propagation) if keydown and not space or enter
- var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13;
- if( event && ( event.type === 'keydown' )
- && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){
- return true;
- }
-
- var $body = this.$el.find( '.dataset-body' );
- expand = ( expand === undefined )?( !$body.is( ':visible' ) ):( expand );
- if( expand ){
- this.expandBody();
- } else {
- this.collapseBody();
- }
- return false;
- },
-
- // ......................................................................... selection
- /** display a (fa-icon) checkbox on the left of the hda that fires events when checked
- * Note: this also hides the primary actions
- */
- showSelector : function(){
- // make sure selected state is represented properly
- if( this.selected ){
- this.select( null, true );
- }
-
- this.selectable = true;
- this.trigger( 'selectable', true, this );
-
- this.$( '.dataset-primary-actions' ).hide();
- this.$( '.dataset-selector' ).show();
- },
-
- /** remove the selection checkbox */
- hideSelector : function(){
- // reverse the process from showSelect
- this.selectable = false;
- this.trigger( 'selectable', false, this );
-
- this.$( '.dataset-selector' ).hide();
- this.$( '.dataset-primary-actions' ).show();
- },
-
- toggleSelector : function(){
- if( !this.$el.find( '.dataset-selector' ).is( ':visible' ) ){
- this.showSelector();
- } else {
- this.hideSelector();
- }
- },
-
- /** event handler for selection (also programmatic selection)
- */
- select : function( event ){
- // switch icon, set selected, and trigger event
- this.$el.find( '.dataset-selector span' )
- .removeClass( 'fa-square-o' ).addClass( 'fa-check-square-o' );
- if( !this.selected ){
- this.trigger( 'selected', this, event );
- this.selected = true;
- }
- return false;
- },
-
- /** event handler for clearing selection (also programmatic deselection)
- */
- deselect : function( event ){
- // switch icon, set selected, and trigger event
- this.$el.find( '.dataset-selector span' )
- .removeClass( 'fa-check-square-o' ).addClass( 'fa-square-o' );
- if( this.selected ){
- this.trigger( 'de-selected', this, event );
- this.selected = false;
- }
- return false;
- },
-
- toggleSelect : function( event ){
- if( this.selected ){
- this.deselect( event );
- } else {
- this.select( event );
- }
- }
-
-});
-
-
//==============================================================================
/** @class Read only view for HistoryDatasetAssociation.
* @name HDABaseView
@@ -156,16 +14,19 @@
* @borrows LoggableMixin#log as #log
* @constructs
*/
-var HDABaseView = HistoryContentBaseView.extend(
+var HDABaseView = historyContentBaseView.HistoryContentBaseView.extend(
/** @lends HDABaseView.prototype */{
///** logger used to record this.log messages, commonly set to console */
//// comment this out to suppress log output
//logger : console,
+ tagName : "div",
className : "dataset hda history-panel-hda",
id : function(){ return 'hda-' + this.model.get( 'id' ); },
+ fxSpeed : 'fast',
+
// ......................................................................... set up
/** Set up the view, cache url templates, bind listeners
* @param {Object} attributes
@@ -253,6 +114,37 @@
return $newRender;
},
+ _queueNewRender : function( $newRender, fade ) {
+ fade = ( fade === undefined )?( true ):( fade );
+ var view = this;
+
+ // fade the old render out (if desired)
+ if( fade ){
+ $( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); });
+ }
+ // empty the old render, update to any new HDA state, swap in the new render contents, handle multi-select
+ $( view ).queue( function( next ){
+ this.$el.empty()
+ .attr( 'class', view.className ).addClass( 'state-' + view.model.get( 'state' ) )
+ .append( $newRender.children() );
+ if( this.selectable ){ this.showSelector( 0 ); }
+ next();
+ });
+ // fade the new in
+ if( fade ){
+ $( view ).queue( function( next ){ this.$el.fadeIn( view.fxSpeed, next ); });
+ }
+ // trigger an event to know we're ready
+ $( view ).queue( function( next ){
+ this.trigger( 'rendered', view );
+ if( this.model.inReadyState() ){
+ this.trigger( 'rendered:ready', view );
+ }
+ if( this.draggable ){ this.draggableOn(); }
+ next();
+ });
+ },
+
/** set up js behaviors, event handlers for elements within the given container
* @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)
*/
@@ -316,11 +208,11 @@
if( Galaxy.frame && Galaxy.frame.active ){
// Create frame with TabularChunkedView.
Galaxy.frame.add({
- title : "Data Viewer: " + self.model.get('name'),
+ title : "Data Viewer: " + self.model.get( 'name' ),
type : "other",
- content : function(parent_elt) {
- var new_dataset = new dataset.TabularDataset({id: self.model.get('id')});
- $.when(new_dataset.fetch()).then(function() {
+ content : function( parent_elt ){
+ var new_dataset = new dataset.TabularDataset({ id: self.model.get( 'id' ) });
+ $.when( new_dataset.fetch() ).then( function(){
dataset.createTabularDatasetChunkedView({
model: new_dataset,
parent_elt: parent_elt,
@@ -558,6 +450,31 @@
'click .dataset-selector' : 'toggleSelect'
},
+ /** Show or hide the body/details of history content.
+ * note: if the model does not have detailed data, fetch that data before showing the body
+ * @param {Event} event the event that triggered this (@link HDABaseView#events)
+ * @param {Boolean} expanded if true, expand; if false, collapse
+ * @fires body-expanded when a body has been expanded
+ * @fires body-collapsed when a body has been collapsed
+ */
+ toggleBodyVisibility : function( event, expand ){
+ // bail (with propagation) if keydown and not space or enter
+ var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13;
+ if( event && ( event.type === 'keydown' )
+ && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){
+ return true;
+ }
+
+ var $body = this.$el.find( '.dataset-body' );
+ expand = ( expand === undefined )?( !$body.is( ':visible' ) ):( expand );
+ if( expand ){
+ this.expandBody();
+ } else {
+ this.collapseBody();
+ }
+ return false;
+ },
+
/** Render and show the full, detailed body of this view including extra data and controls.
* @fires body-expanded when a body has been expanded
*/
@@ -599,6 +516,75 @@
});
},
+ // ......................................................................... selection
+ /** display a (fa-icon) checkbox on the left of the hda that fires events when checked
+ * Note: this also hides the primary actions
+ */
+ showSelector : function(){
+ // make sure selected state is represented properly
+ if( this.selected ){
+ this.select( null, true );
+ }
+
+ this.selectable = true;
+ this.trigger( 'selectable', true, this );
+
+ this.$( '.dataset-primary-actions' ).hide();
+ this.$( '.dataset-selector' ).show();
+ },
+
+ /** remove the selection checkbox */
+ hideSelector : function(){
+ // reverse the process from showSelect
+ this.selectable = false;
+ this.trigger( 'selectable', false, this );
+
+ this.$( '.dataset-selector' ).hide();
+ this.$( '.dataset-primary-actions' ).show();
+ },
+
+ toggleSelector : function(){
+ if( !this.$el.find( '.dataset-selector' ).is( ':visible' ) ){
+ this.showSelector();
+ } else {
+ this.hideSelector();
+ }
+ },
+
+ /** event handler for selection (also programmatic selection)
+ */
+ select : function( event ){
+ // switch icon, set selected, and trigger event
+ this.$el.find( '.dataset-selector span' )
+ .removeClass( 'fa-square-o' ).addClass( 'fa-check-square-o' );
+ if( !this.selected ){
+ this.trigger( 'selected', this, event );
+ this.selected = true;
+ }
+ return false;
+ },
+
+ /** event handler for clearing selection (also programmatic deselection)
+ */
+ deselect : function( event ){
+ // switch icon, set selected, and trigger event
+ this.$el.find( '.dataset-selector span' )
+ .removeClass( 'fa-check-square-o' ).addClass( 'fa-square-o' );
+ if( this.selected ){
+ this.trigger( 'de-selected', this, event );
+ this.selected = false;
+ }
+ return false;
+ },
+
+ toggleSelect : function( event ){
+ if( this.selected ){
+ this.deselect( event );
+ } else {
+ this.select( event );
+ }
+ },
+
// ......................................................................... drag/drop
draggableOn : function(){
this.draggable = true;
@@ -824,7 +810,7 @@
};
//==============================================================================
-return {
- HistoryContentBaseView : HistoryContentBaseView,
- HDABaseView : HDABaseView
-};});
+ return {
+ HDABaseView : HDABaseView
+ };
+});
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/mvc/dataset/hda-edit.js
--- a/static/scripts/mvc/dataset/hda-edit.js
+++ b/static/scripts/mvc/dataset/hda-edit.js
@@ -423,7 +423,7 @@
/** string rep */
toString : function(){
var modelString = ( this.model )?( this.model + '' ):( '(no model)' );
- return 'HDAView(' + modelString + ')';
+ return 'HDAEditView(' + modelString + ')';
}
});
@@ -510,6 +510,7 @@
//==============================================================================
-return {
- HDAEditView : HDAEditView
-};});
+ return {
+ HDAEditView : HDAEditView
+ };
+});
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/mvc/history/history-content-base-view.js
--- /dev/null
+++ b/static/scripts/mvc/history/history-content-base-view.js
@@ -0,0 +1,26 @@
+define([
+ "mvc/base-mvc",
+ "utils/localization"
+], function( baseMVC, _l ){
+/* global Backbone */
+//==============================================================================
+/** @class Read only view for history content views to extend.
+ * @name HistoryContentBaseView
+ *
+ * @augments Backbone.View
+ * @borrows LoggableMixin#logger as #logger
+ * @borrows LoggableMixin#log as #log
+ * @constructs
+ */
+var HistoryContentBaseView = Backbone.View.extend( baseMVC.LoggableMixin ).extend(
+/** @lends HistoryContentBaseView.prototype */{
+});
+
+//TODO: not sure base view class is warranted or even wise
+
+
+//==============================================================================
+ return {
+ HistoryContentBaseView : HistoryContentBaseView
+ };
+});
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/galaxy.workflow_editor.canvas.js
--- a/static/scripts/packed/galaxy.workflow_editor.canvas.js
+++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js
@@ -1,1 +1,1 @@
-function CollectionTypeDescription(a){this.collectionType=a;this.isCollection=true;this.rank=a.split(":").length}$.extend(CollectionTypeDescription.prototype,{append:function(a){if(a===NULL_COLLECTION_TYPE_DESCRIPTION){return this}if(a===ANY_COLLECTION_TYPE_DESCRIPTION){return otherCollectionType}return new CollectionTypeDescription(this.collectionType+":"+a.collectionType)},canMatch:function(a){if(a===NULL_COLLECTION_TYPE_DESCRIPTION){return false}if(a===ANY_COLLECTION_TYPE_DESCRIPTION){return true}return a.collectionType==this.collectionType},canMapOver:function(b){if(b===NULL_COLLECTION_TYPE_DESCRIPTION){return false}if(b===ANY_COLLECTION_TYPE_DESCRIPTION){return false}if(this.rank<=b.rank){return false}var a=b.collectionType;return this._endsWith(this.collectionType,a)},effectiveMapOver:function(a){var c=a.collectionType;var b=this.collectionType.substring(0,this.collectionType.length-c.length-1);return new CollectionTypeDescription(b)},equal:function(a){return a.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(b,a){return b.indexOf(a,b.length-a.length)!==-1}});NULL_COLLECTION_TYPE_DESCRIPTION={isCollection:false,canMatch:function(a){return false},canMapOver:function(a){return false},toString:function(){return"NullCollectionType[]"},append:function(a){return a},equal:function(a){return a===this}};ANY_COLLECTION_TYPE_DESCRIPTION={isCollection:true,canMatch:function(a){return NULL_COLLECTION_TYPE_DESCRIPTION!==a},canMapOver:function(a){return false},toString:function(){return"AnyCollectionType[]"},append:function(a){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(a){return a===this}};var TerminalMapping=Backbone.Model.extend({initialize:function(a){this.mapOver=a.mapOver||NULL_COLLECTION_TYPE_DESCRIPTION;this.terminal=a.terminal;this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(NULL_COLLECTION_TYPE_DESCRIPTION)},setMapOver:function(a){this.mapOver=a;this.trigger("change")}});var TerminalMappingView=Backbone.View.extend({tagName:"div",className:"fa-icon-button fa fa-folder-o",initialize:function(b){var a="Run tool in parallel over collection";this.$el.tooltip({delay:500,title:a});this.model.bind("change",_.bind(this.render,this))},render:function(){if(this.model.mapOver.isCollection){this.$el.show()}else{this.$el.hide()}},});var InputTerminalMappingView=TerminalMappingView.extend({events:{click:"onClick",mouseenter:"onMouseEnter",mouseleave:"onMouseLeave",},onMouseEnter:function(b){var a=this.model;if(!a.terminal.connected()&&a.mapOver.isCollection){this.$el.css("color","red")}},onMouseLeave:function(a){this.$el.css("color","black")},onClick:function(b){var a=this.model;if(!a.terminal.connected()&&a.mapOver.isCollection){a.terminal.resetMapping()}},});var InputTerminalMapping=TerminalMapping;var InputCollectionTerminalMapping=TerminalMapping;var OutputTerminalMapping=TerminalMapping;var OutputTerminalMappingView=TerminalMappingView;var InputCollectionTerminalMappingView=InputTerminalMappingView;var OutputCollectionTerminalMapping=TerminalMapping;var OutputCollectionTerminalMappingView=TerminalMappingView;var Terminal=Backbone.Model.extend({initialize:function(a){this.element=a.element;this.connectors=[]},connect:function(a){this.connectors.push(a);if(this.node){this.node.markChanged()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.markChanged();this.resetMappingIfNeeded()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})},destroyInvalidConnections:function(){_.each(this.connectors,function(a){a.destroyIfInvalid()})},setMapOver:function(a){if(this.multiple){return}if(!this.mapOver().equal(a)){this.terminalMapping.setMapOver(a);_.each(this.node.output_terminals,function(b){b.setMapOver(a)})}},mapOver:function(){if(!this.terminalMapping){return NULL_COLLECTION_TYPE_DESCRIPTION}else{return this.terminalMapping.mapOver}},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){},});var OutputTerminal=Terminal.extend({initialize:function(a){Terminal.prototype.initialize.call(this,a);this.datatypes=a.datatypes},resetMappingIfNeeded:function(){if(!this.node.hasConnectedOutputTerminals()&&!this.node.hasConnectedMappedInputTerminals()){_.each(this.node.mappedInputTerminals(),function(b){b.resetMappingIfNeeded()})}var a=!this.node.hasMappedOverInputTerminals();if(a){this.resetMapping()}},resetMapping:function(){this.terminalMapping.disableMapOver();_.each(this.connectors,function(a){var b=a.handle2;if(b){b.resetMappingIfNeeded();a.destroyIfInvalid()}})}});var BaseInputTerminal=Terminal.extend({initialize:function(a){Terminal.prototype.initialize.call(this,a);this.update(a.input)},canAccept:function(a){if(this._inputFilled()){return false}else{return this.attachable(a)}},resetMappingIfNeeded:function(){var b=this.mapOver();if(!b.isCollection){return}var a=this.node.hasConnectedMappedInputTerminals()||(!this.node.hasConnectedOutputTerminals());if(a){this.resetMapping()}},resetMapping:function(){this.terminalMapping.disableMapOver();if(!this.node.hasMappedOverInputTerminals()){_.each(this.node.output_terminals,function(a){a.resetMapping()})}},connected:function(){return this.connectors.length!==0},_inputFilled:function(){var a;if(!this.connected()){a=false}else{if(this.multiple){if(!this.connected()){a=false}else{var b=this.connectors[0].handle1;if(b===null){a=false}else{if(b.isDataCollectionInput||b.isMappedOver()||b.datatypes.indexOf("input_collection")>0){a=true}else{a=false}}}}else{a=true}}return a},_mappingConstraints:function(){if(!this.node){return[]}var b=this.mapOver();if(b.isCollection){return[b]}var a=[];if(!this.node.hasConnectedOutputTerminals()){_.each(this.node.connectedMappedInputTerminals(),function(c){a.push(c.mapOver())})}else{a.push(_.first(_.values(this.node.output_terminals)).mapOver())}return a},_producesAcceptableDatatype:function(a){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){var h=f[b];if(h=="input"||h=="input_collection"||issubtype(f[b],this.datatypes[c])){return true}}}return false},_otherCollectionType:function(a){var c=NULL_COLLECTION_TYPE_DESCRIPTION;if(a.isDataCollectionInput){c=a.collectionType}else{var b=a.mapOver();if(b.isCollection){c=b}}return c},});var InputTerminal=BaseInputTerminal.extend({update:function(a){this.datatypes=a.extensions;this.multiple=a.multiple;this.collection=false},connect:function(a){BaseInputTerminal.prototype.connect.call(this,a);var b=a.handle1;if(!b){return}var c=this._otherCollectionType(b);if(c.isCollection){this.setMapOver(c)}},attachable:function(b){var d=this._otherCollectionType(b);var a=this.mapOver();if(d.isCollection){if(this.multiple){if(this.connected()){return false}if(d.rank==1){return this._producesAcceptableDatatype(b)}else{return false}}if(a.isCollection&&a.canMatch(d)){return this._producesAcceptableDatatype(b)}else{var c=this._mappingConstraints();if(c.every(_.bind(d.canMatch,d))){return this._producesAcceptableDatatype(b)}else{return false}}}else{if(a.isCollection){return false}}return this._producesAcceptableDatatype(b)}});var InputCollectionTerminal=BaseInputTerminal.extend({update:function(a){this.multiple=false;this.collection=true;this.datatypes=a.extensions;if(a.collection_type){this.collectionType=new CollectionTypeDescription(a.collection_type)}else{this.collectionType=ANY_COLLECTION_TYPE_DESCRIPTION}},connect:function(b){BaseInputTerminal.prototype.connect.call(this,b);var a=b.handle1;if(!a){return}var c=this._effectiveMapOver(a);this.setMapOver(c)},_effectiveMapOver:function(a){var b=this.collectionType;var c=this._otherCollectionType(a);if(!b.canMatch(c)){return c.effectiveMapOver(b)}else{return NULL_COLLECTION_TYPE_DESCRIPTION}},_effectiveCollectionType:function(){var b=this.collectionType;var a=this.mapOver();return a.append(b)},attachable:function(b){var g=this._otherCollectionType(b);if(g.isCollection){var f=this._effectiveCollectionType();var a=this.mapOver();if(f.canMatch(g)){return this._producesAcceptableDatatype(b)}else{if(a.isCollection){return false}else{if(g.canMapOver(this.collectionType)){var d=this._effectiveMapOver(b);if(!d.isCollection){return false}var c=this._mappingConstraints();if(c.every(d.canMatch)){return this._producesAcceptableDatatype(b)}}}}}return false}});var OutputCollectionTerminal=Terminal.extend({initialize:function(a){Terminal.prototype.initialize.call(this,a);this.datatypes=a.datatypes;this.collectionType=new CollectionTypeDescription(a.collection_type);this.isDataCollectionInput=true},update:function(a){var b=new CollectionTypeDescription(a.collection_type);if(b.collectionType!=this.collectionType.collectionType){_.each(this.connectors,function(c){c.destroy()})}this.collectionType=b}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},destroyIfInvalid:function(){if(this.handle1&&this.handle2&&!this.handle2.attachable(this.handle1)){this.destroy()}},redraw:function(){var f=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}f.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var v=function(c){return $(c).offset().left-f.offset().left};var p=function(c){return $(c).offset().top-f.offset().top};if(!this.handle1||!this.handle2){return}var o=v(this.handle1.element)+5;var n=p(this.handle1.element)+5;var x=v(this.handle2.element)+5;var u=p(this.handle2.element)+5;var k=100;var r=Math.min(o,x);var a=Math.max(o,x);var q=Math.min(n,u);var B=Math.max(n,u);var d=Math.min(Math.max(Math.abs(B-q)/2,100),300);var w=r-k;var A=q-k;var y=a-r+2*k;var s=B-q+2*k;this.canvas.style.left=w+"px";this.canvas.style.top=A+"px";this.canvas.setAttribute("width",y);this.canvas.setAttribute("height",s);o-=w;n-=A;x-=w;u-=A;var z=this.canvas.getContext("2d"),h=null,l=null;var g=1;if(this.handle1&&this.handle1.isMappedOver()){var h=[-6,-3,0,3,6];g=5}else{var h=[0]}if(this.handle2&&this.handle2.isMappedOver()){var l=[-6,-3,0,3,6];g=5}else{var l=[0]}var b=this;for(var t=0;t<g;t++){var m=5,j=7;if(h.length>1||l.length>1){m=1;j=3}b.draw_outlined_curve(o,n,x,u,d,m,j,h[t%h.length],l[t%l.length])}},draw_outlined_curve:function(j,i,l,k,a,b,f,g,d){var g=g||0;var d=d||0;var h=this.canvas.getContext("2d");h.lineCap="round";h.strokeStyle=this.outer_color;h.lineWidth=f;h.beginPath();h.moveTo(j,i+g);h.bezierCurveTo(j+a,i+g,l-a,k+d,l,k+d);h.stroke();h.strokeStyle=this.inner_color;h.lineWidth=b;h.beginPath();h.moveTo(j,i+g);h.bezierCurveTo(j+a,i+g,l-a,k+d,l,k+d);h.stroke()}});var Node=Backbone.Model.extend({initialize:function(a){this.element=a.element;this.input_terminals={};this.output_terminals={};this.tool_errors={}},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(b){var a=[];$.each(b,function(c,d){if(d.connectors.length>0){a.push(d)}});return a},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a){if(a[b].connectors.length>0){return true}}return false},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var c=this.input_terminals;for(var b in c){var a=c[b];if(a.connectors.length>0&&a.isMappedOver()){return true}}return false},_connectedMappedTerminals:function(b){var a=[];$.each(b,function(c,d){var f=d.mapOver();if(f.isCollection){if(d.connectors.length>0){a.push(d)}}});return a},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(b){var a=[];$.each(b,function(c,d){var f=d.mapOver();if(f.isCollection){a.push(d)}});return a},hasMappedOverInputTerminals:function(){var a=false;_.each(this.input_terminals,function(b){var c=b.mapOver();if(c.isCollection){a=true}});return a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(b){if(b.type){this.type=b.type}this.name=b.name;this.form_html=b.form_html;this.tool_state=b.tool_state;this.tool_errors=b.tool_errors;this.tooltip=b.tooltip?b.tooltip:"";this.annotation=b.annotation;this.post_job_actions=b.post_job_actions?b.post_job_actions:{};this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var a=this;var c=new NodeView({el:this.element[0],node:a,});a.nodeView=c;$.each(b.data_inputs,function(f,d){c.addDataInput(d)});if((b.data_inputs.length>0)&&(b.data_outputs.length>0)){c.addRule()}$.each(b.data_outputs,function(f,d){c.addDataOutput(d)});c.render();workflow.node_changed(this)},update_field_data:function(d){var c=this;nodeView=c.nodeView;this.tool_state=d.tool_state;this.form_html=d.form_html;this.tool_errors=d.tool_errors;this.annotation=d.annotation;if("post_job_actions" in d){var f=$.parseJSON(d.post_job_actions);this.post_job_actions=f?f:{}}c.nodeView.renderToolErrors();var g=nodeView.$("div.inputs");var a=nodeView.newInputsDiv();var b={};_.each(d.data_inputs,function(h){var i=c.nodeView.addDataInput(h,a);b[h.name]=i});_.each(_.difference(_.values(nodeView.terminalViews),_.values(b)),function(h){h.el.terminal.destroy()});nodeView.terminalViews=b;if(d.data_outputs.length==1&&"collection_type" in d.data_outputs[0]){nodeView.updateDataOutput(d.data_outputs[0])}g.replaceWith(a);this.markChanged();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},markChanged:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node(f.type,f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if(!$.isArray(h)){h=[h]}$.each(h,function(k,j){var m=wf.nodes[j.id];var n=new Connector();n.connect(m.output_terminals[j.output_name],d.input_terminals[i]);n.redraw()})}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node({element:i});g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa fa-times").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}function add_node(b,d,a){var c=prebuild_node(b,d,a);workflow.add_node(c);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview();workflow.activate_node(c);return c}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}var NodeView=Backbone.View.extend({initialize:function(a){this.node=a.node;this.output_width=Math.max(150,this.$el.width());this.tool_body=this.$el.find(".toolFormBody");this.tool_body.find("div").remove();this.newInputsDiv().appendTo(this.tool_body);this.terminalViews={};this.outputTerminlViews={}},render:function(){this.renderToolErrors();this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){if(this.node.tool_errors){this.$el.addClass("tool-node-error")}else{this.$el.removeClass("tool-node-error")}},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(i,d){var j=true;if(!d){d=this.$(".inputs");j=false}var f=this.terminalViews[i.name];var h=(i.input_type=="dataset_collection")?InputCollectionTerminalView:InputTerminalView;if(f&&!(f instanceof h)){f.el.terminal.destroy();f=null}if(!f){f=new h({node:this.node,input:i})}else{var g=f.el.terminal;g.update(i);g.destroyInvalidConnections()}this.terminalViews[i.name]=f;var c=f.el;var b=new DataInputView({terminalElement:c,input:i,nodeView:this,skipResize:j});var a=b.$el;d.append(a.prepend(f.terminalElements()));return f},addDataOutput:function(a){var d=(a.collection_type)?OutputCollectionTerminalView:OutputTerminalView;var c=new d({node:this.node,output:a});var b=new DataOutputView({output:a,terminalElement:c.el,nodeView:this,});this.tool_body.append(b.$el.append(c.terminalElements()))},updateDataOutput:function(b){var a=this.node.output_terminals[b.name];a.update(b)}});var DataInputView=Backbone.View.extend({className:"form-row dataRow input-data-row",initialize:function(a){this.input=a.input;this.nodeView=a.nodeView;this.terminalElement=a.terminalElement;this.$el.attr("name",this.input.name).html(this.input.label);if(!a.skipResize){this.$el.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(this.el);this.nodeView.updateMaxWidth(this.$el.outerWidth());this.$el.css({position:"",left:"",top:"",display:""});this.$el.remove()}},});var OutputCalloutView=Backbone.View.extend({tagName:"div",initialize:function(b){this.label=b.label;this.node=b.node;this.output=b.output;var a=this;this.$el.attr("class","callout "+this.label).css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(a.output.name,a.node.workflow_outputs)!=-1){a.node.workflow_outputs.splice($.inArray(a.output.name,a.node.workflow_outputs),1);a.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{a.node.workflow_outputs.push(a.output.name);a.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."});this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});this.$el.show();this.resetImage()},resetImage:function(){if($.inArray(this.output.name,this.node.workflow_outputs)===-1){this.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{this.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}},hoverImage:function(){this.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")}});var DataOutputView=Backbone.View.extend({className:"form-row dataRow",initialize:function(c){this.output=c.output;this.terminalElement=c.terminalElement;this.nodeView=c.nodeView;var a=this.output;var b=a.name;var f=this.nodeView.node;var d=a.extensions.indexOf("input")>=0||a.extensions.indexOf("input_collection")>=0;if(!d){b=b+" ("+a.extensions.join(", ")+")"}this.$el.html(b);if(f.type=="tool"){var g=new OutputCalloutView({label:b,output:a,node:f,});this.$el.append(g.el);this.$el.hover(function(){g.hoverImage()},function(){g.resetImage()})}this.$el.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(this.el);this.nodeView.updateMaxWidth(this.$el.outerWidth()+17);this.$el.css({position:"",left:"",top:"",display:""}).detach()}});var TerminalView=Backbone.View.extend({setupMappingView:function(b){var c=new this.terminalMappingClass({terminal:b});var a=new this.terminalMappingViewClass({model:c});a.render();b.terminalMappingView=a;this.terminalMappingView=a},terminalElements:function(){if(this.terminalMappingView){return[this.terminalMappingView.el,this.el]}else{return[this.el]}}});var BaseInputTerminalView=TerminalView.extend({className:"terminal input-terminal",initialize:function(c){var f=c.node;var a=c.input;var b=a.name;var d=this.terminalForInput(a);if(!d.multiple){this.setupMappingView(d)}this.el.terminal=d;d.node=f;d.name=b;f.input_terminals[b]=d},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover",},onDropInit:function(b,c){var a=this.el.terminal;return $(c.drag).hasClass("output-terminal")&&a.canAccept(c.drag.terminal)},onDropStart:function(a,b){if(b.proxy.terminal){b.proxy.terminal.connectors[0].inner_color="#BBFFBB"}},onDropEnd:function(a,b){if(b.proxy.terminal){b.proxy.terminal.connectors[0].inner_color="#FFFFFF"}},onDrop:function(b,c){var a=this.el.terminal;new Connector(c.drag.terminal,a).redraw()},onHover:function(){var c=this.el;var b=c.terminal;if(b.connectors.length>0){var a=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){$.each(b.connectors,function(f,d){if(d){d.destroy()}});a.remove()}))).bind("mouseleave",function(){$(this).remove()});a.css({top:$(c).offset().top-2,left:$(c).offset().left-a.width(),"padding-right":$(c).width()}).show()}},});var InputTerminalView=BaseInputTerminalView.extend({terminalMappingClass:InputTerminalMapping,terminalMappingViewClass:InputTerminalMappingView,terminalForInput:function(a){return new InputTerminal({element:this.el,input:a})},});var InputCollectionTerminalView=BaseInputTerminalView.extend({terminalMappingClass:InputCollectionTerminalMapping,terminalMappingViewClass:InputCollectionTerminalMappingView,terminalForInput:function(a){return new InputCollectionTerminal({element:this.el,input:a})},});var BaseOutputTerminalView=TerminalView.extend({className:"terminal output-terminal",initialize:function(c){var f=c.node;var a=c.output;var b=a.name;var d=this.terminalForOutput(a);this.setupMappingView(d);this.el.terminal=d;d.node=f;d.name=b;f.output_terminals[b]=d},events:{drag:"onDrag",dragstart:"onDragStart",dragend:"onDragEnd",},onDrag:function(b,c){var a=function(){var f=$(c.proxy).offsetParent().offset(),d=c.offsetX-f.left,g=c.offsetY-f.top;$(c.proxy).css({left:d,top:g});c.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};a();$("#canvas-container").get(0).scroll_panel.test(b,a)},onDragStart:function(b,f){$(f.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var a=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);a.terminal=new OutputTerminal({element:a});var g=new Connector();g.dragging=true;g.connect(this.el.terminal,a.terminal);return a},onDragEnd:function(a,b){b.proxy.terminal.connectors[0].destroy();$(b.proxy).remove();$(b.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()}});var OutputTerminalView=BaseOutputTerminalView.extend({terminalMappingClass:OutputTerminalMapping,terminalMappingViewClass:OutputTerminalMappingView,terminalForOutput:function(a){var c=a.extensions;var b=new OutputTerminal({element:this.el,datatypes:c});return b},});var OutputCollectionTerminalView=BaseOutputTerminalView.extend({terminalMappingClass:OutputCollectionTerminalMapping,terminalMappingViewClass:OutputCollectionTerminalMappingView,terminalForOutput:function(a){var c=a.collection_type;var b=new OutputCollectionTerminal({element:this.el,collection_type:c,datatypes:a.extensions});return b},});function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
