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3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/61e88903b180/
Changeset: 61e88903b180
Branch: fix-ngs_simulation
User: BjoernGruening
Date: 2014-11-14 14:51:57+00:00
Summary: Created new branch fix-ngs_simulation
Affected #: 0 files
https://bitbucket.org/galaxy/galaxy-central/commits/434fa3779315/
Changeset: 434fa3779315
Branch: fix-ngs_simulation
User: BjoernGruening
Date: 2014-11-14 14:56:28+00:00
Summary: Add rpy requirement.
Affected #: 1 file
diff -r 61e88903b18008068f9693f4eb23903e0e337144 -r 434fa3779315f3b1286ff1af660a8a486dae9bd5 tools/ngs_simulation/ngs_simulation.xml
--- a/tools/ngs_simulation/ngs_simulation.xml
+++ b/tools/ngs_simulation/ngs_simulation.xml
@@ -1,6 +1,9 @@
<tool id="ngs_simulation" name="Simulate" version="1.0.0"><!--<tool id="ngs_simulation" name="Simulate" force_history_refresh="True" version="1.0.0">--><description>Illumina runs</description>
+ <requirements>
+ <requirement type="package" version="1.0.3">rpy</requirement>
+ </requirements><command interpreter="python">
ngs_simulation.py
#if $in_type.input_type == "built-in"
https://bitbucket.org/galaxy/galaxy-central/commits/3ea58a572fef/
Changeset: 3ea58a572fef
User: dan
Date: 2014-11-14 15:10:53+00:00
Summary: Merged in BjoernGruening/galaxy-central-1/fix-ngs_simulation (pull request #563)
Add requirement to the ngs_simulation tool.
Affected #: 1 file
diff -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b -r 3ea58a572fefa03bef988886848af74e05080cff tools/ngs_simulation/ngs_simulation.xml
--- a/tools/ngs_simulation/ngs_simulation.xml
+++ b/tools/ngs_simulation/ngs_simulation.xml
@@ -1,6 +1,9 @@
<tool id="ngs_simulation" name="Simulate" version="1.0.0"><!--<tool id="ngs_simulation" name="Simulate" force_history_refresh="True" version="1.0.0">--><description>Illumina runs</description>
+ <requirements>
+ <requirement type="package" version="1.0.3">rpy</requirement>
+ </requirements><command interpreter="python">
ngs_simulation.py
#if $in_type.input_type == "built-in"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: ToolForm: Fixes for citations, pasting into numeric fields and ui element sizes
by commits-noreply＠bitbucket.org 14 Nov '14
by commits-noreply＠bitbucket.org 14 Nov '14
14 Nov '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3d9e14ac53cc/
Changeset: 3d9e14ac53cc
User: guerler
Date: 2014-11-14 15:08:06+00:00
Summary: ToolForm: Fixes for citations, pasting into numeric fields and ui element sizes
Affected #: 13 files
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -362,15 +362,13 @@
// append citations
if (options.citations) {
- // fetch citations
+ var $citations = $('<div/>');
var citations = new CitationModel.ToolCitationCollection();
citations.tool_id = options.id;
- var citation_list_view = new CitationView.CitationListView({ collection: citations } );
+ var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations } );
citation_list_view.render();
citations.fetch();
-
- // append to element
- this.$el.append(citation_list_view.$el);
+ this.$el.append($citations);
}
// append tool section
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b client/galaxy/scripts/mvc/tools/tools-repeat.js
--- a/client/galaxy/scripts/mvc/tools/tools-repeat.js
+++ b/client/galaxy/scripts/mvc/tools/tools-repeat.js
@@ -73,10 +73,10 @@
// create portlet
var portlet = new Portlet.View({
- id : options.id,
- title : '<b>' + options.title + '</b>',
- cls : 'ui-portlet-repeat',
- operations : {
+ id : options.id,
+ title : '<b>' + options.title + '</b>',
+ cls : 'ui-portlet-repeat',
+ operations : {
button_delete : button_delete
}
});
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b client/galaxy/scripts/mvc/ui/ui-portlet.js
--- a/client/galaxy/scripts/mvc/ui/ui-portlet.js
+++ b/client/galaxy/scripts/mvc/ui/ui-portlet.js
@@ -8,15 +8,16 @@
// defaults options
optionsDefault: {
- title : '',
- icon : '',
- buttons : null,
- body : null,
- scrollable : true,
- nopadding : false,
- operations : null,
- placement : 'bottom',
- cls : 'ui-portlet'
+ title : '',
+ icon : '',
+ buttons : null,
+ body : null,
+ scrollable : true,
+ nopadding : false,
+ operations : null,
+ placement : 'bottom',
+ cls : 'ui-portlet',
+ operations_flt : 'right'
},
// elements
@@ -157,7 +158,7 @@
if (options.title) {
tmpl += '<div id="portlet-header" class="portlet-header">' +
- '<div id="operations" style="float: right;"></div>' +
+ '<div id="operations" style="float: ' + options.operations_flt + ';"></div>' +
'<div class="portlet-title">';
if (options.icon)
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b client/galaxy/scripts/mvc/ui/ui-slider.js
--- a/client/galaxy/scripts/mvc/ui/ui-slider.js
+++ b/client/galaxy/scripts/mvc/ui/ui-slider.js
@@ -46,7 +46,7 @@
this.$el.find('.ui-form-slider-text').css('width', '100%');
}
- // backup integer field
+ // link text input field
this.$text = this.$el.find('#text');
// add text field event
@@ -55,10 +55,17 @@
});
// add text field event
- this.$text.on('keydown', function (event) {
- var v = event.which;
- if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57)
- || (self.options.precise && $(this).val().indexOf('.') == -1) && v == 190)) {
+ var pressed = [];
+ this.$text.on('keyup', function(e) {
+ pressed[e.which] = false;
+ });
+ this.$text.on('keydown', function (e) {
+ var v = e.which;
+ pressed[v] = true;
+ if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || (v >= 48 && v <= 57)
+ || (v == 190 && $(this).val().indexOf('.') == -1 && self.options.precise)
+ || (v == 189 && $(this).val().indexOf('-') == -1)
+ || pressed[91] || pressed[17])) {
event.preventDefault();
}
});
@@ -67,6 +74,11 @@
// value
value : function (new_val) {
if (new_val !== undefined) {
+ // check if its a number
+ if (isNaN(new_val)) {
+ new_val = 0;
+ }
+
// apply limit
if (this.options.max !== null) {
new_val = Math.min(new_val, this.options.max);
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -362,15 +362,13 @@
// append citations
if (options.citations) {
- // fetch citations
+ var $citations = $('<div/>');
var citations = new CitationModel.ToolCitationCollection();
citations.tool_id = options.id;
- var citation_list_view = new CitationView.CitationListView({ collection: citations } );
+ var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations } );
citation_list_view.render();
citations.fetch();
-
- // append to element
- this.$el.append(citation_list_view.$el);
+ this.$el.append($citations);
}
// append tool section
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/scripts/mvc/tools/tools-repeat.js
--- a/static/scripts/mvc/tools/tools-repeat.js
+++ b/static/scripts/mvc/tools/tools-repeat.js
@@ -73,10 +73,10 @@
// create portlet
var portlet = new Portlet.View({
- id : options.id,
- title : '<b>' + options.title + '</b>',
- cls : 'ui-portlet-repeat',
- operations : {
+ id : options.id,
+ title : '<b>' + options.title + '</b>',
+ cls : 'ui-portlet-repeat',
+ operations : {
button_delete : button_delete
}
});
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/scripts/mvc/ui/ui-portlet.js
--- a/static/scripts/mvc/ui/ui-portlet.js
+++ b/static/scripts/mvc/ui/ui-portlet.js
@@ -8,15 +8,16 @@
// defaults options
optionsDefault: {
- title : '',
- icon : '',
- buttons : null,
- body : null,
- scrollable : true,
- nopadding : false,
- operations : null,
- placement : 'bottom',
- cls : 'ui-portlet'
+ title : '',
+ icon : '',
+ buttons : null,
+ body : null,
+ scrollable : true,
+ nopadding : false,
+ operations : null,
+ placement : 'bottom',
+ cls : 'ui-portlet',
+ operations_flt : 'right'
},
// elements
@@ -157,7 +158,7 @@
if (options.title) {
tmpl += '<div id="portlet-header" class="portlet-header">' +
- '<div id="operations" style="float: right;"></div>' +
+ '<div id="operations" style="float: ' + options.operations_flt + ';"></div>' +
'<div class="portlet-title">';
if (options.icon)
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/scripts/mvc/ui/ui-slider.js
--- a/static/scripts/mvc/ui/ui-slider.js
+++ b/static/scripts/mvc/ui/ui-slider.js
@@ -46,7 +46,7 @@
this.$el.find('.ui-form-slider-text').css('width', '100%');
}
- // backup integer field
+ // link text input field
this.$text = this.$el.find('#text');
// add text field event
@@ -55,10 +55,17 @@
});
// add text field event
- this.$text.on('keydown', function (event) {
- var v = event.which;
- if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v == 189 || (v >= 48 && v <= 57)
- || (self.options.precise && $(this).val().indexOf('.') == -1) && v == 190)) {
+ var pressed = [];
+ this.$text.on('keyup', function(e) {
+ pressed[e.which] = false;
+ });
+ this.$text.on('keydown', function (e) {
+ var v = e.which;
+ pressed[v] = true;
+ if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || (v >= 48 && v <= 57)
+ || (v == 190 && $(this).val().indexOf('.') == -1 && self.options.precise)
+ || (v == 189 && $(this).val().indexOf('-') == -1)
+ || pressed[91] || pressed[17])) {
event.preventDefault();
}
});
@@ -67,6 +74,11 @@
// value
value : function (new_val) {
if (new_val !== undefined) {
+ // check if its a number
+ if (isNaN(new_val)) {
+ new_val = 0;
+ }
+
// apply limit
if (this.options.max !== null) {
new_val = Math.min(new_val, this.options.max);
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/scripts/packed/mvc/ui/ui-portlet.js
--- a/static/scripts/packed/mvc/ui/ui-portlet.js
+++ b/static/scripts/packed/mvc/ui/ui-portlet.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:true,nopadding:false,operations:null,placement:"bottom",cls:"ui-portlet"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(e){this.options=a.merge(e,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");this.$title=this.$el.find("#portlet-title-text");var d=this.$el.find("#portlet-content");if(!this.options.scrollable){if(this.options.title){d.addClass("no-scroll")}else{d.addClass("no-scroll-no-title")}}else{d.addClass("scroll")}if(this.options.nopadding){d.css("padding","0px");this.$content.css("padding","0px")}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(f,g){g.$el.prop("id",f);c.$buttons.append(g.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(f,g){g.$el.prop("id",f);c.$operations.append(g.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$title;if(d){c.html(d)}return c.html()},_template:function(d){var c='<div id="'+d.id+'" class="'+d.cls+'">';if(d.title){c+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><div class="portlet-title">';if(d.icon){c+='<i class="icon fa '+d.icon+'"> </i>'}c+='<span id="portlet-title-text" class="portlet-title-text">'+d.title+"</span></div></div>"}c+='<div id="portlet-content" class="portlet-content">';if(d.placement=="top"){c+='<div id="buttons" class="buttons"></div>'}c+='<div id="content" class="content"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons"></div>'}c+="</div></div>";return c}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:true,nopadding:false,operations:null,placement:"bottom",cls:"ui-portlet",operations_flt:"right"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(e){this.options=a.merge(e,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");this.$title=this.$el.find("#portlet-title-text");var d=this.$el.find("#portlet-content");if(!this.options.scrollable){if(this.options.title){d.addClass("no-scroll")}else{d.addClass("no-scroll-no-title")}}else{d.addClass("scroll")}if(this.options.nopadding){d.css("padding","0px");this.$content.css("padding","0px")}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(f,g){g.$el.prop("id",f);c.$buttons.append(g.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(f,g){g.$el.prop("id",f);c.$operations.append(g.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$title;if(d){c.html(d)}return c.html()},_template:function(d){var c='<div id="'+d.id+'" class="'+d.cls+'">';if(d.title){c+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: '+d.operations_flt+';"></div><div class="portlet-title">';if(d.icon){c+='<i class="icon fa '+d.icon+'"> </i>'}c+='<span id="portlet-title-text" class="portlet-title-text">'+d.title+"</span></div></div>"}c+='<div id="portlet-content" class="portlet-content">';if(d.placement=="top"){c+='<div id="buttons" class="buttons"></div>'}c+='<div id="content" class="content"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons"></div>'}c+="</div></div>";return c}});return{View:b}});
\ No newline at end of file
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/scripts/packed/mvc/ui/ui-slider.js
--- a/static/scripts/packed/mvc/ui/ui-slider.js
+++ b/static/scripts/packed/mvc/ui/ui-slider.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(e,f){c.value(f.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");this.$text.on("change",function(){c.value($(this).val())});this.$text.on("keydown",function(f){var e=f.which;if(!(e==8||e==9||e==13||e==37||e==39||e==189||(e>=48&&e<=57)||(c.options.precise&&$(this).val().indexOf(".")==-1)&&e==190)){f.preventDefault()}})},value:function(c){if(c!==undefined){if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}});
\ No newline at end of file
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1307,7 +1307,7 @@
.ui-portlet .portlet-buttons{height:50px;padding:10px}
.ui-portlet .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons{height:50px;padding:10px}
.ui-portlet .no-scroll{height:calc(100% - 80px)}
-.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:0px 2px}
+.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px;display:inline-block}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:0px 2px}
.ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:10px}
.ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
.ui-popover .popover-title{padding:4px 10px}
diff -r 18e4aea56a74618c69b6407a52af03ce179c914b -r 3d9e14ac53cc9d10bd6cf1006e4d2c196cd72e9b static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -205,6 +205,7 @@
border: none;
border-left: solid 3px @form-heading-bg;
border-radius: 5px;
+ display: inline-block;
.portlet-header {
background: @form-heading-bg;
border-radius: 3px;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset e6de07f8c01f
by commits-noreply＠bitbucket.org 14 Nov '14
by commits-noreply＠bitbucket.org 14 Nov '14
14 Nov '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9c1197f1e259/
Changeset: 9c1197f1e259
Branch: stable
User: natefoo
Date: 2014-11-14 14:00:21+00:00
Summary: Update tag latest_2014.10.06 for changeset e6de07f8c01f
Affected #: 1 file
diff -r e6de07f8c01fe8802282eea1bee326c5efba1b78 -r 9c1197f1e259f7925be467f2f6f92fa3e7a5e86c .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -20,4 +20,4 @@
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
-c9759aa6e40f887dec2d27d2f244d6fd7c28e6de latest_2014.10.06
+e6de07f8c01fe8802282eea1bee326c5efba1b78 latest_2014.10.06
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Fix to 31f05a1: restore event handler code based on builtin v. registry
by commits-noreply＠bitbucket.org 13 Nov '14
by commits-noreply＠bitbucket.org 13 Nov '14
13 Nov '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/18e4aea56a74/
Changeset: 18e4aea56a74
User: carlfeberhard
Date: 2014-11-13 21:53:43+00:00
Summary: Fix to 31f05a1: restore event handler code based on builtin v. registry
Affected #: 2 files
diff -r 6f0438d759afd9c36dd80755fa41f145cf370231 -r 18e4aea56a74618c69b6407a52af03ce179c914b templates/webapps/galaxy/page/display.mako
--- a/templates/webapps/galaxy/page/display.mako
+++ b/templates/webapps/galaxy/page/display.mako
@@ -10,8 +10,11 @@
// (b) ...
$('.embedded-item').each( function() {
var container = $(this);
- if( container.hasClass( 'history' )
- || container.hasClass( 'visualization' ) ){ return; }
+ if( container.hasClass( 'history' ) ){ return; }
+ //note: we can't do the same override for visualizations
+ // bc builtins (like trackster) need the handlers/ajax below to work.
+ // instead: (for registry visualizations) we'll clear the handlers below
+ // and add new ones (in embed_in_frame.mako) ...ugh.
