mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_15.03' into dev
This commit is contained in:
guerler
@@ -230,7 +230,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
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title : 'Search',
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tooltip : 'Search help for this tool (Biostar)',
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onclick : function() {
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window.open(options.biostar_url + '/t/' + options.id + '/');
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window.open(options.biostar_url + '/local/search/page/?q=' + options.name);
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}
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});
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};
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File diff suppressed because one or more lines are too long
@@ -4,7 +4,15 @@ return $.extend(true, {}, config_default, {
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category : '',
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library : 'NVD3',
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tag : 'svg',
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keywords : 'small'
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keywords : 'small',
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columns : {
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tooltip : {
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title : 'Data point labels',
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is_text : true,
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is_numeric : true,
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is_auto : true
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}
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}
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});
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});
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@@ -15,71 +15,76 @@ return Backbone.View.extend({
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options.render = function(canvas_id, groups) {
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return self.render(canvas_id, groups)
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};
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// call panel helper
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Tools.panelHelper(app, options);
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},
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// render
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render : function(canvas_id, groups) {
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var chart = this.options.chart;
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var type = this.options.type;
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var makeConfig = this.options.makeConfig;
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// create nvd3 model
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var d3chart = nv.models[type]()
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// request data
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var self = this;
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nv.addGraph(function() {
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try {
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// x axis label
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d3chart.xAxis.axisLabel(chart.settings.get('x_axis_label'));
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// y axis label
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d3chart.yAxis.axisLabel(chart.settings.get('y_axis_label'))
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.axisLabelDistance(30);
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// controls
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d3chart.options({showControls: false});
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// legend
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if (d3chart.showLegend) {
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d3chart.showLegend(chart.settings.get('show_legend') == 'true');
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}
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// make categories
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self._makeAxes(d3chart, groups, chart.settings);
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// custom callback
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if (makeConfig) {
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makeConfig(d3chart);
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}
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// hide controls if in multi-viewer mode
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if (chart.settings.get('use_panels') === 'true') {
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d3chart.options({showControls: false});
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}
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// hide min/max values
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d3chart.xAxis.showMaxMin(false);
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d3chart.yAxis.showMaxMin(chart.definition.showmaxmin);
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// configure tooltips
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d3chart.tooltipContent(function(key, x, y, graph) {
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return '<h3>' + (graph.point.tooltip || key) + '</h3>';
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});
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// draw chart
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if ($('#' + canvas_id).length == 0) {
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return;
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}
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var canvas = d3.select('#' + canvas_id);
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canvas.datum(groups)
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canvas.datum(groups)
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.call(d3chart);
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// add zoom/pan handler
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if (chart.definition.zoomable && chart.definition.zoomable != 'native') {
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// clip edges
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if (d3chart.clipEdge) {
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d3chart.clipEdge(true);
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}
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// add zoom
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Tools.addZoom({
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xAxis : d3chart.xAxis,
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@@ -97,16 +102,16 @@ return Backbone.View.extend({
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self._handleError(chart, err);
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}
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});
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// return
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return true;
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},
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// create axes formatting
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_makeAxes: function(d3chart, groups, settings) {
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// result
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var categories = Tools.makeCategories(groups);
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// make axes
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function makeTickFormat (id) {
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Tools.makeTickFormat({
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@@ -125,7 +130,7 @@ return Backbone.View.extend({
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makeTickFormat('x');
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makeTickFormat('y');
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},
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// handle error
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_handleError: function(chart, err) {
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chart.state('failed', err);
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@@ -6,11 +6,11 @@ return $.extend(true, {}, nvd3_config, {
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zoomable : true,
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columns : {
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x : {
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title : 'Values for x-axis',
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title : 'Values for x-axis',
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is_numeric : true
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},
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y : {
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title : 'Values for y-axis',
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title : 'Values for y-axis',
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is_numeric : true
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}
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}
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@@ -299,7 +299,7 @@ return Backbone.Collection.extend(
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// get/fix value
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var v = column_data[j];