+function CollectionTypeDescription(a){this.collectionType=a;this.isCollection=true;this.rank=a.split(":").length}$.extend(CollectionTypeDescription.prototype,{append:function(a){if(a===NULL_COLLECTION_TYPE_DESCRIPTION){return this}if(a===ANY_COLLECTION_TYPE_DESCRIPTION){return otherCollectionType}return new CollectionTypeDescription(this.collectionType+":"+a.collectionType)},canMatch:function(a){if(a===NULL_COLLECTION_TYPE_DESCRIPTION){return false}if(a===ANY_COLLECTION_TYPE_DESCRIPTION){return true}return a.collectionType==this.collectionType},canMapOver:function(b){if(b===NULL_COLLECTION_TYPE_DESCRIPTION){return false}if(b===ANY_COLLECTION_TYPE_DESCRIPTION){return false}if(this.rank<=b.rank){return false}var a=b.collectionType;return this._endsWith(this.collectionType,a)},effectiveMapOver:function(a){var c=a.collectionType;var b=this.collectionType.substring(0,this.collectionType.length-c.length-1);return new CollectionTypeDescription(b)},equal:function(a){return a.collectionType==this.collectionType},toString:function(){return"CollectionType["+this.collectionType+"]"},_endsWith:function(b,a){return b.indexOf(a,b.length-a.length)!==-1}});NULL_COLLECTION_TYPE_DESCRIPTION={isCollection:false,canMatch:function(a){return false},canMapOver:function(a){return false},toString:function(){return"NullCollectionType[]"},append:function(a){return a},equal:function(a){return a===this}};ANY_COLLECTION_TYPE_DESCRIPTION={isCollection:true,canMatch:function(a){return NULL_COLLECTION_TYPE_DESCRIPTION!==a},canMapOver:function(a){return false},toString:function(){return"AnyCollectionType[]"},append:function(a){throw"Cannot append to ANY_COLLECTION_TYPE_DESCRIPTION"},equal:function(a){return a===this}};var TerminalMapping=Backbone.Model.extend({initialize:function(a){this.mapOver=a.mapOver||NULL_COLLECTION_TYPE_DESCRIPTION;this.terminal=a.terminal;this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(NULL_COLLECTION_TYPE_DESCRIPTION)},setMapOver:function(a){this.mapOver=a;this.trigger("change")}});var TerminalMappingView=Backbone.View.extend({tagName:"div",className:"fa-icon-button fa fa-folder-o",initialize:function(b){var a="Run tool in parallel over collection";this.$el.tooltip({delay:500,title:a});this.model.bind("change",_.bind(this.render,this))},render:function(){if(this.model.mapOver.isCollection){this.$el.show()}else{this.$el.hide()}},});var InputTerminalMappingView=TerminalMappingView.extend({events:{click:"onClick",mouseenter:"onMouseEnter",mouseleave:"onMouseLeave",},onMouseEnter:function(b){var a=this.model;if(!a.terminal.connected()&&a.mapOver.isCollection){this.$el.css("color","red")}},onMouseLeave:function(a){this.$el.css("color","black")},onClick:function(b){var a=this.model;if(!a.terminal.connected()&&a.mapOver.isCollection){a.terminal.resetMapping()}},});var InputTerminalMapping=TerminalMapping;var InputCollectionTerminalMapping=TerminalMapping;var OutputTerminalMapping=TerminalMapping;var OutputTerminalMappingView=TerminalMappingView;var InputCollectionTerminalMappingView=InputTerminalMappingView;var OutputCollectionTerminalMapping=TerminalMapping;var OutputCollectionTerminalMappingView=TerminalMappingView;var Terminal=Backbone.Model.extend({initialize:function(a){this.element=a.element;this.connectors=[]},connect:function(a){this.connectors.push(a);if(this.node){this.node.markChanged()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.markChanged();this.resetMappingIfNeeded()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})},destroyInvalidConnections:function(){_.each(this.connectors,function(a){a.destroyIfInvalid()})},setMapOver:function(a){if(this.multiple){return}if(!this.mapOver().equal(a)){this.terminalMapping.setMapOver(a);_.each(this.node.output_terminals,function(b){b.setMapOver(a)})}},mapOver:function(){if(!this.terminalMapping){return NULL_COLLECTION_TYPE_DESCRIPTION}else{return this.terminalMapping.mapOver}},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){},});var OutputTerminal=Terminal.extend({initialize:function(a){Terminal.prototype.initialize.call(this,a);this.datatypes=a.datatypes},resetMappingIfNeeded:function(){if(!this.node.hasConnectedOutputTerminals()&&!this.node.hasConnectedMappedInputTerminals()){_.each(this.node.mappedInputTerminals(),function(b){b.resetMappingIfNeeded()})}var a=!this.node.hasMappedOverInputTerminals();if(a){this.resetMapping()}},resetMapping:function(){this.terminalMapping.disableMapOver();_.each(this.connectors,function(a){var b=a.handle2;if(b){b.resetMappingIfNeeded();a.destroyIfInvalid()}})}});var BaseInputTerminal=Terminal.extend({initialize:function(a){Terminal.prototype.initialize.call(this,a);this.update(a.input)},canAccept:function(a){if(this._inputFilled()){return false}else{return this.attachable(a)}},resetMappingIfNeeded:function(){var b=this.mapOver();if(!b.isCollection){return}var a=this.node.hasConnectedMappedInputTerminals()||(!this.node.hasConnectedOutputTerminals());if(a){this.resetMapping()}},resetMapping:function(){this.terminalMapping.disableMapOver();if(!this.node.hasMappedOverInputTerminals()){_.each(this.node.output_terminals,function(a){a.resetMapping()})}},connected:function(){return this.connectors.length!==0},_inputFilled:function(){var a;if(!this.connected()){a=false}else{if(this.multiple){if(!this.connected()){a=false}else{var b=this.connectors[0].handle1;if(!b){a=false}else{if(b.isDataCollectionInput||b.isMappedOver()||b.datatypes.indexOf("input_collection")>0){a=true}else{a=false}}}}else{a=true}}return a},_mappingConstraints:function(){if(!this.node){return[]}var b=this.mapOver();if(b.isCollection){return[b]}var a=[];if(!this.node.hasConnectedOutputTerminals()){_.each(this.node.connectedMappedInputTerminals(),function(c){a.push(c.mapOver())})}else{a.push(_.first(_.values(this.node.output_terminals)).mapOver())}return a},_producesAcceptableDatatype:function(a){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){var h=f[b];if(h=="input"||h=="input_collection"||issubtype(f[b],this.datatypes[c])){return true}}}return false},_otherCollectionType:function(a){var c=NULL_COLLECTION_TYPE_DESCRIPTION;if(a.isDataCollectionInput){c=a.collectionType}else{var b=a.mapOver();if(b.isCollection){c=b}}return c},});var InputTerminal=BaseInputTerminal.extend({update:function(a){this.datatypes=a.extensions;this.multiple=a.multiple;this.collection=false},connect:function(a){BaseInputTerminal.prototype.connect.call(this,a);var b=a.handle1;if(!b){return}var c=this._otherCollectionType(b);if(c.isCollection){this.setMapOver(c)}},attachable:function(b){var d=this._otherCollectionType(b);var a=this.mapOver();if(d.isCollection){if(this.multiple){if(this.connected()){return false}if(d.rank==1){return this._producesAcceptableDatatype(b)}else{return false}}if(a.isCollection&&a.canMatch(d)){return this._producesAcceptableDatatype(b)}else{var c=this._mappingConstraints();if(c.every(_.bind(d.canMatch,d))){return this._producesAcceptableDatatype(b)}else{return false}}}else{if(a.isCollection){return false}}return this._producesAcceptableDatatype(b)}});var InputCollectionTerminal=BaseInputTerminal.extend({update:function(a){this.multiple=false;this.collection=true;this.datatypes=a.extensions;if(a.collection_type){this.collectionType=new CollectionTypeDescription(a.collection_type)}else{this.collectionType=ANY_COLLECTION_TYPE_DESCRIPTION}},connect:function(b){BaseInputTerminal.prototype.connect.call(this,b);var a=b.handle1;if(!a){return}var c=this._effectiveMapOver(a);this.setMapOver(c)},_effectiveMapOver:function(a){var b=this.collectionType;var c=this._otherCollectionType(a);if(!b.canMatch(c)){return c.effectiveMapOver(b)}else{return NULL_COLLECTION_TYPE_DESCRIPTION}},_effectiveCollectionType:function(){var b=this.collectionType;var a=this.mapOver();return a.append(b)},attachable:function(b){var g=this._otherCollectionType(b);if(g.isCollection){var f=this._effectiveCollectionType();var a=this.mapOver();if(f.canMatch(g)){return this._producesAcceptableDatatype(b)}else{if(a.isCollection){return false}else{if(g.canMapOver(this.collectionType)){var d=this._effectiveMapOver(b);if(!d.isCollection){return false}var c=this._mappingConstraints();if(c.every(d.canMatch)){return this._producesAcceptableDatatype(b)}}}}}return false}});var OutputCollectionTerminal=Terminal.extend({initialize:function(a){Terminal.prototype.initialize.call(this,a);this.datatypes=a.datatypes;this.collectionType=new CollectionTypeDescription(a.collection_type);this.isDataCollectionInput=true},update:function(a){var b=new CollectionTypeDescription(a.collection_type);if(b.collectionType!=this.collectionType.collectionType){_.each(this.connectors,function(c){c.destroy()})}this.collectionType=b}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},destroyIfInvalid:function(){if(this.handle1&&this.handle2&&!this.handle2.attachable(this.handle1)){this.destroy()}},redraw:function(){var f=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}f.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var v=function(c){return $(c).offset().left-f.offset().left};var p=function(c){return $(c).offset().top-f.offset().top};if(!this.handle1||!this.handle2){return}var o=v(this.handle1.element)+5;var n=p(this.handle1.element)+5;var x=v(this.handle2.element)+5;var u=p(this.handle2.element)+5;var k=100;var r=Math.min(o,x);var a=Math.max(o,x);var q=Math.min(n,u);var B=Math.max(n,u);var d=Math.min(Math.max(Math.abs(B-q)/2,100),300);var w=r-k;var A=q-k;var y=a-r+2*k;var s=B-q+2*k;this.canvas.style.left=w+"px";this.canvas.style.top=A+"px";this.canvas.setAttribute("width",y);this.canvas.setAttribute("height",s);o-=w;n-=A;x-=w;u-=A;var z=this.canvas.getContext("2d"),h=null,l=null;var g=1;if(this.handle1&&this.handle1.isMappedOver()){var h=[-6,-3,0,3,6];g=5}else{var h=[0]}if(this.handle2&&this.handle2.isMappedOver()){var l=[-6,-3,0,3,6];g=5}else{var l=[0]}var b=this;for(var t=0;t<g;t++){var m=5,j=7;if(h.length>1||l.length>1){m=1;j=3}b.draw_outlined_curve(o,n,x,u,d,m,j,h[t%h.length],l[t%l.length])}},draw_outlined_curve:function(j,i,l,k,a,b,f,g,d){var g=g||0;var d=d||0;var h=this.canvas.getContext("2d");h.lineCap="round";h.strokeStyle=this.outer_color;h.lineWidth=f;h.beginPath();h.moveTo(j,i+g);h.bezierCurveTo(j+a,i+g,l-a,k+d,l,k+d);h.stroke();h.strokeStyle=this.inner_color;h.lineWidth=b;h.beginPath();h.moveTo(j,i+g);h.bezierCurveTo(j+a,i+g,l-a,k+d,l,k+d);h.stroke()}});var Node=Backbone.Model.extend({initialize:function(a){this.element=a.element;this.input_terminals={};this.output_terminals={};this.tool_errors={}},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(b){var a=[];$.each(b,function(c,d){if(d.connectors.length>0){a.push(d)}});return a},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a){if(a[b].connectors.length>0){return true}}return false},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var c=this.input_terminals;for(var b in c){var a=c[b];if(a.connectors.length>0&&a.isMappedOver()){return true}}return false},_connectedMappedTerminals:function(b){var a=[];$.each(b,function(c,d){var f=d.mapOver();if(f.isCollection){if(d.connectors.length>0){a.push(d)}}});return a},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(b){var a=[];$.each(b,function(c,d){var f=d.mapOver();if(f.isCollection){a.push(d)}});return a},hasMappedOverInputTerminals:function(){var a=false;_.each(this.input_terminals,function(b){var c=b.mapOver();if(c.isCollection){a=true}});return a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(b){if(b.type){this.type=b.type}this.name=b.name;this.form_html=b.form_html;this.tool_state=b.tool_state;this.tool_errors=b.tool_errors;this.tooltip=b.tooltip?b.tooltip:"";this.annotation=b.annotation;this.post_job_actions=b.post_job_actions?b.post_job_actions:{};this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var a=this;var c=new NodeView({el:this.element[0],node:a,});a.nodeView=c;$.each(b.data_inputs,function(f,d){c.addDataInput(d)});if((b.data_inputs.length>0)&&(b.data_outputs.length>0)){c.addRule()}$.each(b.data_outputs,function(f,d){c.addDataOutput(d)});c.render();workflow.node_changed(this)},update_field_data:function(d){var c=this;nodeView=c.nodeView;this.tool_state=d.tool_state;this.form_html=d.form_html;this.tool_errors=d.tool_errors;this.annotation=d.annotation;if("post_job_actions" in d){var f=$.parseJSON(d.post_job_actions);this.post_job_actions=f?f:{}}c.nodeView.renderToolErrors();var g=nodeView.$("div.inputs");var a=nodeView.newInputsDiv();var b={};_.each(d.data_inputs,function(h){var i=c.nodeView.addDataInput(h,a);b[h.name]=i});_.each(_.difference(_.values(nodeView.terminalViews),_.values(b)),function(h){h.el.terminal.destroy()});nodeView.terminalViews=b;if(d.data_outputs.length==1&&"collection_type" in d.data_outputs[0]){nodeView.updateDataOutput(d.data_outputs[0])}g.replaceWith(a);this.markChanged();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},markChanged:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node(f.type,f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if(!$.isArray(h)){h=[h]}$.each(h,function(k,j){var m=wf.nodes[j.id];var n=new Connector();n.connect(m.output_terminals[j.output_name],d.input_terminals[i]);n.redraw()})}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node({element:i});g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa fa-times").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}function add_node(b,d,a){var c=prebuild_node(b,d,a);workflow.add_node(c);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview();workflow.activate_node(c);return c}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}var NodeView=Backbone.View.extend({initialize:function(a){this.node=a.node;this.output_width=Math.max(150,this.$el.width());this.tool_body=this.$el.find(".toolFormBody");this.tool_body.find("div").remove();this.newInputsDiv().appendTo(this.tool_body);this.terminalViews={};this.outputTerminlViews={}},render:function(){this.renderToolErrors();this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){if(this.node.tool_errors){this.$el.addClass("tool-node-error")}else{this.$el.removeClass("tool-node-error")}},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(i,d){var j=true;if(!d){d=this.$(".inputs");j=false}var f=this.terminalViews[i.name];var h=(i.input_type=="dataset_collection")?InputCollectionTerminalView:InputTerminalView;if(f&&!(f instanceof h)){f.el.terminal.destroy();f=null}if(!f){f=new h({node:this.node,input:i})}else{var g=f.el.terminal;g.update(i);g.destroyInvalidConnections()}this.terminalViews[i.name]=f;var c=f.el;var b=new DataInputView({terminalElement:c,input:i,nodeView:this,skipResize:j});var a=b.$el;d.append(a.prepend(f.terminalElements()));return f},addDataOutput:function(a){var d=(a.collection_type)?OutputCollectionTerminalView:OutputTerminalView;var c=new d({node:this.node,output:a});var b=new DataOutputView({output:a,terminalElement:c.el,nodeView:this,});this.tool_body.append(b.$el.append(c.terminalElements()))},updateDataOutput:function(b){var a=this.node.output_terminals[b.name];a.update(b)}});var DataInputView=Backbone.View.extend({className:"form-row dataRow input-data-row",initialize:function(a){this.input=a.input;this.nodeView=a.nodeView;this.terminalElement=a.terminalElement;this.$el.attr("name",this.input.name).html(this.input.label);if(!a.skipResize){this.$el.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(this.el);this.nodeView.updateMaxWidth(this.$el.outerWidth());this.$el.css({position:"",left:"",top:"",display:""});this.$el.remove()}},});var OutputCalloutView=Backbone.View.extend({tagName:"div",initialize:function(b){this.label=b.label;this.node=b.node;this.output=b.output;var a=this;this.$el.attr("class","callout "+this.label).css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(a.output.name,a.node.workflow_outputs)!=-1){a.node.workflow_outputs.splice($.inArray(a.output.name,a.node.workflow_outputs),1);a.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{a.node.workflow_outputs.push(a.output.name);a.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."});this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});this.$el.show();this.resetImage()},resetImage:function(){if($.inArray(this.output.name,this.node.workflow_outputs)===-1){this.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{this.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}},hoverImage:function(){this.$("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")}});var DataOutputView=Backbone.View.extend({className:"form-row dataRow",initialize:function(c){this.output=c.output;this.terminalElement=c.terminalElement;this.nodeView=c.nodeView;var a=this.output;var b=a.name;var f=this.nodeView.node;var d=a.extensions.indexOf("input")>=0||a.extensions.indexOf("input_collection")>=0;if(!d){b=b+" ("+a.extensions.join(", ")+")"}this.$el.html(b);if(f.type=="tool"){var g=new OutputCalloutView({label:b,output:a,node:f,});this.$el.append(g.el);this.$el.hover(function(){g.hoverImage()},function(){g.resetImage()})}this.$el.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(this.el);this.nodeView.updateMaxWidth(this.$el.outerWidth()+17);this.$el.css({position:"",left:"",top:"",display:""}).detach()}});var TerminalView=Backbone.View.extend({setupMappingView:function(b){var c=new this.terminalMappingClass({terminal:b});var a=new this.terminalMappingViewClass({model:c});a.render();b.terminalMappingView=a;this.terminalMappingView=a},terminalElements:function(){if(this.terminalMappingView){return[this.terminalMappingView.el,this.el]}else{return[this.el]}}});var BaseInputTerminalView=TerminalView.extend({className:"terminal input-terminal",initialize:function(c){var f=c.node;var a=c.input;var b=a.name;var d=this.terminalForInput(a);if(!d.multiple){this.setupMappingView(d)}this.el.terminal=d;d.node=f;d.name=b;f.input_terminals[b]=d},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover",},onDropInit:function(b,c){var a=this.el.terminal;return $(c.drag).hasClass("output-terminal")&&a.canAccept(c.drag.terminal)},onDropStart:function(a,b){if(b.proxy.terminal){b.proxy.terminal.connectors[0].inner_color="#BBFFBB"}},onDropEnd:function(a,b){if(b.proxy.terminal){b.proxy.terminal.connectors[0].inner_color="#FFFFFF"}},onDrop:function(b,c){var a=this.el.terminal;new Connector(c.drag.terminal,a).redraw()},onHover:function(){var c=this.el;var b=c.terminal;if(b.connectors.length>0){var a=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){$.each(b.connectors,function(f,d){if(d){d.destroy()}});a.remove()}))).bind("mouseleave",function(){$(this).remove()});a.css({top:$(c).offset().top-2,left:$(c).offset().left-a.width(),"padding-right":$(c).width()}).show()}},});var InputTerminalView=BaseInputTerminalView.extend({terminalMappingClass:InputTerminalMapping,terminalMappingViewClass:InputTerminalMappingView,terminalForInput:function(a){return new InputTerminal({element:this.el,input:a})},});var InputCollectionTerminalView=BaseInputTerminalView.extend({terminalMappingClass:InputCollectionTerminalMapping,terminalMappingViewClass:InputCollectionTerminalMappingView,terminalForInput:function(a){return new InputCollectionTerminal({element:this.el,input:a})},});var BaseOutputTerminalView=TerminalView.extend({className:"terminal output-terminal",initialize:function(c){var f=c.node;var a=c.output;var b=a.name;var d=this.terminalForOutput(a);this.setupMappingView(d);this.el.terminal=d;d.node=f;d.name=b;f.output_terminals[b]=d},events:{drag:"onDrag",dragstart:"onDragStart",dragend:"onDragEnd",},onDrag:function(b,c){var a=function(){var f=$(c.proxy).offsetParent().offset(),d=c.offsetX-f.left,g=c.offsetY-f.top;$(c.proxy).css({left:d,top:g});c.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};a();$("#canvas-container").get(0).scroll_panel.test(b,a)},onDragStart:function(b,f){$(f.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var a=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);a.terminal=new OutputTerminal({element:a});var g=new Connector();g.dragging=true;g.connect(this.el.terminal,a.terminal);return a},onDragEnd:function(a,b){b.proxy.terminal.connectors[0].destroy();$(b.proxy).remove();$(b.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()}});var OutputTerminalView=BaseOutputTerminalView.extend({terminalMappingClass:OutputTerminalMapping,terminalMappingViewClass:OutputTerminalMappingView,terminalForOutput:function(a){var c=a.extensions;var b=new OutputTerminal({element:this.el,datatypes:c});return b},});var OutputCollectionTerminalView=BaseOutputTerminalView.extend({terminalMappingClass:OutputCollectionTerminalMapping,terminalMappingViewClass:OutputCollectionTerminalMappingView,terminalForOutput:function(a){var c=a.collection_type;var b=new OutputCollectionTerminal({element:this.el,collection_type:c,datatypes:a.extensions});return b},});function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/mvc/collection/dataset-collection-base.js
--- a/static/scripts/packed/mvc/collection/dataset-collection-base.js
+++ b/static/scripts/packed/mvc/collection/dataset-collection-base.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(b,a){var c=a.HistoryContentBaseView.extend({className:"dataset hda history-panel-hda",id:function(){return"hdca-"+this.model.get("id")},initialize:function(d){if(d.logger){this.logger=this.model.logger=d.logger}this.log(this+".initialize:",d);this.selectable=d.selectable||false;this.selected=d.selected||false;this.expanded=d.expanded||false},render:function(e){var d=this._buildNewRender();this._queueNewRender(d,e);return this},templateSkeleton:function(){return['<div class="dataset hda">','<div class="dataset-warnings">',"<% if ( deleted ) { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</div>","<% } %>","<% if ( ! visible ) { %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%= hid %></span> ','<span class="dataset-name"><%= name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("")},templateBody:function(){return['<div class="dataset-body">','<div class="dataset-summary">',"A dataset collection.","</div>"].join("")},_buildNewRender:function(){var d=$(_.template(this.templateSkeleton(),this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);return d},_render_titleButtons:function(){return[]},_render_body:function(){var e=$('<div>Error: unknown state "'+this.model.get("state")+'".</div>'),d=this["_render_body_"+this.model.get("state")];if(_.isFunction(d)){e=d.call(this)}this._setUpBehaviors(e);if(this.expanded){e.show()}return e},_setUpBehaviors:function(d){d=d||this.$el;make_popup_menus(d);d.find("[title]").tooltip({placement:"bottom"})},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var d=this;function e(){d.$el.children(".dataset-body").replaceWith(d._render_body());d.$el.children(".dataset-body").slideDown(d.fxSpeed,function(){d.expanded=true;d.trigger("body-expanded",d.model)})}e()},collapseBody:function(){var d=this;this.$el.children(".dataset-body").slideUp(d.fxSpeed,function(){d.expanded=false;d.trigger("body-collapsed",d.model.id)})},_render_body_ok:function(){var d=$(_.template(this.templateBody(),this.model.toJSON()));if(this.model.get("deleted")){return d}return d}});return{DatasetCollectionBaseView:c}});
\ No newline at end of file
+define(["mvc/history/history-content-base-view","utils/localization"],function(e,b){var c=e.HistoryContentBaseView.extend({className:"dataset hda history-panel-hda",id:function(){return"hdca-"+this.model.get("id")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false},render:function(g){var f=this._buildNewRender();this._queueNewRender(f,g);return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_queueNewRender:function(g,h){h=(h===undefined)?(true):(h);var f=this;if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()})},_render_titleButtons:function(){return[]},_render_body:function(){var g=$('<div>Error: unknown state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model)})}g()},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.id)})},_render_body_ok:function(){var f=$(c.templates.body(this.model.toJSON()));if(this.model.get("deleted")){return f}return f},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this,f);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this,f);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDCABaseView("+f+")"}});var a=_.template(['<div class="dataset hda">','<div class="dataset-warnings">',"<% if ( collection.deleted ) { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',b("This collection has been deleted."),"</div>","<% } %>","<% if ( !collection.visible ) { %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',b("This collection has been hidden."),"</div>","<% } %>","</div>",'<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>','<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%= collection.hid %></span> ','<span class="dataset-name"><%= collection.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join(""));var d=_.template(['<div class="dataset-body">','<div class="dataset-summary">',b("A dataset collection."),"</div>"].join(""));c.templates={skeleton:function(f){return a({_l:b,collection:f})},body:function(f){return d({_l:b,collection:f})}};return{DatasetCollectionBaseView:c}});
\ No newline at end of file
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/mvc/collection/dataset-collection-edit.js
--- a/static/scripts/packed/mvc/collection/dataset-collection-edit.js
+++ b/static/scripts/packed/mvc/collection/dataset-collection-edit.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/collection/dataset-collection-base",],function(b,c){var a=c.DatasetCollectionBaseView.extend({initialize:function(d){c.DatasetCollectionBaseView.prototype.initialize.call(this,d)},_render_titleButtons:function(){return c.DatasetCollectionBaseView.prototype._render_titleButtons.call(this).concat([this._render_deleteButton()])},_render_deleteButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var d=this,e={title:_l("Delete"),classes:"dataset-delete",onclick:function(){d.$el.find(".icon-btn.dataset-delete").trigger("mouseout");d.model["delete"]()}};if(this.model.get("deleted")){e={title:_l("Dataset collection is already deleted"),disabled:true}}e.faIcon="fa-times";return faIconButton(e)}});return{DatasetCollectionEditView:a}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/collection/dataset-collection-base","utils/localization"],function(c,d,b){var a=d.DatasetCollectionBaseView.extend({initialize:function(e){d.DatasetCollectionBaseView.prototype.initialize.call(this,e)},_render_titleButtons:function(){return d.DatasetCollectionBaseView.prototype._render_titleButtons.call(this).concat([this._render_deleteButton()])},_render_deleteButton:function(){if((this.model.get("state")===c.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===c.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var e=this,f={title:b("Delete"),classes:"dataset-delete",onclick:function(){e.$el.find(".icon-btn.dataset-delete").trigger("mouseout");e.model["delete"]()}};if(this.model.get("deleted")){f={title:b("Dataset collection is already deleted"),disabled:true}}f.faIcon="fa-times";return faIconButton(f)},toString:function(){var e=(this.model)?(this.model+""):("(no model)");return"HDCAEditView("+e+")"}});return{DatasetCollectionEditView:a}});
\ No newline at end of file
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/mvc/dataset/hda-base.js
--- a/static/scripts/packed/mvc/dataset/hda-base.js
+++ b/static/scripts/packed/mvc/dataset/hda-base.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/base-mvc","mvc/data","utils/localization"],function(e,b,g,d){var h=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",fxSpeed:"fast",_queueNewRender:function(j,k){k=(k===undefined)?(true):(k);var i=this;if(k){$(i).queue(function(l){this.$el.fadeOut(i.fxSpeed,l)})}$(i).queue(function(l){this.$el.empty().attr("class",i.className).addClass("state-"+i.model.get("state")).append(j.children());if(this.selectable){this.showSelector(0)}l()});if(k){$(i).queue(function(l){this.$el.fadeIn(i.fxSpeed,l)})}$(i).queue(function(l){this.trigger("rendered",i);if(this.model.inReadyState()){this.trigger("rendered:ready",i)}if(this.draggable){this.draggableOn()}l()})},toggleBodyVisibility:function(l,j){var i=32,k=13;if(l&&(l.type==="keydown")&&!(l.keyCode===i||l.keyCode===k)){return true}var m=this.$el.find(".dataset-body");j=(j===undefined)?(!m.is(":visible")):(j);if(j){this.expandBody()}else{this.collapseBody()}return false},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(i){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this,i);this.selected=true}return false},deselect:function(i){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this,i);this.selected=false}return false},toggleSelect:function(i){if(this.selected){this.deselect(i)}else{this.select(i)}}});var c=h.extend({className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+".initialize:",i);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=i.linkTarget||"_blank";this.selectable=i.selectable||false;this.selected=i.selected||false;this.expanded=i.expanded||false;this.draggable=i.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(j,i){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(j){this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var i=this._buildNewRender();this._queueNewRender(i,j);return this},_buildNewRender:function(){var i=$(c.templates.skeleton(this.model.toJSON()));i.find(".dataset-primary-actions").append(this._render_titleButtons());i.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(i);return i},_setUpBehaviors:function(i){i=i||this.$el;make_popup_menus(i);i.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===e.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===e.HistoryDatasetAssociation.STATES.DISCARDED)||(!this.model.get("accessible"))){return null}var j={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){j.disabled=true;j.title=d("Cannot display datasets removed from disk")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.UPLOAD){j.disabled=true;j.title=d("This dataset must finish uploading before it can be viewed")}else{if(this.model.get("state")===e.HistoryDatasetAssociation.STATES.NEW){j.disabled=true;j.title=d("This dataset is not yet viewable")}else{j.title=d("View data");j.href=this.urls.display;var i=this;j.onclick=function(k){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+i.model.get("name"),type:"other",content:function(l){var m=new g.TabularDataset({id:i.model.get("id")});$.when(m.fetch()).then(function(){g.createTabularDatasetChunkedView({model:m,parent_elt:l,embedded:true,height:"100%"})})}});k.preventDefault()}}}}}j.faIcon="fa-eye";return faIconButton(j)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var j=this.urls,k=this.model.get("meta_files");if(_.isEmpty(k)){return $(['<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var l="dataset-"+this.model.get("id")+"-popup",i=['<div popupmenu="'+l+'">','<a href="'+j.download+'">',d("Download dataset"),"</a>","<a>"+d("Additional files")+"</a>",_.map(k,function(m){return['<a class="action-button" href="',j.meta_download+m.file_type,'">',d("Download")," ",m.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+j.download+'" title="'+d("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+l+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(i)},_render_showParamsButton:function(){return faIconButton({title:d("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var j=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),i=this["_render_body_"+this.model.get("state")];if(_.isFunction(i)){j=i.call(this)}this._setUpBehaviors(j);if(this.expanded){j.show()}return j},_render_stateBodyHelper:function(i,l){l=l||[];var j=this,k=$(c.templates.body(_.extend(this.model.toJSON(),{body:i})));k.find(".dataset-actions .left").append(_.map(l,function(m){return m.call(j)}));return k},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+d("This is a new dataset and not all of its data are available yet")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+d("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+d("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+d("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+d("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+d("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+d("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+d('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var i=['<span class="help-text">',d("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){i="<div>"+this.model.get("misc_blurb")+"</div>"+i}return this._render_stateBodyHelper(i,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+d("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var i=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(d("An error occurred setting the metadata for this dataset"))),j=this._render_body_ok();j.prepend(i);return j},_render_body_ok:function(){var i=this,k=$(c.templates.body(this.model.toJSON())),j=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);k.find(".dataset-actions .left").append(_.map(j,function(l){return l.call(i)}));if(this.model.isDeletedOrPurged()){return k}return k},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},expandBody:function(){var i=this;function j(){i.$el.children(".dataset-body").replaceWith(i._render_body());i.$el.children(".dataset-body").slideDown(i.fxSpeed,function(){i.expanded=true;i.trigger("body-expanded",i.model)})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(k){i.urls=i.model.urls();j()})}else{j()}},collapseBody:function(){var i=this;this.$el.children(".dataset-body").slideUp(i.fxSpeed,function(){i.expanded=false;i.trigger("body-collapsed",i.model.id)})},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var i=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);i.addEventListener("dragstart",this.dragStartHandler,false);i.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var i=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);i.removeEventListener("dragstart",this.dragStartHandler,false);i.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(i){this.trigger("dragstart",this);i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(i){this.trigger("dragend",this);return false},remove:function(j){var i=this;this.$el.fadeOut(i.fxSpeed,function(){i.$el.remove();i.off();if(j){j()}})},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+i+")"}});var a=_.template(['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',d("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',d("This dataset has been deleted and removed from disk")+".","</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',d("This dataset has been deleted")+".","</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',d("This dataset has been hidden")+".","</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join(""));var f=_.template(['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',d("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',d("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join(""));c.templates={skeleton:function(i){return a({_l:d,hda:i})},body:function(i){return f({_l:d,hda:i})}};return{HistoryContentBaseView:h,HDABaseView:c}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/history/history-content-base-view","mvc/data","utils/localization"],function(d,g,f,c){var b=g.HistoryContentBaseView.extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(h){if(h.logger){this.logger=this.model.logger=h.logger}this.log(this+".initialize:",h);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=h.linkTarget||"_blank";this.selectable=h.selectable||false;this.selected=h.selected||false;this.expanded=h.expanded||false;this.draggable=h.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(i,h){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(i){this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var h=this._buildNewRender();this._queueNewRender(h,i);return this},_buildNewRender:function(){var h=$(b.templates.skeleton(this.model.toJSON()));h.find(".dataset-primary-actions").append(this._render_titleButtons());h.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(h);return h},_queueNewRender:function(i,j){j=(j===undefined)?(true):(j);var h=this;if(j){$(h).queue(function(k){this.$el.fadeOut(h.fxSpeed,k)})}$(h).queue(function(k){this.$el.empty().attr("class",h.className).addClass("state-"+h.model.get("state")).append(i.children());if(this.selectable){this.showSelector(0)}k()});if(j){$(h).queue(function(k){this.$el.fadeIn(h.fxSpeed,k)})}$(h).queue(function(k){this.trigger("rendered",h);if(this.model.inReadyState()){this.trigger("rendered:ready",h)}if(this.draggable){this.draggableOn()}k()})},_setUpBehaviors:function(h){h=h||this.$el;make_popup_menus(h);h.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(!this.model.get("accessible"))){return null}var i={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){i.disabled=true;i.title=c("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){i.disabled=true;i.title=c("This dataset must finish uploading before it can be viewed")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW){i.disabled=true;i.title=c("This dataset is not yet viewable")}else{i.title=c("View data");i.href=this.urls.display;var h=this;i.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+h.model.get("name"),type:"other",content:function(k){var l=new f.TabularDataset({id:h.model.get("id")});$.when(l.fetch()).then(function(){f.createTabularDatasetChunkedView({model:l,parent_elt:k,embedded:true,height:"100%"})})}});j.preventDefault()}}}}}i.faIcon="fa-eye";return faIconButton(i)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var i=this.urls,j=this.model.get("meta_files");if(_.isEmpty(j)){return $(['<a href="'+i.download+'" title="'+c("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var k="dataset-"+this.model.get("id")+"-popup",h=['<div popupmenu="'+k+'">','<a href="'+i.download+'">',c("Download dataset"),"</a>","<a>"+c("Additional files")+"</a>",_.map(j,function(l){return['<a class="action-button" href="',i.meta_download+l.file_type,'">',c("Download")," ",l.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+i.download+'" title="'+c("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+k+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(h)},_render_showParamsButton:function(){return faIconButton({title:c("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var i=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),h=this["_render_body_"+this.model.get("state")];if(_.isFunction(h)){i=h.call(this)}this._setUpBehaviors(i);if(this.expanded){i.show()}return i},_render_stateBodyHelper:function(h,k){k=k||[];var i=this,j=$(b.templates.body(_.extend(this.model.toJSON(),{body:h})));j.find(".dataset-actions .left").append(_.map(k,function(l){return l.call(i)}));return j},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+c("This is a new dataset and not all of its data are available yet")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+c("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+c("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+c("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+c("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+c("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+c("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var h=['<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){h="<div>"+this.model.get("misc_blurb")+"</div>"+h}return this._render_stateBodyHelper(h,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+c("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var h=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(c("An error occurred setting the metadata for this dataset"))),i=this._render_body_ok();i.prepend(h);return i},_render_body_ok:function(){var h=this,j=$(b.templates.body(this.model.toJSON())),i=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);j.find(".dataset-actions .left").append(_.map(i,function(k){return k.call(h)}));if(this.model.isDeletedOrPurged()){return j}return j},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(k,i){var h=32,j=13;if(k&&(k.type==="keydown")&&!(k.keyCode===h||k.keyCode===j)){return true}var l=this.$el.find(".dataset-body");i=(i===undefined)?(!l.is(":visible")):(i);if(i){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var h=this;function i(){h.$el.children(".dataset-body").replaceWith(h._render_body());h.$el.children(".dataset-body").slideDown(h.fxSpeed,function(){h.expanded=true;h.trigger("body-expanded",h.model)})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(j){h.urls=h.model.urls();i()})}else{i()}},collapseBody:function(){var h=this;this.$el.children(".dataset-body").slideUp(h.fxSpeed,function(){h.expanded=false;h.trigger("body-collapsed",h.model.id)})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(h){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this,h);this.selected=true}return false},deselect:function(h){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this,h);this.selected=false}return false},toggleSelect:function(h){if(this.selected){this.deselect(h)}else{this.select(h)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var h=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);h.addEventListener("dragstart",this.dragStartHandler,false);h.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var h=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);h.removeEventListener("dragstart",this.dragStartHandler,false);h.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(h){this.trigger("dragstart",this);h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(h){this.trigger("dragend",this);return false},remove:function(i){var h=this;this.$el.fadeOut(h.fxSpeed,function(){h.$el.remove();h.off();if(i){i()}})},toString:function(){var h=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+h+")"}});var a=_.template(['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',c("This dataset has been deleted and removed from disk")+".","</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',c("This dataset has been deleted")+".","</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',c("This dataset has been hidden")+".","</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join(""));var e=_.template(['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","<% _.each( hda.display_types, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join(""));b.templates={skeleton:function(h){return a({_l:c,hda:h})},body:function(h){return e({_l:c,hda:h})}};return{HDABaseView:b}});