// Show embedded item.
var show_embedded_item = function() {
diff -r 6f0438d759afd9c36dd80755fa41f145cf370231 -r 18e4aea56a74618c69b6407a52af03ce179c914b templates/webapps/galaxy/visualization/embed_in_frame.mako
--- a/templates/webapps/galaxy/visualization/embed_in_frame.mako
+++ b/templates/webapps/galaxy/visualization/embed_in_frame.mako
@@ -61,7 +61,7 @@
/** 4 elements change when expanding - toggle them all, add the iframe and prevent the url change */
function toggleExpanded( ev ){
var $embeddedObj = $( thisScript ).prev();
- $embeddedObj.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' );
+ $embeddedObj.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' ).show();
$embeddedObj.find( ".summary-content" ).slideToggle( "fast" );
$embeddedObj.find( ".annotation" ).slideToggle( "fast" );
$embeddedObj.find( ".expanded-content" ).slideToggle( "fast" );
@@ -71,8 +71,10 @@
// add expansion to +/- btn and title
$(function(){
- $embeddedObj.find( '.expand-content-btn' ).click( toggleExpanded );
- $embeddedObj.find( '.toggle-embed' ).click( toggleExpanded );
+ var $embeddedObj = $( thisScript ).prev();
+ // clear the handlers (w/ off) created in page/display/mako for visualizations
+ $embeddedObj.find( '.expand-content-btn' ).off().click( toggleExpanded );
+ $embeddedObj.find( '.toggle-embed' ).off().click( toggleExpanded );
});
})();
</script>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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13 Nov '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6f0438d759af/
Changeset: 6f0438d759af
User: guerler
Date: 2014-11-13 21:40:59+00:00
Summary: Charts: Repack scripts
Affected #: 1 file
diff -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 -r 6f0438d759afd9c36dd80755fa41f145cf370231 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
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t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.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.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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'+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$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+'"/>'}}),p=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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-textfield '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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",["mvc/ui/ui-table","mvc/ui/ui-misc","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.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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","mvc/ui/ui-misc","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:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",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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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+'<div class="button">'+'<i id="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),errorText:"No data available.",waitText:"Please wait..."},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$message=$("<div/>"),this.$options=$(this._template(t)),this.$el.append(this.$message),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},wait:function(){this._size()==0&&(this._messageShow(this.options.waitText,"info"),this.$options.hide())},unwait:function(){this._messageHide(),this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.errorText,"danger"),this.$options.hide()):(this._messageHide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$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($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a class="dropdown-item" href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),h=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.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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","mvc/ui/ui-misc","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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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",["mvc/ui/ui-table","mvc/ui/ui-misc","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.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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","mvc/ui/ui-misc","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:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",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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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","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/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
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Ui: Resize select fields
by commits-noreply＠bitbucket.org 13 Nov '14
by commits-noreply＠bitbucket.org 13 Nov '14
13 Nov '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/753a9c257291/
Changeset: 753a9c257291
User: guerler
Date: 2014-11-13 21:38:49+00:00
Summary: Ui: Resize select fields
Affected #: 10 files
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 client/galaxy/scripts/mvc/tools/tools-form.js
--- a/client/galaxy/scripts/mvc/tools/tools-form.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form.js
@@ -334,7 +334,6 @@
this.portlet = new Portlet.View({
icon : 'fa-wrench',
title: '<b>' + this.model.name + '</b> ' + this.model.description,
- cls : 'ui-portlet-short',
operations: {
menu : menu
},
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 client/galaxy/scripts/mvc/ui/ui-select-default.js
--- a/client/galaxy/scripts/mvc/ui/ui-select-default.js
+++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js
@@ -109,7 +109,7 @@
show: function() {
this.unwait();
this.$select.show();
- this.$el.show();
+ this.$el.css('display', 'inline-block');
},
/** Hide the select field
@@ -247,10 +247,10 @@
*/
_template: function(options) {
return '<div id="' + options.id + '">' +
+ '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' +
'<div class="button">' +
'<i id="icon"/>' +
'</div>' +
- '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' +
'</div>';
}
});
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
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n=0;$.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.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" 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btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(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>"}}),h=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.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$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.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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","mvc/ui/ui-misc","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,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=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()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(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.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();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)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},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.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<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=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$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.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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",["mvc/ui/ui-table","mvc/ui/ui-misc","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.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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 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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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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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t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,placement:"bottom",cls:"ui-portlet"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#portlet-title-text");var 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.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div id="'+e.id+'" class="'+e.cls+'">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><div class="portlet-title">',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-title-text" class="portlet-title-text">'+e.title+"</span>"+"</div>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("mvc/ui/ui-select-default",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1,multiple:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.options.multiple?(this.$select.prop("multiple",!0),this.$select.addClass("ui-select-multiple"),this.$icon.remove()):this.$el.addClass("ui-select"),this.update(this.options.data),this.options.visible||this.hide(),this.options.wait?this.wait():this.show();var n=this;this.$select.on("change",function(){n._change()}),this.on("change",function(){n._change()})},value:function(e){return e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait(),this.$select.show(),this.$el.css("display","inline-block")},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$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.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$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()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+'<div class="button">'+'<i id="icon"/>'+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:null,max:null,step:null,precise:!1,split:1e4},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min,this.options.step===null&&(this.options.step=1,this.options.precise&&this.useslider&&(this.options.step=(this.options.max-this.options.min)/this.options.split)),this.useslider?(this.$slider=this.$el.find("#slider"),this.$slider.slider(this.options),this.$slider.on("slide",function(e,t){n.value(t.value)})):this.$el.find(".ui-form-slider-text").css("width","100%"),this.$text=this.$el.find("#text"),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==8||t==9||t==13||t==37||t==39||t==189||t>=48&&t<=57||n.options.precise&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()})},value:function(e){return e!==undefined&&(this.options.max!==null&&(e=Math.min(e,this.options.max)),this.options.min!==null&&(e=Math.max(e,this.options.min)),this.options.onchange&&this.options.onchange(e),this.$slider&&this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),errorText:"No data available.",waitText:"Please wait..."},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$message=$("<div/>"),this.$options=$(this._template(t)),this.$el.append(this.$message),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},validate:function(){var e=this.value();e instanceof Array||(e=[e]);for(var t in e)if([null,"null",undefined].indexOf(e[t])>-1)return!1;return!0},wait:function(){this._size()==0&&(this._messageShow(this.options.waitText,"info"),this.$options.hide())},unwait:function(){this._messageHide(),this._refresh()},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){this._size()==0?(this._messageShow(this.options.errorText,"danger"),this.$options.hide()):(this._messageHide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return"null";if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(e,t){this.$message.show(),this.$message.removeClass(),this.$message.addClass("ui-message alert alert-"+t),this.$message.html(e)},_messageHide:function(){this.$message.hide()}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",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 class="dropdown-item" 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="",n="";e.title?t="width: auto;":n="margin: 0px;";var r='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="dropdown '+e.cls+'">'+'<div class="root button dropdown-toggle" data-toggle="dropdown" style="'+n+'">'+'<i class="icon fa '+e.icon+'"/>';return e.title&&(r+=' <span class="title">'+e.title+"</span>"),r+="</div></div>",r}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=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+'"/>'}}),u=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.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="'+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+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}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$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+'"/>'}}),p=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>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},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 e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-textfield '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),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({type:"PUT",url:config.root+"api/histories/none/contents/"+r,data:{deleted:!0},success: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({type:"POST",url:config.root+"api/tools",data:data,success: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),o.app.storage.save(),o._wait(t,i,s)}},error: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({type:"GET",url:config.root+"api/datasets/"+t.get("dataset_id_job"),data:{},success: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 c(i){l._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(++f<u&&!s){n&&n(parseInt(f/u*100));var l=i.start+r;i=$.extend(!0,a,{start:l}),c(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=e.start||0,s=i+e.query_limit||i+this.app.config.get("query_limit"),o=Math.abs(s-i);if(o<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var u=Math.ceil(o/r)||1,a=$.extend(!0,{},e),f=0,l=this,h=$.extend(!0,a,{start:i});this._get_dataset(e.id,function(){c(h)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request({type:"GET",url:config.root+"api/datasets/"+t,success: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({type:"GET",url:config.root+"api/datasets/"+t.dataset_id,data:{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},success: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("utils/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.queue.length>0&&this.ready()){var e=this.queue[0];this.queue.splice(0,1),e&&e()}})},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"))},reset:function(){this.queue=[]},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","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=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(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.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},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),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$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()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_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="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+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="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/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:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},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,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!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,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(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="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","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",["mvc/ui/ui-table","mvc/ui/ui-misc","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.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<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",["mvc/ui/ui-misc","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,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},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.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(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","mvc/ui/ui-misc","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:1e4,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["x_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["x_axis_precision"]}},{label:"Float",value:"f",operations:{show:["x_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["x_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["x_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["x_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["x_axis_precision"]}}]},x_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_y:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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E=d3.select(this),T=this,N=(u||parseInt(E.style("width"))||960)-s.left-s.right,C=(a||parseInt(E.style("height"))||400)-s.top-s.bottom;x.update=function(){E.call(x)},x.container=this,g.disabled=d.map(function(e){return!!e.disabled});if(!y){var k;y={};for(k in g)g[k]instanceof Array?y[k]=g[k].slice(0):y[k]=g[k]}if(!d||!d.length||!d.filter(function(e){return e.values.length}).length){var L=E.selectAll(".nv-noData").data([b]);return L.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),L.attr("x",s.left+N/2).attr("y",s.top+C/2).text(function(e){return e}),x}E.selectAll(".nv-noData").remove(),v=t.xScale(),m=t.yScale();var A=E.selectAll("g.nv-wrap.nv-historicalBarChart").data([d]),O=A.enter().append("g").attr("class","nvd3 nv-wrap nv-historicalBarChart").append("g"),M=A.select("g");O.append("g").attr("class","nv-x nv-axis"),O.append("g").attr("class","nv-y 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t=e.models.historicalBar(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s={top:30,right:90,bottom:50,left:90},o=e.utils.defaultColor(),u=null,a=null,f=!1,l=!0,c=!0,h=!1,p=!0,d=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},v,m,g={},y=null,b="No Data Available.",w=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),E=0;n.orient("bottom").tickPadding(7),r.orient(h?"right":"left");var S=function(i,s){if(s){var o=d3.select(s).select("svg"),u=o.node()?o.attr("viewBox"):null;if(u){u=u.split(" ");var a=parseInt(o.style("width"))/u[2];i.pos[0]=i.pos[0]*a,i.pos[1]=i.pos[1]*a}}var f=i.pos[0]+(s.offsetLeft||0),l=i.pos[1]+(s.offsetTop||0),c=n.tickFormat()(t.x()(i.point,i.pointIndex)),h=r.tickFormat()(t.y()(i.point,i.pointIndex)),p=d(i.series.key,c,h,i,x);e.tooltip.show([f,l],p,null,null,s)};return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),C.dispatch=S,C.multibar=t,C.legend=i,C.xAxis=n,C.yAxis=r,d3.rebind(C,t,"x","y","xDomain","yDomain","xRange","yRange","forceX","forceY","clipEdge","id","delay","showValues","showBarLabels","valueFormat","stacked","barColor"),C.options=e.utils.optionsFunc.bind(C),C.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,C):o},C.width=function(e){return arguments.length?(u=e,C):u},C.height=function(e){return arguments.length?(a=e,C):a},C.color=function(t){return arguments.length?(f=e.utils.getColor(t),i.color(f),C):f},C.showControls=function(e){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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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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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 e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var 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small",showmaxmin:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/histogram/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogram",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{x_axis_label:{init:"Values"},y_axis_label:{init:"Density"},y_axis_type:{init:"f"},y_axis_precision:{init:".2"}}})}),define("plugin/charts/nvd3/line/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/scatter/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",zoomable:!0,columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/nvd3/stackedarea/config",["plugin/charts/nvd3/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",zoomable:!0,category:"Area charts",keywords:"default small",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/common/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"",category:"",library:"jqPlot",tag:"div",zoomable:!0,keywords:"medium",settings:{separator_grid:{title:"Grids",type:"separator"},x_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the X axis?",type:"radiobutton",init:"false",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]},y_axis_grid:{title:"Axis grid",info:"Would you like to show grid lines for the Y axis?",type:"radiobutton",init:"true",data:[{label:"On",value:"true"},{label:"Off",value:"false"}]}}})}),define("plugin/charts/jqplot/bar/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Regular",category:"Bar diagrams",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/line/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Line chart",category:"Others",columns:{x:{title:"Values for x-axis",is_label:!0,is_auto:!0,is_unique:!0},y:{title:"Values for y-axis",is_numeric:!0}}})}),define("plugin/charts/jqplot/scatter/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",category:"Others",columns:{x:{title:"Values for x-axis",is_numeric:!0},y:{title:"Values for y-axis",is_numeric:!0}},settings:{x_axis_grid:{init:"true"}}})}),define("plugin/charts/jqplot/boxplot/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Box plot",category:"Data processing (requires 'charts' tool from Toolshed)",library:"jqPlot",tag:"div",execute:"boxplot",keywords:"small medium large",columns:{y:{title:"Observations",is_numeric:!0}},settings:{show_legend:{init:"false"}}})}),define("plugin/charts/jqplot/histogram_discrete/config",["plugin/charts/jqplot/common/config"],function(e){return $.extend(!0,{},e,{title:"Discrete Histogram",category:"Data processing (requires 'charts' tool from Toolshed)",execute:"histogramdiscrete",keywords:"small medium large",columns:{x:{title:"Observations",is_label:!0}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/others/heatmap/config",["plugin/charts/forms/default"],function(e){return $.extend(!0,{},e,{title:"Heatmap",category:"Others",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","mvc/ui/ui-misc","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","utils/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 facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -252,6 +252,7 @@
def to_dict( self, trans, view='collection', value_mapper=None ):
d = super(TextToolParameter, self).to_dict(trans)
d['area'] = self.area
+ d['size'] = self.size
return d
class IntegerToolParameter( TextToolParameter ):
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -334,7 +334,6 @@
this.portlet = new Portlet.View({
icon : 'fa-wrench',
title: '<b>' + this.model.name + '</b> ' + this.model.description,
- cls : 'ui-portlet-short',
operations: {
menu : menu
},
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 static/scripts/mvc/ui/ui-select-default.js
--- a/static/scripts/mvc/ui/ui-select-default.js
+++ b/static/scripts/mvc/ui/ui-select-default.js
@@ -109,7 +109,7 @@
show: function() {
this.unwait();
this.$select.show();
- this.$el.show();
+ this.$el.css('display', 'inline-block');
},
/** Hide the select field
@@ -247,10 +247,10 @@
*/
_template: function(options) {
return '<div id="' + options.id + '">' +
+ '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' +
'<div class="button">' +
'<i id="icon"/>' +
'</div>' +
- '<select id="select" class="select ' + options.cls + ' ' + options.id + '"></select>' +
'</div>';
}
});
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 static/scripts/packed/mvc/tools/tools-form.js
--- a/static/scripts/packed/mvc/tools/tools-form.js
+++ b/static/scripts/packed/mvc/tools/tools-form.js