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if (isNaN(v) && !column.is_label) {
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if (isNaN(v) && !column.is_label && !column.is_text) {
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v = 0;
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}
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@@ -145,12 +145,13 @@ return Backbone.View.extend({
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// link this
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var self = this;
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// is a numeric number required
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// available column options
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var is_label = column_definition.is_label;
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var is_auto = column_definition.is_auto;
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var is_numeric = column_definition.is_numeric;
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var is_unique = column_definition.is_unique;
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var is_zero = column_definition.is_zero;
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var is_text = column_definition.is_text;
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// configure columns
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var columns = [];
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@@ -182,7 +183,7 @@ return Backbone.View.extend({
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if (meta[key] == 'int' || meta[key] == 'float') {
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valid = is_numeric;
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} else {
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valid = is_label;
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valid = is_text || is_label;
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}
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// check type
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@@ -230,7 +230,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc',
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title : 'Search',
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tooltip : 'Search help for this tool (Biostar)',
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onclick : function() {
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window.open(options.biostar_url + '/t/' + options.id + '/');
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window.open(options.biostar_url + '/local/search/page/?q=' + options.name);
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}
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});
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};
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@@ -1 +1 @@
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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-section","mvc/tools/tools-tree"],function(f,g,e,j,h,a,d,c,i,b){return Backbone.View.extend({initialize:function(k){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=f.merge(k,this.optionsDefault);console.debug(this.options);var l=parent.Galaxy;if(l&&l.modal){this.modal=l.modal}else{this.modal=new j.Modal.View()}if(l&&l.currUser){this.is_admin=l.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new g();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var k=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.history={};k.options.inputs=m&&m.inputs;this._renderForm(m);var l=this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){k.deferred.reset();k.deferred.execute(function(){var n=k.tree.finalize();if(!_.isEqual(n,l)){l=n;k._updateModel($.extend(true,{},l))}})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}})},reciept:function(k){$(this.container).empty();$(this.container).append(k)},highlight:function(l,m,k){var n=this.element_list[l];if(n){n.error(m||"Please verify this parameter.");if(!k){$("html, body").animate({scrollTop:n.$el.offset().top-20},500)}}},_errors:function(m){this.trigger("reset");if(m&&m.errors){var n=this.tree.matchResponse(m.errors);for(var l in this.element_list){var k=this.element_list[l];if(n[l]){this.highlight(l,n[l],true)}}}},_renderForm:function(s){var r=this;this.message=new j.Message();var l=new j.ButtonMenu({icon:"fa-cubes",title:(!s.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(s.versions&&s.versions.length>1){for(var n in s.versions){var p=s.versions[n];if(p!=s.version){l.addMenu({title:"Switch to "+p,version:p,icon:"fa-cube",onclick:function(){r.options.id=r.options.id.replace(r.options.version,this.version);r.options.version=this.version;r.deferred.reset();r.deferred.execute(function(){r._buildModel()})}})}}}else{l.$el.hide()}var o=new j.ButtonMenu({icon:"fa-caret-down",title:(!s.narrow&&"Options")||null,tooltip:"View available options"});if(s.biostar_url){o.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(s.biostar_url+"/p/new/post/")}});o.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(s.biostar_url+"/t/"+s.id+"/")}})}o.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+s.id)}});if(this.is_admin){o.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+s.id+"/download"}})}if(s.requirements&&s.requirements.length>0){o.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;r.message.update({persistent:true,message:c.requirements(s),status:"info"})}else{this.visible=false;r.message.update({message:""})}}})}if(this.options.sharable_url){o.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(r.options.sharable_url)}})}this.section=new i.View(r,{inputs:s.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new e.View({icon:"fa-wrench",title:"<b>"+s.name+"</b> "+s.description+" (Galaxy Tool Version "+s.version+")",cls:this.options.cls_portlet,operations:{menu:o,versions:l},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(s.help!=""){this.$el.append(c.help(s.help))}if(s.citations){var q=$("<div/>");var k=new h.ToolCitationCollection();k.tool_id=s.id;var m=new a.CitationListView({el:q,collection:k});m.render();k.fetch();this.$el.append(q)}if(s.message){this.message.update({persistent:true,status:"warning",message:s.message})}console.debug("tools-form-base::initialize() - Completed.")}})});
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define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-section","mvc/tools/tools-tree"],function(f,g,e,j,h,a,d,c,i,b){return Backbone.View.extend({initialize:function(k){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=f.merge(k,this.optionsDefault);console.debug(this.options);var l=parent.Galaxy;if(l&&l.modal){this.modal=l.modal}else{this.modal=new j.Modal.View()}if(l&&l.currUser){this.is_admin=l.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new g();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var k=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.history={};k.options.inputs=m&&m.inputs;this._renderForm(m);var l=this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){k.deferred.reset();k.deferred.execute(function(){var n=k.tree.finalize();if(!_.isEqual(n,l)){l=n;k._updateModel($.extend(true,{},l))}})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}})},reciept:function(k){$(this.container).empty();$(this.container).append(k)},highlight:function(l,m,k){var n=this.element_list[l];if(n){n.error(m||"Please verify this parameter.");if(!k){$("html, body").animate({scrollTop:n.$el.offset().top-20},500)}}},_errors:function(m){this.trigger("reset");if(m&&m.errors){var n=this.tree.matchResponse(m.errors);for(var l in this.element_list){var k=this.element_list[l];if(n[l]){this.highlight(l,n[l],true)}}}},_renderForm:function(s){var r=this;this.message=new j.Message();var l=new j.ButtonMenu({icon:"fa-cubes",title:(!s.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(s.versions&&s.versions.length>1){for(var n in s.versions){var p=s.versions[n];if(p!=s.version){l.addMenu({title:"Switch to "+p,version:p,icon:"fa-cube",onclick:function(){r.options.id=r.options.id.replace(r.options.version,this.version);r.options.version=this.version;r.deferred.reset();r.deferred.execute(function(){r._buildModel()})}})}}}else{l.$el.hide()}var o=new j.ButtonMenu({icon:"fa-caret-down",title:(!s.narrow&&"Options")||null,tooltip:"View available options"});if(s.biostar_url){o.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(s.biostar_url+"/p/new/post/")}});o.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(s.biostar_url+"/local/search/page/?q="+s.name)}})}o.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+s.id)}});if(this.is_admin){o.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+s.id+"/download"}})}if(s.requirements&&s.requirements.length>0){o.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;r.message.update({persistent:true,message:c.requirements(s),status:"info"})}else{this.visible=false;r.message.update({message:""})}}})}if(this.options.sharable_url){o.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(r.options.sharable_url)}})}this.section=new i.View(r,{inputs:s.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new e.View({icon:"fa-wrench",title:"<b>"+s.name+"</b> "+s.description+" (Galaxy Tool Version "+s.version+")",cls:this.options.cls_portlet,operations:{menu:o,versions:l},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(s.help!=""){this.$el.append(c.help(s.help))}if(s.citations){var q=$("<div/>");var k=new h.ToolCitationCollection();k.tool_id=s.id;var m=new a.CitationListView({el:q,collection:k});m.render();k.fetch();this.$el.append(q)}if(s.message){this.message.update({persistent:true,status:"warning",message:s.message})}console.debug("tools-form-base::initialize() - Completed.")}})});
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