\ No newline at end of file
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/mvc/dataset/hda-edit.js
--- a/static/scripts/packed/mvc/dataset/hda-edit.js
+++ b/static/scripts/packed/mvc/dataset/hda-edit.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations","utils/localization"],function(g,b,a,e,f){var h=b.HDABaseView.extend({initialize:function(i){b.HDABaseView.prototype.initialize.call(this,i);this.hasUser=i.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.purgeAllowed=i.purgeAllowed||false;this.tagsEditorShown=i.tagsEditorShown||false;this.annotationEditorShown=i.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===g.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===g.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var k=this.model.get("purged"),i=this.model.get("deleted"),j={title:f("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(i||k){j.disabled=true;if(k){j.title=f("Cannot edit attributes of datasets removed from disk")}else{if(i){j.title=f("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===g.HistoryDatasetAssociation.STATES.UPLOAD){j.disabled=true;j.title=f("This dataset must finish uploading before it can be edited")}else{if(this.model.get("state")===g.HistoryDatasetAssociation.STATES.NEW){j.disabled=true;j.title=f("This dataset is not yet editable")}}}j.faIcon="fa-pencil";return faIconButton(j)},_render_deleteButton:function(){if((this.model.get("state")===g.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this,j={title:f("Delete"),classes:"dataset-delete",onclick:function(){i.$el.find(".icon-btn.dataset-delete").trigger("mouseout");i.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){j={title:f("Dataset is already deleted"),disabled:true}}j.faIcon="fa-times";return faIconButton(j)},_render_errButton:function(){if(this.model.get("state")!==g.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:f("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:f("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var i=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(i))){return null}if(_.isObject(i[0])){return this._render_visualizationsFrameworkButton(i)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),o=this.urls.visualization,l={},p={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){p.dbkey=k}var j=faIconButton({title:f("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function m(q){if(q==="trackster"){return c(o,p,k)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:o+"/"+q+"?"+$.param(p)})}}function n(q){return q.charAt(0).toUpperCase()+q.slice(1)}if(i.length===1){j.attr("data-original-title",f("Visualize in")+" "+f(n(i[0])));j.click(m(i[0]))}else{_.each(i,function(q){l[f(n(q))]=m(q)});make_popupmenu(j,l)}return j},_render_visualizationsFrameworkButton:function(i){if(!(this.model.hasData())||!(i&&!_.isEmpty(i))){return null}var k=faIconButton({title:f("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(i.length===1){var j=i[0];k.attr("data-original-title",f("Visualize in")+" "+j.html);k.attr("href",j.href)}else{var l=[];_.each(i,function(m){m.func=function(n){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:m.href});n.preventDefault();return false}return true};l.push(m);return false});PopupMenu.create(k,l)}return k},_buildNewRender:function(){var i=b.HDABaseView.prototype._buildNewRender.call(this);var j="<br />",l=".",k=function(m,n){return['<a href="javascript:void(0)" class="',n,'">',m,"</a>"].join("")};i.find(".dataset-deleted-msg").append([j,k(f("Undelete it"),"dataset-undelete"),l].join(""));if(this.purgeAllowed){i.find(".dataset-deleted-msg").append([j,k(f("Permanently remove it from disk"),"dataset-purge"),l].join(""))}i.find(".dataset-hidden-msg").append([j,k(f("Unhide it"),"dataset-unhide"),l].join(""));return i},_render_body_failed_metadata:function(){var j=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(f("set it manually or retry auto-detection")),i=$("<span/>").text(". "+f("You may be able to")+" ").append(j),k=b.HDABaseView.prototype._render_body_failed_metadata.call(this);k.find(".warningmessagesmall strong").append(i);return k},_render_body_error:function(){var i=b.HDABaseView.prototype._render_body_error.call(this);i.find(".dataset-actions .left").prepend(this._render_errButton());return i},_render_body_ok:function(){var i=b.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return i}this.makeDbkeyEditLink(i);if(this.hasUser){i.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(i);this._renderAnnotation(i)}return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.tagsEditorShown=true},onhide:function(){j.tagsEditorShown=false},$activator:faIconButton({title:f("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(i){var j=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:i.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.annotationEditorShown=true},onhide:function(){j.annotationEditorShown=false},$activator:faIconButton({title:f("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(j){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var i=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);j.find(".dataset-dbkey .value").replaceWith(i)}},events:_.extend(_.clone(b.HDABaseView.prototype.events),{"click .dataset-undelete":function(i){this.model.undelete();return false},"click .dataset-unhide":function(i){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function d(i){this.model.purge();return false},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDAView("+i+")"}});function c(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.Galaxy.modal.hide()},"View in saved visualization":function(){n.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:m,buttons:{Cancel:function(){n.Galaxy.modal.hide()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){n.Galaxy.modal.hide();var o=$(this).val();k.id=o;n.Galaxy.frame.add({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)})})}}})},"View in new visualization":function(){n.Galaxy.modal.hide();var o=i+"/trackster?"+$.param(k);n.Galaxy.frame.add({title:"Trackster",type:"url",content:o})}}})}});return false}}return{HDAEditView:h}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/tags","mvc/annotations","utils/localization"],function(g,b,a,e,f){var h=b.HDABaseView.extend({initialize:function(i){b.HDABaseView.prototype.initialize.call(this,i);this.hasUser=i.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.purgeAllowed=i.purgeAllowed||false;this.tagsEditorShown=i.tagsEditorShown||false;this.annotationEditorShown=i.annotationEditorShown||false},_render_titleButtons:function(){return b.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===g.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===g.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var k=this.model.get("purged"),i=this.model.get("deleted"),j={title:f("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(i||k){j.disabled=true;if(k){j.title=f("Cannot edit attributes of datasets removed from disk")}else{if(i){j.title=f("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===g.HistoryDatasetAssociation.STATES.UPLOAD){j.disabled=true;j.title=f("This dataset must finish uploading before it can be edited")}else{if(this.model.get("state")===g.HistoryDatasetAssociation.STATES.NEW){j.disabled=true;j.title=f("This dataset is not yet editable")}}}j.faIcon="fa-pencil";return faIconButton(j)},_render_deleteButton:function(){if((this.model.get("state")===g.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this,j={title:f("Delete"),classes:"dataset-delete",onclick:function(){i.$el.find(".icon-btn.dataset-delete").trigger("mouseout");i.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){j={title:f("Dataset is already deleted"),disabled:true}}j.faIcon="fa-times";return faIconButton(j)},_render_errButton:function(){if(this.model.get("state")!==g.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:f("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:f("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var i=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(i))){return null}if(_.isObject(i[0])){return this._render_visualizationsFrameworkButton(i)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),o=this.urls.visualization,l={},p={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){p.dbkey=k}var j=faIconButton({title:f("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});function m(q){if(q==="trackster"){return c(o,p,k)}return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:o+"/"+q+"?"+$.param(p)})}}function n(q){return q.charAt(0).toUpperCase()+q.slice(1)}if(i.length===1){j.attr("data-original-title",f("Visualize in")+" "+f(n(i[0])));j.click(m(i[0]))}else{_.each(i,function(q){l[f(n(q))]=m(q)});make_popupmenu(j,l)}return j},_render_visualizationsFrameworkButton:function(i){if(!(this.model.hasData())||!(i&&!_.isEmpty(i))){return null}var k=faIconButton({title:f("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(i.length===1){var j=i[0];k.attr("data-original-title",f("Visualize in")+" "+j.html);k.attr("href",j.href)}else{var l=[];_.each(i,function(m){m.func=function(n){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:m.href});n.preventDefault();return false}return true};l.push(m);return false});PopupMenu.create(k,l)}return k},_buildNewRender:function(){var i=b.HDABaseView.prototype._buildNewRender.call(this);var j="<br />",l=".",k=function(m,n){return['<a href="javascript:void(0)" class="',n,'">',m,"</a>"].join("")};i.find(".dataset-deleted-msg").append([j,k(f("Undelete it"),"dataset-undelete"),l].join(""));if(this.purgeAllowed){i.find(".dataset-deleted-msg").append([j,k(f("Permanently remove it from disk"),"dataset-purge"),l].join(""))}i.find(".dataset-hidden-msg").append([j,k(f("Unhide it"),"dataset-unhide"),l].join(""));return i},_render_body_failed_metadata:function(){var j=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(f("set it manually or retry auto-detection")),i=$("<span/>").text(". "+f("You may be able to")+" ").append(j),k=b.HDABaseView.prototype._render_body_failed_metadata.call(this);k.find(".warningmessagesmall strong").append(i);return k},_render_body_error:function(){var i=b.HDABaseView.prototype._render_body_error.call(this);i.find(".dataset-actions .left").prepend(this._render_errButton());return i},_render_body_ok:function(){var i=b.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return i}this.makeDbkeyEditLink(i);if(this.hasUser){i.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(i);this._renderAnnotation(i)}return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.tagsEditorShown=true},onhide:function(){j.tagsEditorShown=false},$activator:faIconButton({title:f("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(i){var j=this;this.annotationEditor=new e.AnnotationEditor({model:this.model,el:i.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.annotationEditorShown=true},onhide:function(){j.annotationEditorShown=false},$activator:faIconButton({title:f("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(j){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var i=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);j.find(".dataset-dbkey .value").replaceWith(i)}},events:_.extend(_.clone(b.HDABaseView.prototype.events),{"click .dataset-undelete":function(i){this.model.undelete();return false},"click .dataset-unhide":function(i){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function d(i){this.model.purge();return false},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"HDAEditView("+i+")"}});function c(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.Galaxy.modal.hide()},"View in saved visualization":function(){n.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:m,buttons:{Cancel:function(){n.Galaxy.modal.hide()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){n.Galaxy.modal.hide();var o=$(this).val();k.id=o;n.Galaxy.frame.add({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)})})}}})},"View in new visualization":function(){n.Galaxy.modal.hide();var o=i+"/trackster?"+$.param(k);n.Galaxy.frame.add({title:"Trackster",type:"url",content:o})}}})}});return false}}return{HDAEditView:h}});
\ No newline at end of file
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/mvc/history/history-content-base-view.js
--- /dev/null
+++ b/static/scripts/packed/mvc/history/history-content-base-view.js
@@ -0,0 +1,1 @@
+define(["mvc/base-mvc","utils/localization"],function(a,b){var c=Backbone.View.extend(a.LoggableMixin).extend({});return{HistoryContentBaseView:c}});
\ No newline at end of file
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/mvc/history/history-contents.js
--- a/static/scripts/packed/mvc/history/history-contents.js
+++ b/static/scripts/packed/mvc/history/history-contents.js
@@ -1,1 +1,1 @@
-define(["mvc/history/history-content-base","mvc/dataset/hda-model","mvc/collection/hdca-model","mvc/base-mvc","utils/localization"],function(b,d,f,a,c){var g=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){console.debug("HistoryContents.model:",i);if(i.history_content_type==="dataset"){return new d.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){return new f.HistoryDatasetCollectionAssociation(i,h)}}throw new TypeError("Unknown history_content_type:"+i.history_content_type)},initialize:function(i,h){h=h||{};console.debug("new HistoryContents",i,h);this.historyId=h.historyId},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new g(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new g(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m;var n=b.HistoryContent.typeIdStr(l.history_content_type,l.id);var o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function e(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){console.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){console.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},toString:function(){return(["HistoryContents(",[this.parentId,this.length].join(),")"].join(""))}});return{HistoryContents:g}});
\ No newline at end of file
+define(["mvc/history/history-content-base","mvc/dataset/hda-model","mvc/collection/hdca-model","mvc/base-mvc","utils/localization"],function(b,d,f,a,c){var g=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new d.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){return new f.HistoryDatasetCollectionAssociation(i,h)}}throw new TypeError("Unknown history_content_type:"+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new g(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new g(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m;var n=b.HistoryContent.typeIdStr(l.history_content_type,l.id);var o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function e(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){console.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){console.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},toString:function(){return(["HistoryContents(",[this.parentId,this.length].join(),")"].join(""))}});return{HistoryContents:g}});
\ No newline at end of file
diff -r 65ec063664eb0ce100d76d985fba93f200ac5178 -r cef33a0617405e7b3f25c79955890c72e69dc14b static/scripts/packed/mvc/ui/ui-frames.js
--- a/static/scripts/packed/mvc/ui/ui-frames.js
+++ b/static/scripts/packed/mvc/ui/ui-frames.js
@@ -1,1 +1,1 @@
-define([],function(){var a=Backbone.View.extend({options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:true,onchange:null},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:null,initialize:function(c){var b=this;if(c){this.options=_.defaults(c,this.options)}this.visible=this.options.visible;this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var d="#frame-shadow";$(this.el).append(this._template_shadow(d.substring(1)));this.frame_shadow={id:d,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[d]=this.frame_shadow;this._panel_refresh();if(!this.visible){this.hide()}else{this.show()}var b=this;$(window).resize(function(){if(b.visible){b._panel_refresh()}})},add:function(c){var f={title:"",content:null,target:"",type:null};if(c){c=_.defaults(c,f)}else{c=f}if(!c.content){return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var d="#frame-"+(this.frame_counter_id++);if($(d).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;var e=null;if(c.type==="url"){e=$(this._template_frame_url(d.substring(1),c.title,c.content))}else{if(c.type==="other"){e=$(this._template_frame(d.substring(1),c.title));var b=e.find(".f-content");console.log(b);if(_.isFunction(c.content)){c.content(b)}else{b.append(c.content)}}}$(this.el).append(e);var g={id:d,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};c.width=this._to_pixel_coord("width",this.options.frame.cols);c.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(g.id).css("z-index"));this.frame_list[d]=g;this.frame_counter++;this._frame_resize(g,{width:c.width,height:c.height});this._frame_insert(g,{top:0,left:0},true);if(!this.visible){this.show()}},show:function(){this.visible=true;this.$el.find(".frame").fadeIn("fast");this.$el.find(this.frame_shadow.id).hide();this.$el.find(".frame-background").show();this._panel_refresh();this._menu_refresh()},hide:function(){if(this.event.type!==null){return}this.visible=false;this.$el.find(".frame").fadeOut("fast");this.$el.find(".frame-background").hide();this.$el.find(".frame-menu").hide();this._menu_refresh()},length:function(){return this.frame_counter},setOnChange:function(b){this.options.onchange=b},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_hide","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(b){if(this.event.type!==null){return}if($(b.target).hasClass("f-header")||$(b.target).hasClass("f-title")){this.event.type="drag"}if($(b.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}b.preventDefault();this.event.target=this._frame_identify(b.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:b.originalEvent.pageX,y:b.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(h){if(this.event.type!="drag"&&this.event.type!="resize"){return}var f={x:h.originalEvent.pageX,y:h.originalEvent.pageY};var c={x:f.x-this.event.xy.x,y:f.y-this.event.xy.y};this.event.xy=f;var g=this._frame_screen(this.event.target);if(this.event.type=="resize"){g.width+=c.x;g.height+=c.y;var d=this.options.cell-this.options.margin-1;g.width=Math.max(g.width,d);g.height=Math.max(g.height,d);this._frame_resize(this.event.target,g);g.width=this._to_grid_coord("width",g.width)+1;g.height=this._to_grid_coord("height",g.height)+1;g.width=this._to_pixel_coord("width",g.width);g.height=this._to_pixel_coord("height",g.height);this._frame_resize(this.frame_shadow,g);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",g.top),left:this._to_grid_coord("left",g.left)})}if(this.event.type=="drag"){g.left+=c.x;g.top+=c.y;this._frame_offset(this.event.target,g);var b={top:this._to_grid_coord("top",g.top),left:this._to_grid_coord("left",g.left)};if(b.left!==0){b.left++}this._frame_insert(this.frame_shadow,b)}},_event_frame_mouse_up:function(b){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);var b=this;$(d.id).fadeOut("fast",function(){$(d.id).remove();delete b.frame_list[d.id];b.frame_counter--;b._panel_refresh(true);b._panel_animation_complete();if(b.visible&&b.frame_counter==0){b.hide()}})},_event_frame_lock:function(b){if(this.event.type!==null){return}b.preventDefault();var c=this._frame_identify(b.target);if(c.grid_lock){c.grid_lock=false;$(c.id).find(".f-pin").removeClass("toggle");$(c.id).find(".f-header").removeClass("f-not-allowed");$(c.id).find(".f-title").removeClass("f-not-allowed");$(c.id).find(".f-resize").show();$(c.id).find(".f-close").show()}else{c.grid_lock=true;$(c.id).find(".f-pin").addClass("toggle");$(c.id).find(".f-header").addClass("f-not-allowed");$(c.id).find(".f-title").addClass("f-not-allowed");$(c.id).find(".f-resize").hide();$(c.id).find(".f-close").hide()}},_event_hide:function(b){if(this.event.type!==null){return}this.hide()},_event_panel_scroll:function(b){if(this.event.type!==null||!this.visible){return}var c=$(b.srcElement).parents(".frame");if(c.length!==0){b.stopPropagation();return}b.preventDefault();var d=b.originalEvent.detail?b.originalEvent.detail:b.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(b){if(this.event.type!==null){return}b.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(b){if(this.event.type!==null){return}b.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(b){return this.frame_list["#"+$(b).closest(".frame").attr("id")]},_frame_drag_start:function(c){this._frame_focus(c,true);var b=this._frame_screen(c);this._frame_resize(this.frame_shadow,b);this._frame_grid(this.frame_shadow,c.grid_location);c.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(c){this._frame_focus(c,false);var b=this._frame_screen(this.frame_shadow);this._frame_resize(c,b);this._frame_grid(c,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(d,c){var b=(d=="width"||d=="height")?1:-1;if(d=="top"){c-=this.top}return parseInt((c+b*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(d,e){var b=(d=="width"||d=="height")?1:-1;var c=(e*this.options.cell)-b*this.options.margin;if(d=="top"){c+=this.top}return c},_to_grid:function(b){return{top:this._to_grid_coord("top",b.top),left:this._to_grid_coord("left",b.left),width:this._to_grid_coord("width",b.width),height:this._to_grid_coord("height",b.height)}},_to_pixel:function(b){return{top:this._to_pixel_coord("top",b.top),left:this._to_pixel_coord("left",b.left),width:this._to_pixel_coord("width",b.width),height:this._to_pixel_coord("height",b.height)}},_is_collision:function(d){function b(g,f){return !(g.left>f.left+f.width-1||g.left+g.width-1<f.left||g.top>f.top+f.height-1||g.top+g.height-1<f.top)}for(var c in this.frame_list){var e=this.frame_list[c];if(e.grid_location===null){continue}if(b(d,e.grid_location)){return true}}return false},_location_rank:function(b){return(b.top*this.cols)+b.left},_menu_refresh:function(){if(this.visible){if(this.top==this.options.top_min){$(".frame-scroll-up").hide()}else{$(".frame-scroll-up").show()}if(this.top==this.top_max){$(".frame-scroll-down").hide()}else{$(".frame-scroll-down").show()}}if(this.options.onchange){this.options.onchange()}},_panel_animation_complete:function(){var b=this;$(".frame").promise().done(function(){b._panel_scroll(0,true)})},_panel_refresh:function(b){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this._frame_insert(null,null,b)},_panel_scroll:function(g,b){var d=this.top-this.options.scroll*g;d=Math.max(d,this.top_max);d=Math.min(d,this.options.top_min);if(this.top!=d){for(var c in this.frame_list){var f=this.frame_list[c];if(f.grid_location!==null){var e={top:f.screen_location.top-(this.top-d),left:f.screen_location.left};this._frame_offset(f,e,b)}}this.top=d}this._menu_refresh()},_frame_insert:function(h,b,d){var c=[];if(h){h.grid_location=null;c.push([h,this._location_rank(b)])}var e=null;for(e in this.frame_list){var g=this.frame_list[e];if(g.grid_location!==null&&!g.grid_lock){g.grid_location=null;c.push([g,g.grid_rank])}}c.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(e=0;e<c.length;e++){this._frame_place(c[e][0],d)}this.top_max=0;for(var e in this.frame_list){var h=this.frame_list[e];if(h.grid_location!==null){this.top_max=Math.max(this.top_max,h.grid_location.top+h.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this._menu_refresh()},_frame_place:function(h,c){h.grid_location=null;var f=this._to_grid(this._frame_screen(h));var b=false;for(var e=0;e<this.options.rows;e++){for(var d=0;d<Math.max(1,this.cols-f.width);d++){f.top=e;f.left=d;if(!this._is_collision(f)){b=true;break}}if(b){break}}if(b){this._frame_grid(h,f,c)}else{console.log("Grid dimensions exceeded.")}},_frame_focus:function(d,b){var c=this.frame_z+(b?1:0);$(d.id).css("z-index",c)},_frame_offset:function(e,d,c){e.screen_location.left=d.left;e.screen_location.top=d.top;if(c){this._frame_focus(e,true);var b=this;$(e.id).animate({top:d.top,left:d.left},"fast",function(){b._frame_focus(e,false)})}else{$(e.id).css({top:d.top,left:d.left})}},_frame_resize:function(c,b){$(c.id).css({width:b.width,height:b.height});c.screen_location.width=b.width;c.screen_location.height=b.height},_frame_grid:function(d,b,c){d.grid_location=b;this._frame_offset(d,this._to_pixel(b),c);d.grid_rank=this._location_rank(b)},_frame_screen:function(c){var b=c.screen_location;return{top:b.top,left:b.left,width:b.width,height:b.height}},_template:function(){return'<div class="galaxy-frame"></div>'},_template_frame:function(c,b){if(!b){b=""}return'<div id="'+c+'" class="frame corner"><div class="f-header corner"><span class="f-title">'+b+'</span><span class="f-icon f-close fa fa-trash-o"></span><span class="f-icon f-pin fa fa-thumb-tack"></span></div><div class="f-content"><div class="f-cover"></div></div><span class="f-resize f-icon corner fa fa-resize-full"></span></div>'},_template_frame_url:function(e,d,b){if(b.indexOf("?")==-1){b+="?"}else{b+="&"}b+="widget=True";var c=$(this._template_frame(e,d));c.find(".f-content").append('<iframe scrolling="auto" class="f-iframe" src="'+b+'"></iframe>');return c},_template_shadow:function(b){return'<div id="'+b+'" class="frame-shadow corner"></div>'},_template_background:function(){return'<div class="frame-background"></div>'},_template_menu:function(){return'<div class="frame-scroll-up frame-menu fa fa-chevron-up fa-2x"></div><div class="frame-scroll-down frame-menu fa fa-chevron-down fa-2x"></div>'}});return{View:a}});
\ No newline at end of file
+define([],function(){var a=Backbone.View.extend({options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9,visible:true,onchange:null},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:null,initialize:function(c){var b=this;if(c){this.options=_.defaults(c,this.options)}this.visible=this.options.visible;this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var d="#frame-shadow";$(this.el).append(this._template_shadow(d.substring(1)));this.frame_shadow={id:d,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[d]=this.frame_shadow;this._panel_refresh();if(!this.visible){this.hide()}else{this.show()}var b=this;$(window).resize(function(){if(b.visible){b._panel_refresh()}})},add:function(c){var f={title:"",content:null,target:"",type:null};if(c){c=_.defaults(c,f)}else{c=f}if(!c.content){return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var d="#frame-"+(this.frame_counter_id++);if($(d).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;var e=null;if(c.type==="url"){e=$(this._template_frame_url(d.substring(1),c.title,c.content))}else{if(c.type==="other"){e=$(this._template_frame(d.substring(1),c.title));var b=e.find(".f-content");if(_.isFunction(c.content)){c.content(b)}else{b.append(c.content)}}}$(this.el).append(e);var g={id:d,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};c.width=this._to_pixel_coord("width",this.options.frame.cols);c.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(g.id).css("z-index"));this.frame_list[d]=g;this.frame_counter++;this._frame_resize(g,{width:c.width,height:c.height});this._frame_insert(g,{top:0,left:0},true);if(!this.visible){this.show()}},show:function(){this.visible=true;this.$el.find(".frame").fadeIn("fast");this.$el.find(this.frame_shadow.id).hide();this.$el.find(".frame-background").show();this._panel_refresh();this._menu_refresh()},hide:function(){if(this.event.type!==null){return}this.visible=false;this.$el.find(".frame").fadeOut("fast");this.$el.find(".frame-background").hide();this.$el.find(".frame-menu").hide();this._menu_refresh()},length:function(){return this.frame_counter},setOnChange:function(b){this.options.onchange=b},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_hide","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(b){if(this.event.type!==null){return}if($(b.target).hasClass("f-header")||$(b.target).hasClass("f-title")){this.event.type="drag"}if($(b.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}b.preventDefault();this.event.target=this._frame_identify(b.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:b.originalEvent.pageX,y:b.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(h){if(this.event.type!="drag"&&this.event.type!="resize"){return}var f={x:h.originalEvent.pageX,y:h.originalEvent.pageY};var c={x:f.x-this.event.xy.x,y:f.y-this.event.xy.y};this.event.xy=f;var g=this._frame_screen(this.event.target);if(this.event.type=="resize"){g.width+=c.x;g.height+=c.y;var d=this.options.cell-this.options.margin-1;g.width=Math.max(g.width,d);g.height=Math.max(g.height,d);this._frame_resize(this.event.target,g);g.width=this._to_grid_coord("width",g.width)+1;g.height=this._to_grid_coord("height",g.height)+1;g.width=this._to_pixel_coord("width",g.width);g.height=this._to_pixel_coord("height",g.height);this._frame_resize(this.frame_shadow,g);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",g.top),left:this._to_grid_coord("left",g.left)})}if(this.event.type=="drag"){g.left+=c.x;g.top+=c.y;this._frame_offset(this.event.target,g);var b={top:this._to_grid_coord("top",g.top),left:this._to_grid_coord("left",g.left)};if(b.left!==0){b.left++}this._frame_insert(this.frame_shadow,b)}},_event_frame_mouse_up:function(b){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);var b=this;$(d.id).fadeOut("fast",function(){$(d.id).remove();delete b.frame_list[d.id];b.frame_counter--;b._panel_refresh(true);b._panel_animation_complete();if(b.visible&&b.frame_counter==0){b.hide()}})},_event_frame_lock:function(b){if(this.event.type!==null){return}b.preventDefault();var c=this._frame_identify(b.target);if(c.grid_lock){c.grid_lock=false;$(c.id).find(".f-pin").removeClass("toggle");$(c.id).find(".f-header").removeClass("f-not-allowed");$(c.id).find(".f-title").removeClass("f-not-allowed");$(c.id).find(".f-resize").show();$(c.id).find(".f-close").show()}else{c.grid_lock=true;$(c.id).find(".f-pin").addClass("toggle");$(c.id).find(".f-header").addClass("f-not-allowed");$(c.id).find(".f-title").addClass("f-not-allowed");$(c.id).find(".f-resize").hide();$(c.id).find(".f-close").hide()}},_event_hide:function(b){if(this.event.type!==null){return}this.hide()},_event_panel_scroll:function(b){if(this.event.type!==null||!this.visible){return}var c=$(b.srcElement).parents(".frame");if(c.length!==0){b.stopPropagation();return}b.preventDefault();var 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commit/galaxy-central: carlfeberhard: HDA & History Managers: move serialization logic for bootstrapping into view, display_by_username_and_slug, and root/history into Managers in order to display dataset collections
by commits-noreply＠bitbucket.org 10 Jul '14
by commits-noreply＠bitbucket.org 10 Jul '14
10 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/65ec063664eb/
Changeset: 65ec063664eb
User: carlfeberhard
Date: 2014-07-10 15:56:17
Summary: HDA & History Managers: move serialization logic for bootstrapping into view, display_by_username_and_slug, and root/history into Managers in order to display dataset collections
Affected #: 7 files
diff -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 -r 65ec063664eb0ce100d76d985fba93f200ac5178 lib/galaxy/managers/__init__.py
--- a/lib/galaxy/managers/__init__.py
+++ b/lib/galaxy/managers/__init__.py
@@ -1,4 +1,33 @@
-""" 'Business logic' independent of web transactions/user context (trans)
-should be pushed into models - but logic that requires the context trans
-should be placed under this module.