@@ -1,1 +1,1 @@
-define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-short",operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
+define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}});
\ No newline at end of file
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 static/scripts/packed/mvc/ui/ui-select-default.js
--- a/static/scripts/packed/mvc/ui/ui-select-default.js
+++ b/static/scripts/packed/mvc/ui/ui-select-default.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><div class="button"><i id="icon"/></div><select id="select" class="select '+c.cls+" "+c.id+'"></select></div>'}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find("#select");this.$icon=this.$el.find("#icon");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c)}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.css("display","inline-block")},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i id="icon"/></div></div>'}});return{View:b}});
\ No newline at end of file
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1279,7 +1279,7 @@
.upload-ftp .upload-ftp-help{margin-bottom:10px}
.upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px}
.upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop}
-.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-short,.ui-portlet-repeat{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;}
+.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-repeat{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;}
.ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px}
.ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px}
.ui-table tbody{cursor:pointer}
@@ -1302,12 +1302,11 @@
.ui-button-icon-plain{border:none !important;background:none !important;height:inherit !important;width:inherit !important;padding-right:3px !important}
.ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px}
.ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer}
-.ui-portlet,.ui-portlet-short,.ui-portlet-repeat,.ui-portlet-short,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header,.ui-portlet-short .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title .portlet-title-text,.ui-portlet-short .portlet-header .portlet-title .portlet-title-text{vertical-align:middle}
-.ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-short .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle}
-.ui-portlet .portlet-buttons,.ui-portlet-short .portlet-buttons{height:50px;padding:10px}
-.ui-portlet .portlet-content,.ui-portlet-short .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content,.ui-portlet-short .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons,.ui-portlet-short .portlet-content .content .buttons{height:50px;padding:10px}
-.ui-portlet .no-scroll,.ui-portlet-short .no-scroll{height:calc(100% - 80px)}
-.ui-portlet-short .portlet-content{max-width:600px}
+.ui-portlet,.ui-portlet-repeat,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title .portlet-title-text{vertical-align:middle}
+.ui-portlet .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle}
+.ui-portlet .portlet-buttons{height:50px;padding:10px}
+.ui-portlet .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons{height:50px;padding:10px}
+.ui-portlet .no-scroll{height:calc(100% - 80px)}
.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:0px 2px}
.ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:10px}
.ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
@@ -1319,9 +1318,8 @@
.ui-form-slider .ui-form-slider-element{width:calc(100% - 110px);float:left;top:8px;left:10px}
.ui-radiobutton{width:100%}.ui-radiobutton label{height:23px;line-height:1em}
.ui-radiobutton i{padding-right:5px}
-.ui-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.ui-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;background:#f2f2f2;text-align:center;line-height:25px}
-.ui-select select{position:absolute;top:0px;height:100%;width:100%;padding-left:5px;cursor:pointer;background:transparent;border:0;border-radius:0;-webkit-appearance:none}
-.ui-select-multiple{height:100% !important;width:100% !important}
+.ui-select{position:relative}.ui-select .button{position:absolute;top:5px;right:5px}
+.ui-select select{position:relative;top:0px;height:27px;width:100%;padding-left:5px;padding-right:20px;cursor:pointer;background:transparent;-webkit-appearance:none;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}
.libraryRow{background-color:#ebd9b2}
.datasetHighlighted{background-color:#f9f9f9}
.libraryItemDeleted-True{font-style:italic}
diff -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 -r 753a9c25729169dfb7ddd9bbbc2b37f7250957e5 static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -200,13 +200,6 @@
}
}
-.ui-portlet-short {
- &:extend(.ui-portlet all);
- .portlet-content {
- max-width: 600px;
- }
-}
-
.ui-portlet-repeat {
&:extend(.ui-portlet);
border: none;
@@ -292,39 +285,27 @@
.ui-select {
position: relative;
- height: 27px;
- overflow: hidden;
- border: 1px solid @border-default-color;
- -moz-border-radius: @border-radius-base;
- border-radius: @border-radius-base;
-
.button {
+ position: absolute;
+ top: 5px;
+ right: 5px;
+ }
+ select {
position: relative;
- width: 25px;
- height: 100%;
- float: right;
- border-left: 1px solid @border-default-color;
- background: @btn-default-bg;
- text-align: center;
- line-height: 25px;
- }
-
- select {
- position: absolute;
top: 0px;
- height: 100%;
+ height: 27px;
width: 100%;
padding-left:5px;
+ padding-right: 20px;
cursor: pointer;
background: transparent;
- border: 0;
- border-radius: 0;
-webkit-appearance: none;
+ border: 1px solid @border-default-color;
+ -moz-border-radius: @border-radius-base;
+ border-radius: @border-radius-base;
}
}
.ui-select-multiple {
&:extend(.ui-input);
- height: 100% !important;
- width: 100% !important;
}
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: open citation url in _blank (prevents browser's insecure content error messages while trying to open in the middle pane - https vs http)
by commits-noreply＠bitbucket.org 13 Nov '14
by commits-noreply＠bitbucket.org 13 Nov '14
13 Nov '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e6de07f8c01f/
Changeset: e6de07f8c01f
Branch: stable
User: martenson
Date: 2014-11-13 19:41:49+00:00
Summary: open citation url in _blank (prevents browser's insecure content error messages while trying to open in the middle pane - https vs http)
Affected #: 3 files
diff -r f01e2504095a477b16970f9570eb68361f031287 -r e6de07f8c01fe8802282eea1bee326c5efba1b78 client/galaxy/scripts/mvc/citation/citation-view.js
--- a/client/galaxy/scripts/mvc/citation/citation-view.js
+++ b/client/galaxy/scripts/mvc/citation/citation-view.js
@@ -58,11 +58,11 @@
var doiUrl = "";
if( fields.doi ) {
doiUrl = 'http://dx.doi.org/' + fields.doi;
- ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]";
+ ref += '[<a href="' + doiUrl + '" target="_blank">doi:' + fields.doi + "</a>]";
}
var url = fields.url || doiUrl;
if( url ) {
- ref += '[<a href="' + url + '">Link</a>]';
+ ref += '[<a href="' + url + '" target="_blank">Link</a>]';
}
return ref;
},
@@ -185,4 +185,4 @@
CitationListView : CitationListView
};
-});
\ No newline at end of file
+});
diff -r f01e2504095a477b16970f9570eb68361f031287 -r e6de07f8c01fe8802282eea1bee326c5efba1b78 static/scripts/mvc/citation/citation-view.js
--- a/static/scripts/mvc/citation/citation-view.js
+++ b/static/scripts/mvc/citation/citation-view.js
@@ -58,11 +58,11 @@
var doiUrl = "";
if( fields.doi ) {
doiUrl = 'http://dx.doi.org/' + fields.doi;
- ref += '[<a href="' + doiUrl + '">doi:' + fields.doi + "</a>]";
+ ref += '[<a href="' + doiUrl + '" target="_blank">doi:' + fields.doi + "</a>]";
}
var url = fields.url || doiUrl;
if( url ) {
- ref += '[<a href="' + url + '">Link</a>]';
+ ref += '[<a href="' + url + '" target="_blank">Link</a>]';
}
return ref;
},
@@ -185,4 +185,4 @@
CitationListView : CitationListView
};
-});
\ No newline at end of file
+});
diff -r f01e2504095a477b16970f9570eb68361f031287 -r e6de07f8c01fe8802282eea1bee326c5efba1b78 static/scripts/packed/mvc/citation/citation-view.js
--- a/static/scripts/packed/mvc/citation/citation-view.js
+++ b/static/scripts/packed/mvc/citation/citation-view.js
@@ -1,1 +1,1 @@
-define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var k=this.model;var i=k.entryType();var l=k.fields();var g="";var o=this._asSentence((l.author?l.author:"")+(l.year?(" ("+l.year+")"):""))+" ";var n=l.title||"";var h=l.pages?("pp. "+l.pages):"";var p=l.address;if(i=="article"){var j=(l.volume?l.volume:"")+(l.number?(" ("+l.number+")"):"")+(h?", "+h:"");g=o+this._asSentence(n)+(l.journal?("In <em>"+l.journal+", "):"")+this._asSentence(j)+this._asSentence(l.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=o+this._asSentence(n)+(l.booktitle?("In <em>"+l.booktitle+", "):"")+(h?h:"")+(p?", "+p:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=o+this._asSentence(n)+(l.howpublished?l.howpublished+". ":"")+(l.note?l.note+".":"")}else{if(i=="techreport"){g=o+this._asSentence(n)+this._asSentence(l.institution)+this._asSentence(l.number)+this._asSentence(l.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=o+" "+this._formatBookInfo(l)}else{g=o+" "+this._asSentence(n)+this._asSentence(l.howpublished)+this._asSentence(l.note)}}}}}var m="";if(l.doi){m="http://dx.doi.org/"+l.doi;g+='[<a href="'+m+'">doi:'+l.doi+"</a>]"}var f=l.url||m;if(f){g+='[<a href="'+f+'">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}});
\ No newline at end of file
+define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,d,c){var b=Backbone.View.extend({tagName:"div",className:"citations",render:function(){this.$el.append("<p>"+this.formattedReference()+"</p>");return this},formattedReference:function(){var k=this.model;var i=k.entryType();var l=k.fields();var g="";var o=this._asSentence((l.author?l.author:"")+(l.year?(" ("+l.year+")"):""))+" ";var n=l.title||"";var h=l.pages?("pp. "+l.pages):"";var p=l.address;if(i=="article"){var j=(l.volume?l.volume:"")+(l.number?(" ("+l.number+")"):"")+(h?", "+h:"");g=o+this._asSentence(n)+(l.journal?("In <em>"+l.journal+", "):"")+this._asSentence(j)+this._asSentence(l.address)+"</em>"}else{if(i=="inproceedings"||i=="proceedings"){g=o+this._asSentence(n)+(l.booktitle?("In <em>"+l.booktitle+", "):"")+(h?h:"")+(p?", "+p:"")+".</em>"}else{if(i=="mastersthesis"||i=="phdthesis"){g=o+this._asSentence(n)+(l.howpublished?l.howpublished+". ":"")+(l.note?l.note+".":"")}else{if(i=="techreport"){g=o+this._asSentence(n)+this._asSentence(l.institution)+this._asSentence(l.number)+this._asSentence(l.type)}else{if(i=="book"||i=="inbook"||i=="incollection"){g=o+" "+this._formatBookInfo(l)}else{g=o+" "+this._asSentence(n)+this._asSentence(l.howpublished)+this._asSentence(l.note)}}}}}var m="";if(l.doi){m="http://dx.doi.org/"+l.doi;g+='[<a href="'+m+'" target="_blank">doi:'+l.doi+"</a>]"}var f=l.url||m;if(f){g+='[<a href="'+f+'" target="_blank">Link</a>]'}return g},_formatBookInfo:function(f){var g="";if(f.chapter){g+=f.chapter+" in "}if(f.title){g+="<em>"+f.title+"</em>"}if(f.editor){g+=", Edited by "+f.editor+", "}if(f.publisher){g+=", "+f.publisher}if(f.pages){g+=", pp. "+f.pages+""}if(f.series){g+=", <em>"+f.series+"</em>"}if(f.volume){g+=", Vol."+f.volume}if(f.issn){g+=", ISBN: "+f.issn}return g+"."},_asSentence:function(f){return(f&&f.trim())?f+". ":""}});var e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(g){var f=new b({model:g});this.$(".citations-formatted").append(f.render().el);var h=this.$(".citations-bibtex-text");h.val(h.val()+"\n\r"+g.attributes.content)},render:function(){this.$el.html(this.citationsElement());this.collection.each(function(f){this.renderCitation(f)},this);this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show();this.$(".citations-to-bibtex").hide();this.$(".citations-bibtex").show();this.$(".citations-formatted").hide();this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide();this.$(".citations-to-bibtex").show();this.$(".citations-bibtex").hide();this.$(".citations-formatted").show()},partialWarningElement:function(){if(this.collection.partial){return['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',"</div>",].join("")}else{return""}},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <i class="fa fa-pencil-square-o citations-to-bibtex" title="Select all as BibTeX."></i>',' <i class="fa fa-times citations-to-formatted" title="Return to formatted citation list."></i>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:b,CitationListView:e}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1
0
13 Nov '14
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: bb6100d9ee75650217f5729e2566c34c8e8f2bf7
https://github.com/galaxyproject/usegalaxy-playbook/commit/bb6100d9ee756502…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2014-11-13 (Thu, 13 Nov 2014)
Changed paths:
M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml
M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml
Log Message:
-----------
Reinstall EMBOSS tools on Main.
1
0
7 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d1864ea200ce/
Changeset: d1864ea200ce
User: jmchilton
Date: 2014-11-13 18:47:38+00:00
Summary: Dynamically load workflow module descriptions in mako editor.
This again falls under the umbrella of making workflow modules more like true plugins. This should allow one to add new modules downstream without needing to modify templates/webapps/galaxy/workflow/editor.mako. One can imagine a new API endpoint for the new load_module_sections method will be useful as the editor UI shifts to a single page app and actual API clients need to determine what workflow modules are available. Such an API endpoint is not included but would be easy to add now.
Affected #: 2 files
diff -r c9b13e2f3f6bb7f35f6ed9a012159c42519fac02 -r d1864ea200ce16992c26a4a642381be71310c4a2 lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -773,6 +773,24 @@
module_factory = WorkflowModuleFactory( module_types )
+def load_module_sections( trans ):
+ """ Get abstract description of the workflow modules this Galaxy instance
+ is configured with.
+ """
+ inputs_section = {
+ "name": "inputs",
+ "title": "Inputs",
+ "modules": [
+ {"name": "data_input", "title": "Input Dataset", "description": "Input dataset"},
+ {"name": "data_collection_input", "title": "Input Dataset Collection", "description": "Input dataset collection"},
+ ],
+ }
+ module_sections = [
+ inputs_section
+ ]
+ return module_sections
+
+
class MissingToolException( Exception ):
""" WorkflowModuleInjector will raise this if the tool corresponding to the
module is missing. """
diff -r c9b13e2f3f6bb7f35f6ed9a012159c42519fac02 -r d1864ea200ce16992c26a4a642381be71310c4a2 templates/webapps/galaxy/workflow/editor.mako
--- a/templates/webapps/galaxy/workflow/editor.mako
+++ b/templates/webapps/galaxy/workflow/editor.mako
@@ -332,19 +332,27 @@
<em><strong>Search did not match any tools.</strong></em></div><div> </div>
+
<div class="toolMenuGroupHeader">Workflow control</div>
- <div class="toolSectionTitle" id="title___workflow__input__">
- <span>Inputs</span>
- </div>
- <div id="__workflow__input__" class="toolSectionBody">
+ <%
+ from galaxy.workflow.modules import load_module_sections
+ %>
+ %for module_section in load_module_sections( trans ):
+ <% section_title = module_section["title"] %>
+ <% section_name = module_section["name"] %>
+ <div class="toolSectionTitle" id="title___workflow__${section_name}__">
+ <span>${section_title}</span>
+ </div>
+ <div id="__workflow__${section_name}__" class="toolSectionBody"><div class="toolSectionBg">
+ %for module in module_section["modules"]:
<div class="toolTitle">
- <a href="#" onclick="add_node_for_module( 'data_input', 'Input Dataset' )">Input dataset</a>
- </div>
- <div class="toolTitle">
- <a href="#" onclick="add_node_for_module( 'data_collection_input', 'Input Dataset Collection' )">Input dataset collection</a>
- </div>
+ <a href="#" onclick="add_node_for_module( '${module['name']}', '${module['title']}' )">${module['description']}</a>
+ </div><!-- end toolTitle -->
+ %endfor
</div>
+ </div>
+ %endfor
</div></div></div>
https://bitbucket.org/galaxy/galaxy-central/commits/f6dcea371b03/
Changeset: f6dcea371b03
User: jmchilton
Date: 2014-11-13 18:47:38+00:00
Summary: Implement workflow scheduling 'plugin' framework.
Models:
Workflow invocations have been augmented with significantly more state - inputs, parameters, runtime step state, are all being tracked now. Workflow invocations have a state that can be changed over time, the UUIDs generated for workflow invocations in Pull Request #465 have to be persisted so they can be reused when scheduling new jobs for theworkflow invocation. Workflow invocation steps now have an action parameter for persisting state provided by users during the execution of the workflow (see forthcoming PauseModule for further details).
Some initial elements of these model changes were based on model changes in Kyle Ellrott's Galaxy farm work (https://bitbucket.org/kellrott/galaxy-farm/branch/workflow_migrate) I made heavy modifications to the model to enforce referential integrity on parameter to workflow step mappings and made some cosmetic changes various other details.
Scheduling Plugins:
Used the pattern setup with dependency resolvers and job metrics to build a dynamic plugin infrastructure for defining workflow schedulers. I hesistate calling anything with only one implementation a plugin infrastructure, but I am confident enough that the combination of persisted workflow request combined with scheduler tag could be used to build a galaxy-farm plugin that would wait for another Galaxy instance to become available and it would pull the workflow down and
This work piggy backs on Galaxy job handlers to have workflow scheduled in the background (i.e. during submission each workflow being scheduled in the background is assigned a unique job handler and only that job handler thread will process the workflow). It should be pretty easy to allow the definition of a new kind of handler - that is a workflow handler instead of a job handler if that is of interest.
I will probably move a bunch of stuff that is happening in workflow/scheduling_manager.py more into the scheduler itself so that it can be more configurable and closer to a true plugin.
API:
There are a number of new API points here for flushing out dealing with workflow invocations (called usages in existing parlance).
- POST /api/workflows/{encoded_workflow_id}/usage
Schedule a worklfow to be run in the background and return just the workflow invocation information.
RESTfully speaking this should be plural but the matching GET endpoint is likewise usage and not usages - so I am favoring consistency over RESTful correctness here. Also, likewise creating a 'usage' feel like odd - I would like to make all of the usage endpoints aliases to a more RESTfully correct invocations endpoints.
The existing workflow run API endpoints still work and still work the way they use usually - but the output now includes all of the workflow invocation to_dict stuff as well as the list of outputs it initially used. Once everything is scheduled this way - that list of outputs is going to have to disappear but hopefully people can start using the invocation stuff now to help the transition.
- DELETE /api/workflows/{workflow_id}/usage/{usage_id}
Cancel a scheduled workflow invocation.
- GET /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
Get information about a workflow invocation step.
- PUT /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
Update a workflow invocation step - for ones with modifiable state. Extension point added to workflow modules to support this but it is unused by all existing worklfow modules. A subsequent PauseModule will use this to either continue or cancel a workflow invocation at a particular step.
Modules:
Workflow modules can now define new methods for dealing with recovering state and interacting with user requests.
Testing:
One can issue a workflow request by running the following test.
./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_request
Affected #: 23 files
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f .hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -67,6 +67,7 @@
shed_data_manager_conf.xml
object_store_conf.xml
job_metrics_conf.xml
+workflow_schedulers_conf.xml
config/*
static/welcome.html.*
static/welcome.html
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f config/workflow_schedulers_conf.xml.sample
--- /dev/null
+++ b/config/workflow_schedulers_conf.xml.sample
@@ -0,0 +1,14 @@
+<?xml version="1.0"?>
+<!-- If workflow_schedulers_conf.xml exists it defines the workflow scheduling
+ plugins to load and how to configure them. Currently only the core workflow
+ scheduling is available.
+-->
+<workflow_schedulers default="core">
+ <!-- Each element in this file corresponds to a workflow scheduling plugin
+ in lib/galaxy/workflow/schedulers. -->
+
+ <!-- Core plugin schedules whole workflow at outset inside Galaxy and doesn't
+ require any external dependencies. -->
+ <core id="core" />
+
+</workflow_schedulers>
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -142,6 +142,11 @@
self.proxy_manager = ProxyManager( self.config )
# Initialize the external service types
self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self )
+
+ from galaxy.workflow import scheduling_manager
+ # Must be initialized after job_config.
+ self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self )
+
self.model.engine.dispose()
self.control_worker = GalaxyQueueWorker(self,
galaxy.queues.control_queue_from_config(self.config),
@@ -150,6 +155,7 @@
self.control_worker.start()
def shutdown( self ):
+ self.workflow_scheduling_manager.shutdown()
self.job_manager.shutdown()
self.object_store.shutdown()
if self.heartbeat:
@@ -171,3 +177,6 @@
self.trace_logger = FluentTraceLogger( 'galaxy', self.config.fluent_host, self.config.fluent_port )
else:
self.trace_logger = None
+
+ def is_job_handler( self ):
+ return (self.config.track_jobs_in_database and self.job_config.is_handler(self.config.server_name)) or not self.config.track_jobs_in_database
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -139,6 +139,7 @@
self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ]
self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root )
+ self.workflow_schedulers_config_file = resolve_path( kwargs.get( 'workflow_schedulers_config_file', 'config/workflow_schedulers_conf.xml' ), self.root )
self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) )
self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) )
self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") )
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/jobs/manager.py
--- a/lib/galaxy/jobs/manager.py
+++ b/lib/galaxy/jobs/manager.py
@@ -18,7 +18,7 @@
"""
def __init__( self, app ):
self.app = app
- if (self.app.config.track_jobs_in_database and self.app.job_config.is_handler(self.app.config.server_name)) or not self.app.config.track_jobs_in_database:
+ if self.app.is_job_handler():
log.debug("Starting job handler")
self.job_handler = handler.JobHandler( app )
self.job_queue = self.job_handler.job_queue
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/managers/workflows.py
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -1,5 +1,6 @@
from galaxy import model
from galaxy import exceptions
+from galaxy.workflow import modules
class WorkflowsManager( object ):
@@ -49,6 +50,46 @@
self.check_security( trans, workflow_invocation, check_ownership=True, check_accessible=False )
return workflow_invocation
+ def cancel_invocation( self, trans, decoded_invocation_id ):
+ workflow_invocation = self.get_invocation( trans, decoded_invocation_id )
+ cancelled = workflow_invocation.cancel()
+
+ if cancelled:
+ trans.sa_session.add( workflow_invocation )
+ trans.sa_session.flush()
+ else:
+ # TODO: More specific exception?
+ raise exceptions.MessageException( "Cannot cancel an inactive workflow invocation." )
+
+ return workflow_invocation
+
+ def get_invocation_step( self, trans, decoded_workflow_invocation_step_id ):
+ try:
+ workflow_invocation_step = trans.sa_session.query(
+ model.WorkflowInvocationStep
+ ).get( decoded_workflow_invocation_step_id )
+ except Exception:
+ raise exceptions.ObjectNotFound()
+ self.check_security( trans, workflow_invocation_step.workflow_invocation, check_ownership=True, check_accessible=False )
+ return workflow_invocation_step
+
+ def update_invocation_step( self, trans, decoded_workflow_invocation_step_id, action ):
+ if action is None:
+ raise exceptions.RequestParameterMissingException( "Updating workflow invocation step requires an action parameter. " )
+
+ workflow_invocation_step = self.get_invocation_step( trans, decoded_workflow_invocation_step_id )
+ workflow_invocation = workflow_invocation_step.workflow_invocation
+ if not workflow_invocation.active:
+ raise exceptions.RequestParameterInvalidException( "Attempting to modify the state of an completed workflow invocation." )
+
+ step = workflow_invocation_step.workflow_step
+ module = modules.module_factory.from_workflow_step( trans, step )
+ performed_action = module.do_invocation_step_action( step, action )
+ workflow_invocation_step.action = performed_action
+ trans.sa_session.add( workflow_invocation_step )
+ trans.sa_session.flush()
+ return workflow_invocation_step
+
def build_invocations_query( self, trans, decoded_stored_workflow_id ):
try:
stored_workflow = trans.sa_session.query(
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -39,6 +39,7 @@
from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField,
PasswordField, SelectField, TextArea, TextField, WorkflowField,
WorkflowMappingField)
+from galaxy.model.orm import and_, or_
from sqlalchemy.orm import object_session
from sqlalchemy.orm import joinedload
from sqlalchemy.sql.expression import func
@@ -3096,8 +3097,74 @@
class WorkflowInvocation( object, Dictifiable ):
- dict_collection_visible_keys = ( 'id', 'update_time', 'workflow_id' )
- dict_element_visible_keys = ( 'id', 'update_time', 'workflow_id' )
+ dict_collection_visible_keys = ( 'id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state' )
+ dict_element_visible_keys = ( 'id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state' )
+ states = Bunch(
+ NEW='new', # Brand new workflow invocation... maybe this should be same as READY
+ READY='ready', # Workflow ready for another iteration of scheduling.
+ SCHEDULED='scheduled', # Workflow has been scheduled.
+ CANCELLED='cancelled',
+ FAILED='failed',
+ )
+
+ @property
+ def active( self ):
+ """ Indicates the workflow invocation is somehow active - and in
+ particular valid actions may be performed on its
+ ``WorkflowInvocationStep``s.
+ """
+ states = WorkflowInvocation.states
+ return self.state in [ states.NEW, states.READY ]
+
+ def cancel( self ):
+ if not self.active:
+ return False
+ else:
+ self.state = WorkflowInvocation.states.CANCELLED
+ return True
+
+ def fail( self ):
+ self.state = WorkflowInvocation.states.FAILED
+
+ def step_states_by_step_id( self ):
+ step_states = {}
+ for step_state in self.step_states:
+ step_id = step_state.workflow_step_id
+ step_states[ step_id ] = step_state
+ return step_states
+
+ def step_invocations_by_step_id( self ):
+ step_invocations = {}
+ for invocation_step in self.steps:
+ step_id = invocation_step.workflow_step_id
+ if step_id not in step_invocations:
+ step_invocations[ step_id ] = []
+ step_invocations[ step_id ].append( invocation_step )
+ return step_invocations
+
+ @staticmethod
+ def poll_active_workflow_ids(
+ sa_session,
+ scheduler=None,
+ handler=None
+ ):
+ and_conditions = [
+ or_(
+ WorkflowInvocation.state == WorkflowInvocation.states.NEW,
+ WorkflowInvocation.state == WorkflowInvocation.states.READY
+ ),
+ ]
+ if scheduler is not None:
+ and_conditions.append( WorkflowInvocation.scheduler == scheduler )
+ if handler is not None:
+ and_conditions.append( WorkflowInvocation.handler == handler )
+
+ query = sa_session.query(
+ WorkflowInvocation
+ ).filter( and_( *and_conditions ) )
+ # Immediately just load all ids into memory so time slicing logic
+ # is relatively intutitive.
+ return map( lambda wi: wi.id, query.all() )
def to_dict( self, view='collection', value_mapper=None ):
rval = super( WorkflowInvocation, self ).to_dict( view=view, value_mapper=value_mapper )
@@ -3123,14 +3190,63 @@
class WorkflowInvocationStep( object, Dictifiable ):
- dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' )
- dict_element_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id' )
+ dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' )
+ dict_element_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' )
def to_dict( self, view='collection', value_mapper=None ):
rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper )
rval['order_index'] = self.workflow_step.order_index
return rval
+
+class WorkflowRequest( object, Dictifiable ):
+ dict_collection_visible_keys = [ 'id', 'name', 'type', 'state', 'history_id', 'workflow_id' ]
+ dict_element_visible_keys = [ 'id', 'name', 'type', 'state', 'history_id', 'workflow_id' ]
+
+ def to_dict( self, view='collection', value_mapper=None ):
+ rval = super( WorkflowRequest, self ).to_dict( view=view, value_mapper=value_mapper )
+ return rval
+
+
+class WorkflowRequestInputParameter(object, Dictifiable):
+ """ Workflow-related parameters not tied to steps or inputs.
+ """
+ dict_collection_visible_keys = ['id', 'name', 'value', 'type']
+ types = Bunch(
+ REPLACEMENT_PARAMETERS='replacements',
+ META_PARAMETERS='meta', #
+ )
+
+ def __init__( self, name=None, value=None, type=None ):
+ self.name = name
+ self.value = value
+ self.type = type
+
+
+class WorkflowRequestStepState(object, Dictifiable):
+ """ Workflow step value parameters.
+ """
+ dict_collection_visible_keys = ['id', 'name', 'value', 'workflow_step_id']
+
+ def __init__( self, workflow_step=None, name=None, value=None ):
+ self.workflow_step = workflow_step
+ self.name = name
+ self.value = value
+ self.type = type
+
+
+class WorkflowRequestToInputDatasetAssociation(object, Dictifiable):
+ """ Workflow step input dataset parameters.
+ """
+ dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name' ]
+
+
+class WorkflowRequestToInputDatasetCollectionAssociation(object, Dictifiable):
+ """ Workflow step input dataset collection parameters.
+ """
+ dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name' ]
+
+
class MetadataFile( object ):
def __init__( self, dataset=None, name=None ):
@@ -4038,6 +4154,18 @@
self.value = None
self.user_value = None
+
+class WorkRequestTagAssociation( ItemTagAssociation ):
+ def __init__( self, id=None, user=None, workflow_request_id=None, tag_id=None, user_tname=None, value=None ):
+ self.id = id
+ self.user = user
+ self.workflow_request_id = workflow_request_id
+ self.tag_id = tag_id
+ self.user_tname = user_tname
+ self.value = None
+ self.user_value = None
+
+
# Item annotation classes.
class HistoryAnnotationAssociation( object ):
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/model/mapping.py
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -710,6 +710,46 @@
## Column( "input_connections", JSONType )
)
+
+model.WorkflowRequestStepState.table = Table(
+ "workflow_request_step_states", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" )),
+ Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id" )),
+ Column( "value", JSONType ),
+)
+
+
+model.WorkflowRequestInputParameter.table = Table(
+ "workflow_request_input_parameters", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" )),
+ Column( "name", Unicode(255) ),
+ Column( "value", TEXT ),
+ Column( "type", Unicode(255) ),
+)
+
+
+model.WorkflowRequestToInputDatasetAssociation.table = Table(
+ "workflow_request_to_input_dataset", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "name", String(255) ),
+ Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
+ Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
+ Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
+)
+
+
+model.WorkflowRequestToInputDatasetCollectionAssociation.table = Table(
+ "workflow_request_to_input_collection_dataset", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "name", String(255) ),
+ Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
+ Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
+ Column( "dataset_collection_id", Integer, ForeignKey( "history_dataset_collection_association.id" ), index=True ),
+)
+
+
model.WorkflowStepConnection.table = Table( "workflow_step_connection", metadata,
Column( "id", Integer, primary_key=True ),
Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
@@ -728,8 +768,13 @@
Column( "id", Integer, primary_key=True ),
Column( "create_time", DateTime, default=now ),
Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False )
- )
+ Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ),
+ Column( "state", TrimmedString( 64 ), index=True ),
+ Column( "scheduler", TrimmedString( 255 ), index=True ),
+ Column( "handler", TrimmedString( 255 ), index=True ),
+ Column( 'uuid', UUIDType() ),
+ Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
+)
model.WorkflowInvocationStep.table = Table( "workflow_invocation_step", metadata,
Column( "id", Integer, primary_key=True ),
@@ -737,8 +782,9 @@
Column( "update_time", DateTime, default=now, onupdate=now ),
Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ),
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True )
- )
+ Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True ),
+ Column( "action", JSONType, nullable=True ),
+)
model.StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata,
Column( "id", Integer, primary_key=True ),
@@ -1968,6 +2014,11 @@
mapper( model.WorkflowInvocation, model.WorkflowInvocation.table,
properties=dict(
+ history=relation( model.History ),
+ input_parameters=relation( model.WorkflowRequestInputParameter ),
+ step_states=relation( model.WorkflowRequestStepState ),
+ input_datasets=relation( model.WorkflowRequestToInputDatasetAssociation ),
+ input_dataset_collections=relation( model.WorkflowRequestToInputDatasetCollectionAssociation ),
steps=relation( model.WorkflowInvocationStep, backref='workflow_invocation', lazy=False ),
workflow=relation( model.Workflow ) ) )
@@ -1976,6 +2027,33 @@
workflow_step = relation( model.WorkflowStep ),
job = relation( model.Job, backref=backref( 'workflow_invocation_step', uselist=False ) ) ) )
+simple_mapping(
+ model.WorkflowRequestInputParameter,
+ workflow_invocation=relation( model.WorkflowInvocation ),
+)
+
+simple_mapping(
+ model.WorkflowRequestStepState,
+ workflow_invocation=relation( model.WorkflowInvocation ),
+ workflow_step=relation( model.WorkflowStep ),
+)
+
+simple_mapping(
+ model.WorkflowRequestToInputDatasetAssociation,
+ workflow_invocation=relation( model.WorkflowInvocation ),
+ workflow_step=relation( model.WorkflowStep ),
+ dataset=relation( model.HistoryDatasetAssociation ),
+)
+
+
+simple_mapping(
+ model.WorkflowRequestToInputDatasetCollectionAssociation,
+ workflow_invocation=relation( model.WorkflowInvocation ),
+ workflow_step=relation( model.WorkflowStep ),
+ dataset_collection=relation( model.HistoryDatasetCollectionAssociation ),
+)
+
+
mapper( model.MetadataFile, model.MetadataFile.table,
properties=dict( history_dataset=relation( model.HistoryDatasetAssociation ), library_dataset=relation( model.LibraryDatasetDatasetAssociation ) ) )
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
--- /dev/null
+++ b/lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
@@ -0,0 +1,144 @@
+"""
+Migration script for workflow request tables.
+"""
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+from galaxy.model.custom_types import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData()
+
+
+WorkflowRequestInputParameter_table = Table(
+ "workflow_request_input_parameters", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" )),
+ Column( "name", Unicode(255) ),
+ Column( "type", Unicode(255) ),
+ Column( "value", TEXT ),
+)
+
+
+WorkflowRequestStepState_table = Table(
+ "workflow_request_step_states", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE" )),
+ Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id" )),
+ Column( "value", JSONType ),
+)
+
+
+WorkflowRequestToInputDatasetAssociation_table = Table(
+ "workflow_request_to_input_dataset", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "name", String(255) ),
+ Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
+ Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
+ Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
+)
+
+
+WorkflowRequestToInputDatasetCollectionAssociation_table = Table(
+ "workflow_request_to_input_collection_dataset", metadata,
+ Column( "id", Integer, primary_key=True ),
+ Column( "name", String(255) ),
+ Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True ),
+ Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id") ),
+ Column( "dataset_collection_id", Integer, ForeignKey( "history_dataset_collection_association.id" ), index=True ),
+)
+
+
+TABLES = [
+ WorkflowRequestInputParameter_table,
+ WorkflowRequestStepState_table,
+ WorkflowRequestToInputDatasetAssociation_table,
+ WorkflowRequestToInputDatasetCollectionAssociation_table,
+]
+
+
+def upgrade(migrate_engine):
+ metadata.bind = migrate_engine
+ print __doc__
+ metadata.reflect()
+
+ for table in TABLES:
+ __create(table)
+
+ History_column = Column( "history_id", Integer, ForeignKey( "history.id" ), nullable=True )
+ State_column = Column( "state", TrimmedString( 64 ) )
+
+ # TODO: Handle indexes correctly
+ SchedulerId_column = Column( "scheduler", TrimmedString(255) )
+ HandlerId_column = Column( "handler", TrimmedString(255) )
+ WorkflowUUID_column = Column( "uuid", UUIDType, nullable=True )
+ __add_column( History_column, "workflow_invocation", metadata )
+ __add_column( State_column, "workflow_invocation", metadata )
+ __add_column( SchedulerId_column, "workflow_invocation", metadata, index_nane="id_workflow_invocation_scheduler" )
+ __add_column( HandlerId_column, "workflow_invocation", metadata, index_name="id_workflow_invocation_handler" )
+ __add_column( WorkflowUUID_column, "workflow_invocation", metadata )
+
+ # All previous invocations have been scheduled...
+ cmd = "UPDATE workflow_invocation SET state = 'scheduled'"
+ try:
+ migrate_engine.execute( cmd )
+ except Exception, e:
+ log.debug( "failed to update past workflow invocation states: %s" % ( str( e ) ) )
+
+ WorkflowInvocationStepAction_column = Column( "action", JSONType, nullable=True )
+ __add_column( WorkflowInvocationStepAction_column, "workflow_invocation_step", metadata )
+
+
+def downgrade(migrate_engine):
+ metadata.bind = migrate_engine
+ metadata.reflect()
+
+ for table in TABLES:
+ __drop(table)
+
+ __drop_column( "state", "workflow_invocation", metadata )
+ __drop_column( "scheduler_id", "workflow_invocation", metadata )
+ __drop_column( "uuid", "workflow_invocation", metadata )
+ __drop_column( "history_id", "workflow_invocation", metadata )
+ __drop_column( "handler_id", "workflow_invocation", metadata )
+ __drop_column( "action", "workflow_invocation_step", metadata )
+
+
+def __add_column(column, table_name, metadata, **kwds):
+ try:
+ table = Table( table_name, metadata, autoload=True )
+ column.create( table, **kwds )
+ except Exception as e:
+ print str(e)
+ log.exception( "Adding column %s column failed." % column)
+
+
+def __drop_column( column_name, table_name, metadata ):
+ try:
+ table = Table( table_name, metadata, autoload=True )
+ getattr( table.c, column_name ).drop()
+ except Exception as e:
+ print str(e)
+ log.exception( "Dropping column %s failed." % column_name )
+
+
+def __create(table):
+ try:
+ table.create()
+ except Exception as e:
+ print str(e)
+ log.exception("Creating %s table failed: %s" % (table.name, str( e ) ) )
+
+
+def __drop(table):
+ try:
+ table.drop()
+ except Exception as e:
+ print str(e)
+ log.exception("Dropping %s table failed: %s" % (table.name, str( e ) ) )
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -16,7 +16,7 @@
from galaxy.web.base.controller import UsesHistoryMixin
from galaxy.web.base.controller import SharableMixin
from galaxy.workflow.extract import extract_workflow
-from galaxy.workflow.run import invoke
+from galaxy.workflow.run import invoke, queue_invoke
from galaxy.workflow.run_request import build_workflow_run_config
log = logging.getLogger(__name__)
@@ -224,7 +224,7 @@
# invoke may throw MessageExceptions on tool erors, failure
# to match up inputs, etc...
- outputs = invoke(
+ outputs, invocation = invoke(
trans=trans,
workflow=workflow,
workflow_run_config=run_config,
@@ -235,14 +235,19 @@
# Build legacy output - should probably include more information from
# outputs.
rval = {}
- rval['history'] = trans.security.encode_id(history.id)
+ rval['history'] = trans.security.encode_id( history.id )
rval['outputs'] = []
for step in workflow.steps:
if step.type == 'tool' or step.type is None:
for v in outputs[ step.id ].itervalues():
rval[ 'outputs' ].append( trans.security.encode_id( v.id ) )
- return rval
+ # Newer version of this API just returns the invocation as a dict, to
+ # facilitate migration - produce the newer style response and blend in
+ # the older information.