"""
+Classes that manage resources (models, tools, etc.) by using the current
+Transaction.
+
+Encapsulates the intersection of trans (or trans.sa_session), models,
+and Controllers.
+
+Responsibilities:
+ model operations that involve the trans/sa_session (CRUD)
+ security:
+ ownership, accessibility
+ common aspect-oriented operations via new mixins:
+ sharable, annotatable, tagable, ratable
+
+Not responsible for:
+ encoding/decoding ids
+ any http gobblygook
+ formatting of returned data (always python structures)
+ formatting of raised errors
+
+The goal is to have Controllers only handle:
+ query-string/payload parsing and encoding/decoding ids
+ http
+ return formatting
+
+and:
+ control, improve namespacing in Controllers
+ DRY for Controller ops (define here - use in both UI/API Controllers)
+
+In other words, 'Business logic' independent of web transactions/user context
+(trans) should be pushed into models - but logic that requires the context
+trans should be placed under this module.
+"""
diff -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 -r 65ec063664eb0ce100d76d985fba93f200ac5178 lib/galaxy/managers/base.py
--- /dev/null
+++ b/lib/galaxy/managers/base.py
@@ -0,0 +1,7 @@
+
+
+class ModelManager( object ):
+ pass
+
+class ModelSerializer( object ):
+ pass
diff -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 -r 65ec063664eb0ce100d76d985fba93f200ac5178 lib/galaxy/managers/hdas.py
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -1,16 +1,35 @@
+"""
+Manager and Serializer for HDAs.
+
+HistoryDatasetAssociations (HDAs) are datasets contained or created in a
+history.
+"""
+
from galaxy import exceptions
-from ..managers import histories
+from galaxy.managers import base as manager_base
+from galaxy.managers import histories as history_manager
-class HDAManager( object ):
+import galaxy.web
+import galaxy.datatypes.metadata
+from galaxy import objectstore
+
+class HDAManager( manager_base.ModelManager ):
+ """
+ Interface/service object for interacting with HDAs.
+ """
def __init__( self ):
- self.histories_mgr = histories.HistoryManager()
+ """
+ Set up and initialize other managers needed by hdas.
+ """
+ self.histories_mgr = history_manager.HistoryManager()
def get( self, trans, unencoded_id, check_ownership=True, check_accessible=True ):
"""
+ Get an HDA by its unencoded db id, checking ownership (via its history)
+ or accessibility (via dataset shares/permissions).
"""
- # this is a replacement for UsesHistoryDatasetAssociationMixin because mixins are a bad soln/structure
hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( unencoded_id )
if hda is None:
raise exceptions.ObjectNotFound()
@@ -19,7 +38,8 @@
def secure( self, trans, hda, check_ownership=True, check_accessible=True ):
"""
- checks if (a) user owns item or (b) item is accessible to user.
+ check ownership (via its history) or accessibility (via dataset
+ shares/permissions).
"""
# all items are accessible to an admin
if trans.user and trans.user_is_admin():
@@ -31,12 +51,18 @@
return hda
def can_access_dataset( self, trans, hda ):
+ """
+ Use security agent to see if current user has access to dataset.
+ """
current_user_roles = trans.get_current_user_roles()
return trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset )
#TODO: is_owner, is_accessible
def check_ownership( self, trans, hda ):
+ """
+ Use history to see if current user owns HDA.
+ """
if not trans.user:
#if hda.history == trans.history:
# return hda
@@ -51,6 +77,9 @@
"HistoryDatasetAssociation is not owned by the current user", type='error' )
def check_accessible( self, trans, hda ):
+ """
+ Raise error if HDA is not accessible.
+ """
if trans.user and trans.user_is_admin():
return hda
# check for access of the containing history...
@@ -62,6 +91,151 @@
"HistoryDatasetAssociation is not accessible to the current user", type='error' )
def err_if_uploading( self, trans, hda ):
+ """
+ Raise error if HDA is still uploading.
+ """
if hda.state == trans.model.Dataset.states.UPLOAD:
raise exceptions.Conflict( "Please wait until this dataset finishes uploading" )
return hda
+
+ def get_hda_dict( self, trans, hda ):
+ """
+ Return full details of this HDA in dictionary form.
+ """
+ #precondition: the user's access to this hda has already been checked
+ #TODO:?? postcondition: all ids are encoded (is this really what we want at this level?)
+ expose_dataset_path = trans.user_is_admin() or trans.app.config.expose_dataset_path
+ hda_dict = hda.to_dict( view='element', expose_dataset_path=expose_dataset_path )
+ hda_dict[ 'api_type' ] = "file"
+
+ # Add additional attributes that depend on trans must be added here rather than at the model level.
+ can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset )
+ can_access_hda = ( trans.user_is_admin() or can_access_hda )
+ if not can_access_hda:
+ return self.get_inaccessible_hda_dict( trans, hda )
+ hda_dict[ 'accessible' ] = True
+
+ #TODO: I'm unclear as to which access pattern is right
+ hda_dict[ 'annotation' ] = hda.get_item_annotation_str( trans.sa_session, hda.history.user, hda )
+ #annotation = getattr( hda, 'annotation', hda.get_item_annotation_str( trans.sa_session, trans.user, hda ) )
+
+ # ---- return here if deleted AND purged OR can't access
+ purged = ( hda.purged or hda.dataset.purged )
+ if ( hda.deleted and purged ):
+ #TODO: to_dict should really go AFTER this - only summary data
+ return trans.security.encode_dict_ids( hda_dict )
+
+ if expose_dataset_path:
+ try:
+ hda_dict[ 'file_name' ] = hda.file_name
+ except objectstore.ObjectNotFound:
+ log.exception( 'objectstore.ObjectNotFound, HDA %s.', hda.id )
+
+ hda_dict[ 'download_url' ] = galaxy.web.url_for( 'history_contents_display',
+ history_id = trans.security.encode_id( hda.history.id ),
+ history_content_id = trans.security.encode_id( hda.id ) )
+
+ # indeces, assoc. metadata files, etc.
+ meta_files = []
+ for meta_type in hda.metadata.spec.keys():
+ if isinstance( hda.metadata.spec[ meta_type ].param, galaxy.datatypes.metadata.FileParameter ):
+ meta_files.append( dict( file_type=meta_type ) )
+ if meta_files:
+ hda_dict[ 'meta_files' ] = meta_files
+
+ # currently, the viz reg is optional - handle on/off
+ if trans.app.visualizations_registry:
+ hda_dict[ 'visualizations' ] = trans.app.visualizations_registry.get_visualizations( trans, hda )
+ else:
+ hda_dict[ 'visualizations' ] = hda.get_visualizations()
+ #TODO: it may also be wiser to remove from here and add as API call that loads the visualizations
+ # when the visualizations button is clicked (instead of preloading/pre-checking)
+
+ # ---- return here if deleted
+ if hda.deleted and not purged:
+ return trans.security.encode_dict_ids( hda_dict )
+
+ return trans.security.encode_dict_ids( hda_dict )
+
+ def get_inaccessible_hda_dict( self, trans, hda ):
+ """
+ Return truncated serialization of HDA when inaccessible to user.
+ """
+ return trans.security.encode_dict_ids({
+ 'id' : hda.id,
+ 'history_id': hda.history.id,
+ 'hid' : hda.hid,
+ 'name' : hda.name,
+ 'state' : hda.state,
+ 'deleted' : hda.deleted,
+ 'visible' : hda.visible,
+ 'accessible': False
+ })
+
+ def get_hda_dict_with_error( self, trans, hda=None, history_id=None, id=None, error_msg='Error' ):
+ """
+ Return truncated serialization of HDA when error raised getting
+ details.
+ """
+ return trans.security.encode_dict_ids({
+ 'id' : hda.id if hda else id,
+ 'history_id': hda.history.id if hda else history_id,
+ 'hid' : hda.hid if hda else '(unknown)',
+ 'name' : hda.name if hda else '(unknown)',
+ 'error' : error_msg,
+ 'state' : trans.model.Dataset.states.NEW
+ })
+
+ def get_display_apps( self, trans, hda ):
+ """
+ Return dictionary containing new-style display app urls.
+ """
+ display_apps = []
+ for display_app in hda.get_display_applications( trans ).itervalues():
+
+ app_links = []
+ for link_app in display_app.links.itervalues():
+ app_links.append({
+ 'target': link_app.url.get( 'target_frame', '_blank' ),
+ 'href' : link_app.get_display_url( hda, trans ),
+ 'text' : gettext( link_app.name )
+ })
+ if app_links:
+ display_apps.append( dict( label=display_app.name, links=app_links ) )
+
+ return display_apps
+
+ def get_old_display_applications( self, trans, hda ):
+ """
+ Return dictionary containing old-style display app urls.
+ """
+ display_apps = []
+ if not trans.app.config.enable_old_display_applications:
+ return display_apps
+
+ for display_app in hda.datatype.get_display_types():
+ target_frame, display_links = hda.datatype.get_display_links( hda,
+ display_app, trans.app, trans.request.base )
+
+ if len( display_links ) > 0:
+ display_label = hda.datatype.get_display_label( display_app )
+
+ app_links = []
+ for display_name, display_link in display_links:
+ app_links.append({
+ 'target': target_frame,
+ 'href' : display_link,
+ 'text' : gettext( display_name )
+ })
+ if app_links:
+ display_apps.append( dict( label=display_label, links=app_links ) )
+
+ return display_apps
+
+
+# =============================================================================
+class HistorySerializer( manager_base.ModelSerializer ):
+ """
+ Interface/service object for serializing HDAs into dictionaries.
+ """
+ pass
diff -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 -r 65ec063664eb0ce100d76d985fba93f200ac5178 lib/galaxy/managers/histories.py
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -1,9 +1,32 @@
+"""
+Manager and Serializer for histories.
+
+Histories are containers for datasets or dataset collections
+created (or copied) by users over the course of an analysis.
+"""
+
from galaxy import exceptions
from galaxy.model import orm
+from galaxy.managers import base as manager_base
+import galaxy.managers.hdas
-class HistoryManager( object ):
+import galaxy.web
+import galaxy.dataset_collections.util
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+# =============================================================================
+class HistoryManager( manager_base.ModelManager ):
+ """
+ Interface/service object for interacting with HDAs.
+ """
+
#TODO: all the following would be more useful if passed the user instead of defaulting to trans.user
+ def __init__( self, *args, **kwargs ):
+ super( HistoryManager, self ).__init__( *args, **kwargs )
def get( self, trans, unencoded_id, check_ownership=True, check_accessible=True, deleted=None ):
"""
@@ -44,7 +67,7 @@
def secure( self, trans, history, check_ownership=True, check_accessible=True ):
"""
- checks if (a) user owns item or (b) item is accessible to user.
+ Checks if (a) user owns item or (b) item is accessible to user.
"""
# all items are accessible to an admin
if trans.user and trans.user_is_admin():
@@ -56,15 +79,28 @@
return history
def is_current( self, trans, history ):
+ """
+ True if the given history is the user's current history.
+
+ Returns False if the session has no current history.
+ """
+ if trans.history is None:
+ return False
return trans.history == history
def is_owner( self, trans, history ):
+ """
+ True if the current user is the owner of the given history.
+ """
# anon users are only allowed to view their current history
if not trans.user:
return self.is_current( trans, history )
return trans.user == history.user
def check_ownership( self, trans, history ):
+ """
+ Raises error if the current user is not the owner of the history.
+ """
if trans.user and trans.user_is_admin():
return history
if not trans.user and not self.is_current( trans, history ):
@@ -74,6 +110,9 @@
raise exceptions.ItemOwnershipException( "History is not owned by the current user", type='error' )
def is_accessible( self, trans, history ):
+ """
+ True if the user can access (read) the current history.
+ """
# admin always have access
if trans.user and trans.user_is_admin():
return True
@@ -88,6 +127,103 @@
return False
def check_accessible( self, trans, history ):
+ """
+ Raises error if the current user can't access the history.
+ """
if self.is_accessible( trans, history ):
return history
raise exceptions.ItemAccessibilityException( "History is not accessible to the current user", type='error' )
+
+ #TODO: bleh...
+ def _get_history_data( self, trans, history ):
+ """
+ Returns a dictionary containing ``history`` and ``contents``, serialized
+ history and an array of serialized history contents respectively.
+ """
+ hda_mgr = galaxy.managers.hdas.HDAManager()
+ collection_dictifier = galaxy.dataset_collections.util.dictify_dataset_collection_instance
+
+ history_dictionary = {}
+ contents_dictionaries = []
+ try:
+ #for content in history.contents_iter( **contents_kwds ):
+ for content in history.contents_iter( types=[ 'dataset', 'dataset_collection' ] ):
+ hda_dict = {}
+
+ if isinstance( content, trans.app.model.HistoryDatasetAssociation ):
+ try:
+ hda_dict = hda_mgr.get_hda_dict( trans, content )
+ except Exception, exc:
+ # don't fail entire list if hda err's, record and move on
+ log.exception( 'Error bootstrapping hda: %s', exc )
+ hda_dict = hda_mgr.get_hda_dict_with_error( trans, content, str( exc ) )
+
+ elif isinstance( content, trans.app.model.HistoryDatasetCollectionAssociation ):
+ try:
+ service = trans.app.dataset_collections_service
+ dataset_collection_instance = service.get_dataset_collection_instance(
+ trans=trans,
+ instance_type='history',
+ id=trans.security.encode_id( content.id ),
+ )
+ hda_dict = collection_dictifier( dataset_collection_instance,
+ security=trans.security, parent=dataset_collection_instance.history, view="element" )
+
+ except Exception, exc:
+ log.exception( "Error in history API at listing dataset collection: %s", exc )
+ #TODO: return some dict with the error
+
+ contents_dictionaries.append( hda_dict )
+
+ # re-use the hdas above to get the history data...
+ history_dictionary = self.get_history_dict( trans, history, contents_dictionaries=contents_dictionaries )
+
+ except Exception, exc:
+ user_id = str( trans.user.id ) if trans.user else '(anonymous)'
+ log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) )
+ message = ( 'An error occurred getting the history data from the server. '
+ + 'Please contact a Galaxy administrator if the problem persists.' )
+ history_dictionary[ 'error' ] = message
+
+ return {
+ 'history' : history_dictionary,
+ 'contents' : contents_dictionaries
+ }
+
+ def get_history_dict( self, trans, history, contents_dictionaries=None ):
+ """
+ Returns history data in the form of a dictionary.
+ """
+ #TODO: to serializer
+ history_dict = history.to_dict( view='element', value_mapper={ 'id':trans.security.encode_id })
+ history_dict[ 'user_id' ] = None
+ if history.user_id:
+ history_dict[ 'user_id' ] = trans.security.encode_id( history.user_id )
+
+ history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True )
+ history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, history.user, history )
+ if not history_dict[ 'annotation' ]:
+ history_dict[ 'annotation' ] = ''
+
+ #TODO: item_slug url
+ if history_dict[ 'importable' ] and history_dict[ 'slug' ]:
+ username_and_slug = ( '/' ).join(( 'u', history.user.username, 'h', history_dict[ 'slug' ] ))
+ history_dict[ 'username_and_slug' ] = username_and_slug
+
+#TODO: re-add
+ #hda_summaries = hda_dictionaries if hda_dictionaries else self.get_hda_summary_dicts( trans, history )
+ ##TODO remove the following in v2
+ #( state_counts, state_ids ) = self._get_hda_state_summaries( trans, hda_summaries )
+ #history_dict[ 'state_details' ] = state_counts
+ #history_dict[ 'state_ids' ] = state_ids
+ #history_dict[ 'state' ] = self._get_history_state_from_hdas( trans, history, state_counts )
+
+ return history_dict
+
+
+# =============================================================================
+class HistorySerializer( manager_base.ModelSerializer ):
+ """
+ Interface/service object for serializing histories into dictionaries.
+ """
+ pass
diff -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 -r 65ec063664eb0ce100d76d985fba93f200ac5178 lib/galaxy/webapps/galaxy/api/history_contents.py
--- a/lib/galaxy/webapps/galaxy/api/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/history_contents.py
@@ -92,7 +92,7 @@
else:
types = [ 'dataset', "dataset_collection" ]
- contents_kwds = {'types': types}
+ contents_kwds = { 'types': types }
if ids:
ids = map( lambda id: trans.security.decode_id( id ), ids.split( ',' ) )
contents_kwds[ 'ids' ] = ids
@@ -110,14 +110,14 @@
details = util.listify( details )
for content in history.contents_iter( **contents_kwds ):
- if isinstance(content, trans.app.model.HistoryDatasetAssociation):
+ if isinstance( content, trans.app.model.HistoryDatasetAssociation ):
encoded_content_id = trans.security.encode_id( content.id )
detailed = details == 'all' or ( encoded_content_id in details )
if detailed:
rval.append( self._detailed_hda_dict( trans, content ) )
else:
rval.append( self._summary_hda_dict( trans, history_id, content ) )
- elif isinstance(content, trans.app.model.HistoryDatasetCollectionAssociation):
+ elif isinstance( content, trans.app.model.HistoryDatasetCollectionAssociation ):
rval.append( self.__collection_dict( trans, content ) )
return rval
@@ -149,7 +149,8 @@
}
def __collection_dict( self, trans, dataset_collection_instance, view="collection" ):
- return dictify_dataset_collection_instance( dataset_collection_instance, security=trans.security, parent=dataset_collection_instance.history, view=view )
+ return dictify_dataset_collection_instance( dataset_collection_instance,
+ security=trans.security, parent=dataset_collection_instance.history, view=view )
def _detailed_hda_dict( self, trans, hda ):
"""
@@ -201,8 +202,7 @@
)
return self.__collection_dict( trans, dataset_collection_instance, view="element" )
except Exception, e:
- msg = "Error in history API at listing dataset collection: %s" % ( str(e) )
- log.error( msg, exc_info=True )
+ log.exception( "Error in history API at listing dataset collection: %s", e )
trans.response.status = 500
return msg
diff -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 -r 65ec063664eb0ce100d76d985fba93f200ac5178 lib/galaxy/webapps/galaxy/controllers/history.py
--- a/lib/galaxy/webapps/galaxy/controllers/history.py
+++ b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -4,6 +4,7 @@
import galaxy.util
from galaxy import model
from galaxy import web
+from galaxy import managers
from galaxy.datatypes.data import nice_size
from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
from galaxy.model.orm import and_, eagerload_all, func
@@ -194,6 +195,12 @@
class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings,
UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, ExportsHistoryMixin,
ImportsHistoryMixin ):
+ def __init__( self, app ):
+ super( HistoryController, self ).__init__( app )
+ self.mgrs = util.bunch.Bunch(
+ histories=managers.histories.HistoryManager()
+ )
+
@web.expose
def index( self, trans ):
return ""
@@ -204,6 +211,7 @@
trans.response.set_content_type( 'text/xml' )
return trans.fill_template( "/history/list_as_xml.mako" )
+ # ......................................................................... lists
stored_list_grid = HistoryListGrid()
shared_list_grid = SharedHistoryListGrid()
published_list_grid = HistoryAllPublishedGrid()
@@ -437,6 +445,7 @@
# Render the list view
return self.shared_list_grid( trans, status=status, message=message, **kwargs )
+ # ......................................................................... html
@web.expose
def display_structured( self, trans, id=None ):
"""
@@ -512,6 +521,435 @@
return trans.fill_template( "history/display_structured.mako", items=items, history=history )
@web.expose
+ def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ):
+ """
+ View a history. If a history is importable, then it is viewable by any user.
+ """
+ # Get history to view.
+ if not id:
+ return trans.show_error_message( "You must specify a history you want to view." )
+
+ show_deleted = galaxy.util.string_as_bool( show_deleted )
+ show_hidden = galaxy.util.string_as_bool( show_hidden )
+ use_panels = galaxy.util.string_as_bool( use_panels )
+
+ history_dictionary = {}
+ hda_dictionaries = []
+ user_is_owner = False
+ try:
+ history_to_view = self.get_history( trans, id, check_ownership=False, check_accessible=False )
+ if not history_to_view:
+ return trans.show_error_message( "The specified history does not exist." )
+ if history_to_view.user == trans.user:
+ user_is_owner = True
+
+ if( ( history_to_view.user != trans.user )
+ # Admin users can view any history
+ and ( not trans.user_is_admin() )
+ and ( not history_to_view.importable )
+ and ( trans.user not in history_to_view.users_shared_with_dot_users ) ):
+ return trans.show_error_message( "Either you are not allowed to view this history"
+ + " or the owner of this history has not made it accessible." )
+
+ # include all datasets: hidden, deleted, and purged
+ history_data = self.mgrs.histories._get_history_data( trans, history_to_view )
+ history_dictionary = history_data[ 'history' ]
+ hda_dictionaries = history_data[ 'contents' ]
+
+ except Exception, exc:
+ user_id = str( trans.user.id ) if trans.user else '(anonymous)'
+ log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) )
+ history_dictionary[ 'error' ] = ( 'An error occurred getting the history data from the server. '
+ + 'Please contact a Galaxy administrator if the problem persists.' )
+
+ return trans.fill_template_mako( "history/view.mako",
+ history=history_dictionary, hdas=hda_dictionaries, user_is_owner=user_is_owner,
+ show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels )
+
+ @web.expose
+ def display_by_username_and_slug( self, trans, username, slug ):
+ """
+ Display history based on a username and slug.
+ """
+ # Get history.
+ session = trans.sa_session
+ user = session.query( model.User ).filter_by( username=username ).first()
+ history = trans.sa_session.query( model.History ).filter_by( user=user, slug=slug, deleted=False ).first()
+ if history is None:
+ raise web.httpexceptions.HTTPNotFound()
+ # Security check raises error if user cannot access history.
+ self.security_check( trans, history, False, True)
+
+ # Get rating data.