+ invocation_response = self.__encode_invocation( trans, invocation )
+ invocation_response.update( rval )
+ return invocation_response
@expose_api
def workflow_dict( self, trans, workflow_id, **kwd ):
@@ -370,6 +375,32 @@
return item
@expose_api
+ def workflow_request( self, trans, workflow_id, payload, **kwd ):
+ """
+ POST /api/workflows/{encoded_workflow_id}/usage
+
+ Schedule the workflow specified by `workflow_id` to run.
+ """
+ # /usage is awkward in this context but is consistent with the rest of
+ # this module. Would prefer to redo it all to use /invocation(s).
+ # Get workflow + accessibility check.
+ stored_workflow = self.__get_stored_accessible_workflow( trans, workflow_id )
+ workflow = stored_workflow.latest_workflow
+
+ run_config = build_workflow_run_config( trans, workflow, payload )
+ workflow_scheduler_id = payload.get( "scheduler", None )
+ # TODO: workflow scheduler hints
+ work_request_params = dict( scheduler=workflow_scheduler_id )
+
+ workflow_invocation = queue_invoke(
+ trans=trans,
+ workflow=workflow,
+ workflow_run_config=run_config,
+ request_params=work_request_params
+ )
+ return self.encode_all_ids( trans, workflow_invocation.to_dict(), recursive=True )
+
+ @expose_api
def workflow_usage(self, trans, workflow_id, **kwd):
"""
GET /api/workflows/{workflow_id}/usage
@@ -407,6 +438,87 @@
return self.__encode_invocation( trans, workflow_invocation )
return None
+ @expose_api
+ def cancel_workflow_invocation(self, trans, workflow_id, usage_id, **kwd):
+ """
+ DELETE /api/workflows/{workflow_id}/usage/{usage_id}
+ Cancel the specified workflow invocation.
+
+ :param workflow_id: the workflow id (required)
+ :type workflow_id: str
+
+ :param usage_id: the usage id (required)
+ :type usage_id: str
+
+ :raises: exceptions.MessageException, exceptions.ObjectNotFound
+ """
+ decoded_workflow_invocation_id = self.__decode_id( trans, usage_id )
+ workflow_invocation = self.workflow_manager.cancel_invocation( trans, decoded_workflow_invocation_id )
+ return self.__encode_invocation( trans, workflow_invocation )
+
+ @expose_api
+ def workflow_invocation_step(self, trans, workflow_id, usage_id, step_id, **kwd):
+ """
+ GET /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
+
+ :param workflow_id: the workflow id (required)
+ :type workflow_id: str
+
+ :param usage_id: the usage id (required)
+ :type usage_id: str
+
+ :param step_id: encoded id of the WorkflowInvocationStep (required)
+ :type step_id: str
+
+ :param payload: payload containing update action information
+ for running workflow.
+
+ :raises: exceptions.MessageException, exceptions.ObjectNotFound
+ """
+ decoded_invocation_step_id = self.__decode_id( trans, step_id )
+ invocation_step = self.workflow_manager.get_invocation_step(
+ trans,
+ decoded_invocation_step_id
+ )
+ return self.__encode_invocation_step( trans, invocation_step )
+
+ @expose_api
+ def workflow_invocation_step_update(self, trans, workflow_id, usage_id, step_id, payload, **kwd):
+ """
+ PUT /api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}
+ Update state of running workflow step invocation - still very nebulous
+ but this would be for stuff like confirming paused steps can proceed
+ etc....
+
+
+ :param workflow_id: the workflow id (required)
+ :type workflow_id: str
+
+ :param usage_id: the usage id (required)
+ :type usage_id: str
+
+ :param step_id: encoded id of the WorkflowInvocationStep (required)
+ :type step_id: str
+
+ :raises: exceptions.MessageException, exceptions.ObjectNotFound
+ """
+ decoded_invocation_step_id = self.__decode_id( trans, step_id )
+ action = payload.get( "action", None )
+
+ invocation_step = self.workflow_manager.update_invocation_step(
+ trans,
+ decoded_invocation_step_id,
+ action=action,
+ )
+ return self.__encode_invocation_step( trans, invocation_step )
+
+ def __encode_invocation_step( self, trans, invocation_step ):
+ return self.encode_all_ids(
+ trans,
+ invocation_step.to_dict( 'element' ),
+ True
+ )
+
def __get_stored_accessible_workflow( self, trans, workflow_id ):
stored_workflow = self.__get_stored_workflow( trans, workflow_id )
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -227,7 +227,12 @@
webapp.mapper.connect( 'import_shared_workflow_deprecated', '/api/workflows/import', controller='workflows', action='import_shared_workflow_deprecated', conditions=dict( method=['POST'] ) )
webapp.mapper.connect( 'workflow_usage', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_usage', conditions=dict(method=['GET']))
webapp.mapper.connect( 'workflow_usage_contents', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='workflow_usage_contents', conditions=dict(method=['GET']))
+ webapp.mapper.connect( 'cancel_workflow_invocation', '/api/workflows/{workflow_id}/usage/{usage_id}', controller='workflows', action='cancel_workflow_invocation', conditions=dict(method=['DELETE']))
+ webapp.mapper.connect( 'workflow_invocation_step', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step', conditions=dict(method=['GET']))
+ webapp.mapper.connect( 'workflow_invocation_step_update', '/api/workflows/{workflow_id}/usage/{usage_id}/steps/{step_id}', controller='workflows', action='workflow_invocation_step_update', conditions=dict(method=['PUT']))
+
+ webapp.mapper.connect( 'workflow_request', '/api/workflows/{workflow_id}/usage', controller='workflows', action='workflow_request', conditions=dict( method=['POST'] ) )
# ============================
# ===== AUTHENTICATE API =====
# ============================
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1295,7 +1295,7 @@
copy_inputs_to_history=new_history is not None
)
- outputs = invoke(
+ outputs, invocation = invoke(
trans=trans,
workflow=workflow,
workflow_run_config=run_config
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/work/context.py
--- /dev/null
+++ b/lib/galaxy/work/context.py
@@ -0,0 +1,46 @@
+from galaxy.managers.context import (
+ ProvidesAppContext,
+ ProvidesUserContext,
+ ProvidesHistoryContext
+)
+
+
+class WorkRequestContext( ProvidesAppContext, ProvidesUserContext, ProvidesHistoryContext ):
+ """ Stripped down implementation of Galaxy web transaction god object for
+ work request handling outside of web threads - uses mix-ins shared with
+ GalaxyWebTransaction to provide app, user, and history context convience
+ methods - but nothing related to HTTP handling, mako views, etc....
+
+ Things that only need app shouldn't be consuming trans - but there is a
+ need for actions potentially tied to users and histories and hopefully
+ this can define that stripped down interface providing access to user and
+ history information - but not dealing with web request and response
+ objects.
+ """
+
+ def __init__( self, app, user=None, history=None ):
+ self.app = app
+ self.security = app.security
+ self.__user = user
+ self.__history = history
+ self.api_inherit_admin = False
+
+ def get_history( self, create=False ):
+ if create:
+ raise NotImplementedError( "Cannot create histories from a work request context." )
+ return self.__history
+
+ def set_history( self ):
+ raise NotImplementedError( "Cannot change histories from a work request context." )
+
+ history = property( get_history, set_history )
+
+ def get_user( self ):
+ """Return the current user if logged in or None."""
+ return self.__user
+
+ def set_user( self, user ):
+ """Set the current user."""
+ raise NotImplementedError( "Cannot change users from a work request context." )
+
+ user = property( get_user, set_user )
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -171,6 +171,21 @@
"""
raise TypeError( "Abstract method" )
+ def do_invocation_step_action( self, step, action ):
+ """ Update or set the workflow invocation state action - generic
+ extension point meant to allows users to interact with interactive
+ workflow modules. The action object returned from this method will
+ be attached to the WorkflowInvocationStep and be available the next
+ time the workflow scheduler visits the workflow.
+ """
+ raise exceptions.RequestParameterInvalidException( "Attempting to perform invocation step action on module that does not support actions." )
+
+ def recover_mapping( self, step, step_invocations, progress ):
+ """ Re-populate progress object with information about connections
+ from previously executed steps recorded via step_invocations.
+ """
+ raise TypeError( "Abstract method" )
+
class InputModule( WorkflowModule ):
@@ -240,6 +255,19 @@
state.inputs = dict( input=None )
return state
+ def recover_runtime_state( self, runtime_state ):
+ """ Take secure runtime state from persisted invocation and convert it
+ into a DefaultToolState object for use during workflow invocation.
+ """
+ fake_tool = Bunch( inputs=self.get_runtime_inputs() )
+ state = galaxy.tools.DefaultToolState()
+ state.decode( runtime_state, fake_tool, self.trans.app, secure=False )
+ return state
+
+ def normalize_runtime_state( self, runtime_state ):
+ fake_tool = Bunch( inputs=self.get_runtime_inputs() )
+ return runtime_state.encode( fake_tool, self.trans.app, secure=False )
+
def encode_runtime_state( self, trans, state ):
fake_tool = Bunch( inputs=self.get_runtime_inputs() )
return state.encode( fake_tool, trans.app )
@@ -291,6 +319,9 @@
progress.set_outputs_for_input( step, step_outputs )
return job
+ def recover_mapping( self, step, step_invocations, progress ):
+ progress.set_outputs_for_input( step )
+
class InputDataModule( InputModule ):
type = "data_input"
@@ -439,6 +470,18 @@
)
self.state.inputs = self.tool.params_from_strings( state, app, **params_from_kwds )
+ def recover_runtime_state( self, runtime_state ):
+ """ Take secure runtime state from persisted invocation and convert it
+ into a DefaultToolState object for use during workflow invocation.
+ """
+ state = galaxy.tools.DefaultToolState()
+ app = self.trans.app
+ state.decode( runtime_state, self.tool, app, secure=False )
+ return state
+
+ def normalize_runtime_state( self, runtime_state ):
+ return runtime_state.encode( self.tool, self.trans.app, secure=False )
+
@classmethod
def __get_tool_version( cls, trans, tool_id ):
# Return a ToolVersion if one exists for tool_id.
@@ -664,7 +707,7 @@
param_combinations=param_combinations,
history=invocation.history,
collection_info=collection_info,
- workflow_invocation_uuid=invocation.uuid
+ workflow_invocation_uuid=invocation.uuid.hex
)
if collection_info:
step_outputs = dict( execution_tracker.created_collections )
@@ -731,6 +774,23 @@
visit_input_values( self.tool.inputs, self.state.inputs, callback )
+ def recover_mapping( self, step, step_invocations, progress ):
+ # Grab a job representing this invocation - for normal workflows
+ # there will be just one job but if this step was mapped over there
+ # may be many.
+ job_0 = step_invocations[ 0 ].job
+
+ outputs = {}
+ for job_output in job_0.output_datasets:
+ replacement_name = job_output.name
+ replacement_value = job_output.dataset
+ # If was a mapping step, grab the output mapped collection for
+ # replacement instead.
+ if replacement_value.hidden_beneath_collection_instance:
+ replacement_value = replacement_value.hidden_beneath_collection_instance
+ outputs[ replacement_name ] = replacement_value
+ progress.set_step_outputs( step, outputs )
+
class WorkflowModuleFactory( object ):
@@ -796,6 +856,14 @@
module is missing. """
+class DelayedWorkflowEvaluation(Exception):
+ pass
+
+
+class CancelWorkflowEvaluation(Exception):
+ pass
+
+
class WorkflowModuleInjector(object):
""" Injects workflow step objects from the ORM with appropriate module and
module generated/influenced state. """
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/workflow/run.py
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -6,54 +6,110 @@
from galaxy.util.odict import odict
from galaxy.workflow import modules
from galaxy.workflow.run_request import WorkflowRunConfig
+from galaxy.workflow.run_request import workflow_run_config_to_request
import logging
log = logging.getLogger( __name__ )
-def invoke( trans, workflow, workflow_run_config, populate_state=False ):
+def invoke( trans, workflow, workflow_run_config, workflow_invocation=None, populate_state=False ):
""" Run the supplied workflow in the supplied target_history.
"""
if populate_state:
modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map )
- return WorkflowInvoker(
+ invoker = WorkflowInvoker(
trans,
workflow,
workflow_run_config,
- ).invoke()
+ workflow_invocation=workflow_invocation,
+ )
+ try:
+ outputs = invoker.invoke()
+ except modules.CancelWorkflowEvaluation:
+ if workflow_invocation:
+ if workflow_invocation.cancel():
+ trans.sa_session.add( workflow_invocation )
+ outputs = []
+ except Exception:
+ log.exception("Failed to execute scheduled workflow.")
+ if workflow_invocation:
+ # Running workflow invocation in background, just mark
+ # persistent workflow invocation as failed.
+ workflow_invocation.fail()
+ trans.sa_session.add( workflow_invocation )
+ else:
+ # Running new transient workflow invocation in legacy
+ # controller action - propage the exception up.
+ raise
+ outputs = []
+
+ if workflow_invocation:
+ # Be sure to update state of workflow_invocation.
+ trans.sa_session.flush()
+
+ return outputs, invoker.workflow_invocation
+
+
+def queue_invoke( trans, workflow, workflow_run_config, request_params ):
+ modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map )
+ workflow_invocation = workflow_run_config_to_request( trans, workflow_run_config, workflow )
+ workflow_invocation.workflow = workflow
+ return trans.app.workflow_scheduling_manager.queue(
+ workflow_invocation,
+ request_params
+ )
class WorkflowInvoker( object ):
- def __init__( self, trans, workflow, workflow_run_config ):
+ def __init__( self, trans, workflow, workflow_run_config, workflow_invocation=None ):
self.trans = trans
self.workflow = workflow
- workflow_invocation = model.WorkflowInvocation()
- workflow_invocation.workflow = self.workflow
- self.workflow_invocation = workflow_invocation
- self.progress = WorkflowProgress( self.workflow_invocation, workflow_run_config.inputs )
+ if workflow_invocation is None:
+ invocation_uuid = uuid.uuid1()
- invocation_uuid = uuid.uuid1().hex
+ workflow_invocation = model.WorkflowInvocation()
+ workflow_invocation.workflow = self.workflow
- # In one way or another, following attributes will become persistent
- # so they are available during delayed/revisited workflow scheduling.
- self.workflow_invocation.uuid = invocation_uuid
- self.workflow_invocation.history = workflow_run_config.target_history
+ # In one way or another, following attributes will become persistent
+ # so they are available during delayed/revisited workflow scheduling.
+ workflow_invocation.uuid = invocation_uuid
+ workflow_invocation.history = workflow_run_config.target_history
+
+ self.workflow_invocation = workflow_invocation
+ else:
+ self.workflow_invocation = workflow_invocation
+
self.workflow_invocation.copy_inputs_to_history = workflow_run_config.copy_inputs_to_history
self.workflow_invocation.replacement_dict = workflow_run_config.replacement_dict
+ module_injector = modules.WorkflowModuleInjector( trans )
+ self.progress = WorkflowProgress( self.workflow_invocation, workflow_run_config.inputs, module_injector )
+
def invoke( self ):
workflow_invocation = self.workflow_invocation
remaining_steps = self.progress.remaining_steps()
+ delayed_steps = False
for step in remaining_steps:
- jobs = self._invoke_step( step )
- for job in util.listify( jobs ):
- # Record invocation
- workflow_invocation_step = model.WorkflowInvocationStep()
- workflow_invocation_step.workflow_invocation = workflow_invocation
- workflow_invocation_step.workflow_step = step
- workflow_invocation_step.job = job
+ jobs = None
+ try:
+ jobs = self._invoke_step( step )
+ for job in (util.listify( jobs ) or [None]):
+ # Record invocation
+ workflow_invocation_step = model.WorkflowInvocationStep()
+ workflow_invocation_step.workflow_invocation = workflow_invocation
+ workflow_invocation_step.workflow_step = step
+ workflow_invocation_step.job = job
+ except modules.DelayedWorkflowEvaluation:
+ delayed_steps = True
+ self.progress.mark_step_outputs_delayed( step )
+
+ if delayed_steps:
+ state = model.WorkflowInvocation.states.READY
+ else:
+ state = model.WorkflowInvocation.states.SCHEDULED
+ workflow_invocation.state = state
# All jobs ran successfully, so we can save now
self.trans.sa_session.add( workflow_invocation )
@@ -66,18 +122,35 @@
jobs = step.module.execute( self.trans, self.progress, self.workflow_invocation, step )
return jobs
+STEP_OUTPUT_DELAYED = object()
+
class WorkflowProgress( object ):
- def __init__( self, workflow_invocation, inputs_by_step_id ):
+ def __init__( self, workflow_invocation, inputs_by_step_id, module_injector ):
self.outputs = odict()
+ self.module_injector = module_injector
self.workflow_invocation = workflow_invocation
self.inputs_by_step_id = inputs_by_step_id
def remaining_steps(self):
+ # Previously computed and persisted step states.