+ user_item_rating = 0
+ if trans.get_user():
+ user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), history )
+ if user_item_rating:
+ user_item_rating = user_item_rating.rating
+ else:
+ user_item_rating = 0
+ ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, history )
+
+ # create ownership flag for template, dictify models
+ user_is_owner = trans.user == history.user
+ history_data = self.mgrs.histories._get_history_data( trans, history )
+ history_dict = history_data[ 'history' ]
+ hda_dicts = history_data[ 'contents' ]
+
+ history_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, history )
+ # note: adding original annotation since this is published - get_dict returns user-based annos
+ #for hda_dict in hda_dicts:
+ # hda_dict[ 'annotation' ] = hda.annotation
+ # dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset )
+
+ return trans.stream_template_mako( "history/display.mako", item=history, item_data=[],
+ user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts,
+ user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings )
+
+ # ......................................................................... sharing & publishing
+ @web.expose
+ @web.require_login( "share Galaxy histories" )
+ def sharing( self, trans, id=None, histories=[], **kwargs ):
+ """ Handle history sharing. """
+
+ # Get session and histories.
+ session = trans.sa_session
+ # Id values take precedence over histories passed in; last resort is current history.
+ if id:
+ ids = galaxy.util.listify( id )
+ if ids:
+ histories = [ self.get_history( trans, history_id ) for history_id in ids ]
+ elif not histories:
+ histories = [ trans.history ]
+
+ # Do operation on histories.
+ for history in histories:
+ if 'make_accessible_via_link' in kwargs:
+ self._make_item_accessible( trans.sa_session, history )
+ elif 'make_accessible_and_publish' in kwargs:
+ self._make_item_accessible( trans.sa_session, history )
+ history.published = True
+ elif 'publish' in kwargs:
+ if history.importable:
+ history.published = True
+ else:
+ # TODO: report error here.
+ pass
+ elif 'disable_link_access' in kwargs:
+ history.importable = False
+ elif 'unpublish' in kwargs:
+ history.published = False
+ elif 'disable_link_access_and_unpublish' in kwargs:
+ history.importable = history.published = False
+ elif 'unshare_user' in kwargs:
+ user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( kwargs[ 'unshare_user' ] ) )
+ # Look for and delete sharing relation for history-user.
+ deleted_sharing_relation = False
+ husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=user, history=history ).all()
+ if husas:
+ deleted_sharing_relation = True
+ for husa in husas:
+ trans.sa_session.delete( husa )
+ if not deleted_sharing_relation:
+ message = "History '%s' does not seem to be shared with user '%s'" % ( history.name, user.email )
+ return trans.fill_template( '/sharing_base.mako', item=history,
+ message=message, status='error' )
+
+
+ # Legacy issue: histories made accessible before recent updates may not have a slug. Create slug for any histories that need them.
+ for history in histories:
+ if history.importable and not history.slug:
+ self._make_item_accessible( trans.sa_session, history )
+
+ session.flush()
+
+ return trans.fill_template( "/sharing_base.mako", item=history )
+
+ @web.expose
+ @web.require_login( "share histories with other users" )
+ def share( self, trans, id=None, email="", **kwd ):
+ # If a history contains both datasets that can be shared and others that cannot be shared with the desired user,
+ # then the entire history is shared, and the protected datasets will be visible, but inaccessible ( greyed out )
+ # in the copyd history
+ params = Params( kwd )
+ user = trans.get_user()
+ # TODO: we have too many error messages floating around in here - we need
+ # to incorporate the messaging system used by the libraries that will display
+ # a message on any page.
+ err_msg = galaxy.util.restore_text( params.get( 'err_msg', '' ) )
+ if not email:
+ if not id:
+ # Default to the current history
+ id = trans.security.encode_id( trans.history.id )
+ id = galaxy.util.listify( id )
+ send_to_err = err_msg
+ histories = []
+ for history_id in id:
+ histories.append( self.get_history( trans, history_id ) )
+ return trans.fill_template( "/history/share.mako",
+ histories=histories,
+ email=email,
+ send_to_err=send_to_err )
+ histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email )
+ if not send_to_users:
+ if not send_to_err:
+ send_to_err += "%s is not a valid Galaxy user. %s" % ( email, err_msg )
+ return trans.fill_template( "/history/share.mako",
+ histories=histories,
+ email=email,
+ send_to_err=send_to_err )
+ if params.get( 'share_button', False ):
+ # The user has not yet made a choice about how to share, so dictionaries will be built for display
+ can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \
+ self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err, unique=True )
+ send_to_err += err_msg
+ if cannot_change and not no_change_needed and not can_change:
+ send_to_err = "The histories you are sharing do not contain any datasets that can be accessed by the users with which you are sharing."
+ return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err )
+ if can_change or cannot_change:
+ return trans.fill_template( "/history/share.mako",
+ histories=histories,
+ email=email,
+ send_to_err=send_to_err,
+ can_change=can_change,
+ cannot_change=cannot_change,
+ no_change_needed=unique_no_change_needed )
+ if no_change_needed:
+ return self._share_histories( trans, user, send_to_err, histories=no_change_needed )
+ elif not send_to_err:
+ # User seems to be sharing an empty history
+ send_to_err = "You cannot share an empty history. "
+ return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err )
+
+ @web.expose
+ @web.require_login( "share restricted histories with other users" )
+ def share_restricted( self, trans, id=None, email="", **kwd ):
+ if 'action' in kwd:
+ action = kwd[ 'action' ]
+ else:
+ err_msg = "Select an action. "
+ return trans.response.send_redirect( url_for( controller='history',
+ action='share',
+ id=id,
+ email=email,
+ err_msg=err_msg,
+ share_button=True ) )
+ user = trans.get_user()
+ user_roles = user.all_roles()
+ histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email )
+ send_to_err = ''
+ # The user has made a choice, so dictionaries will be built for sharing
+ can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \
+ self._populate_restricted( trans, user, histories, send_to_users, action, send_to_err )
+ # Now that we've populated the can_change, cannot_change, and no_change_needed dictionaries,
+ # we'll populate the histories_for_sharing dictionary from each of them.
+ histories_for_sharing = {}
+ if no_change_needed:
+ # Don't need to change anything in cannot_change, so populate as is
+ histories_for_sharing, send_to_err = \
+ self._populate( trans, histories_for_sharing, no_change_needed, send_to_err )
+ if cannot_change:
+ # Can't change anything in cannot_change, so populate as is
+ histories_for_sharing, send_to_err = \
+ self._populate( trans, histories_for_sharing, cannot_change, send_to_err )
+ # The action here is either 'public' or 'private', so we'll continue to populate the
+ # histories_for_sharing dictionary from the can_change dictionary.
+ for send_to_user, history_dict in can_change.items():
+ for history in history_dict:
+ # Make sure the current history has not already been shared with the current send_to_user
+ if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+ .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id,
+ trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
+ .count() > 0:
+ send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
+ else:
+ # Only deal with datasets that have not been purged
+ for hda in history.activatable_datasets:
+ # If the current dataset is not public, we may need to perform an action on it to
+ # make it accessible by the other user.
+ if not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
+ # The user with which we are sharing the history does not have access permission on the current dataset
+ if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations:
+ # The current user has authority to change permissions on the current dataset because
+ # they have permission to manage permissions on the dataset and the dataset is not associated
+ # with a library.
+ if action == "private":
+ trans.app.security_agent.privately_share_dataset( hda.dataset, users=[ user, send_to_user ] )
+ elif action == "public":
+ trans.app.security_agent.make_dataset_public( hda.dataset )
+ # Populate histories_for_sharing with the history after performing any requested actions on
+ # its datasets to make them accessible by the other user.
+ if send_to_user not in histories_for_sharing:
+ histories_for_sharing[ send_to_user ] = [ history ]
+ elif history not in histories_for_sharing[ send_to_user ]:
+ histories_for_sharing[ send_to_user ].append( history )
+ return self._share_histories( trans, user, send_to_err, histories=histories_for_sharing )
+
+ def _get_histories_and_users( self, trans, user, id, email ):
+ if not id:
+ # Default to the current history
+ id = trans.security.encode_id( trans.history.id )
+ id = galaxy.util.listify( id )
+ send_to_err = ""
+ histories = []
+ for history_id in id:
+ histories.append( self.get_history( trans, history_id ) )
+ send_to_users = []
+ for email_address in galaxy.util.listify( email ):
+ email_address = email_address.strip()
+ if email_address:
+ if email_address == user.email:
+ send_to_err += "You cannot send histories to yourself. "
+ else:
+ send_to_user = trans.sa_session.query( trans.app.model.User ) \
+ .filter( and_( trans.app.model.User.table.c.email==email_address,
+ trans.app.model.User.table.c.deleted==False ) ) \
+ .first()
+ if send_to_user:
+ send_to_users.append( send_to_user )
+ else:
+ send_to_err += "%s is not a valid Galaxy user. " % email_address
+ return histories, send_to_users, send_to_err
+
+ def _populate( self, trans, histories_for_sharing, other, send_to_err ):
+ # This method will populate the histories_for_sharing dictionary with the users and
+ # histories in other, eliminating histories that have already been shared with the
+ # associated user. No security checking on datasets is performed.
+ # If not empty, the histories_for_sharing dictionary looks like:
+ # { userA: [ historyX, historyY ], userB: [ historyY ] }
+ # other looks like:
+ # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
+ for send_to_user, history_dict in other.items():
+ for history in history_dict:
+ # Make sure the current history has not already been shared with the current send_to_user
+ if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+ .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id,
+ trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
+ .count() > 0:
+ send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
+ else:
+ # Build the dict that will be used for sharing
+ if send_to_user not in histories_for_sharing:
+ histories_for_sharing[ send_to_user ] = [ history ]
+ elif history not in histories_for_sharing[ send_to_user ]:
+ histories_for_sharing[ send_to_user ].append( history )
+ return histories_for_sharing, send_to_err
+
+ def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err, unique=False ):
+ # The user may be attempting to share histories whose datasets cannot all be accessed by other users.
+ # If this is the case, the user sharing the histories can:
+ # 1) action=='public': choose to make the datasets public if he is permitted to do so
+ # 2) action=='private': automatically create a new "sharing role" allowing protected
+ # datasets to be accessed only by the desired users
+ # This method will populate the can_change, cannot_change and no_change_needed dictionaries, which
+ # are used for either displaying to the user, letting them make 1 of the choices above, or sharing
+ # after the user has made a choice. They will be used for display if 'unique' is True, and will look
+ # like: {historyX : [hda, hda], historyY : [hda] }
+ # For sharing, they will look like:
+ # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
+ can_change = {}
+ cannot_change = {}
+ no_change_needed = {}
+ unique_no_change_needed = {}
+ user_roles = user.all_roles()
+ for history in histories:
+ for send_to_user in send_to_users:
+ # Make sure the current history has not already been shared with the current send_to_user
+ if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
+ .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id,
+ trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
+ .count() > 0:
+ send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
+ else:
+ # Only deal with datasets that have not been purged
+ for hda in history.activatable_datasets:
+ if trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
+ # The no_change_needed dictionary is a special case. If both of can_change
+ # and cannot_change are empty, no_change_needed will used for sharing. Otherwise
+ # unique_no_change_needed will be used for displaying, so we need to populate both.
+ # Build the dictionaries for display, containing unique histories only
+ if history not in unique_no_change_needed:
+ unique_no_change_needed[ history ] = [ hda ]
+ else:
+ unique_no_change_needed[ history ].append( hda )
+ # Build the dictionaries for sharing
+ if send_to_user not in no_change_needed:
+ no_change_needed[ send_to_user ] = {}
+ if history not in no_change_needed[ send_to_user ]:
+ no_change_needed[ send_to_user ][ history ] = [ hda ]
+ else:
+ no_change_needed[ send_to_user ][ history ].append( hda )
+ else:
+ # The user with which we are sharing the history does not have access permission on the current dataset
+ if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ):
+ # The current user has authority to change permissions on the current dataset because
+ # they have permission to manage permissions on the dataset.
+ # NOTE: ( gvk )There may be problems if the dataset also has an ldda, but I don't think so
+ # because the user with which we are sharing will not have the "manage permission" permission
+ # on the dataset in their history. Keep an eye on this though...
+ if unique:
+ # Build the dictionaries for display, containing unique histories only
+ if history not in can_change:
+ can_change[ history ] = [ hda ]
+ else:
+ can_change[ history ].append( hda )
+ else:
+ # Build the dictionaries for sharing
+ if send_to_user not in can_change:
+ can_change[ send_to_user ] = {}
+ if history not in can_change[ send_to_user ]:
+ can_change[ send_to_user ][ history ] = [ hda ]
+ else:
+ can_change[ send_to_user ][ history ].append( hda )
+ else:
+ if action in [ "private", "public" ]:
+ # The user has made a choice, so 'unique' doesn't apply. Don't change stuff
+ # that the user doesn't have permission to change
+ continue
+ if unique:
+ # Build the dictionaries for display, containing unique histories only
+ if history not in cannot_change:
+ cannot_change[ history ] = [ hda ]
+ else:
+ cannot_change[ history ].append( hda )
+ else:
+ # Build the dictionaries for sharing
+ if send_to_user not in cannot_change:
+ cannot_change[ send_to_user ] = {}
+ if history not in cannot_change[ send_to_user ]:
+ cannot_change[ send_to_user ][ history ] = [ hda ]
+ else:
+ cannot_change[ send_to_user ][ history ].append( hda )
+ return can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err
+
+ def _share_histories( self, trans, user, send_to_err, histories=None ):
+ # histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] }
+ histories = histories or {}
+ msg = ""
+ sent_to_emails = []
+ for send_to_user in histories.keys():
+ sent_to_emails.append( send_to_user.email )
+ emails = ",".join( e for e in sent_to_emails )
+ if not histories:
+ send_to_err += "No users have been specified or no histories can be sent without changing permissions or associating a sharing role. "
+ else:
+ for send_to_user, send_to_user_histories in histories.items():
+ shared_histories = []
+ for history in send_to_user_histories:
+ share = trans.app.model.HistoryUserShareAssociation()
+ share.history = history
+ share.user = send_to_user
+ trans.sa_session.add( share )
+ self.create_item_slug( trans.sa_session, history )
+ trans.sa_session.flush()
+ if history not in shared_histories:
+ shared_histories.append( history )
+ if send_to_err:
+ msg += send_to_err
+ return self.sharing( trans, histories=shared_histories, msg=msg )
+
+ # ......................................................................... actions/orig. async
+ @web.expose
def delete_hidden_datasets( self, trans ):
"""
This method deletes all hidden datasets in the current history.
@@ -839,451 +1277,6 @@
#TODO: used in history/view, display, embed
@web.expose
- def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ):
- """
- View a history. If a history is importable, then it is viewable by any user.
- """
- # Get history to view.
- if not id:
- return trans.show_error_message( "You must specify a history you want to view." )
-
- show_deleted = galaxy.util.string_as_bool( show_deleted )
- show_hidden = galaxy.util.string_as_bool( show_hidden )
- use_panels = galaxy.util.string_as_bool( use_panels )
-
- history_dictionary = {}
- hda_dictionaries = []
- user_is_owner = False
- try:
- history_to_view = self.get_history( trans, id, check_ownership=False, check_accessible=False )
- if not history_to_view:
- return trans.show_error_message( "The specified history does not exist." )
- if history_to_view.user == trans.user:
- user_is_owner = True
-
- if( ( history_to_view.user != trans.user )
- # Admin users can view any history
- and ( not trans.user_is_admin() )
- and ( not history_to_view.importable )
- and ( trans.user not in history_to_view.users_shared_with_dot_users ) ):
- return trans.show_error_message( "Either you are not allowed to view this history"
- + " or the owner of this history has not made it accessible." )
-
- # include all datasets: hidden, deleted, and purged
- hdas = self.get_history_datasets( trans, history_to_view,
- show_deleted=True, show_hidden=True, show_purged=True )
- for hda in hdas:
- hda_dict = {}
- try:
- hda_dict = self.get_hda_dict( trans, hda )
-
- except Exception, exc:
- # don't fail entire list if hda err's, record and move on
- log.error( 'Error bootstrapping hda %d: %s', hda.id, str( exc ), exc_info=True )
- hda_dict = self.get_hda_dict_with_error( trans, hda, str( exc ) )
-
- hda_dictionaries.append( hda_dict )
-
- # re-use the hdas above to get the history data...
- history_dictionary = self.get_history_dict( trans, history_to_view, hda_dictionaries=hda_dictionaries )
-
- except Exception, exc:
- user_id = str( trans.user.id ) if trans.user else '(anonymous)'
- log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) )
- history_dictionary[ 'error' ] = ( 'An error occurred getting the history data from the server. '
- + 'Please contact a Galaxy administrator if the problem persists.' )
-
- return trans.fill_template_mako( "history/view.mako",
- history=history_dictionary, hdas=hda_dictionaries, user_is_owner=user_is_owner,
- show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels )
-
- @web.expose
- def display_by_username_and_slug( self, trans, username, slug ):
- """
- Display history based on a username and slug.
- """
- # Get history.
- session = trans.sa_session
- user = session.query( model.User ).filter_by( username=username ).first()
- history = trans.sa_session.query( model.History ).filter_by( user=user, slug=slug, deleted=False ).first()
- if history is None:
- raise web.httpexceptions.HTTPNotFound()
- # Security check raises error if user cannot access history.
- self.security_check( trans, history, False, True)
-
- # Get datasets and annotations
- datasets = self.get_history_datasets( trans, history )
- history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history )
- for dataset in datasets:
- dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset )
-
- # Get rating data.
- user_item_rating = 0
- if trans.get_user():
- user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), history )
- if user_item_rating:
- user_item_rating = user_item_rating.rating
- else:
- user_item_rating = 0
- ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, history )
-
- # create ownership flag for template, dictify models
- # note: adding original annotation since this is published - get_dict returns user-based annos
- user_is_owner = trans.user == history.user
- hda_dicts = []
- for hda in datasets:
- hda_dict = self.get_hda_dict( trans, hda )
- hda_dict[ 'annotation' ] = hda.annotation
- hda_dicts.append( hda_dict )
- history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts )
- history_dict[ 'annotation' ] = history.annotation
-
- return trans.stream_template_mako( "history/display.mako", item=history, item_data=datasets,
- user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts,
- user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings )
-
- @web.expose
- @web.require_login( "share Galaxy histories" )
- def sharing( self, trans, id=None, histories=[], **kwargs ):
- """ Handle history sharing. """
-
- # Get session and histories.
- session = trans.sa_session
- # Id values take precedence over histories passed in; last resort is current history.
- if id:
- ids = galaxy.util.listify( id )
- if ids:
- histories = [ self.get_history( trans, history_id ) for history_id in ids ]
- elif not histories:
- histories = [ trans.history ]
-
- # Do operation on histories.
- for history in histories:
- if 'make_accessible_via_link' in kwargs:
- self._make_item_accessible( trans.sa_session, history )
- elif 'make_accessible_and_publish' in kwargs:
- self._make_item_accessible( trans.sa_session, history )
- history.published = True
- elif 'publish' in kwargs:
- if history.importable:
- history.published = True
- else:
- # TODO: report error here.
- pass
- elif 'disable_link_access' in kwargs:
- history.importable = False
- elif 'unpublish' in kwargs:
- history.published = False
- elif 'disable_link_access_and_unpublish' in kwargs:
- history.importable = history.published = False
- elif 'unshare_user' in kwargs:
- user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( kwargs[ 'unshare_user' ] ) )
- # Look for and delete sharing relation for history-user.
- deleted_sharing_relation = False
- husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=user, history=history ).all()
- if husas:
- deleted_sharing_relation = True
- for husa in husas:
- trans.sa_session.delete( husa )
- if not deleted_sharing_relation:
- message = "History '%s' does not seem to be shared with user '%s'" % ( history.name, user.email )
- return trans.fill_template( '/sharing_base.mako', item=history,
- message=message, status='error' )
-
-
- # Legacy issue: histories made accessible before recent updates may not have a slug. Create slug for any histories that need them.
- for history in histories:
- if history.importable and not history.slug:
- self._make_item_accessible( trans.sa_session, history )
-
- session.flush()
-
- return trans.fill_template( "/sharing_base.mako", item=history )
-
- @web.expose
- @web.require_login( "share histories with other users" )
- def share( self, trans, id=None, email="", **kwd ):
- # If a history contains both datasets that can be shared and others that cannot be shared with the desired user,
- # then the entire history is shared, and the protected datasets will be visible, but inaccessible ( greyed out )
- # in the copyd history
- params = Params( kwd )
- user = trans.get_user()
- # TODO: we have too many error messages floating around in here - we need
- # to incorporate the messaging system used by the libraries that will display
- # a message on any page.
- err_msg = galaxy.util.restore_text( params.get( 'err_msg', '' ) )
- if not email:
- if not id:
- # Default to the current history
- id = trans.security.encode_id( trans.history.id )
- id = galaxy.util.listify( id )
- send_to_err = err_msg
- histories = []
- for history_id in id:
- histories.append( self.get_history( trans, history_id ) )
- return trans.fill_template( "/history/share.mako",
- histories=histories,
- email=email,
- send_to_err=send_to_err )
- histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email )
- if not send_to_users:
- if not send_to_err:
- send_to_err += "%s is not a valid Galaxy user. %s" % ( email, err_msg )
- return trans.fill_template( "/history/share.mako",
- histories=histories,
- email=email,
- send_to_err=send_to_err )
- if params.get( 'share_button', False ):
- # The user has not yet made a choice about how to share, so dictionaries will be built for display
- can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \
- self._populate_restricted( trans, user, histories, send_to_users, None, send_to_err, unique=True )
- send_to_err += err_msg
- if cannot_change and not no_change_needed and not can_change:
- send_to_err = "The histories you are sharing do not contain any datasets that can be accessed by the users with which you are sharing."
- return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err )
- if can_change or cannot_change:
- return trans.fill_template( "/history/share.mako",
- histories=histories,
- email=email,
- send_to_err=send_to_err,
- can_change=can_change,
- cannot_change=cannot_change,
- no_change_needed=unique_no_change_needed )
- if no_change_needed:
- return self._share_histories( trans, user, send_to_err, histories=no_change_needed )
- elif not send_to_err:
- # User seems to be sharing an empty history
- send_to_err = "You cannot share an empty history. "
- return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err )
-
- @web.expose
- @web.require_login( "share restricted histories with other users" )
- def share_restricted( self, trans, id=None, email="", **kwd ):
- if 'action' in kwd:
- action = kwd[ 'action' ]
- else:
- err_msg = "Select an action. "
- return trans.response.send_redirect( url_for( controller='history',
- action='share',
- id=id,
- email=email,
- err_msg=err_msg,
- share_button=True ) )
- user = trans.get_user()
- user_roles = user.all_roles()
- histories, send_to_users, send_to_err = self._get_histories_and_users( trans, user, id, email )
- send_to_err = ''
- # The user has made a choice, so dictionaries will be built for sharing
- can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err = \
- self._populate_restricted( trans, user, histories, send_to_users, action, send_to_err )
- # Now that we've populated the can_change, cannot_change, and no_change_needed dictionaries,
- # we'll populate the histories_for_sharing dictionary from each of them.
- histories_for_sharing = {}
- if no_change_needed:
- # Don't need to change anything in cannot_change, so populate as is
- histories_for_sharing, send_to_err = \
- self._populate( trans, histories_for_sharing, no_change_needed, send_to_err )
- if cannot_change:
- # Can't change anything in cannot_change, so populate as is
- histories_for_sharing, send_to_err = \
- self._populate( trans, histories_for_sharing, cannot_change, send_to_err )
- # The action here is either 'public' or 'private', so we'll continue to populate the
- # histories_for_sharing dictionary from the can_change dictionary.
- for send_to_user, history_dict in can_change.items():
- for history in history_dict:
- # Make sure the current history has not already been shared with the current send_to_user
- if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
- .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id,
- trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
- .count() > 0:
- send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
- else:
- # Only deal with datasets that have not been purged
- for hda in history.activatable_datasets:
- # If the current dataset is not public, we may need to perform an action on it to
- # make it accessible by the other user.
- if not trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
- # The user with which we are sharing the history does not have access permission on the current dataset
- if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ) and not hda.dataset.library_associations:
- # The current user has authority to change permissions on the current dataset because
- # they have permission to manage permissions on the dataset and the dataset is not associated
- # with a library.
- if action == "private":
- trans.app.security_agent.privately_share_dataset( hda.dataset, users=[ user, send_to_user ] )
- elif action == "public":
- trans.app.security_agent.make_dataset_public( hda.dataset )
- # Populate histories_for_sharing with the history after performing any requested actions on
- # its datasets to make them accessible by the other user.
- if send_to_user not in histories_for_sharing:
- histories_for_sharing[ send_to_user ] = [ history ]
- elif history not in histories_for_sharing[ send_to_user ]:
- histories_for_sharing[ send_to_user ].append( history )
- return self._share_histories( trans, user, send_to_err, histories=histories_for_sharing )
-
- def _get_histories_and_users( self, trans, user, id, email ):
- if not id:
- # Default to the current history
- id = trans.security.encode_id( trans.history.id )
- id = galaxy.util.listify( id )
- send_to_err = ""
- histories = []
- for history_id in id:
- histories.append( self.get_history( trans, history_id ) )
- send_to_users = []
- for email_address in galaxy.util.listify( email ):
- email_address = email_address.strip()
- if email_address:
- if email_address == user.email:
- send_to_err += "You cannot send histories to yourself. "
- else:
- send_to_user = trans.sa_session.query( trans.app.model.User ) \
- .filter( and_( trans.app.model.User.table.c.email==email_address,
- trans.app.model.User.table.c.deleted==False ) ) \
- .first()
- if send_to_user:
- send_to_users.append( send_to_user )
- else:
- send_to_err += "%s is not a valid Galaxy user. " % email_address
- return histories, send_to_users, send_to_err
-
- def _populate( self, trans, histories_for_sharing, other, send_to_err ):
- # This method will populate the histories_for_sharing dictionary with the users and
- # histories in other, eliminating histories that have already been shared with the
- # associated user. No security checking on datasets is performed.
- # If not empty, the histories_for_sharing dictionary looks like:
- # { userA: [ historyX, historyY ], userB: [ historyY ] }
- # other looks like:
- # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
- for send_to_user, history_dict in other.items():
- for history in history_dict:
- # Make sure the current history has not already been shared with the current send_to_user
- if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
- .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id,
- trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
- .count() > 0:
- send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
- else:
- # Build the dict that will be used for sharing
- if send_to_user not in histories_for_sharing:
- histories_for_sharing[ send_to_user ] = [ history ]
- elif history not in histories_for_sharing[ send_to_user ]:
- histories_for_sharing[ send_to_user ].append( history )
- return histories_for_sharing, send_to_err
-
- def _populate_restricted( self, trans, user, histories, send_to_users, action, send_to_err, unique=False ):
- # The user may be attempting to share histories whose datasets cannot all be accessed by other users.
- # If this is the case, the user sharing the histories can:
- # 1) action=='public': choose to make the datasets public if he is permitted to do so
- # 2) action=='private': automatically create a new "sharing role" allowing protected
- # datasets to be accessed only by the desired users
- # This method will populate the can_change, cannot_change and no_change_needed dictionaries, which
- # are used for either displaying to the user, letting them make 1 of the choices above, or sharing
- # after the user has made a choice. They will be used for display if 'unique' is True, and will look
- # like: {historyX : [hda, hda], historyY : [hda] }
- # For sharing, they will look like:
- # { userA: {historyX : [hda, hda], historyY : [hda]}, userB: {historyY : [hda]} }
- can_change = {}
- cannot_change = {}
- no_change_needed = {}
- unique_no_change_needed = {}
- user_roles = user.all_roles()
- for history in histories:
- for send_to_user in send_to_users:
- # Make sure the current history has not already been shared with the current send_to_user
- if trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \
- .filter( and_( trans.app.model.HistoryUserShareAssociation.table.c.user_id == send_to_user.id,
- trans.app.model.HistoryUserShareAssociation.table.c.history_id == history.id ) ) \
- .count() > 0:
- send_to_err += "History (%s) already shared with user (%s)" % ( history.name, send_to_user.email )
- else:
- # Only deal with datasets that have not been purged
- for hda in history.activatable_datasets:
- if trans.app.security_agent.can_access_dataset( send_to_user.all_roles(), hda.dataset ):
- # The no_change_needed dictionary is a special case. If both of can_change
- # and cannot_change are empty, no_change_needed will used for sharing. Otherwise
- # unique_no_change_needed will be used for displaying, so we need to populate both.
- # Build the dictionaries for display, containing unique histories only
- if history not in unique_no_change_needed:
- unique_no_change_needed[ history ] = [ hda ]
- else:
- unique_no_change_needed[ history ].append( hda )
- # Build the dictionaries for sharing
- if send_to_user not in no_change_needed:
- no_change_needed[ send_to_user ] = {}
- if history not in no_change_needed[ send_to_user ]:
- no_change_needed[ send_to_user ][ history ] = [ hda ]
- else:
- no_change_needed[ send_to_user ][ history ].append( hda )
- else:
- # The user with which we are sharing the history does not have access permission on the current dataset
- if trans.app.security_agent.can_manage_dataset( user_roles, hda.dataset ):
- # The current user has authority to change permissions on the current dataset because
- # they have permission to manage permissions on the dataset.
- # NOTE: ( gvk )There may be problems if the dataset also has an ldda, but I don't think so
- # because the user with which we are sharing will not have the "manage permission" permission
- # on the dataset in their history. Keep an eye on this though...