+ step_states = self.workflow_invocation.step_states_by_step_id()
steps = self.workflow_invocation.workflow.steps
+ remaining_steps = []
+ step_invocations_by_id = self.workflow_invocation.step_invocations_by_step_id()
+ for step in steps:
+ if not hasattr( step, 'module' ):
+ self.module_injector.inject( step )
+ runtime_state = step_states[ step.id ].value
+ step.state = step.module.recover_runtime_state( runtime_state )
- return steps
+ invocation_steps = step_invocations_by_id.get( step.id, None )
+ if invocation_steps:
+ self._recover_mapping( step, invocation_steps )
+ else:
+ remaining_steps.append( step )
+ return remaining_steps
def replacement_for_tool_input( self, step, input, prefixed_name ):
""" For given workflow 'step' that has had input_connections_by_name
@@ -100,6 +173,8 @@
def replacement_for_connection( self, connection ):
step_outputs = self.outputs[ connection.output_step.id ]
+ if step_outputs is STEP_OUTPUT_DELAYED:
+ raise modules.DelayedWorkflowEvaluation()
return step_outputs[ connection.output_name ]
def set_outputs_for_input( self, step, outputs={} ):
@@ -111,5 +186,13 @@
def set_step_outputs(self, step, outputs):
self.outputs[ step.id ] = outputs
+ def mark_step_outputs_delayed(self, step):
+ self.outputs[ step.id ] = STEP_OUTPUT_DELAYED
+
+ def _recover_mapping( self, step, step_invocations ):
+ try:
+ step.module.recover_mapping( step, step_invocations, self )
+ except modules.DelayedWorkflowEvaluation:
+ self.mark_step_outputs_delayed( step )
__all__ = [ invoke, WorkflowRunConfig ]
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/workflow/run_request.py
--- a/lib/galaxy/workflow/run_request.py
+++ b/lib/galaxy/workflow/run_request.py
@@ -1,9 +1,15 @@
+import uuid
+
from galaxy import exceptions
+from galaxy import model
from galaxy.managers import histories
INPUT_STEP_TYPES = [ 'data_input', 'data_collection_input' ]
+import logging
+log = logging.getLogger( __name__ )
+
class WorkflowRunConfig( object ):
""" Wrapper around all the ways a workflow execution can be parameterized.
@@ -231,6 +237,96 @@
return run_config
+def workflow_run_config_to_request( trans, run_config, workflow ):
+ param_types = model.WorkflowRequestInputParameter.types
+
+ workflow_invocation = model.WorkflowInvocation()
+ workflow_invocation.uuid = uuid.uuid1()
+ workflow_invocation.history = run_config.target_history
+
+ def add_parameter( name, value, type ):
+ parameter = model.WorkflowRequestInputParameter(
+ name=name,
+ value=value,
+ type=type,
+ )
+ workflow_invocation.input_parameters.append( parameter )
+
+ replacement_dict = run_config.replacement_dict
+ for name, value in replacement_dict.iteritems():
+ add_parameter(
+ name=name,
+ value=value,
+ type=param_types.REPLACEMENT_PARAMETERS,
+ )
+
+ for step_id, content in run_config.inputs.iteritems():
+ if content.history_content_type == "dataset":
+ request_to_content = model.WorkflowRequestToInputDatasetAssociation()
+ request_to_content.dataset = content
+ request_to_content.workflow_step_id = step_id
+ workflow_invocation.input_datasets.append( request_to_content )
+ else:
+ request_to_content = model.WorkflowRequestToInputDatasetCollectionAssociation()
+ request_to_content.dataset_collection = content
+ request_to_content.workflow_step_id = step_id
+ workflow_invocation.input_dataset_collections.append( request_to_content )
+
+ for step in workflow.steps:
+ state = step.state
+ serializable_runtime_state = step.module.normalize_runtime_state( state )
+ step_state = model.WorkflowRequestStepState()
+ step_state.workflow_step_id = step.id
+ step_state.value = serializable_runtime_state
+ workflow_invocation.step_states.append( step_state )
+
+ add_parameter( "copy_inputs_to_history", "true" if run_config.copy_inputs_to_history else "false", param_types.META_PARAMETERS )
+ return workflow_invocation
+
+
+def workflow_request_to_run_config( work_request_context, workflow_invocation ):
+ param_types = model.WorkflowRequestInputParameter.types
+
+ history = workflow_invocation.history
+ replacement_dict = {}
+ inputs = {}
+ param_map = {}
+ copy_inputs_to_history = None
+
+ for parameter in workflow_invocation.input_parameters:
+ parameter_type = parameter.type
+
+ if parameter_type == param_types.REPLACEMENT_PARAMETERS:
+ replacement_dict[ parameter.name ] = parameter.value
+ elif parameter_type == param_types.META_PARAMETERS:
+ if parameter.name == "copy_inputs_to_history":
+ copy_inputs_to_history = (parameter.value == "true")
+
+ #for parameter in workflow_invocation.step_parameters:
+ # step_id = parameter.workflow_step_id
+ # if step_id not in param_map:
+ # param_map[ step_id ] = {}
+ # param_map[ step_id ][ parameter.name ] = parameter.value
+
+ for input_association in workflow_invocation.input_datasets:
+ inputs[ input_association.workflow_step_id ] = input_association.dataset
+
+ for input_association in workflow_invocation.input_dataset_collections:
+ inputs[ input_association.workflow_step_id ] = input_association.dataset_collection
+
+ if copy_inputs_to_history is None:
+ raise exceptions.InconsistentDatabase("Failed to find copy_inputs_to_history parameter loading workflow_invocation from database.")
+
+ workflow_run_config = WorkflowRunConfig(
+ target_history=history,
+ replacement_dict=replacement_dict,
+ inputs=inputs,
+ param_map=param_map,
+ copy_inputs_to_history=copy_inputs_to_history,
+ )
+ return workflow_run_config
+
+
def __decode_id( trans, workflow_id, model_type="workflow" ):
try:
return trans.security.decode_id( workflow_id )
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/workflow/schedulers/__init__.py
--- /dev/null
+++ b/lib/galaxy/workflow/schedulers/__init__.py
@@ -0,0 +1,41 @@
+""" Module containing Galaxy workflow scheduling plugins. Galaxy's interface
+for workflow scheduling is highly experimental and the interface required for
+scheduling plugins will almost certainly change.
+"""
+from abc import ABCMeta
+from abc import abstractmethod
+
+
+class WorkflowSchedulingPlugin( object ):
+ """ A plugin defining how Galaxy should schedule plugins. By default
+ plugins are passive and should monitor Galaxy's work queue for
+ WorkflowRequests. Inherit from ActiveWorkflowSchedulingPlugin instead if
+ the scheduling plugin should be forced (i.e. if scheduling happen all at
+ once or the request will be stored and monitored outside of Galaxy.)
+ """
+ __metaclass__ = ABCMeta
+
+ @property
+ @abstractmethod
+ def plugin_type( self ):
+ """ Short string providing labelling this plugin """
+
+ def startup( self, app ):
+ """ Called when Galaxy starts up if the plugin is enabled.
+ """
+
+ def shutdown( self ):
+ """ Called when Galaxy is shutting down, workflow scheduling should
+ end.
+ """
+
+
+class ActiveWorkflowSchedulingPlugin( WorkflowSchedulingPlugin ):
+ __metaclass__ = ABCMeta
+
+ @abstractmethod
+ def schedule( self, workflow_invocation ):
+ """ Optionally return one or more commands to instrument job. These
+ commands will be executed on the compute server prior to the job
+ running.
+ """
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/workflow/schedulers/core.py
--- /dev/null
+++ b/lib/galaxy/workflow/schedulers/core.py
@@ -0,0 +1,46 @@
+""" The class defines the stock Galaxy workflow scheduling plugin - currently
+it simply schedules the whole workflow up front when offered.
+"""
+from ..schedulers import ActiveWorkflowSchedulingPlugin
+
+from galaxy.work import context
+
+from galaxy.workflow import run
+from galaxy.workflow import run_request
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+class CoreWorkflowSchedulingPlugin( ActiveWorkflowSchedulingPlugin ):
+ plugin_type = "core"
+
+ def __init__( self, **kwds ):
+ pass
+
+ def startup( self, app ):
+ self.app = app
+
+ def shutdown( self ):
+ pass
+
+ def schedule( self, workflow_invocation ):
+ workflow = workflow_invocation.workflow
+ history = workflow_invocation.history
+ request_context = context.WorkRequestContext(
+ app=self.app,
+ history=history,
+ user=history.user
+ ) # trans-like object not tied to a web-thread.
+ workflow_run_config = run_request.workflow_request_to_run_config(
+ request_context,
+ workflow_invocation
+ )
+ run.invoke(
+ trans=request_context,
+ workflow=workflow,
+ workflow_run_config=workflow_run_config,
+ workflow_invocation=workflow_invocation,
+ )
+
+__all__ = [ CoreWorkflowSchedulingPlugin ]
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f lib/galaxy/workflow/scheduling_manager.py
--- /dev/null
+++ b/lib/galaxy/workflow/scheduling_manager.py
@@ -0,0 +1,197 @@
+import os
+import time
+import logging
+import threading
+
+from xml.etree import ElementTree
+
+from galaxy import model
+from galaxy.util import plugin_config
+
+import galaxy.workflow.schedulers
+
+log = logging.getLogger( __name__ )
+
+DEFAULT_SCHEDULER_ID = "default" # well actually this should be called DEFAULT_DEFAULT_SCHEDULER_ID...
+DEFAULT_SCHEDULER_PLUGIN_TYPE = "core"
+
+EXCEPTION_MESSAGE_SHUTDOWN = "Exception raised while attempting to shutdown workflow scheduler."
+EXCEPTION_MESSAGE_NO_SCHEDULERS = "Failed to defined workflow schedulers - no workflow schedulers defined."
+EXCEPTION_MESSAGE_NO_DEFAULT_SCHEDULER = "Failed to defined workflow schedulers - no workflow scheduler found for default id '%s'."
+EXCEPTION_MESSAGE_DUPLICATE_SCHEDULERS = "Failed to defined workflow schedulers - workflow scheduling plugin id '%s' duplicated."
+
+
+class WorkflowSchedulingManager( object ):
+ """ A workflow scheduling manager based loosely on pattern established by
+ ``galaxy.manager.JobManager``. Only schedules workflows on handler
+ processes.
+ """
+
+ def __init__( self, app ):
+ self.app = app
+ self.__job_config = app.job_config
+ self.workflow_schedulers = {}
+ self.active_workflow_schedulers = {} # Passive workflow schedulers
+ # won't need to be monitored I
+ # guess.
+ self.request_monitor = None
+
+ self.__plugin_classes = self.__plugins_dict()
+ self.__init_schedulers()
+
+ if self._is_workflow_handler():
+ log.debug("Starting workflow schedulers")
+ self.__start_schedulers()
+ if self.active_workflow_schedulers:
+ self.__start_request_monitor()
+ else:
+ # Process should not schedule workflows - do nothing.
+ pass
+
+ # Provide a handler config-like interface by delegating to job handler
+ # config. Perhaps it makes sense to let there be explicit workflow
+ # handlers?
+ def _is_workflow_handler( self ):
+ return self.app.is_job_handler()
+
+ def _get_handler( self ):
+ return self.__job_config.get_handler( None )
+
+ def shutdown( self ):
+ for workflow_scheduler in self.workflow_schedulers.itervalues():
+ try:
+ workflow_scheduler.shutdown()
+ except Exception:
+ log.exception( EXCEPTION_MESSAGE_SHUTDOWN )
+ if self.request_monitor:
+ try:
+ self.request_monitor.shutdown()
+ except Exception:
+ log.exception( "Failed to shutdown worklfow request monitor." )
+
+ def queue( self, workflow_invocation, request_params ):
+ workflow_invocation.state = model.WorkflowInvocation.states.NEW
+ scheduler = request_params.get( "scheduler", None ) or self.default_scheduler_id
+ handler = self._get_handler()
+
+ workflow_invocation.scheduler = scheduler
+ workflow_invocation.handler = handler
+
+ sa_session = self.app.model.context
+ sa_session.add( workflow_invocation )
+ sa_session.flush()
+ return workflow_invocation
+
+ def __start_schedulers( self ):
+ for workflow_scheduler in self.workflow_schedulers.itervalues():
+ workflow_scheduler.startup( self.app )
+
+ def __plugins_dict( self ):
+ return plugin_config.plugins_dict( galaxy.workflow.schedulers, 'plugin_type' )
+
+ def __init_schedulers( self ):
+ config_file = self.app.config.workflow_schedulers_config_file
+ use_default_scheduler = False
+ if not config_file:
+ log.info( "Not workflow schedulers plugin config file defined, using default scheduler." )
+ use_default_scheduler = True
+ elif not os.path.exists( config_file ):
+ log.info( "Cannot find workflow schedulers plugin config file '%s', using default scheduler." % config_file )
+ use_default_scheduler = True
+
+ if use_default_scheduler:
+ self.__init_default_scheduler()
+ else:
+ plugins_element = ElementTree.parse( config_file ).getroot()
+ self.__init_schedulers_for_element( plugins_element )
+
+ def __init_default_scheduler( self ):
+ self.default_scheduler_id = DEFAULT_SCHEDULER_ID
+ self.__init_plugin( DEFAULT_SCHEDULER_PLUGIN_TYPE )
+
+ def __init_schedulers_for_element( self, plugins_element ):
+ plugins_kwds = dict( plugins_element.items() )
+ self.default_scheduler_id = plugins_kwds.get( 'default', DEFAULT_SCHEDULER_ID )
+
+ for plugin_element in plugins_element.getchildren():
+ plugin_type = plugin_element.tag
+ plugin_kwds = dict( plugin_element.items() )
+ plugin_kwds.update( self.extra_kwargs )
+ workflow_scheduler_id = plugin_kwds.get( 'id', None )
+ self.__init_plugin( plugin_type, workflow_scheduler_id, **plugin_kwds )
+
+ if not self.workflow_schedulers:
+ raise Exception( EXCEPTION_MESSAGE_NO_SCHEDULERS )
+ if self.default_scheduler_id not in self.workflow_schedulers:
+ raise Exception( EXCEPTION_MESSAGE_NO_DEFAULT_SCHEDULER % self.default_scheduler_id )
+
+ def __init_plugin( self, plugin_type, workflow_scheduler_id=None, **kwds ):
+ workflow_scheduler_id = workflow_scheduler_id or self.default_scheduler_id
+
+ if workflow_scheduler_id in self.workflow_schedulers:
+ raise Exception( EXCEPTION_MESSAGE_DUPLICATE_SCHEDULERS % workflow_scheduler_id )
+
+ workflow_scheduler = self.__plugin_classes[ plugin_type ]( **kwds )
+ self.workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler
+ if isinstance( workflow_scheduler, galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin ):
+ self.active_workflow_schedulers[ workflow_scheduler_id ] = workflow_scheduler
+
+ def __start_request_monitor( self ):
+ self.request_monitor = WorkflowRequestMonitor( self.app, self )
+
+
+class WorkflowRequestMonitor( object ):
+
+ def __init__( self, app, workflow_scheduling_manager ):
+ self.app = app
+ self.active = True
+ self.workflow_scheduling_manager = workflow_scheduling_manager
+ self.monitor_thread = threading.Thread( name="WorkflowRequestMonitor.monitor_thread", target=self.__monitor )
+ self.monitor_thread.setDaemon( True )
+ self.monitor_thread.start()
+
+ def __monitor( self ):
+ to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers
+ while self.active:
+ for workflow_scheduler_id, workflow_scheduler in to_monitor.iteritems():
+ if not self.active:
+ return
+
+ self.__schedule( workflow_scheduler_id, workflow_scheduler )
+ time.sleep(1) # TODO: wake if stopped
+
+ def __schedule( self, workflow_scheduler_id, workflow_scheduler ):
+ invocation_ids = self.__active_invocation_ids( workflow_scheduler_id )
+ for invocation_id in invocation_ids:
+ self.__attempt_schedule( invocation_id, workflow_scheduler )
+ if not self.active:
+ return
+
+ def __attempt_schedule( self, invocation_id, workflow_scheduler ):
+ sa_session = self.app.model.context
+ workflow_invocation = sa_session.query( model.WorkflowInvocation ).get( invocation_id )
+
+ if not workflow_invocation or not workflow_invocation.active:
+ return False
+
+ try:
+ workflow_scheduler.schedule( workflow_invocation )
+ except Exception:
+ # TODO: eventually fail this - or fail it right away?
+ log.exception( "Exception raised while attempting to schedule workflow request." )
+ return False
+
+ # A workflow was obtained and scheduled...
+ return True
+
+ def __active_invocation_ids( self, scheduler_id ):
+ sa_session = self.app.model.context
+ handler = self.app.config.server_name
+ return model.WorkflowInvocation.poll_active_workflow_ids(
+ sa_session,
+ scheduler=scheduler_id,
+ handler=handler,
+ )
+
+ def shutdown( self ):
+ self.active = False
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -135,9 +135,28 @@
# TODO: This should really be a post to workflows/<workflow_id>/run or
# something like that.
run_workflow_response = self._post( "workflows", data=workflow_request )
+
+ invocation_id = run_workflow_response.json()[ "id" ]
+ invocation = self._invocation_details( workflow_request[ "workflow_id" ], invocation_id )
+ assert invocation[ "state" ] == "scheduled", invocation
+
self._assert_status_code_is( run_workflow_response, 200 )
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+ def test_workflow_request( self ):
+ workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
+ workflow_request, history_id = self._setup_workflow_run( workflow )
+ # TODO: This should really be a post to workflows/<workflow_id>/run or
+ # something like that.
+ url = "workflows/%s/request" % ( workflow_request[ "workflow_id" ] )
+ del workflow_request[ "workflow_id" ]
+ run_workflow_response = self._post( url, data=workflow_request )
+
+ self._assert_status_code_is( run_workflow_response, 200 )
+ # Give some time for workflow to get scheduled before scanning the history.