- if unique:
- # Build the dictionaries for display, containing unique histories only
- if history not in can_change:
- can_change[ history ] = [ hda ]
- else:
- can_change[ history ].append( hda )
- else:
- # Build the dictionaries for sharing
- if send_to_user not in can_change:
- can_change[ send_to_user ] = {}
- if history not in can_change[ send_to_user ]:
- can_change[ send_to_user ][ history ] = [ hda ]
- else:
- can_change[ send_to_user ][ history ].append( hda )
- else:
- if action in [ "private", "public" ]:
- # The user has made a choice, so 'unique' doesn't apply. Don't change stuff
- # that the user doesn't have permission to change
- continue
- if unique:
- # Build the dictionaries for display, containing unique histories only
- if history not in cannot_change:
- cannot_change[ history ] = [ hda ]
- else:
- cannot_change[ history ].append( hda )
- else:
- # Build the dictionaries for sharing
- if send_to_user not in cannot_change:
- cannot_change[ send_to_user ] = {}
- if history not in cannot_change[ send_to_user ]:
- cannot_change[ send_to_user ][ history ] = [ hda ]
- else:
- cannot_change[ send_to_user ][ history ].append( hda )
- return can_change, cannot_change, no_change_needed, unique_no_change_needed, send_to_err
-
- def _share_histories( self, trans, user, send_to_err, histories=None ):
- # histories looks like: { userA: [ historyX, historyY ], userB: [ historyY ] }
- histories = histories or {}
- msg = ""
- sent_to_emails = []
- for send_to_user in histories.keys():
- sent_to_emails.append( send_to_user.email )
- emails = ",".join( e for e in sent_to_emails )
- if not histories:
- send_to_err += "No users have been specified or no histories can be sent without changing permissions or associating a sharing role. "
- else:
- for send_to_user, send_to_user_histories in histories.items():
- shared_histories = []
- for history in send_to_user_histories:
- share = trans.app.model.HistoryUserShareAssociation()
- share.history = history
- share.user = send_to_user
- trans.sa_session.add( share )
- self.create_item_slug( trans.sa_session, history )
- trans.sa_session.flush()
- if history not in shared_histories:
- shared_histories.append( history )
- if send_to_err:
- msg += send_to_err
- return self.sharing( trans, histories=shared_histories, msg=msg )
-
- @web.expose
@web.require_login( "rename histories" )
def rename( self, trans, id=None, name=None, **kwd ):
user = trans.get_user()
@@ -1361,7 +1354,8 @@
name += " (active items only)"
new_history = history.copy( name=name, target_user=user )
if len( histories ) == 1:
- msg = 'New history "<a href="%s" target="_top">%s</a>" has been created.' % ( url_for( controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) ) , new_history.name )
+ switch_url = url_for( controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) )
+ msg = 'New history "<a href="%s" target="_top">%s</a>" has been created.' % ( switch_url, new_history.name )
else:
msg = 'Copied and created %d new histories.' % len( histories )
return trans.show_ok_message( msg )
diff -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 -r 65ec063664eb0ce100d76d985fba93f200ac5178 lib/galaxy/webapps/galaxy/controllers/root.py
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -7,20 +7,28 @@
from paste.httpexceptions import HTTPNotFound, HTTPBadGateway
+from galaxy.web.base.controller import BaseUIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin
+from galaxy import managers
+
from galaxy import web
from galaxy.web import url_for
from galaxy.model.item_attrs import UsesAnnotations
+from galaxy import util
from galaxy.util import listify, Params, string_as_bool, string_as_bool_or_none
-from galaxy.web.base.controller import BaseUIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin
from galaxy.util.json import to_json_string
-from galaxy.util.debugging import SimpleProfiler
-
import logging
log = logging.getLogger( __name__ )
class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesAnnotations ):
- """Controller class that maps to the url root of Galaxy (i.e. '/')."""
+ """
+ Controller class that maps to the url root of Galaxy (i.e. '/').
+ """
+ def __init__( self, app ):
+ super( RootController, self ).__init__( app )
+ self.mgrs = util.bunch.Bunch(
+ histories=managers.histories.HistoryManager()
+ )
@web.expose
def default(self, trans, target1=None, target2=None, **kwd):
@@ -100,42 +108,6 @@
show_deleted=string_as_bool( show_deleted ),
show_hidden=string_as_bool( show_hidden ) )
- def _get_current_history_data( self, trans ):
- history_dictionary = {}
- hda_dictionaries = []
-
- try:
- history = trans.get_history( create=True )
- hdas = self.get_history_datasets( trans, history,
- show_deleted=True, show_hidden=True, show_purged=True )
-
- for hda in hdas:
- hda_dict = {}
- try:
- hda_dict = self.get_hda_dict( trans, hda )
-
- except Exception, exc:
- # don't fail entire list if hda err's, record and move on
- log.error( 'Error bootstrapping hda %d: %s', hda.id, str( exc ), exc_info=True )
- hda_dict = self.get_hda_dict_with_error( trans, hda, str( exc ) )
-
- hda_dictionaries.append( hda_dict )
-
- # re-use the hdas above to get the history data...
- history_dictionary = self.get_history_dict( trans, history, hda_dictionaries=hda_dictionaries )
-
- except Exception, exc:
- user_id = str( trans.user.id ) if trans.user else '(anonymous)'
- log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) )
- message = ( 'An error occurred getting the history data from the server. '
- + 'Please contact a Galaxy administrator if the problem persists.' )
- history_dictionary[ 'error' ] = message
-
- return {
- 'history' : history_dictionary,
- 'hdas' : hda_dictionaries
- }
-
@web.expose
def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, **kwd ):
"""
@@ -154,11 +126,11 @@
show_hidden = string_as_bool_or_none( show_hidden )
history_dictionary = {}
- hda_dictionaries = []
+ hda_dictionaries = []
try:
- history_data = self._get_current_history_data( trans )
+ history_data = self.mgrs.histories._get_history_data( trans, trans.get_history( create=True ) )
history_dictionary = history_data[ 'history' ]
- hda_dictionaries = history_data[ 'hdas' ]
+ hda_dictionaries = history_data[ 'contents' ]
except Exception, exc:
user_id = str( trans.user.id ) if trans.user else '(anonymous)'
@@ -170,6 +142,7 @@
history = history_dictionary, hdas = hda_dictionaries,
show_deleted=show_deleted, show_hidden=show_hidden )
+
## ---- Dataset display / editing ----------------------------------------
@web.expose
def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", encoded_id=None, **kwd ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Fix bug related to undefined attribute error in workflow editor.
by commits-noreply＠bitbucket.org 09 Jul '14
by commits-noreply＠bitbucket.org 09 Jul '14
09 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1861cbcc610d/
Changeset: 1861cbcc610d
User: jmchilton
Date: 2014-07-10 00:39:00
Summary: Fix bug related to undefined attribute error in workflow editor.
Affected #: 1 file
diff -r 5e74f91d068bedde58cf4ec9d8299bd05fdff697 -r 1861cbcc610da6e519c7760e1c829ec3b66887f4 static/scripts/galaxy.workflow_editor.canvas.js
--- a/static/scripts/galaxy.workflow_editor.canvas.js
+++ b/static/scripts/galaxy.workflow_editor.canvas.js
@@ -306,7 +306,7 @@
inputFilled = false;
} else {
var firstOutput = this.connectors[ 0 ].handle1;
- if( firstOutput === null ){
+ if( ! firstOutput ){
inputFilled = false;
} else {
if( firstOutput.isDataCollectionInput || firstOutput.isMappedOver() || firstOutput.datatypes.indexOf( "input_collection" ) > 0 ) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Remove debugging statement.
by commits-noreply＠bitbucket.org 09 Jul '14
by commits-noreply＠bitbucket.org 09 Jul '14
09 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5e74f91d068b/
Changeset: 5e74f91d068b
User: jgoecks
Date: 2014-07-09 22:36:47
Summary: Remove debugging statement.
Affected #: 1 file
diff -r 64d51b16a55173bfec78dc22ee802d3e085dd4fc -r 5e74f91d068bedde58cf4ec9d8299bd05fdff697 static/scripts/mvc/ui/ui-frames.js
--- a/static/scripts/mvc/ui/ui-frames.js
+++ b/static/scripts/mvc/ui/ui-frames.js
@@ -196,7 +196,6 @@
// Load content into frame.
var content_elt = $frame_el.find('.f-content');
- console.log(content_elt);
if (_.isFunction(options.content)) {
options.content(content_elt);
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: davebgx: Fix test_history_functions test 80, copying history items.
by commits-noreply＠bitbucket.org 09 Jul '14
by commits-noreply＠bitbucket.org 09 Jul '14
09 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/64d51b16a551/
Changeset: 64d51b16a551
User: davebgx
Date: 2014-07-09 22:11:50
Summary: Fix test_history_functions test 80, copying history items.
Affected #: 2 files
diff -r 50a273de6cd76b770eb78861fee2b0a97621fa3b -r 64d51b16a55173bfec78dc22ee802d3e085dd4fc test/base/twilltestcase.py
--- a/test/base/twilltestcase.py
+++ b/test/base/twilltestcase.py
@@ -506,13 +506,13 @@
self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' )
self.wait() # wait for the format convert tool to finish before returning
- def copy_history_item( self, source_dataset_id=None, target_history_id=None, all_target_history_ids=[],
+ def copy_history_item( self, source_history_id=None, source_dataset_id=None, target_history_id=None, all_target_history_ids=[],
deleted_history_ids=[] ):
"""
Copy 1 history_dataset_association to 1 history (Limited by twill since it doesn't support multiple
field names, such as checkboxes
"""
- self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_id ) )
+ self.visit_url( "/dataset/copy_datasets" )
self.check_page_for_string( 'Source History:' )
# Make sure all of users active histories are displayed
for id in all_target_history_ids:
@@ -524,9 +524,11 @@
raise AssertionError( "deleted history id %d displayed in list of target histories" % id )
except:
pass
-
- tc.fv( '1', 'target_history_id', target_history_id )
- tc.submit( 'do_copy' )
+ form_values = [ ( 'source_history', source_history_id ),
+ ( 'target_history_id', target_history_id ),
+ ( 'source_content_ids', 'dataset|%s' % source_dataset_id ),
+ ( 'do_copy', True ) ]
+ self.visit_url( "/dataset/copy_datasets", params=form_values )
check_str = '1 dataset copied to 1 history'
self.check_page_for_string( check_str )
diff -r 50a273de6cd76b770eb78861fee2b0a97621fa3b -r 64d51b16a55173bfec78dc22ee802d3e085dd4fc test/functional/test_history_functions.py
--- a/test/functional/test_history_functions.py
+++ b/test/functional/test_history_functions.py
@@ -831,7 +831,8 @@
deleted_history_ids = [ self.security.encode_id( history1.id ), self.security.encode_id( history2.id ) ]
# Test copying to the current history
target_history_id = self.security.encode_id( history6.id )
- self.copy_history_item( source_dataset_id=source_dataset_ids,
+ self.copy_history_item( source_history_id=self.security.encode_id( history6.id ),
+ source_dataset_id=source_dataset_ids,
target_history_id=target_history_id,
all_target_history_ids=all_target_history_ids,
deleted_history_ids=deleted_history_ids )
@@ -852,7 +853,8 @@
all_target_history_ids = [ self.security.encode_id( hda.id ) for hda in admin_user.active_histories ]
# Test copying to the a history that is not the current history
self.security.encode_id( history7.id )
- self.copy_history_item( source_dataset_id=source_dataset_ids,
+ self.copy_history_item( source_history_id=self.security.encode_id( history6.id ),
+ source_dataset_id=source_dataset_ids,
target_history_id=target_history_id,
all_target_history_ids=all_target_history_ids,
deleted_history_ids=deleted_history_ids )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: History panel: refactoring for dataset collections
by commits-noreply＠bitbucket.org 09 Jul '14
by commits-noreply＠bitbucket.org 09 Jul '14
09 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/50a273de6cd7/
Changeset: 50a273de6cd7
User: carlfeberhard
Date: 2014-07-09 19:40:43
Summary: History panel: refactoring for dataset collections
Affected #: 17 files
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/collection/hdca-model.js
--- /dev/null
+++ b/static/scripts/mvc/collection/hdca-model.js
@@ -0,0 +1,69 @@
+define([
+ "mvc/history/history-content-base",
+ "utils/localization"
+], function( historyContent, _l ){
+//==============================================================================
+var HistoryDatasetCollectionAssociation = historyContent.HistoryContent.extend(
+/** @lends HistoryDatasetCollectionAssociation.prototype */{
+ /** default attributes for a model */
+ defaults : {
+ // parent (containing) history
+ history_id : null,
+ // often used with tagging
+ model_class : 'HistoryDatasetCollectionAssociation',
+ history_content_type : 'dataset_collection',
+ hid : 0,
+
+ id : null,
+ name : '(unnamed dataset collection)',
+ // one of HistoryDatasetAssociation.STATES, calling them all 'ok' for now.
+ state : 'ok',
+
+ accessible : true,
+ deleted : false,
+ visible : true,
+
+ purged : false, // Purged doesn't make sense for collections - at least right now.
+
+ tags : [],
+ annotation : ''
+ },
+ urls : function(){
+ },
+
+ inReadyState : function(){
+ return true; // TODO
+ },
+
+ // ........................................................................ search
+ /** what attributes of an collection will be used in a text search */
+ searchAttributes : [
+ 'name'
+ ],
+
+ /** our attr keys don't often match the labels we display to the user - so, when using
+ * attribute specifiers ('name="bler"') in a term, allow passing in aliases for the
+ * following attr keys.
+ */
+ searchAliases : {
+ title : 'name'
+ // TODO: Add tag...
+ },
+
+ // ........................................................................ misc
+ /** String representation */
+ toString : function(){
+ var nameAndId = this.get( 'id' ) || '';
+ if( this.get( 'name' ) ){
+ nameAndId = this.get( 'hid' ) + ' :"' + this.get( 'name' ) + '",' + nameAndId;
+ }
+ return 'HDCA-' + this.get( 'collection_type' ) + '(' + nameAndId + ')';
+ }
+});
+
+
+//==============================================================================
+ return {
+ HistoryDatasetCollectionAssociation : HistoryDatasetCollectionAssociation
+ };
+});
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/dataset/hda-model.js
--- a/static/scripts/mvc/dataset/hda-model.js
+++ b/static/scripts/mvc/dataset/hda-model.js
@@ -1,169 +1,7 @@
define([
- "mvc/base-mvc",
+ "mvc/history/history-content-base",
"utils/localization"
-], function( baseMVC, _l ){
-//==============================================================================
-/** @class model for contents related to a history.
- * @name HistoryContent
- *
- * @augments Backbone.Model
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
- */
-var HistoryContent = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( {
- idAttribute : 'type_id',
-
- /** fetch location of this HDA's history in the api */
- urlRoot: galaxy_config.root + 'api/histories/',
-
- constructor : function( attrs, options ){
- attrs.type_id = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id );
- Backbone.Model.apply( this, arguments );
- },
-
- initialize : function( attrs, options ){
- // assumes type won't change
- this.on( 'change:id', this._createTypeId );
- //TODO: not sure this covers all the bases...
- },
-
- /** full url spec. for this HDA */
- url : function(){
- return this.urlRoot + this.get( 'history_id' ) + '/contents/' + this.get('history_content_type') + 's/' + this.get( 'id' );
- },
-
- /** the more common alias of visible */
- hidden : function(){
- return !this.get( 'visible' );
- },
-
- // ........................................................................ ajax
-
- /** save this HDA, _Mark_ing it as deleted (just a flag) */
- 'delete' : function _delete( options ){
- if( this.get( 'deleted' ) ){ return jQuery.when(); }
- return this.save( { deleted: true }, options );
- },
- /** save this HDA, _Mark_ing it as undeleted */
- undelete : function _undelete( options ){
- if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }
- return this.save( { deleted: false }, options );
- },
-
- /** save this HDA as not visible */
- hide : function _hide( options ){
- if( !this.get( 'visible' ) ){ return jQuery.when(); }
- return this.save( { visible: false }, options );
- },
- /** save this HDA as visible */
- unhide : function _uhide( options ){
- if( this.get( 'visible' ) ){ return jQuery.when(); }
- return this.save( { visible: true }, options );
- },
-
- /** based on show_deleted, show_hidden (gen. from the container control),
- * would this ds show in the list of ds's?
- * @param {Boolean} show_deleted are we showing deleted hdas?
- * @param {Boolean} show_hidden are we showing hidden hdas?
- */
- isVisible : function( show_deleted, show_hidden ){
- var isVisible = true;
- if( ( !show_deleted )
- && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){
- isVisible = false;
- }
- if( ( !show_hidden )
- && ( !this.get( 'visible' ) ) ){
- isVisible = false;
- }
- return isVisible;
- },
-
- /** search the attribute with key attrKey for the string searchFor; T/F if found */
- searchAttribute : function( attrKey, searchFor ){
- var attrVal = this.get( attrKey );
- //console.debug( 'searchAttribute', attrKey, attrVal, searchFor );
- // bail if empty searchFor or unsearchable values
- if( !searchFor
- || ( attrVal === undefined || attrVal === null ) ){
- return false;
- }
- // pass to sep. fn for deep search of array attributes
- if( _.isArray( attrVal ) ){ return this._searchArrayAttribute( attrVal, searchFor ); }
- return ( attrVal.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 );
- },
-
- /** deep(er) search for array attributes; T/F if found */
- _searchArrayAttribute : function( array, searchFor ){
- //console.debug( '_searchArrayAttribute', array, searchFor );
- searchFor = searchFor.toLowerCase();
- //precondition: searchFor has already been validated as non-empty string
- //precondition: assumes only 1 level array
- //TODO: could possibly break up searchFor more (CSV...)
- return _.any( array, function( elem ){
- return ( elem.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 );
- });
- },
-
- /** search all searchAttributes for the string searchFor,
- * returning a list of keys of attributes that contain searchFor
- */
- search : function( searchFor ){
- var model = this;
- return _.filter( this.searchAttributes, function( key ){
- return model.searchAttribute( key, searchFor );
- });
- },
-
- /** alias of search, but returns a boolean; accepts attribute specifiers where
- * the attributes searched can be narrowed to a single attribute using
- * the form: matches( 'genome_build=hg19' )
- * (the attribute keys allowed can also be aliases to the true attribute key;
- * see searchAliases above)
- * @param {String} term plain text or ATTR_SPECIFIER sep. key=val pair
- * @returns {Boolean} was term found in (any) attribute(s)
- */
- matches : function( term ){
- var ATTR_SPECIFIER = '=',
- split = term.split( ATTR_SPECIFIER );
- // attribute is specified - search only that
- if( split.length >= 2 ){
- var attrKey = split[0];
- attrKey = this.searchAliases[ attrKey ] || attrKey;
- return this.searchAttribute( attrKey, split[1] );
- }
- // no attribute is specified - search all attributes in searchAttributes
- return !!this.search( term ).length;
- },
-
- /** an implicit AND search for all terms; IOW, an hda must match all terms given
- * where terms is a whitespace separated value string.
- * e.g. given terms of: 'blah bler database=hg19'
- * an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19
- * To include whitespace in terms: wrap the term in double quotations.
- */
- matchesAll : function( terms ){
- var model = this;
- // break the terms up by whitespace and filter out the empty strings
- terms = terms.match( /(".*"|\w*=".*"|\S*)/g ).filter( function( s ){ return !!s; });
- return _.all( terms, function( term ){
- term = term.replace( /"/g, '' );
- return model.matches( term );
- });
- },
-
- _createTypeId : function(){
- this.set( 'type_id', TypeIdModel.typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) ) );
- },
-
-} );
-
-/** create a type + id string for use in mixed collections */
-HistoryContent.typeIdStr = function _typeId( type, id ){
- return [ type, id ].join( '-' );
-};
-
+], function( historyContent, _l ){
//==============================================================================
/** @class (HDA) model for a Galaxy dataset
* related to a history.
@@ -174,7 +12,7 @@
* @borrows LoggableMixin#log as #log
* @constructs
*/
-var HistoryDatasetAssociation = HistoryContent.extend(
+var HistoryDatasetAssociation = historyContent.HistoryContent.extend(
/** @lends HistoryDatasetAssociation.prototype */{
///** logger used to record this.log messages, commonly set to console */
@@ -456,326 +294,9 @@
HistoryDatasetAssociation.STATES.NEW
];
-//==============================================================================
-/** @class Backbone collection of (HDA) models
- * TODO: Rename HistoryContentCollection
- *
- * @borrows LoggableMixin#logger as #logger
- * @borrows LoggableMixin#log as #log
- * @constructs
- */
-var HDACollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend(
-/** @lends HDACollection.prototype */{
- model : function( attrs, options ) {
- if( attrs.history_content_type == "dataset" ) {
- return new HistoryDatasetAssociation( attrs, options );
- } else if( attrs.history_content_type == "dataset_collection" ) {
- return new HistoryDatasetCollectionAssociation( attrs, options );
- } else {
- // TODO: Handle unknown history_content_type...
- }
- },
-
- ///** logger used to record this.log messages, commonly set to console */
- //// comment this out to suppress log output
- //logger : console,
-
- /** root api url */
- urlRoot : galaxy_config.root + 'api/histories',
- /** complete api url */
- url : function(){
- return this.urlRoot + '/' + this.historyId + '/contents';
- },
-
- /** Set up.
- * @see Backbone.Collection#initialize
- */
- initialize : function( models, options ){
- options = options || {};
- this.historyId = options.historyId;
- //this._setUpListeners();
- },
-
- //_setUpListeners : function(){
- //},
-
- // ........................................................................ common queries
- /** Get the ids of every hda in this collection
- * @returns array of encoded ids
- */
- ids : function(){
- return this.map( function( hda ){ return hda.get('id'); });
- },
-
- /** Get hdas that are not ready
- * @returns array of HDAs
- */
- notReady : function(){
- return this.filter( function( hda ){
- return !hda.inReadyState();
- });
- },
-
- /** Get the id of every hda in this collection not in a 'ready' state (running).
- * @returns an array of hda ids
- * @see HistoryDatasetAssociation#inReadyState
- */
- running : function(){
- var idList = [];
- this.each( function( item ){
- if( !item.inReadyState() ){
- idList.push( item.get( 'id' ) );
- }
- });
- return idList;
- },
-
- /** Get the hda with the given hid
- * @param {Int} hid the hid to search for
- * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found
- */
- getByHid : function( hid ){
- return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) );
- },
-
- /** Get every 'shown' hda in this collection based on show_deleted/hidden
- * @param {Boolean} show_deleted are we showing deleted hdas?
- * @param {Boolean} show_hidden are we showing hidden hdas?
- * @returns array of hda models
- * @see HistoryDatasetAssociation#isVisible
- */
- getVisible : function( show_deleted, show_hidden, filters ){
- filters = filters || [];
- //console.debug( 'filters:', filters );
- //TODO:?? why doesn't this return a collection?
- // always filter by show deleted/hidden first
- var filteredHdas = new HDACollection( this.filter( function( item ){
- return item.isVisible( show_deleted, show_hidden );
- }));
-
- _.each( filters, function( filter_fn ){
- if( !_.isFunction( filter_fn ) ){ return; }
- filteredHdas = new HDACollection( filteredHdas.filter( filter_fn ) );
- });
- //if( filteredHdas.length ){
- // console.debug( 'filteredHdas:' );
- // filteredHdas.each( function( hda ){
- // console.debug( '\t', hda );
- // });
- //} else {
- // console.warn( 'no visible hdas' );
- //}
- return filteredHdas;
- },
-
- /** return true if any hdas don't have details */
- haveDetails : function(){
- return this.all( function( hda ){ return hda.hasDetails(); });
- },
-
- // ........................................................................ ajax
- /** fetch detailed model data for all HDAs in this collection */
- fetchAllDetails : function( options ){
- options = options || {};
- var detailsFlag = { details: 'all' };
- options.data = ( options.data )?( _.extend( options.data, detailsFlag ) ):( detailsFlag );
- return this.fetch( options );
- },
-
- /** using a queue, perform hdaModelAjaxFn on each of the hdas in this collection */
- ajaxQueue : function( hdaAjaxFn, options ){
- var deferred = jQuery.Deferred(),
- startingLength = this.length,
- responses = [];
-
- if( !startingLength ){
- deferred.resolve([]);
- return deferred;
- }
-
- // use reverse order (stylistic choice)
- var ajaxFns = this.chain().reverse().map( function( hda, i ){
- return function(){
- var xhr = hdaAjaxFn.call( hda, options );
- // if successful, notify using the deferred to allow tracking progress
- xhr.done( function( response ){
- deferred.notify({ curr: i, total: startingLength, response: response, model: hda });
- });
- // (regardless of previous error or success) if not last ajax call, shift and call the next
- // if last fn, resolve deferred
- xhr.always( function( response ){
- responses.push( response );
- if( ajaxFns.length ){
- ajaxFns.shift()();
- } else {
- deferred.resolve( responses );
- }
- });
- };
- }).value();
- // start the queue
- ajaxFns.shift()();
-
- return deferred;
- },
-
- // ........................................................................ sorting/filtering
- /** return a new collection of HDAs whose attributes contain the substring matchesWhat */
- matches : function( matchesWhat ){
- return this.filter( function( hda ){
- return hda.matches( matchesWhat );
- });
- },
-
- // ........................................................................ misc
- set : function( models, options ){
- // arrrrrrrrrrrrrrrrrg...
- // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone)
- // w/o this partial models from the server will fill in missing data with model defaults
- // and overwrite existing data on the client
- // see Backbone.Collection.set and _prepareModel
- var collection = this;
- models = _.map( models, function( model ){
- var attrs = model.attributes || model; // Handle raw json or Backbone model.
- var typeId = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id );
- var existing = collection.get( typeId );
- if( !existing ){ return model; }
-
- // merge the models _BEFORE_ calling the superclass version
- var merged = existing.toJSON();
- _.extend( merged, model );
- return merged;
- });
- // now call superclass when the data is filled
- Backbone.Collection.prototype.set.call( this, models, options );
- },
-
- /** Convert this ad-hoc collection of HDAs to a formal collection tracked
- by the server.
- **/
- promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){
- options = options || {};
- options.url = this.url();
- options.type = "POST";
- var full_collection_type = collection_type;
- var element_identifiers = [],
- name = null;
-
- // This mechanism is rough - no error handling, allows invalid selections, no way
- // for user to pick/override element identifiers. This is only really meant
- if( collection_type == "list" ) {
- this.chain().each( function( hda ) {
- // TODO: Handle duplicate names.
- var name = hda.attributes.name;
- var id = hda.get('id');
- var content_type = hda.attributes.history_content_type;
- if( content_type == "dataset" ) {
- if( full_collection_type != "list" ) {
- console.log( "Invalid collection type" );
- }
- element_identifiers.push( { name: name, src: "hda", id: id } );
- } else {
- if( full_collection_type == "list" ) {
- full_collection_type = "list:" + hda.attributes.collection_type;
- } else {
- if( full_collection_type != "list:" + hda.attributes.collection_type ) {
- console.log( "Invalid collection type" );
- }
- }
- element_identifiers.push( { name: name, src: "hdca", id: id } );
- }
- });
- name = "New Dataset List";
- } else if( collection_type == "paired" ) {
- var ids = this.ids();
- if( ids.length != 2 ){
- // TODO: Do something...
- }
- element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } );
- element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } );
- name = "New Dataset Pair";
- }
- options.data = {type: "dataset_collection",
- name: name,
- collection_type: full_collection_type,
- element_identifiers: JSON.stringify(element_identifiers),
- };
-
- var xhr = jQuery.ajax( options );
- xhr.done( function( message, status, responseObj ){
- history.refresh( );
- });
- xhr.fail( function( xhr, status, message ){
- if( xhr.responseJSON && xhr.responseJSON.error ){
- error = xhr.responseJSON.error;
- } else {
- error = xhr.responseJSON;
- }
- xhr.responseText = error;
- // Do something?
- });
- return xhr;
- },
-
- /** String representation. */
- toString : function(){
- return ([ 'HDACollection(', [ this.historyId, this.length ].join(), ')' ].join( '' ));
- }
-});
-
-var HistoryDatasetCollectionAssociation = HistoryContent.extend(
-/** @lends HistoryDatasetCollectionAssociation.prototype */{
- /** default attributes for a model */
- defaults : {
- // parent (containing) history
- history_id : null,
- // often used with tagging
- model_class : 'HistoryDatasetCollectionAssociation',
- history_content_type : 'dataset_collection',
- hid : 0,
-
- id : null,
- name : '(unnamed dataset collection)',
- // one of HistoryDatasetAssociation.STATES, calling them all 'ok' for now.
- state : 'ok',
-
- accessible : true,
- deleted : false,
- visible : true,
-
- purged : false, // Purged doesn't make sense for collections - at least right now.
-
- tags : [],
- annotation : ''
- },
- urls : function(){
- },
-
- inReadyState : function(){
- return true; // TODO
- },
-
- // ........................................................................ search
- /** what attributes of an collection will be used in a text search */
- searchAttributes : [
- 'name'
- ],
-
- /** our attr keys don't often match the labels we display to the user - so, when using
- * attribute specifiers ('name="bler"') in a term, allow passing in aliases for the
- * following attr keys.
- */
- searchAliases : {
- title : 'name'
- // TODO: Add tag...
- },
-
-});
-
-
//==============================================================================
-return {
- HistoryDatasetAssociation : HistoryDatasetAssociation,
- HDACollection : HDACollection
-};});
+ return {
+ HistoryDatasetAssociation : HistoryDatasetAssociation
+ };
+});
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/current-history-panel.js
--- a/static/scripts/mvc/history/current-history-panel.js
+++ b/static/scripts/mvc/history/current-history-panel.js
@@ -53,7 +53,7 @@
noneFoundMsg : _l( "No matching datasets found" ),
// ......................................................................... SET UP
- /** Set up the view, set up storage, bind listeners to HDACollection events
+ /** Set up the view, set up storage, bind listeners to HistoryContents events
* @param {Object} attributes
*/
initialize : function( attributes ){
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-content-base.js
--- /dev/null
+++ b/static/scripts/mvc/history/history-content-base.js
@@ -0,0 +1,181 @@
+define([
+ "mvc/base-mvc",
+ "utils/localization"
+], function( baseMVC, _l ){
+//==============================================================================
+/** @class base model for content items contained in a history or hdca.
+ * @name HistoryContent
+ *
+ * @augments Backbone.Model
+ * @borrows LoggableMixin#logger as #logger
+ * @borrows LoggableMixin#log as #log
+ * @constructs
+ */
+var HistoryContent = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( {
+ idAttribute : 'type_id',
+
+ constructor : function( attrs, options ){
+ attrs.type_id = HistoryContent.typeIdStr( attrs.history_content_type, attrs.id );
+ Backbone.Model.apply( this, arguments );
+ },
+
+ initialize : function( attrs, options ){
+ // assumes type won't change
+ this.on( 'change:id', this._createTypeId );
+ //TODO: not sure this covers all the bases...
+ },
+ _createTypeId : function(){
+ this.set( 'type_id', TypeIdModel.typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) ) );
+ },
+
+ // ........................................................................ common queries
+ /** the more common alias of visible */
+ hidden : function(){
+ return !this.get( 'visible' );
+ },
+
+ /** based on show_deleted, show_hidden (gen. from the container control),
+ * would this ds show in the list of ds's?
+ * @param {Boolean} show_deleted are we showing deleted hdas?
+ * @param {Boolean} show_hidden are we showing hidden hdas?
+ */
+ isVisible : function( show_deleted, show_hidden ){
+ var isVisible = true;
+ if( ( !show_deleted )
+ && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){
+ isVisible = false;
+ }
+ if( ( !show_hidden )
+ && ( !this.get( 'visible' ) ) ){
+ isVisible = false;
+ }
+ return isVisible;
+ },
+
+ // ........................................................................ ajax
+ /** */
+ urlRoot: galaxy_config.root + 'api/histories/',
+
+ /** full url spec. for this HDA */
+ url : function(){
+ return this.urlRoot + this.get( 'history_id' ) + '/contents/'
+ + this.get('history_content_type') + 's/' + this.get( 'id' );
+ },
+
+ /** save this HDA, _Mark_ing it as deleted (just a flag) */
+ 'delete' : function _delete( options ){
+ if( this.get( 'deleted' ) ){ return jQuery.when(); }
+ return this.save( { deleted: true }, options );
+ },
+ /** save this HDA, _Mark_ing it as undeleted */
+ undelete : function _undelete( options ){
+ if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }
+ return this.save( { deleted: false }, options );
+ },
+
+ /** save this HDA as not visible */
+ hide : function _hide( options ){
+ if( !this.get( 'visible' ) ){ return jQuery.when(); }
+ return this.save( { visible: false }, options );
+ },
+ /** save this HDA as visible */
+ unhide : function _uhide( options ){
+ if( this.get( 'visible' ) ){ return jQuery.when(); }
+ return this.save( { visible: true }, options );
+ },
+
+ // ........................................................................ searching
+ /** search the attribute with key attrKey for the string searchFor; T/F if found */
+ searchAttribute : function( attrKey, searchFor ){
+ var attrVal = this.get( attrKey );
+ //console.debug( 'searchAttribute', attrKey, attrVal, searchFor );
+ // bail if empty searchFor or unsearchable values
+ if( !searchFor
+ || ( attrVal === undefined || attrVal === null ) ){
+ return false;
+ }
+ // pass to sep. fn for deep search of array attributes
+ if( _.isArray( attrVal ) ){ return this._searchArrayAttribute( attrVal, searchFor ); }
+ return ( attrVal.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 );
+ },
+
+ /** deep(er) search for array attributes; T/F if found */
+ _searchArrayAttribute : function( array, searchFor ){
+ //console.debug( '_searchArrayAttribute', array, searchFor );
+ searchFor = searchFor.toLowerCase();
+ //precondition: searchFor has already been validated as non-empty string
+ //precondition: assumes only 1 level array
+ //TODO: could possibly break up searchFor more (CSV...)
+ return _.any( array, function( elem ){
+ return ( elem.toString().toLowerCase().indexOf( searchFor.toLowerCase() ) !== -1 );
+ });
+ },
+
+ /** search all searchAttributes for the string searchFor,
+ * returning a list of keys of attributes that contain searchFor
+ */
+ search : function( searchFor ){
+ var model = this;
+ return _.filter( this.searchAttributes, function( key ){
+ return model.searchAttribute( key, searchFor );
+ });
+ },
+
+ /** alias of search, but returns a boolean; accepts attribute specifiers where
+ * the attributes searched can be narrowed to a single attribute using
+ * the form: matches( 'genome_build=hg19' )
+ * (the attribute keys allowed can also be aliases to the true attribute key;
+ * see searchAliases above)
+ * @param {String} term plain text or ATTR_SPECIFIER sep. key=val pair
+ * @returns {Boolean} was term found in (any) attribute(s)
+ */
+ matches : function( term ){
+ var ATTR_SPECIFIER = '=',
+ split = term.split( ATTR_SPECIFIER );
+ // attribute is specified - search only that
+ if( split.length >= 2 ){
+ var attrKey = split[0];
+ attrKey = this.searchAliases[ attrKey ] || attrKey;
+ return this.searchAttribute( attrKey, split[1] );
+ }
+ // no attribute is specified - search all attributes in searchAttributes
+ return !!this.search( term ).length;
+ },
+
+ /** an implicit AND search for all terms; IOW, an hda must match all terms given
+ * where terms is a whitespace separated value string.
+ * e.g. given terms of: 'blah bler database=hg19'
+ * an HDA would have to have attributes containing blah AND bler AND a genome_build == hg19
+ * To include whitespace in terms: wrap the term in double quotations.
+ */
+ matchesAll : function( terms ){
+ var model = this;
+ // break the terms up by whitespace and filter out the empty strings
+ terms = terms.match( /(".*"|\w*=".*"|\S*)/g ).filter( function( s ){ return !!s; });
+ return _.all( terms, function( term ){
+ term = term.replace( /"/g, '' );
+ return model.matches( term );
+ });
+ },
+
+ // ........................................................................ misc
+ /** String representation */
+ toString : function(){
+ var nameAndId = this.get( 'id' ) || '';
+ if( this.get( 'name' ) ){
+ nameAndId = this.get( 'hid' ) + ' :"' + this.get( 'name' ) + '",' + nameAndId;
+ }
+ return 'HistoryContent(' + nameAndId + ')';
+ }
+});
+
+/** create a type + id string for use in mixed collections */
+HistoryContent.typeIdStr = function _typeId( type, id ){
+ return [ type, id ].join( '-' );
+};
+
+
+//==============================================================================
+return {
+ HistoryContent : HistoryContent
+};});
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-contents.js
--- /dev/null
+++ b/static/scripts/mvc/history/history-contents.js
@@ -0,0 +1,277 @@
+define([
+ "mvc/history/history-content-base",
+ "mvc/dataset/hda-model",
+ "mvc/collection/hdca-model",
+ "mvc/base-mvc",
+ "utils/localization"
+], function( historyContent, hdaModel, hdcaModel, baseMVC, _l ){
+//==============================================================================
+/** @class Backbone collection for history content.
+ * NOTE: history content seems like a dataset collection, but differs in that it is mixed:
+ * each element can be either an HDA (dataset) or a DatasetCollection and co-exist on
+ * the same level.
+ * Dataset collections on the other hand are not mixed and (so far) can only contain either
+ * HDAs or child dataset collections on one level.
+ * This is why this does not inherit from any of the DatasetCollections (currently).
+ *
+ * @borrows LoggableMixin#logger as #logger
+ * @borrows LoggableMixin#log as #log
+ * @constructs
+ */
+var HistoryContents = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend(
+/** @lends HistoryContents.prototype */{
+
+ ///** logger used to record this.log messages, commonly set to console */
+ //// comment this out to suppress log output
+ //logger : console,
+
+ /** since history content is a mix, override model fn into a factory, creating based on history_content_type */
+ model : function( attrs, options ) {
+ if( attrs.history_content_type === "dataset" ) {
+ return new hdaModel.HistoryDatasetAssociation( attrs, options );
+ } else if( attrs.history_content_type === "dataset_collection" ) {
+ return new hdcaModel.HistoryDatasetCollectionAssociation( attrs, options );
+ }
+ // TODO: Handle unknown history_content_type...
+ throw new TypeError( 'Unknown history_content_type:' + attrs.history_content_type );
+ },
+
+ /** Set up.
+ * @see Backbone.Collection#initialize
+ */
+ initialize : function( models, options ){
+ options = options || {};
+ this.historyId = options.historyId;
+ //this._setUpListeners();
+ },
+
+ /** root api url */
+ urlRoot : galaxy_config.root + 'api/histories',
+ /** complete api url */
+ url : function(){
+ return this.urlRoot + '/' + this.historyId + '/contents';
+ },
+
+ // ........................................................................ common queries
+ /** Get the ids of every hda in this collection
+ * @returns array of encoded ids
+ */
+ ids : function(){
+ return this.map( function( hda ){ return hda.get('id'); });
+ },
+
+ /** Get hdas that are not ready
+ * @returns array of HDAs
+ */
+ notReady : function(){
+ return this.filter( function( hda ){
+ return !hda.inReadyState();
+ });
+ },
+
+ /** Get the id of every hda in this collection not in a 'ready' state (running).
+ * @returns an array of hda ids
+ * @see HistoryDatasetAssociation#inReadyState
+ */
+ running : function(){
+ var idList = [];
+ this.each( function( item ){
+ if( !item.inReadyState() ){
+ idList.push( item.get( 'id' ) );
+ }
+ });
+ return idList;
+ },
+
+ /** Get the hda with the given hid
+ * @param {Int} hid the hid to search for
+ * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found
+ */
+ getByHid : function( hid ){
+ return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) );
+ },
+
+ /** Get every 'shown' hda in this collection based on show_deleted/hidden
+ * @param {Boolean} show_deleted are we showing deleted hdas?
+ * @param {Boolean} show_hidden are we showing hidden hdas?
+ * @returns array of hda models
+ * @see HistoryDatasetAssociation#isVisible
+ */
+ getVisible : function( show_deleted, show_hidden, filters ){
+ filters = filters || [];
+ //console.debug( 'filters:', filters );
+ //TODO:?? why doesn't this return a collection?
+ // always filter by show deleted/hidden first
+ var filteredHdas = new HistoryContents( this.filter( function( item ){
+ return item.isVisible( show_deleted, show_hidden );
+ }));
+
+ _.each( filters, function( filter_fn ){
+ if( !_.isFunction( filter_fn ) ){ return; }
+ filteredHdas = new HistoryContents( filteredHdas.filter( filter_fn ) );
+ });
+ return filteredHdas;
+ },
+
+ /** return true if any hdas don't have details */
+ haveDetails : function(){
+ return this.all( function( hda ){ return hda.hasDetails(); });
+ },
+
+ // ........................................................................ ajax
+ /** fetch detailed model data for all HDAs in this collection */
+ fetchAllDetails : function( options ){
+ options = options || {};
+ var detailsFlag = { details: 'all' };
+ options.data = ( options.data )?( _.extend( options.data, detailsFlag ) ):( detailsFlag );
+ return this.fetch( options );
+ },
+
+ /** using a queue, perform hdaModelAjaxFn on each of the hdas in this collection */
+ ajaxQueue : function( hdaAjaxFn, options ){
+ var deferred = jQuery.Deferred(),
+ startingLength = this.length,
+ responses = [];
+
+ if( !startingLength ){
+ deferred.resolve([]);
+ return deferred;
+ }
+
+ // use reverse order (stylistic choice)
+ var ajaxFns = this.chain().reverse().map( function( hda, i ){
+ return function(){
+ var xhr = hdaAjaxFn.call( hda, options );
+ // if successful, notify using the deferred to allow tracking progress
+ xhr.done( function( response ){
+ deferred.notify({ curr: i, total: startingLength, response: response, model: hda });
+ });
+ // (regardless of previous error or success) if not last ajax call, shift and call the next
+ // if last fn, resolve deferred
+ xhr.always( function( response ){
+ responses.push( response );
+ if( ajaxFns.length ){
+ ajaxFns.shift()();
+ } else {
+ deferred.resolve( responses );
+ }
+ });
+ };
+ }).value();
+ // start the queue
+ ajaxFns.shift()();
+
+ return deferred;
+ },
+
+ // ........................................................................ sorting/filtering
+ /** return a new collection of HDAs whose attributes contain the substring matchesWhat */
+ matches : function( matchesWhat ){
+ return this.filter( function( hda ){
+ return hda.matches( matchesWhat );
+ });
+ },
+
+ // ........................................................................ misc
+ set : function( models, options ){
+ // arrrrrrrrrrrrrrrrrg...
+ // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone)
+ // w/o this partial models from the server will fill in missing data with model defaults
+ // and overwrite existing data on the client
+ // see Backbone.Collection.set and _prepareModel
+ var collection = this;
+ models = _.map( models, function( model ){
+ var attrs = model.attributes || model; // Handle raw json or Backbone model.
+ var typeId = historyContent.HistoryContent.typeIdStr( attrs.history_content_type, attrs.id );
+ var existing = collection.get( typeId );
+ if( !existing ){ return model; }
+
+ // merge the models _BEFORE_ calling the superclass version
+ var merged = existing.toJSON();
+ _.extend( merged, model );
+ return merged;
+ });
+ // now call superclass when the data is filled
+ Backbone.Collection.prototype.set.call( this, models, options );
+ },
+
+ /** Convert this ad-hoc collection of HDAs to a formal collection tracked
+ by the server.
+ **/
+ promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){
+ options = options || {};
+ options.url = this.url();
+ options.type = "POST";
+ var full_collection_type = collection_type;
+ var element_identifiers = [],
+ name = null;
+
+ // This mechanism is rough - no error handling, allows invalid selections, no way
+ // for user to pick/override element identifiers. This is only really meant
+ if( collection_type === "list" ) {
+ this.chain().each( function( hda ) {
+ // TODO: Handle duplicate names.
+ var name = hda.attributes.name;
+ var id = hda.get('id');
+ var content_type = hda.attributes.history_content_type;
+ if( content_type === "dataset" ) {
+ if( full_collection_type !== "list" ) {
+ console.log( "Invalid collection type" );
+ }
+ element_identifiers.push( { name: name, src: "hda", id: id } );
+ } else {
+ if( full_collection_type === "list" ) {
+ full_collection_type = "list:" + hda.attributes.collection_type;
+ } else {
+ if( full_collection_type !== "list:" + hda.attributes.collection_type ) {
+ console.log( "Invalid collection type" );
+ }
+ }
+ element_identifiers.push( { name: name, src: "hdca", id: id } );
+ }
+ });
+ name = "New Dataset List";
+ } else if( collection_type === "paired" ) {
+ var ids = this.ids();
+ if( ids.length !== 2 ){
+ // TODO: Do something...
+ }
+ element_identifiers.push( { name: "forward", src: "hda", id: ids[ 0 ] } );
+ element_identifiers.push( { name: "reverse", src: "hda", id: ids[ 1 ] } );
+ name = "New Dataset Pair";
+ }
+ options.data = {
+ type: "dataset_collection",
+ name: name,
+ collection_type: full_collection_type,
+ element_identifiers: JSON.stringify( element_identifiers )
+ };
+
+ var xhr = jQuery.ajax( options );
+ xhr.done( function( message, status, responseObj ){
+ history.refresh( );
+ });
+ xhr.fail( function( xhr, status, message ){
+ if( xhr.responseJSON && xhr.responseJSON.error ){
+ error = xhr.responseJSON.error;
+ } else {
+ error = xhr.responseJSON;
+ }
+ xhr.responseText = error;
+ // Do something?
+ });
+ return xhr;
+ },
+
+ /** String representation. */
+ toString : function(){
+ return ([ 'HistoryContents(', [ this.parentId, this.length ].join(), ')' ].join( '' ));
+ }
+});
+
+
+//==============================================================================
+ return {
+ HistoryContents : HistoryContents
+ };
+});
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-model.js
--- a/static/scripts/mvc/history/history-model.js
+++ b/static/scripts/mvc/history/history-model.js
@@ -1,8 +1,8 @@
define([
- "mvc/dataset/hda-model",
+ "mvc/history/history-contents",
"mvc/base-mvc",
"utils/localization"
-], function( hdaModel, baseMVC, _l ){
+], function( historyContents, baseMVC, _l ){
//==============================================================================
/** @class Model for a Galaxy history resource - both a record of user
* tool use and a collection of the datasets those tools produced.
@@ -45,8 +45,8 @@
this.logger = options.logger || null;
this.log( this + ".initialize:", historyJSON, hdaJSON, options );
- /** HDACollection of the HDAs contained in this history. */
- this.hdas = new hdaModel.HDACollection( hdaJSON || [], { historyId: this.get( 'id' )});
+ /** HistoryContents collection of the HDAs contained in this history. */
+ this.hdas = new historyContents.HistoryContents( hdaJSON || [], { historyId: this.get( 'id' )});
// if we've got hdas passed in the constructor, load them
if( hdaJSON && _.isArray( hdaJSON ) ){
this.hdas.reset( hdaJSON );
@@ -230,12 +230,12 @@
}
var data = {};
if( hdaDetailIds.length ) {
- data[ "dataset_details" ] = hdaDetailIds.join( ',' );
+ data.dataset_details = hdaDetailIds.join( ',' );
}
if( hdcaDetailIds.length ) {
// for symmetry, not actually used by backend of consumed
// by frontend.
- data[ "dataset_collection_details" ] = hdcaDetailIds.join( ',' );
+ data.dataset_collection_details = hdcaDetailIds.join( ',' );
}
return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyData.id + '/contents', { data: data });
}
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/history-panel.js
--- a/static/scripts/mvc/history/history-panel.js
+++ b/static/scripts/mvc/history/history-panel.js
@@ -2,11 +2,12 @@
"mvc/dataset/hda-model",
"mvc/dataset/hda-edit",
"mvc/collection/dataset-collection-edit",
+ "mvc/history/history-contents",
"mvc/history/readonly-history-panel",
"mvc/tags",
"mvc/annotations",
"utils/localization"
-], function( hdaModel, hdaEdit, datasetCollectionEdit, readonlyPanel, tagsMod, annotationsMod, _l ){
+], function( hdaModel, hdaEdit, datasetCollectionEdit, historyContents, readonlyPanel, tagsMod, annotationsMod, _l ){
/* =============================================================================
TODO:
@@ -36,7 +37,7 @@
HDAViewClass : hdaEdit.HDAEditView,
// ......................................................................... SET UP
- /** Set up the view, set up storage, bind listeners to HDACollection events
+ /** Set up the view, set up storage, bind listeners to HistoryContents events
* @param {Object} attributes
*/
initialize : function( attributes ){
@@ -493,7 +494,7 @@
/** return an HdaCollection of the models of all currenly selected hdas */
getSelectedHdaCollection : function(){
- return new hdaModel.HDACollection( _.map( this.getSelectedHdaViews(), function( hdaView ){
+ return new historyContents.HistoryContents( _.map( this.getSelectedHdaViews(), function( hdaView ){
return hdaView.model;
}), { historyId: this.model.id });
},
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/mvc/history/readonly-history-panel.js
--- a/static/scripts/mvc/history/readonly-history-panel.js
+++ b/static/scripts/mvc/history/readonly-history-panel.js
@@ -97,7 +97,7 @@
noneFoundMsg : _l( 'No matching datasets found' ),
// ......................................................................... SET UP
- /** Set up the view, set up storage, bind listeners to HDACollection events
+ /** Set up the view, set up storage, bind listeners to HistoryContents events
* @param {Object} attributes optional settings for the panel
*/
initialize : function( attributes ){
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/collection/hdca-model.js
--- /dev/null
+++ b/static/scripts/packed/mvc/collection/hdca-model.js
@@ -0,0 +1,1 @@
+define(["mvc/history/history-content-base","utils/localization"],function(b,c){var a=b.HistoryContent.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},toString:function(){var d=this.get("id")||"";if(this.get("name")){d=this.get("hid")+' :"'+this.get("name")+'",'+d}return"HDCA-"+this.get("collection_type")+"("+d+")"}});return{HistoryDatasetCollectionAssociation:a}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/dataset/hda-model.js
--- a/static/scripts/packed/mvc/dataset/hda-model.js
+++ b/static/scripts/packed/mvc/dataset/hda-model.js
@@ -1,1 +1,1 @@
-define(["mvc/base-mvc","utils/localization"],function(e,c){var a=Backbone.Model.extend(e.LoggableMixin).extend({idAttribute:"type_id",urlRoot:galaxy_config.root+"api/histories/",constructor:function(o,n){o.type_id=a.typeIdStr(o.history_content_type,o.id);Backbone.Model.apply(this,arguments)},initialize:function(o,n){this.on("change:id",this._createTypeId)},url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},hidden:function(){return !this.get("visible")},"delete":function f(n){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},n)},undelete:function j(n){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},n)},hide:function d(n){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},n)},unhide:function i(n){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},n)},isVisible:function(o,p){var n=true;if((!o)&&(this.get("deleted")||this.get("purged"))){n=false}if((!p)&&(!this.get("visible"))){n=false}return n},searchAttribute:function(p,n){var o=this.get(p);if(!n||(o===undefined||o===null)){return false}if(_.isArray(o)){return this._searchArrayAttribute(o,n)}return(o.toString().toLowerCase().indexOf(n.toLowerCase())!==-1)},_searchArrayAttribute:function(o,n){n=n.toLowerCase();return _.any(o,function(p){return(p.toString().toLowerCase().indexOf(n.toLowerCase())!==-1)})},search:function(n){var o=this;return _.filter(this.searchAttributes,function(p){return o.searchAttribute(p,n)})},matches:function(o){var q="=",n=o.split(q);if(n.length>=2){var p=n[0];p=this.searchAliases[p]||p;return this.searchAttribute(p,n[1])}return !!this.search(o).length},matchesAll:function(o){var n=this;o=o.match(/(".*"|\w*=".*"|\S*)/g).filter(function(p){return !!p});return _.all(o,function(p){p=p.replace(/"/g,"");return n.matches(p)})},_createTypeId:function(){this.set("type_id",TypeIdModel.typeIdStr(this.get("history_content_type"),this.get("id")))},});a.typeIdStr=function h(n,o){return[n,o].join("-")};var m=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var o=this.get("id");if(!o){return{}}var n={purge:galaxy_config.root+"datasets/"+o+"/purge_async",display:galaxy_config.root+"datasets/"+o+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+o+"/edit",download:galaxy_config.root+"datasets/"+o+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+o,rerun:galaxy_config.root+"tool_runner/rerun?id="+o,show_params:galaxy_config.root+"datasets/"+o+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+o,set:galaxy_config.root+"dataset/annotate_async?id="+o},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+o+"&metadata_name="};return n},initialize:function(n){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",m.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(o,n){this.log(this+" has changed state:",o,n);if(this.inReadyState()){this.trigger("state:ready",o,n,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var n=_.contains(m.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||n)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function f(n){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},n)},undelete:function j(n){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},n)},hide:function d(n){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},n)},unhide:function i(n){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},n)},purge:function g(n){if(this.get("purged")){return jQuery.when()}n=n||{};n.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var o=this,p=jQuery.ajax(n);p.done(function(s,q,r){o.set({deleted:true,purged:true})});p.fail(function(u,q,t){var r=c("Unable to purge dataset");var s=("Removal of datasets by users is not allowed in this Galaxy instance");if(u.responseJSON&&u.responseJSON.error){r=u.responseJSON.error}else{if(u.responseText.indexOf(s)!==-1){r=s}}u.responseText=r;o.trigger("error",o,u,n,c(r),{error:r})});return p},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var n=this.get("id")||"";if(this.get("name")){n=this.get("hid")+' :"'+this.get("name")+'",'+n}return"HDA("+n+")"}});m.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};m.READY_STATES=[m.STATES.OK,m.STATES.EMPTY,m.STATES.PAUSED,m.STATES.FAILED_METADATA,m.STATES.NOT_VIEWABLE,m.STATES.DISCARDED,m.STATES.ERROR];m.NOT_READY_STATES=[m.STATES.UPLOAD,m.STATES.QUEUED,m.STATES.RUNNING,m.STATES.SETTING_METADATA,m.STATES.NEW];var b=Backbone.Collection.extend(e.LoggableMixin).extend({model:function(o,n){if(o.history_content_type=="dataset"){return new m(o,n)}else{if(o.history_content_type=="dataset_collection"){return new k(o,n)}else{}}},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(o,n){n=n||{};this.historyId=n.historyId},ids:function(){return this.map(function(n){return n.get("id")})},notReady:function(){return this.filter(function(n){return !n.inReadyState()})},running:function(){var n=[];this.each(function(o){if(!o.inReadyState()){n.push(o.get("id"))}});return n},getByHid:function(n){return _.first(this.filter(function(o){return o.get("hid")===n}))},getVisible:function(n,q,p){p=p||[];var o=new b(this.filter(function(r){return r.isVisible(n,q)}));_.each(p,function(r){if(!_.isFunction(r)){return}o=new b(o.filter(r))});return o},haveDetails:function(){return this.all(function(n){return n.hasDetails()})},fetchAllDetails:function(o){o=o||{};var n={details:"all"};o.data=(o.data)?(_.extend(o.data,n)):(n);return this.fetch(o)},ajaxQueue:function(q,p){var o=jQuery.Deferred(),n=this.length,s=[];if(!n){o.resolve([]);return o}var r=this.chain().reverse().map(function(u,t){return function(){var v=q.call(u,p);v.done(function(w){o.notify({curr:t,total:n,response:w,model:u})});v.always(function(w){s.push(w);if(r.length){r.shift()()}else{o.resolve(s)}})}}).value();r.shift()();return o},matches:function(n){return this.filter(function(o){return o.matches(n)})},set:function(p,n){var o=this;p=_.map(p,function(s){var r=s.attributes||s;var t=a.typeIdStr(r.history_content_type,r.id);var u=o.get(t);if(!u){return s}var q=u.toJSON();_.extend(q,s);return q});Backbone.Collection.prototype.set.call(this,p,n)},promoteToHistoryDatasetCollection:function l(s,q,o){o=o||{};o.url=this.url();o.type="POST";var u=q;var r=[],n=null;if(q=="list"){this.chain().each(function(x){var v=x.attributes.name;var y=x.get("id");var w=x.attributes.history_content_type;if(w=="dataset"){if(u!="list"){console.log("Invalid collection type")}r.push({name:v,src:"hda",id:y})}else{if(u=="list"){u="list:"+x.attributes.collection_type}else{if(u!="list:"+x.attributes.collection_type){console.log("Invalid collection type")}}r.push({name:v,src:"hdca",id:y})}});n="New Dataset List"}else{if(q=="paired"){var p=this.ids();if(p.length!=2){}r.push({name:"forward",src:"hda",id:p[0]});r.push({name:"reverse",src:"hda",id:p[1]});n="New Dataset Pair"}}o.data={type:"dataset_collection",name:n,collection_type:u,element_identifiers:JSON.stringify(r),};var t=jQuery.ajax(o);t.done(function(x,v,w){s.refresh()});t.fail(function(x,v,w){if(x.responseJSON&&x.responseJSON.error){error=x.responseJSON.error}else{error=x.responseJSON}x.responseText=error});return t},toString:function(){return(["HDACollection(",[this.historyId,this.length].join(),")"].join(""))}});var k=a.extend({defaults:{history_id:null,model_class:"HistoryDatasetCollectionAssociation",history_content_type:"dataset_collection",hid:0,id:null,name:"(unnamed dataset collection)",state:"ok",accessible:true,deleted:false,visible:true,purged:false,tags:[],annotation:""},urls:function(){},inReadyState:function(){return true},searchAttributes:["name"],searchAliases:{title:"name"},});return{HistoryDatasetAssociation:m,HDACollection:b}});
\ No newline at end of file
+define(["mvc/history/history-content-base","utils/localization"],function(e,f){var d=e.HistoryContent.extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",history_content_type:"dataset",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:"",file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:[],annotation:""},urls:function(){var j=this.get("id");if(!j){return{}}var i={purge:galaxy_config.root+"datasets/"+j+"/purge_async",display:galaxy_config.root+"datasets/"+j+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+j+"/edit",download:galaxy_config.root+"datasets/"+j+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+j,rerun:galaxy_config.root+"tool_runner/rerun?id="+j,show_params:galaxy_config.root+"datasets/"+j+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+j,set:galaxy_config.root+"dataset/annotate_async?id="+j},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+j+"&metadata_name="};return i},initialize:function(i){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(j,i){this.log(this+" has changed state:",j,i);if(this.inReadyState()){this.trigger("state:ready",j,i,this.previous("state"))}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var i=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||i)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(i){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},i)},undelete:function a(i){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},i)},hide:function b(i){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},i)},unhide:function h(i){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},i)},purge:function g(i){if(this.get("purged")){return jQuery.when()}i=i||{};i.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var j=this,k=jQuery.ajax(i);k.done(function(n,l,m){j.set({deleted:true,purged:true})});k.fail(function(p,l,o){var m=f("Unable to purge dataset");var n=("Removal of datasets by users is not allowed in this Galaxy instance");if(p.responseJSON&&p.responseJSON.error){m=p.responseJSON.error}else{if(p.responseText.indexOf(n)!==-1){m=n}}p.responseText=m;j.trigger("error",j,p,i,f(m),{error:m})});return k},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var i=this.get("id")||"";if(this.get("name")){i=this.get("hid")+' :"'+this.get("name")+'",'+i}return"HDA("+i+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA,d.STATES.NEW];return{HistoryDatasetAssociation:d}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-content-base.js
--- /dev/null
+++ b/static/scripts/packed/mvc/history/history-content-base.js
@@ -0,0 +1,1 @@
+define(["mvc/base-mvc","utils/localization"],function(b,e){var f=Backbone.Model.extend(b.LoggableMixin).extend({idAttribute:"type_id",constructor:function(j,i){j.type_id=f.typeIdStr(j.history_content_type,j.id);Backbone.Model.apply(this,arguments)},initialize:function(j,i){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",TypeIdModel.typeIdStr(this.get("history_content_type"),this.get("id")))},hidden:function(){return !this.get("visible")},isVisible:function(j,k){var i=true;if((!j)&&(this.get("deleted")||this.get("purged"))){i=false}if((!k)&&(!this.get("visible"))){i=false}return i},urlRoot:galaxy_config.root+"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id")},"delete":function d(i){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},i)},undelete:function a(i){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},i)},hide:function c(i){if(!this.get("visible")){return jQuery.when()}return this.save({visible:false},i)},unhide:function g(i){if(this.get("visible")){return jQuery.when()}return this.save({visible:true},i)},searchAttribute:function(k,i){var j=this.get(k);if(!i||(j===undefined||j===null)){return false}if(_.isArray(j)){return this._searchArrayAttribute(j,i)}return(j.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)},_searchArrayAttribute:function(j,i){i=i.toLowerCase();return _.any(j,function(k){return(k.toString().toLowerCase().indexOf(i.toLowerCase())!==-1)})},search:function(i){var j=this;return _.filter(this.searchAttributes,function(k){return j.searchAttribute(k,i)})},matches:function(j){var l="=",i=j.split(l);if(i.length>=2){var k=i[0];k=this.searchAliases[k]||k;return this.searchAttribute(k,i[1])}return !!this.search(j).length},matchesAll:function(j){var i=this;j=j.match(/(".*"|\w*=".*"|\S*)/g).filter(function(k){return !!k});return _.all(j,function(k){k=k.replace(/"/g,"");return i.matches(k)})},toString:function(){var i=this.get("id")||"";if(this.get("name")){i=this.get("hid")+' :"'+this.get("name")+'",'+i}return"HistoryContent("+i+")"}});f.typeIdStr=function h(i,j){return[i,j].join("-")};return{HistoryContent:f}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-contents.js
--- /dev/null
+++ b/static/scripts/packed/mvc/history/history-contents.js
@@ -0,0 +1,1 @@