+ time.sleep( 5 )
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+
def test_cannot_run_inaccessible_workflow( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" )
workflow_request, history_id = self._setup_workflow_run( workflow )
@@ -563,11 +582,18 @@
@skip_without_tool( "cat1" )
def test_invocation_usage( self ):
workflow_id, usage = self._run_workflow_once_get_invocation( "test_usage")
- usage_details = self._invocation_details( workflow_id, usage[ "id" ] )
+ invocation_id = usage[ "id" ]
+ usage_details = self._invocation_details( workflow_id, invocation_id )
# Assert some high-level things about the structure of data returned.
self._assert_has_keys( usage_details, "inputs", "steps" )
- for step in usage_details[ "steps" ]:
+ invocation_steps = usage_details[ "steps" ]
+ for step in invocation_steps:
self._assert_has_keys( step, "workflow_step_id", "order_index", "id" )
+ an_invocation_step = invocation_steps[ 0 ]
+ step_id = an_invocation_step[ "id" ]
+ step_response = self._get( "workflows/%s/usage/%s/steps/%s" % ( workflow_id, invocation_id, step_id ) )
+ self._assert_status_code_is( step_response, 200 )
+ self._assert_has_keys( step_response.json(), "id", "order_index" )
def _invocation_details( self, workflow_id, invocation_id ):
invocation_details_response = self._get( "workflows/%s/usage/%s" % ( workflow_id, invocation_id ) )
diff -r d1864ea200ce16992c26a4a642381be71310c4a2 -r f6dcea371b036e423488bf5478e3395d5501fd8f test/unit/test_galaxy_mapping.py
--- a/test/unit/test_galaxy_mapping.py
+++ b/test/unit/test_galaxy_mapping.py
@@ -1,6 +1,7 @@
# -*- coding: utf-8 -*-
import unittest
import galaxy.model.mapping as mapping
+import uuid
class MappingTests( unittest.TestCase ):
@@ -358,6 +359,54 @@
assert contents_iter_names( ids=[ d1.id, d3.id ] ) == [ "1", "3" ]
+ def test_workflows( self ):
+ model = self.model
+ user = model.User(
+ email="testworkflows(a)bx.psu.edu",
+ password="password"
+ )
+ stored_workflow = model.StoredWorkflow()
+ stored_workflow.user = user
+ workflow = model.Workflow()
+ workflow_step = model.WorkflowStep()
+ workflow.steps = [ workflow_step ]
+ workflow.stored_workflow = stored_workflow
+
+ self.persist( workflow )
+ assert workflow_step.id is not None
+
+ invocation_uuid = uuid.uuid1()
+
+ workflow_invocation = model.WorkflowInvocation()
+ workflow_invocation.uuid = invocation_uuid
+
+ workflow_invocation_step1 = model.WorkflowInvocationStep()
+ workflow_invocation_step1.workflow_invocation = workflow_invocation
+ workflow_invocation_step1.workflow_step = workflow_step
+
+ workflow_invocation_step2 = model.WorkflowInvocationStep()
+ workflow_invocation_step2.workflow_invocation = workflow_invocation
+ workflow_invocation_step2.workflow_step = workflow_step
+
+ workflow_invocation.workflow = workflow
+
+ h1 = model.History( name="WorkflowHistory1", user=user)
+ d1 = self.new_hda( h1, name="1" )
+ workflow_request_dataset = model.WorkflowRequestToInputDatasetAssociation()
+ workflow_request_dataset.workflow_invocation = workflow_invocation
+ workflow_request_dataset.workflow_step = workflow_step
+ workflow_request_dataset.dataset = d1
+ self.persist( workflow_invocation )
+ assert workflow_request_dataset is not None
+ assert workflow_invocation.id is not None
+
+ self.expunge()
+
+ loaded_invocation = self.query( model.WorkflowInvocation ).get( workflow_invocation.id )
+ assert loaded_invocation.uuid == invocation_uuid, "%s != %s" % (loaded_invocation.uuid, invocation_uuid)
+ assert loaded_invocation
+ assert len( loaded_invocation.steps ) == 2
+
def new_hda( self, history, **kwds ):
return history.add_dataset( self.model.HistoryDatasetAssociation( create_dataset=True, sa_session=self.model.session, **kwds ) )
https://bitbucket.org/galaxy/galaxy-central/commits/504aad0d9688/
Changeset: 504aad0d9688
User: jmchilton
Date: 2014-11-13 18:47:39+00:00
Summary: Update workflow invocations when their jobs complete.
This could allow more efficient checks when recovering workflow state.
Affected #: 3 files
diff -r f6dcea371b036e423488bf5478e3395d5501fd8f -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -918,7 +918,7 @@
self.pause( dep_job_assoc.job, "Execution of this dataset's job is paused because its input datasets are in an error state." )
self.sa_session.add( dataset )
self.sa_session.flush()
- job.state = job.states.ERROR
+ job.set_final_state( job.states.ERROR )
job.command_line = self.command_line
job.info = message
# TODO: Put setting the stdout, stderr, and exit code in one place
@@ -1243,7 +1243,7 @@
# Finally set the job state. This should only happen *after* all
# dataset creation, and will allow us to eliminate force_history_refresh.
- job.state = final_job_state
+ job.set_final_state( final_job_state )
if not job.tasks:
# If job was composed of tasks, don't attempt to recollect statisitcs
self._collect_metrics( job )
diff -r f6dcea371b036e423488bf5478e3395d5501fd8f -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -680,11 +680,11 @@
except Empty:
pass
for job, error_msg in jobs_to_check:
+ final_state = job.states.DELETED
if error_msg is not None:
- job.state = job.states.ERROR
+ final_state = job.states.ERROR
job.info = error_msg
- else:
- job.state = job.states.DELETED
+ job.set_final_state( final_state )
self.sa_session.add( job )
self.sa_session.flush()
if job.job_runner_name is not None:
diff -r f6dcea371b036e423488bf5478e3395d5501fd8f -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -28,6 +28,7 @@
import galaxy.security.passwords
from galaxy.datatypes.metadata import MetadataCollection
from galaxy.model.item_attrs import Dictifiable, UsesAnnotations
+import galaxy.model.orm.now
from galaxy.security import get_permitted_actions
from galaxy.util import is_multi_byte, nice_size, Params, restore_text, send_mail
from galaxy.util import ready_name_for_url
@@ -551,6 +552,11 @@
return rval
+ def set_final_state( self, final_state ):
+ self.state = final_state
+ if self.workflow_invocation_step:
+ self.workflow_invocation_step.update()
+
class Task( object, HasJobMetrics ):
"""
@@ -3188,11 +3194,17 @@
rval['inputs'] = inputs
return rval
+ def update( self ):
+ self.update_time = galaxy.model.orm.now.now()
+
class WorkflowInvocationStep( object, Dictifiable ):
dict_collection_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' )
dict_element_visible_keys = ( 'id', 'update_time', 'job_id', 'workflow_step_id', 'action' )
+ def update( self ):
+ self.workflow_invocation.update()
+
def to_dict( self, view='collection', value_mapper=None ):
rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper )
rval['order_index'] = self.workflow_step.order_index
https://bitbucket.org/galaxy/galaxy-central/commits/5324504e9175/
Changeset: 5324504e9175
User: jmchilton
Date: 2014-11-13 18:47:39+00:00
Summary: Implement pause module for workflows.
New module type that pauses a workflow and gives time for the runner to review it before proceeding with execution.
- Introduce concept of beta workflow modules - I guess we should just keep the pause module as beta until their is a UI to support it.
- Extracts base class ouptut of InputModule for modules that are "simple" - i.e. their configuration state is represented as a dictionary and configuration form is rendered via the generic template.
- Test Cases (for this changeset and a bunch of stuff that is now testable with the pause module in place from the scheduling framework commit).
Affected #: 5 files
diff -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 -r 5324504e91756088158af4214bbe8592daa879ff lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -192,6 +192,11 @@
self.local_task_queue_workers = int(kwargs.get("local_task_queue_workers", 2))
# The transfer manager and deferred job queue
self.enable_beta_job_managers = string_as_bool( kwargs.get( 'enable_beta_job_managers', 'False' ) )
+ # These workflow modules should not be considered part of Galaxy's
+ # public API yet - the module state definitions may chnage and
+ # workflows built using these modules may not function in the
+ # future.
+ self.enable_beta_workflow_modules = string_as_bool( kwargs.get( 'enable_beta_workflow_modules', 'False' ) )
# Per-user Job concurrency limitations
self.cache_user_job_count = string_as_bool( kwargs.get( 'cache_user_job_count', False ) )
self.user_job_limit = int( kwargs.get( 'user_job_limit', 0 ) )
diff -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 -r 5324504e91756088158af4214bbe8592daa879ff lib/galaxy/workflow/modules.py
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -187,7 +187,7 @@
raise TypeError( "Abstract method" )
-class InputModule( WorkflowModule ):
+class SimpleWorkflowModule( WorkflowModule ):
@classmethod
def new( Class, trans, tool_id=None ):
@@ -215,46 +215,17 @@
"""
raise TypeError( "Abstract method" )
- def get_runtime_input_dicts( self, step_annotation ):
- name = self.state.get( "name", self.default_name )
- return [ dict( name=name, description=step_annotation ) ]
-
- def recover_state( self, state, **kwds ):
- """ Recover state `dict` from simple dictionary describing configuration
- state (potentially from persisted step state).
-
- Sub-classes should supply `default_state` method and `state_fields`
- attribute which are used to build up the state `dict`.
- """
- self.state = self.default_state()
- for key in self.state_fields:
- if state and key in state:
- self.state[ key ] = state[ key ]
-
def save_to_step( self, step ):
step.type = self.type
step.tool_id = None
step.tool_inputs = self.state
- def get_data_inputs( self ):
- return []
-
- def get_config_form( self ):
- form = self._abstract_config_form( )
- return self.trans.fill_template( "workflow/editor_generic_form.mako",
- module=self, form=form )
-
def get_state( self, secure=True ):
return dumps( self.state )
def update_state( self, incoming ):
self.recover_state( incoming )
- def get_runtime_state( self ):
- state = galaxy.tools.DefaultToolState()
- state.inputs = dict( input=None )
- return state
-
def recover_runtime_state( self, runtime_state ):
""" Take secure runtime state from persisted invocation and convert it
into a DefaultToolState object for use during workflow invocation.
@@ -275,7 +246,8 @@
def decode_runtime_state( self, trans, string ):
fake_tool = Bunch( inputs=self.get_runtime_inputs() )
state = galaxy.tools.DefaultToolState()
- state.decode( string, fake_tool, trans.app )
+ if string:
+ state.decode( string, fake_tool, trans.app )
return state
def update_runtime_state( self, trans, state, values ):
@@ -288,7 +260,7 @@
return errors
def compute_runtime_state( self, trans, step_updates=None ):
- if step_updates:
+ if step_updates and "tool_state" in step_updates:
# Fix this for multiple inputs
state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) )
step_errors = self.update_runtime_state( trans, state, step_updates )
@@ -298,6 +270,38 @@
return state, step_errors
+ def recover_state( self, state, **kwds ):
+ """ Recover state `dict` from simple dictionary describing configuration
+ state (potentially from persisted step state).
+
+ Sub-classes should supply `default_state` method and `state_fields`
+ attribute which are used to build up the state `dict`.
+ """
+ self.state = self.default_state()
+ for key in self.state_fields:
+ if state and key in state:
+ self.state[ key ] = state[ key ]
+
+ def get_config_form( self ):
+ form = self._abstract_config_form( )
+ return self.trans.fill_template( "workflow/editor_generic_form.mako",
+ module=self, form=form )
+
+
+class InputModule( SimpleWorkflowModule ):
+
+ def get_runtime_state( self ):
+ state = galaxy.tools.DefaultToolState()
+ state.inputs = dict( input=None )
+ return state
+
+ def get_runtime_input_dicts( self, step_annotation ):
+ name = self.state.get( "name", self.default_name )
+ return [ dict( name=name, description=step_annotation ) ]
+
+ def get_data_inputs( self ):
+ return []
+
def execute( self, trans, progress, invocation, step ):
job, step_outputs = None, dict( output=step.state.inputs['input'])
@@ -389,6 +393,76 @@
return [ dict( name='output', extensions=['input_collection'], collection_type=self.state[ 'collection_type' ] ) ]
+class PauseModule( SimpleWorkflowModule ):
+ """ Initially this module will unconditionally pause a workflow - will aim
+ to allow conditional pausing later on.
+ """
+ type = "pause"
+ name = "Pause for dataset review"
+ default_name = "Pause for Dataset Review"
+ state_fields = [ "name" ]
+
+ @classmethod
+ def default_state( Class ):
+ return dict( name=Class.default_name )
+
+ def get_data_inputs( self ):
+ input = dict(
+ name="input",
+ label="Dataset for Review",
+ multiple=False,
+ extensions='input',
+ input_type="dataset",
+ )
+ return [ input ]
+
+ def get_data_outputs( self ):
+ return [ dict( name="output", label="Reviewed Dataset", extensions=['input'] ) ]
+
+ def _abstract_config_form( self ):
+ form = formbuilder.FormBuilder(
+ title=self.name
+ ).add_text( "name", "Name", value=self.state['name'] )
+ return form
+
+ def get_runtime_inputs( self, **kwds ):
+ return dict( )
+
+ def get_runtime_input_dicts( self, step_annotation ):
+ return []
+
+ def get_runtime_state( self ):
+ state = galaxy.tools.DefaultToolState()
+ state.inputs = dict( )
+ return state
+
+ def execute( self, trans, progress, invocation, step ):
+ progress.mark_step_outputs_delayed( step )
+ return None
+
+ def recover_mapping( self, step, step_invocations, progress ):
+ if step_invocations:
+ step_invocation = step_invocations[0]
+ action = step_invocation.action
+ if action:
+ connection = step.input_connections_by_name[ "input" ][ 0 ]
+ replacement = progress.replacement_for_connection( connection )
+ progress.set_step_outputs( step, { 'output': replacement } )
+ return
+ elif action is False:
+ raise CancelWorkflowEvaluation()
+ raise DelayedWorkflowEvaluation()
+
+ def do_invocation_step_action( self, step, action ):
+ """ Update or set the workflow invocation state action - generic
+ extension point meant to allows users to interact with interactive
+ workflow modules. The action object returned from this method will
+ be attached to the WorkflowInvocationStep and be available the next
+ time the workflow scheduler visits the workflow.
+ """
+ return bool( action )
+
+
class ToolModule( WorkflowModule ):
type = "tool"
@@ -828,6 +902,7 @@
module_types = dict(
data_input=InputDataModule,
data_collection_input=InputDataCollectionModule,
+ pause=PauseModule,
tool=ToolModule,
)
module_factory = WorkflowModuleFactory( module_types )
@@ -848,6 +923,16 @@
module_sections = [
inputs_section
]
+ if trans.app.config.enable_beta_workflow_modules:
+ experimental_modules = {
+ "name": "experimental",
+ "title": "Experimental",
+ "modules": [
+ {"name": "pause", "title": "Pause Workflow for Dataset Review", "description": "Pause for Review"},
+ ],
+ }
+ module_sections.append(experimental_modules)
+
return module_sections
@@ -901,7 +986,6 @@
# Populate module.
module = step.module = module_factory.from_workflow_step( trans, step )
- # Calculating step errors and state depends on whether step is a tool step or not.
if not module:
step.module = None
step.state = None
diff -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 -r 5324504e91756088158af4214bbe8592daa879ff templates/webapps/galaxy/workflow/editor.mako
--- a/templates/webapps/galaxy/workflow/editor.mako
+++ b/templates/webapps/galaxy/workflow/editor.mako
@@ -353,7 +353,6 @@
</div></div>
%endfor
- </div></div></div>
diff -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 -r 5324504e91756088158af4214bbe8592daa879ff test/api/test_workflow_pause.ga
--- /dev/null
+++ b/test/api/test_workflow_pause.ga
@@ -0,0 +1,118 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "test_workflow_pause",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 199.9201512336731,
+ "top": 251.4826512336731
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "1": {
+ "annotation": "",
+ "id": 1,
+ "input_connections": {
+ "input1": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "name": "Concatenate datasets (for test workflows)",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 516.7257237434387,
+ "top": 187.28126573562622
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "cat",
+ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[]\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "user_outputs": []
+ },
+ "2": {
+ "annotation": "",
+ "id": 2,
+ "input_connections": {
+ "input": {
+ "id": 1,
+ "output_name": "out_file1"
+ }
+ },
+ "inputs": [
+ {
+ "description": "",
+ "name": "Pause for Dataset Review"
+ }
+ ],
+ "name": "Pause for dataset review",
+ "outputs": [],
+ "position": {
+ "left": 862.715301990509,
+ "top": 197.28126573562622
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Pause for Dataset Review\"}",
+ "tool_version": null,
+ "type": "pause",
+ "user_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "id": 3,
+ "input_connections": {
+ "input1": {
+ "id": 2,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "name": "Concatenate datasets (for test workflows)",
+ "outputs": [
+ {
+ "name": "out_file1",
+ "type": "input"
+ }
+ ],
+ "position": {
+ "left": 1181.9722595214844,
+ "top": 181.52084350585938
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "cat1",
+ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[]\"}",
+ "tool_version": "1.0.0",
+ "type": "tool",
+ "user_outputs": []
+ }
+ },
+ "uuid": "9058956e-76b6-4909-bab3-c12b2cc394c7"
+}
\ No newline at end of file
diff -r 504aad0d96887e8eb7e9fee9445bc1a968fccbb8 -r 5324504e91756088158af4214bbe8592daa879ff test/api/test_workflows.py
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -9,6 +9,7 @@
from .helpers import skip_without_tool
from requests import delete
+from requests import put
from galaxy.exceptions import error_codes
@@ -146,9 +147,7 @@
def test_workflow_request( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
workflow_request, history_id = self._setup_workflow_run( workflow )
- # TODO: This should really be a post to workflows/<workflow_id>/run or
- # something like that.
- url = "workflows/%s/request" % ( workflow_request[ "workflow_id" ] )
+ url = "workflows/%s/usage" % ( workflow_request[ "workflow_id" ] )
del workflow_request[ "workflow_id" ]
run_workflow_response = self._post( url, data=workflow_request )
@@ -157,6 +156,110 @@
time.sleep( 5 )
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+ def test_workflow_pause( self ):
+ workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_pause" )
+ uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
+ history_id = self.dataset_populator.new_history()
+ hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
+ index_map = {
+ '0': self._ds_entry(hda1),
+ }
+ invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
+ # Give some time for workflow to get scheduled before scanning the history.
+ time.sleep( 5 )
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+
+ # Wait for all the datasets to complete, make sure the workflow invocation
+ # is not complete.
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] != 'scheduled', invocation
+
+ self.__review_paused_steps( uploaded_workflow_id, invocation_id, order_index=2, action=True )
+
+ time.sleep( 5 )
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] == 'scheduled', invocation
+
+ def test_workflow_pause_cancel( self ):
+ workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_pause" )
+ uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
+ history_id = self.dataset_populator.new_history()
+ hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
+ index_map = {
+ '0': self._ds_entry(hda1),
+ }
+ invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
+ # Give some time for workflow to get scheduled before scanning the history.
+ time.sleep( 5 )
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+
+ # Wait for all the datasets to complete, make sure the workflow invocation
+ # is not complete.
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] != 'scheduled'
+
+ self.__review_paused_steps( uploaded_workflow_id, invocation_id, order_index=2, action=False )
+ # Not immediately cancelled, must wait until workflow scheduled again.
+ time.sleep( 4 )
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] == 'cancelled', invocation
+
+ def test_workflow_map_reduce_pause( self ):
+ workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_map_reduce_pause" )
+ uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
+ history_id = self.dataset_populator.new_history()
+ hda1 = self.dataset_populator.new_dataset( history_id, content="reviewed\nunreviewed" )
+ hdca1 = self.dataset_collection_populator.create_list_in_history( history_id, contents=["1\n2\n3", "4\n5\n6"] ).json()
+ index_map = {
+ '0': self._ds_entry(hda1),
+ '1': self._ds_entry(hdca1),
+ }
+ invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
+ # Give some time for workflow to get scheduled before scanning the history.
+ time.sleep( 5 )
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+
+ # Wait for all the datasets to complete, make sure the workflow invocation
+ # is not complete.
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] != 'scheduled'
+
+ self.__review_paused_steps( uploaded_workflow_id, invocation_id, order_index=4, action=True )
+
+ time.sleep( 5 )
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] == 'scheduled'
+ self.assertEquals("reviewed\n1\nreviewed\n4\n", self.dataset_populator.get_history_dataset_content( history_id ) )
+
+ def test_cancel_workflow_invocation( self ):
+ workflow = self.workflow_populator.load_workflow_from_resource( "test_workflow_pause" )
+ uploaded_workflow_id = self.workflow_populator.create_workflow( workflow )
+ history_id = self.dataset_populator.new_history()
+ hda1 = self.dataset_populator.new_dataset( history_id, content="1 2 3" )
+ index_map = {
+ '0': self._ds_entry(hda1),
+ }
+ invocation_id = self.__invoke_workflow( history_id, uploaded_workflow_id, index_map )
+ # Give some time for workflow to get scheduled before scanning the history.
+ time.sleep( 5 )
+ self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+
+ # Wait for all the datasets to complete, make sure the workflow invocation
+ # is not complete.
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] != 'scheduled'
+
+ invocation_url = self._api_url( "workflows/%s/usage/%s" % (uploaded_workflow_id, invocation_id), use_key=True )
+ delete_response = delete( invocation_url )
+ self._assert_status_code_is( delete_response, 200 )
+
+ # Wait for all the datasets to complete, make sure the workflow invocation
+ # is not complete.
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ assert invocation[ 'state' ] == 'cancelled'
+
def test_cannot_run_inaccessible_workflow( self ):
workflow = self.workflow_populator.load_workflow( name="test_for_run_cannot_access" )
workflow_request, history_id = self._setup_workflow_run( workflow )
@@ -601,6 +704,21 @@
invocation_details = invocation_details_response.json()
return invocation_details
+ def _invocation_step_details( self, workflow_id, invocation_id, step_id ):
+ invocation_step_response = self._get( "workflows/%s/usage/%s/steps/%s" % ( workflow_id, invocation_id, step_id ) )
+ self._assert_status_code_is( invocation_step_response, 200 )
+ invocation_step_details = invocation_step_response.json()
+ return invocation_step_details
+
+ def _execute_invocation_step_action( self, workflow_id, invocation_id, step_id, action ):
+ raw_url = "workflows/%s/usage/%s/steps/%s" % ( workflow_id, invocation_id, step_id )
+ url = self._api_url( raw_url, use_key=True )
+ payload = dumps( dict( action=action ) )
+ action_response = put( url, data=payload )
+ self._assert_status_code_is( action_response, 200 )
+ invocation_step_details = action_response.json()
+ return invocation_step_details
+
def _run_workflow_once_get_invocation( self, name ):
workflow = self.workflow_populator.load_workflow( name=name )
workflow_request, history_id = self._setup_workflow_run( workflow )
@@ -689,6 +807,15 @@
names = self.__workflow_names()
assert name in names, "No workflows with name %s in users workflows <%s>" % ( name, names )
+ def __review_paused_steps( self, uploaded_workflow_id, invocation_id, order_index, action=True ):
+ invocation = self._invocation_details( uploaded_workflow_id, invocation_id )
+ invocation_steps = invocation[ "steps" ]
+ pause_steps = [ s for s in invocation_steps if s[ 'order_index' ] == order_index ]
+ for pause_step in pause_steps:
+ pause_step_id = pause_step[ 'id' ]
+
+ self._execute_invocation_step_action( uploaded_workflow_id, invocation_id, pause_step_id, action=action )
+
def __assert_lines_hid_line_count_is( self, history, hid, lines ):
contents_url = "histories/%s/contents" % history
history_contents_response = self._get( contents_url )
@@ -698,6 +825,22 @@
self._assert_status_code_is( hda_info_response, 200 )
self.assertEquals( hda_info_response.json()[ "metadata_data_lines" ], lines )
+ def __invoke_workflow( self, history_id, workflow_id, inputs, assert_ok=True ):
+ workflow_request = dict(
+ history="hist_id=%s" % history_id,
+ )
+ workflow_request[ "inputs" ] = dumps( inputs )
+ workflow_request[ "inputs_by" ] = 'step_index'
+ url = "workflows/%s/usage" % ( workflow_id )
+
+ invocation_response = self._post( url, data=workflow_request )
+ if assert_ok:
+ self._assert_status_code_is( invocation_response, 200 )
+ invocation_id = invocation_response.json()[ "id" ]
+ return invocation_id
+ else:
+ return invocation_response
+
def __workflow_names( self ):
index_response = self._get( "workflows" )
self._assert_status_code_is( index_response, 200 )
https://bitbucket.org/galaxy/galaxy-central/commits/45eae5a7f3ba/
Changeset: 45eae5a7f3ba
User: jmchilton
Date: 2014-11-13 18:47:40+00:00
Summary: Conditionally force traditional workflow invocations paths through scheduling framework.
Workflow with pause modules have to be run through the new workflow scheduling plugin framework - so these will always force jobs to be queued in the background. The deployer can also now choose to have workflows scheduled this way if a workflow has a minimum number of steps (set at a very high 250 right now) or if it uses collections (currently this defaults to False). These options are meant as transient options that will disappear once all workflows a scheduled this way - but there needs to be better UI in place before making that switch as well as more testing. These options are just meant to give people running really large workflows a way to start exploring the scheduling framework option.
Affected #: 5 files
diff -r 5324504e91756088158af4214bbe8592daa879ff -r 45eae5a7f3baff113f5d264a40117e991e083212 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -193,10 +193,19 @@
# The transfer manager and deferred job queue
self.enable_beta_job_managers = string_as_bool( kwargs.get( 'enable_beta_job_managers', 'False' ) )
# These workflow modules should not be considered part of Galaxy's
- # public API yet - the module state definitions may chnage and
+ # public API yet - the module state definitions may change and
# workflows built using these modules may not function in the
# future.
self.enable_beta_workflow_modules = string_as_bool( kwargs.get( 'enable_beta_workflow_modules', 'False' ) )
+
+ # Certain modules such as the pause module will automatically cause
+ # workflows to be scheduled in job handlers the way all workflows will
+ # be someday - the following two properties can also be used to force this
+ # behavior in under conditions - namely for workflows that have a minimum
+ # number of steps or that consume collections.
+ self.force_beta_workflow_scheduled_min_steps = int( kwargs.get( 'force_beta_workflow_scheduled_min_steps', '250' ) )
+ self.force_beta_workflow_scheduled_for_collections = string_as_bool( kwargs.get( 'force_beta_workflow_scheduled_for_collections', 'False' ) )
+
# Per-user Job concurrency limitations
self.cache_user_job_count = string_as_bool( kwargs.get( 'cache_user_job_count', False ) )
self.user_job_limit = int( kwargs.get( 'user_job_limit', 0 ) )
diff -r 5324504e91756088158af4214bbe8592daa879ff -r 45eae5a7f3baff113f5d264a40117e991e083212 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1250,6 +1250,7 @@
try: # use a try/finally block to restore the user's current history
default_target_history = trans.get_history()
module_injector = WorkflowModuleInjector( trans )
+ scheduled = True
if kwargs:
# If kwargs were provided, the states for each step should have
# been POSTed
@@ -1300,13 +1301,18 @@
workflow=workflow,
workflow_run_config=run_config
)
-
+ invocation_state = invocation.state
+ # Just use last invocation - right now not really
+ # possible to have some invocations scheduled and not
+ # others.
+ scheduled = invocation_state == model.WorkflowInvocation.states.SCHEDULED
invocations.append({'outputs': outputs,
'new_history': new_history})
trans.sa_session.flush()
if invocations:
return trans.fill_template( "workflow/run_complete.mako",
workflow=stored,
+ scheduled=scheduled,
invocations=invocations )
else:
# Prepare each step
diff -r 5324504e91756088158af4214bbe8592daa879ff -r 45eae5a7f3baff113f5d264a40117e991e083212 lib/galaxy/workflow/run.py
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -12,7 +12,48 @@
log = logging.getLogger( __name__ )
+# Entry point for direct invoke via controllers. Deprecated to some degree.
def invoke( trans, workflow, workflow_run_config, workflow_invocation=None, populate_state=False ):
+ if force_queue( trans, workflow ):
+ invocation = queue_invoke( trans, workflow, workflow_run_config, populate_state=populate_state )
+ return [], invocation
+ else:
+ return __invoke( trans, workflow, workflow_run_config, workflow_invocation, populate_state )
+
+
+# Entry point for core workflow scheduler.
+def schedule( trans, workflow, workflow_run_config, workflow_invocation ):
+ return __invoke( trans, workflow, workflow_run_config, workflow_invocation )
+
+
+BASIC_WORKFLOW_STEP_TYPES = [ None, "tool", "data_input", "data_collection_input" ]
+
+
+def force_queue( trans, workflow ):
+ # Default behavior is still to just schedule workflows completley right
+ # away. This can be modified here in various ways.
+ config = trans.app.config
+ force_for_collection = config.force_beta_workflow_scheduled_for_collections
+ force_min_steps = config.force_beta_workflow_scheduled_min_steps
+
+ step_count = len( workflow.steps )
+ if step_count > force_min_steps:
+ log.info("Workflow has many steps %d, backgrounding execution" % step_count)
+ return True
+ for step in workflow.steps:
+ if step.type not in BASIC_WORKFLOW_STEP_TYPES:
+ log.info("Found non-basic workflow step type - backgrounding execution")
+ # Force all new beta modules types to be use force queueing of
+ # workflow.
+ return True
+ if step.type == "data_collection_input" and force_for_collection:
+ log.info("Found collection input step - backgrounding execution")
+ return True
+
+ return False
+
+
+def __invoke( trans, workflow, workflow_run_config, workflow_invocation=None, populate_state=False ):
""" Run the supplied workflow in the supplied target_history.
"""
if populate_state:
@@ -51,8 +92,9 @@
return outputs, invoker.workflow_invocation
-def queue_invoke( trans, workflow, workflow_run_config, request_params ):
- modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map )
+def queue_invoke( trans, workflow, workflow_run_config, request_params={}, populate_state=True ):
+ if populate_state:
+ modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map )
workflow_invocation = workflow_run_config_to_request( trans, workflow_run_config, workflow )
workflow_invocation.workflow = workflow
return trans.app.workflow_scheduling_manager.queue(
diff -r 5324504e91756088158af4214bbe8592daa879ff -r 45eae5a7f3baff113f5d264a40117e991e083212 lib/galaxy/workflow/schedulers/core.py
--- a/lib/galaxy/workflow/schedulers/core.py
+++ b/lib/galaxy/workflow/schedulers/core.py
@@ -36,7 +36,7 @@
request_context,
workflow_invocation
)
- run.invoke(
+ run.schedule(
trans=request_context,
workflow=workflow,
workflow_run_config=workflow_run_config,
diff -r 5324504e91756088158af4214bbe8592daa879ff -r 45eae5a7f3baff113f5d264a40117e991e083212 templates/webapps/galaxy/workflow/run_complete.mako
--- a/templates/webapps/galaxy/workflow/run_complete.mako
+++ b/templates/webapps/galaxy/workflow/run_complete.mako
@@ -1,6 +1,7 @@
<%inherit file="/base.mako"/><div class="donemessagelarge">
+%if scheduled:
Successfully ran workflow "${util.unicodify( workflow.name )}". The following datasets have been added to the queue:
%for invocation in invocations:
<div class="workflow-invocation-complete">
@@ -21,6 +22,11 @@
</div></div>
%endfor
+%else:
+ The requested workflows have been queued and datasets will appear
+ as jobs are created - you will need to refresh your history panel
+ to see these.
+%endif
</div><script type="text/javascript">
https://bitbucket.org/galaxy/galaxy-central/commits/114b22292fb6/
Changeset: 114b22292fb6
User: kellrott
Date: 2014-11-13 18:47:40+00:00
Summary: Fixing id lookup on GET /api/workflows/<uuid>/usage
Affected #: 1 file
diff -r 45eae5a7f3baff113f5d264a40117e991e083212 -r 114b22292fb6a32b8c6102ff8554872f1977f2a7 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -411,8 +411,8 @@
:raises: exceptions.MessageException, exceptions.ObjectNotFound
"""
- decoded_stored_workflow_invocation_id = self.__decode_id( trans, workflow_id )
- results = self.workflow_manager.build_invocations_query( trans, decoded_stored_workflow_invocation_id )
+ stored_workflow = self.__get_stored_workflow(trans, workflow_id)
+ results = self.workflow_manager.build_invocations_query( trans, stored_workflow.id )
out = []
for r in results:
out.append( self.__encode_invocation( trans, r ) )
https://bitbucket.org/galaxy/galaxy-central/commits/facd14607d28/
Changeset: facd14607d28
User: kellrott
Date: 2014-11-13 18:47:41+00:00
Summary: Adding job state info to WorkflowInvocationStep to_dict
Affected #: 1 file
diff -r 114b22292fb6a32b8c6102ff8554872f1977f2a7 -r facd14607d28535545e460bd1f4c7a8ef6b8dff5 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3208,6 +3208,7 @@
def to_dict( self, view='collection', value_mapper=None ):
rval = super( WorkflowInvocationStep, self ).to_dict( view=view, value_mapper=value_mapper )
rval['order_index'] = self.workflow_step.order_index
+ rval['state'] = self.job.state if self.job is not None else None
return rval
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Fix toolshed bootstrapping for Macs.
by commits-noreply＠bitbucket.org 13 Nov '14
by commits-noreply＠bitbucket.org 13 Nov '14
13 Nov '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c9b13e2f3f6b/
Changeset: c9b13e2f3f6b
User: dan
Date: 2014-11-13 17:43:26+00:00
Summary: Fix toolshed bootstrapping for Macs.
Affected #: 1 file
diff -r 77676b9852282c0a240ebebb410374b233a1fa36 -r c9b13e2f3f6bb7f35f6ed9a012159c42519fac02 lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
--- a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
+++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh
@@ -47,7 +47,7 @@
echo " done."
-sed -i "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" ${TOOL_SHED_CONFIG_FILE}
+sed -i"bak" "s/#admin_users = user1@example.org,user2@example.org/admin_users = $admin_user_email/" "${TOOL_SHED_CONFIG_FILE}"
echo -n "Starting tool shed in order to populate users and categories... "
if [ -f tool_shed_bootstrap.pid ] ; then
@@ -76,7 +76,7 @@
done
echo -n "Retrieving admin user's API key from $local_shed_url..."
-api_key=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/ | sed 's/.\+api_key[^0-9a-f]\+\([0-9a-f]\+\).\+/\1/'`
+api_key=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/ | sed 's/..*api_key[^0-9a-f][^0-9a-f]*\([0-9a-f]*\)..*/\1/'`
if [[ -z $api_key && ${api_key+x} ]] ; then
stop_err "Error getting API key for user $admin_user_email."
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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