+define(["mvc/history/history-content-base","mvc/dataset/hda-model","mvc/collection/hdca-model","mvc/base-mvc","utils/localization"],function(b,d,f,a,c){var g=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){console.debug("HistoryContents.model:",i);if(i.history_content_type==="dataset"){return new d.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){return new f.HistoryDatasetCollectionAssociation(i,h)}}throw new TypeError("Unknown history_content_type:"+i.history_content_type)},initialize:function(i,h){h=h||{};console.debug("new HistoryContents",i,h);this.historyId=h.historyId},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];var i=new g(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new g(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m;var n=b.HistoryContent.typeIdStr(l.history_content_type,l.id);var o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function e(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){console.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){console.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},toString:function(){return(["HistoryContents(",[this.parentId,this.length].join(),")"].join(""))}});return{HistoryContents:g}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-model.js
--- a/static/scripts/packed/mvc/history/history-model.js
+++ b/static/scripts/packed/mvc/history/history-model.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/base-mvc","utils/localization"],function(c,a,b){var e=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new c.HDACollection(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||e.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});e.UPDATE_DELAY=4000;e.getHistoryData=function f(h,s){s=s||{};var m=s.hdaDetailIds||[];var j=s.hdcaDetailIds||[];var o=jQuery.Deferred(),n=null;function i(t){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(t){if(!t||!t.state_ids){return 0}return _.reduce(t.state_ids,function(u,w,v){return u+w.length},0)}function r(u){if(!g(u)){return[]}if(_.isFunction(m)){m=m(u)}if(_.isFunction(j)){j=j(u)}var t={};if(m.length){t.dataset_details=m.join(",")}if(j.length){t.dataset_collection_details=j.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+u.id+"/contents",{data:t})}var q=s.historyFn||i,p=s.hdaFn||r;var l=q(h);l.done(function(t){n=t;o.notify({status:"history data retrieved",historyJSON:n})});l.fail(function(v,t,u){o.reject(v,"loading the history")});var k=l.then(p);k.then(function(t){o.notify({status:"dataset data retrieved",historyJSON:n,hdaJSON:t});o.resolve(n,t)});k.fail(function(v,t,u){o.reject(v,"loading the datasets",{history:n})});return o};var d=Backbone.Collection.extend(a.LoggableMixin).extend({model:e,urlRoot:galaxy_config.root+"api/histories"});return{History:e,HistoryCollection:d}});
\ No newline at end of file
+define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(e,a,b){var d=Backbone.Model.extend(a.LoggableMixin).extend({defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(h,i,g){g=g||{};this.logger=g.logger||null;this.log(this+".initialize:",h,i,g);this.hdas=new e.HistoryContents(i||[],{historyId:this.get("id")});if(i&&_.isArray(i)){this.hdas.reset(i)}this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(h,k,g,j,i){this.errorHandler(h,k,g,j,i)});if(this.hdas){this.listenTo(this.hdas,"error",function(){this.trigger.apply(this,["error:hdas"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(h,g){if(this.hdas){this.hdas.historyId=g}},this)},errorHandler:function(h,k,g,j,i){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},hdaCount:function(){return _.reduce(_.values(this.get("state_details")),function(g,h){return g+h},0)},checkForUpdates:function(g){if(this.hdas.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(g)){g.call(this)}}return this},setUpdateTimeout:function(g){g=g||d.UPDATE_DELAY;var h=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){h.refresh()},g);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(h,g){h=h||[];g=g||{};var i=this;g.data=g.data||{};if(h.length){g.data.details=h.join(",")}var j=this.hdas.fetch(g);j.done(function(k){i.checkForUpdates(function(){this.fetch()})});return j},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}});d.UPDATE_DELAY=4000;d.getHistoryData=function f(h,s){s=s||{};var m=s.hdaDetailIds||[];var j=s.hdcaDetailIds||[];var o=jQuery.Deferred(),n=null;function i(t){return jQuery.ajax(galaxy_config.root+"api/histories/"+h)}function g(t){if(!t||!t.state_ids){return 0}return _.reduce(t.state_ids,function(u,w,v){return u+w.length},0)}function r(u){if(!g(u)){return[]}if(_.isFunction(m)){m=m(u)}if(_.isFunction(j)){j=j(u)}var t={};if(m.length){t.dataset_details=m.join(",")}if(j.length){t.dataset_collection_details=j.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+u.id+"/contents",{data:t})}var q=s.historyFn||i,p=s.hdaFn||r;var l=q(h);l.done(function(t){n=t;o.notify({status:"history data retrieved",historyJSON:n})});l.fail(function(v,t,u){o.reject(v,"loading the history")});var k=l.then(p);k.then(function(t){o.notify({status:"dataset data retrieved",historyJSON:n,hdaJSON:t});o.resolve(n,t)});k.fail(function(v,t,u){o.reject(v,"loading the datasets",{history:n})});return o};var c=Backbone.Collection.extend(a.LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories"});return{History:d,HistoryCollection:c}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/mvc/history/history-panel.js
--- a/static/scripts/packed/mvc/history/history-panel.js
+++ b/static/scripts/packed/mvc/history/history-panel.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});k.push({html:e("Build List of Dataset Pairs (Experimental)"),func:_.bind(j._showPairedCollectionModal,j)});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_showPairedCollectionModal:function(){var i=this,j=i.getSelectedHdaCollection().toJSON().filter(function(k){return k.history_content_type==="dataset"&&k.state===f.HistoryDatasetAssociation.STATES.OK});if(j.length){require(["mvc/collection/paired-collection-creator"],function(k){window.creator=k.pairedCollectionCreatorModal(j,{historyId:i.model.id})})}else{}},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.id,l=j.get("history_content_type"),k=null;if(l==="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l==="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(m,l){if(!l){return}var k=[];if((l.shiftKey)&&(i.lastSelectedViewId&&_.has(i.hdaViews,i.lastSelectedViewId))){var o=i.hdaViews[i.lastSelectedViewId];k=i.selectDatasetRange(m,o).map(function(p){return p.model.id})}else{var n=m.model.id;i.lastSelectedViewId=n;k=[n]}i.selectedHdaIds=_.union(i.selectedHdaIds,k)});j.on("de-selected",function(l,k){var m=l.model.id;i.selectedHdaIds=_.without(i.selectedHdaIds,m)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){this.lastSelectedViewId=null;_.each(this.hdaViews,function(j){j.deselect(i)})},selectDatasetRange:function(k,j){var i=this.hdaViewRange(k,j);_.each(i,function(l){l.select()});return i},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/history-contents","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,h,b,g,c,d,i,a){var e=c.ReadOnlyHistoryPanel.extend({HDAViewClass:h.HDAEditView,initialize:function(j){j=j||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=j.purgeAllowed||false;this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this.tagsEditorShown=j.tagsEditorShown||false;c.ReadOnlyHistoryPanel.prototype.initialize.call(this,j)},_setUpModelEventHandlers:function(){c.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this)},renderModel:function(){var j=$("<div/>");j.append(e.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(j).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}j.find(".history-secondary-actions").prepend(this._renderSelectButton());j.find(".history-dataset-actions").toggle(this.selecting);j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},_renderTags:function(j){var k=this;this.tagsEditor=new d.TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:a("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))})},_renderAnnotation:function(j){var k=this;this.annotationEditor=new i.AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:a("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))})},_renderSelectButton:function(j){return faIconButton({title:a("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;c.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,j);if(!this.model){return}this._setUpDatasetActionsPopup(j);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",a("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){var m=k.model.get("name");if(l&&l!==m){k.$el.find(".history-name").text(l);k.model.save({name:l}).fail(function(){k.$el.find(".history-name").text(k.model.previous("name"))})}else{k.$el.find(".history-name").text(m)}}})},_setUpDatasetActionsPopup:function(j){var k=this,l=[{html:a("Hide datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(m)}},{html:a("Unhide datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(m)}},{html:a("Delete datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(m)}},{html:a("Undelete datasets"),func:function(){var m=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(m)}}];if(k.purgeAllowed){l.push({html:a("Permanently delete datasets"),func:function(){if(confirm(a("This will permanently remove the data in your datasets. Are you sure?"))){var m=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(m)}}})}l.push({html:a("Build Dataset List (Experimental)"),func:function(){k.getSelectedHdaCollection().promoteToHistoryDatasetCollection(k.model,"list")}});l.push({html:a("Build Dataset Pair (Experimental)"),func:function(){k.getSelectedHdaCollection().promoteToHistoryDatasetCollection(k.model,"paired")}});l.push({html:a("Build List of Dataset Pairs (Experimental)"),func:_.bind(k._showPairedCollectionModal,k)});return new PopupMenu(j.find(".history-dataset-action-popup-btn"),l)},_showPairedCollectionModal:function(){var j=this,k=j.getSelectedHdaCollection().toJSON().filter(function(l){return l.history_content_type==="dataset"&&l.state===f.HistoryDatasetAssociation.STATES.OK});if(k.length){require(["mvc/collection/paired-collection-creator"],function(l){window.creator=l.pairedCollectionCreatorModal(k,{historyId:j.model.id})})}else{}},_handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},_handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},_createContentView:function(k){var j=k.id,m=k.get("history_content_type"),l=null;if(m==="dataset"){l=new this.HDAViewClass({model:k,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[j],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(m==="dataset_collection"){l=new b.DatasetCollectionEditView({model:k,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[j],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(l);return l},_setUpHdaListeners:function(k){var j=this;c.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,k);k.on("selected",function(n,m){if(!m){return}var l=[];if((m.shiftKey)&&(j.lastSelectedViewId&&_.has(j.hdaViews,j.lastSelectedViewId))){var p=j.hdaViews[j.lastSelectedViewId];l=j.selectDatasetRange(n,p).map(function(q){return q.model.id})}else{var o=n.model.id;j.lastSelectedViewId=o;l=[o]}j.selectedHdaIds=_.union(j.selectedHdaIds,l)});k.on("de-selected",function(m,l){var n=m.model.id;j.selectedHdaIds=_.without(j.selectedHdaIds,n)})},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.trigger("empty-history",j);j._renderEmptyMsg()}})},events:_.extend(_.clone(c.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(j){j=(j!==undefined)?(j):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(j){j=(j!==undefined)?(j):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(j){_.each(this.hdaViews,function(k){k.select(j)})},deselectAllDatasets:function(j){this.lastSelectedViewId=null;_.each(this.hdaViews,function(k){k.deselect(j)})},selectDatasetRange:function(l,k){var j=this.hdaViewRange(l,k);_.each(j,function(m){m.select()});return j},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new g.HistoryContents(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:e}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/viz/trackster/tracks.js
--- a/static/scripts/packed/viz/trackster/tracks.js
+++ b/static/scripts/packed/viz/trackster/tracks.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){if(this.view.reference_track.tiles_div.is(":visible")){this.view.resize_viewport()}var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/viz_views","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(ab,w,V,j,s,J,h,X,P,R){var o=ab.extend;var l={};var i=function(ac,ad){l[ac.attr("id")]=ad};var k=function(ac,ad,af,ae){af=".group";l[ac.attr("id")]=ae;ac.bind("drag",{handle:"."+ad,relative:true},function(an,ao){var am=$(this),ar=$(this).parent(),aj=ar.children(".track,.group"),al=l[$(this).attr("id")],ai,ah,ap,ag,ak;ah=$(this).parents(af);if(ah.length!==0){ap=ah.position().top;ag=ap+ah.outerHeight();var aq=l[ah.attr("id")];if(ao.offsetY<ap){$(this).insertBefore(ah);aq.remove_drawable(al);aq.container.add_drawable_before(al,aq);return}else{if(ao.offsetY>ag){$(this).insertAfter(ah);aq.remove_drawable(al);aq.container.add_drawable(al);return}}}ah=null;for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));ap=ai.position().top;ag=ap+ai.outerHeight();if(ai.is(af)&&this!==ai.get(0)&&ao.offsetY>=ap&&ao.offsetY<=ag){if(ao.offsetY-ap<ag-ao.offsetY){ai.find(".content-div").prepend(this)}else{ai.find(".content-div").append(this)}if(al.container){al.container.remove_drawable(al)}l[ai.attr("id")].add_drawable(al);return}}for(ak=0;ak<aj.length;ak++){ai=$(aj.get(ak));if(ao.offsetY<ai.position().top&&!(ai.hasClass("reference-track")||ai.hasClass("intro"))){break}}if(ak===aj.length){if(this!==aj.get(ak-1)){ar.append(this);l[ar.attr("id")].move_drawable(al,ak)}}else{if(this!==aj.get(ak)){$(this).insertBefore(aj.get(ak));l[ar.attr("id")].move_drawable(al,(ao.deltaY>0?ak-1:ak))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var p=function(ad,ac,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ag.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ag.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=null;if(ag.header!==false){var ae=new V.TrackHeaderView({model:this,id:this.id});this.header_div=ae.$el;this.container_div.append(this.header_div);var af=ae.icons_div;this.action_icons=ae.action_icons;this.container_div.hover(function(){af.show()},function(){af.hide()})}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.config.get_value("content_visible")){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.config.set_value("content_visible",false)}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.config.set_value("content_visible",true);ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ad){var ac=new R.ConfigSettingCollectionView({collection:ad.config});ac.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.config.get_value("name");this.config.set_value("name",ac)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){p.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=n(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var N=function(ad,ac,af){o(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.filters_manager.parent_div.after($("<div style='clear: both'/>"));this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new h.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){this.action_icons.composite_icon.toggle(this.drawables[0] instanceof e);this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new h.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}this.action_icons.filters_icon.toggle(this.filters_manager.filters.length>0)}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){o(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ac.name})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(n(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})},minLength:2})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get_value(ac.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){this.intro_div.toggle(this.drawables.length===0)},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new B(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,af=ac.chrom_data.length;aj<af;aj++){var ai=ac.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ag.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad===undefined&&aj===undefined){ae.low=0;ae.high=ae.max_high}else{ae.low=(ad!==undefined?Math.max(ad,0):0);if(aj===undefined){ae.low=Math.max(ae.low-15,0);ae.high=ae.low+30}else{ae.high=Math.min(aj,ae.max_high)}}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):undefined),ac=(ad[2]?parseInt(ad[2],10):undefined);this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_viewport:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height())},resize_window:function(){this.resize_viewport();this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ac){P.Tool.prototype.initialize.call(this,ac);var ad=true;if(ac.tool_state!==undefined&&ac.tool_state.hidden!==undefined){ad=ac.tool_state.hidden}this.set("hidden",ad);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ac){return ab.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ae=this.$el.addClass("param-row"),af=this.model;var ac=$("<div>").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("<div/>").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("<div style='clear: both;'/>").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new t({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("<div>").addClass("param-row").appendTo(parent_div);var ag=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(af);var ac=$("<input type='submit'>").attr("value","Run on visible region").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){this.$el.toggle(this.model.is_visible())},update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},run_on_dataset:function(){var ac=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){Galaxy.modal.show({title:ac.get("name")+" is Running",body:ac.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ad=this.model.get("track"),ag=this.model,ai=new w.GenomeRegion({chrom:ad.view.chrom,start:ad.view.low,end:ad.view.high}),aj={target_dataset_id:ad.dataset.id,action:"rerun",tool_id:ag.id,regions:[ai.toJSON()]},ah=ad,al=ag.get("name")+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ak=new N(view,view,{name:ad.config.get_value("name")});var af=ah.container.replace_drawable(ah,ak,false);ak.container_div.insertBefore(ah.view.content_div.children()[af]);ak.add_drawable(ah);ah.container_div.appendTo(ak.content_div);ac=ak}else{ac=ah.container}var ae=new ah.constructor(view,ac,{name:al,hda_ldda:"hda"});ae.init_for_tool_data();ae.change_mode(ah.mode);ae.set_filters_manager(ah.filters_manager.copy(ae));ae.update_icons();ac.add_drawable(ae);ae.tiles_div.text("Starting job.");this.run(aj,ae,function(am){ae.set_dataset(new X.Dataset(am));ae.tiles_div.text("Running job.");ae.init()})},run:function(ac,ae,af){ac.inputs=this.model.get_inputs_dict();var ad=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var C=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ae;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ac,af,ag,ad,ae){b.call(this,ac,af,ag,ad,ae)};K.prototype.predisplay_actions=function(){};var M=function(ae,aj,al,ad,ag,ah,am,ac,ai,af,ak){b.call(this,ae,aj,al,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ai;this.has_icons=false;this.incomplete_features=af;this.seq_data=ak};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}af=$("<div/>").attr("id",ak).addClass("feature-popup");var au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?U(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ad,ac,ae){o(ae,{drag_handle_class:"draghandle"});p.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:new X.Dataset(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ac){ac.view.set_overview(ac)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.config.get_value("name")+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get_value("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.config.get_value("content_visible")){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.set_value("height",ac.visible_height_px);ac.changed()}).appendTo(ac.container_div)},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ac){this.tiles_div.remove();return $("<span/>").addClass("message").html(ac).appendTo(this.content_div)},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");ad.tiles_div=$("<div/>").addClass("tiles").appendTo(ad.content_div);if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");var ah=ad.show_message(m);if(ag.message){ah.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ag.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ah.append($("<span/>").text(" "));ah.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.show_message(H)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.show_message(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.show_message(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_default_value("min_value",ae);ac.config.set_default_value("max_value",ag);ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},get_drawables:function(){return this}});var L=function(ae,ad,ag){f.call(this,ae,ad,ag);var ac=this;k(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new h.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new q(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();o(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.config.get_value("min_value")))||isNaN(parseFloat(ac.config.get_value("max_value")))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_value("min_value",ae);ac.config.set_value("max_value",ag)}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.set_value("mode",ad);if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;ac.action_icons.filters_icon.toggle(ac.filters_available);ac.action_icons.tools_icon.toggle(ac.tool!==null);ac.action_icons.param_space_viz_icon.toggle(ac.tool!==null)},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*Q)),ak,am,ah,ai=[],ao=[];while((ac*Q*af)<ag){ak=Math.floor(ac*Q*af);am=new w.GenomeRegion({chrom:this.view.chrom,start:ak,end:Math.min(ak+Math.ceil(Q*af),this.view.max_high)});ah=this.draw_helper(am,ap,aq);ai.push(ah);$.when(ah).then(function(ar){ao.push(ar)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();ao=ab.filter(ao,function(ar){return ar!==null});if(ao.length!==0){ae.postdraw_actions(ao,ad,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ae=this.container_div.find(".yaxislabel."+ag);ah=ah||function(){ad.request_draw({clear_tile_cache:true})};if(ae.length!==0){ae.text(ad.config.get_value(ac))}else{ae=$("<div/>").text(ad.config.get_value(ac)).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.config.get_value("label_color"));this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof K)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof K)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(A,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(ab.find(ap,function(aD){return j.is_deferred(aD)})){ae.tile_cache.set_elt(am,undefined);$.when(ae.draw_helper(al,an,ao)).then(function(aD){ac.resolve(aD)});return}if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new K(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css("left",ag);if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height()-2);ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){f.call(this,ad,ac,{resize:false,header:false});this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div/>").addClass("label-container");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div/>").addClass("label").text(commatize(ac)).css({left:ai}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var e=function(ad,ac,ag){L.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=n(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof S){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ac=this.visible_height_px;ab.each(this.drawables,function(ad){ad.visible_height_px=ac});f.prototype.on_resize.call(this)},change_mode:function(ac){L.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new N(this.view,this.container,{name:this.config.get_value("name")}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){var ad=ab.min(ab.map(this.drawables,function(ae){return ae.config.get_value("min_value")})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.config.get_value("max_value")}));this.config.set_value("min_value",ad);this.config.set_value("max_value",ac);ab.each(this.drawables,function(ae){ae.config.set_value("min_value",ad);ae.config.set_value("max_value",ac)})},update_all_min_max:function(){var ad=this,ac=this.config.get_value("min_value"),ae=this.config.get_value("max_value");ab.each(this.drawables,function(af){af.config.set_value("min_value",ac);af.config.set_value("max_value",ae)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){var ag=-1,ae;for(ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){L.call(this,ac,{content_div:ac.top_labeltrack},{resize:false,header:false});this.left_offset=ac.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ah,ad){var ac=this.tiles_div.is(":visible"),ag,ae=null;if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();ag=true;ae=L.prototype.draw_helper.call(this,af,ah,ad)}else{ag=false;this.tiles_div.hide()}if(ac!==ag){this.view.resize_viewport()}return ae},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;ag<ai;ag++){ak.fillStyle=this.view.get_base_color(aj[ag]);ak.fillText(aj[ag],Math.floor(ag*al),10)}return new b(this,ah,al,ac,ad)}});var g=function(ad,ac,ae){this.mode="Histogram";L.call(this,ad,ac,ae)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ac,ad,af,ae,ag){return this._draw_line_track_tile(ac,ad,af,ae,ag)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ad,ac,ae){this.mode="Heatmap";L.call(this,ad,ac,ae)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:ab.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new J.DiagonalHeatmapPainter(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah);ad.draw(ae,af.width,af.height,ai);return new b(this,ag,ai,af,ac.data)}});var c=function(ad,ac,ae){L.call(this,ad,ac,ae);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ao,af,aq,an){L.prototype.postdraw_actions.call(this,ao,af,aq,an);var ah=this,ai,am=ab.filter(ao,function(ar){return(ar instanceof K)});if(am.length===0){var ac={};ab.each(ab.pluck(ao,"incomplete_features"),function(ar){ab.each(ar,function(at){ac[at[0]]=at})});var ap=this;ab.each(ao,function(ar){ap.draw_tile({data:ab.values(ac)},ar.canvas.getContext("2d"),ar.mode,ar.region,aq,ar.seq_data,true)})}if(ah.filters_manager){var ag=ah.filters_manager.filters,ak;for(ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<ao.length;ai++){if(ao[ai].data.length){al=ao[ai].data[0];for(ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(ao[0] instanceof M){var ad=true;for(ai=0;ai<ao.length;ai++){if(!ao[ai].all_slotted){ad=false;break}}this.action_icons.show_more_rows_icon.toggle(!ad)}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(an,at,aq,ag,ak,af,ao){var ar=this,ae=at.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,at,aq,ag,ak)}var aj=[],ap=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ap)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.config.to_key_value_dict(),aq,aC,aA,af,function(aE){return ar.view.get_base_color(aE)});var ax=null;at.fillStyle=this.config.get_value("block_color");at.font=at.canvas.manager.default_font;at.textAlign="right";if(an.data){var ac=aB.draw(at,ae.width,ae.height,ak,ap);ax=ac.feature_mapper;incomplete_features=ac.incomplete_features;ax.translation=-ah}if(!ao){return new M(ar,ag,ak,ae,an.data,aq,an.message,all_slotted,ax,incomplete_features,af)}}});var Z=function(ad,ac,ae){L.call(this,ad,ac,ae);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:ab.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ac,af,ah,ag,ai){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ai)}else{var ae=this.view,ad=new (this.painter)(ac.data,ag.get("start"),ag.get("end"),this.config.to_key_value_dict(),ah,function(aj){return ae.get_base_color(aj)});ad.draw(af,af.canvas.width,af.canvas.height,ai);return new b(this,ag,ai,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}var af=new (this.painter)(null,null,null,this.config.to_key_value_dict(),ag);return af.get_required_height(ad)}},predraw_init:function(){var ac=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ag,ah,aj,ad){L.prototype.postdraw_actions.call(this,ag,ah,aj,ad);var af=ab.filter(ag,function(ak){return(ak instanceof K)});var ae=this.dataset.get_metadata("sample_names");if(af.length===0&&this.config.get_value("show_labels")&&ae&&ae.length>1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.config.get_value("summary_height")-ac)/2+"px"}));if(this.config.get_value("show_sample_data")){var ai=ae.join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ad,ac,ae){c.call(this,ad,ac,ae);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:ab.union(p.prototype.config_params,[{key:"block_color",label:"Histogram color",type:"color"},{key:"detail_block_color",label:"Sense strand block color",type:"color",default_value:"#AAAAAA"},{key:"reverse_strand_color",label:"Antisense strand block color",type:"color",default_value:"#DDDDDD"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var n=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Z,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/viz/trackster_ui.js
--- a/static/scripts/packed/viz/trackster_ui.js
+++ b/static/scripts/packed/viz/trackster_ui.js
@@ -1,1 +1,1 @@
-define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].config.get_value("name")===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});this.set_up_router({view:l});return l},set_up_router:function(k){new h.TrackBrowserRouter(k);Backbone.history.start()},init_keyboard_nav:function(k){$(document).keyup(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}});
\ No newline at end of file
+define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(f.extend(p,{header:false}));l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].config.get_value("name")===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});this.set_up_router({view:l});return l},set_up_router:function(k){new h.TrackBrowserRouter(k);Backbone.history.start()},init_keyboard_nav:function(k){$(document).keyup(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}});
\ No newline at end of file
diff -r 83a3792548db71c8bf69e278bf745bc5df123db7 -r 50a273de6cd76b770eb78861fee2b0a97621fa3b static/scripts/packed/viz/viz_views.js
--- /dev/null
+++ b/static/scripts/packed/viz/viz_views.js
@@ -0,0 +1,1 @@
+define(["libs/underscore"],function(a){var b=Backbone.View.extend({className:"track-header",initialize:function(){this.model.config.get("name").on("change:value",this.update_name,this);this.render()},render:function(){this.$el.append($("<div/>").addClass(this.model.drag_handle_class));this.$el.append($("<div/>").addClass("track-name").text(this.model.config.get_value("name")));this.action_icons={};this.render_action_icons();this.$el.dblclick(function(c){c.stopPropagation()});this.$el.append($("<div style='clear: both'/>"))},update_name:function(){this.$el.find(".track-name").text(this.model.config.get_value("name"))},render_action_icons:function(){var c=this;this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.$el);a.each(this.model.action_icons_def,function(d){c.add_action_icon(d.name,d.title,d.css_class,d.on_click_fn,d.prepend,d.hide)});this.set_display_modes(this.model.display_modes)},add_action_icon:function(e,i,h,g,d,f){var c=this;this.action_icons[e]=$("<a/>").attr("title",i).addClass("icon-button").addClass(h).tooltip().click(function(){g(c.model)}).appendTo(this.icons_div);if(f){this.action_icons[e].hide()}},set_display_modes:function(g,k){if(!g){return}this.model.display_modes=g;this.model.mode=(k||this.model.config.get_value("mode")||this.model.display_modes[0]);this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var e=this,d=this.model,h={};for(var f=0,c=d.display_modes.length;f<c;f++){var j=d.display_modes[f];h[j]=function(i){return function(){d.change_mode(i)}}(j)}make_popupmenu(this.action_icons.mode_icon,h)}});return{TrackHeaderView:b}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: In the dynamic job function mapper, get the user directly from the job instead of from the history.
by commits-noreply＠bitbucket.org 09 Jul '14
by commits-noreply＠bitbucket.org 09 Jul '14
09 Jul '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/83a3792548db/
Changeset: 83a3792548db
User: natefoo
Date: 2014-07-09 19:10:43
Summary: In the dynamic job function mapper, get the user directly from the job instead of from the history.
Affected #: 1 file
diff -r cbe3fe407093b0161469e1de662623d1d13bf532 -r 83a3792548db71c8bf69e278bf745bc5df123db7 lib/galaxy/jobs/mapper.py
--- a/lib/galaxy/jobs/mapper.py
+++ b/lib/galaxy/jobs/mapper.py
@@ -83,7 +83,7 @@
if "job" in function_arg_names or "user" in function_arg_names or "user_email" in function_arg_names or "resource_params" in function_arg_names:
job = self.job_wrapper.get_job()
history = job.history
- user = history and history.user
+ user = job.user
user_email = user and str(user.email)
if "job" in function_arg_names:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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