3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e184e48b8e2d/ Changeset: e184e48b8e2d User: jeremy goecks Date: 2014-01-21 23:24:14 Summary: Trailing whitespace fixes. Affected #: 1 file diff -r 13114825942ff71c6dac143bba6ed31a7cb8d584 -r e184e48b8e2d6f723ea55e351ab3820a8735c03e static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -17,7 +17,7 @@ // To the right of screen? eltBRect.left > svgBRect.right || // Above screen? - eltBRect.bottom < 0 || + eltBRect.bottom < 0 || // Below screen? eltBRect.top > svgBRect.bottom) { return false; @@ -125,7 +125,7 @@ /** * Renders a full circster visualization. - */ + */ var CircsterView = Backbone.View.extend({ className: 'circster', @@ -174,7 +174,7 @@ min_dimension = Math.min(this.$el.width(), this.$el.height()), // Compute radius start based on model, will be centered // and fit entirely inside element by default. - radius_start = min_dimension / 2 - + radius_start = min_dimension / 2 - circular_tracks.length * (this.dataset_arc_height + this.track_gap) - (this.label_arc_height + this.track_gap), @@ -212,7 +212,7 @@ // Do zoom, drag. var scale = d3.event.scale; svg.attr("transform", - "translate(" + d3.event.translate + ")" + + "translate(" + d3.event.translate + ")" + " scale(" + scale + ")"); // Propagate scale changes to views. @@ -320,7 +320,7 @@ // Update chords tracks. _.each(this.chords_views, function(track_view) { track_view.update_radius_bounds(new_track_bounds[0]); - }); + }); // Render new track. var track_index = this.circular_views.length, @@ -510,8 +510,8 @@ self._update_data_bounds(); // Find chromosome arc to draw data on. - var chrom_arc = _.find(self.chroms_layout, function(layout) { - return layout.data.chrom === chrom; + var chrom_arc = _.find(self.chroms_layout, function(layout) { + return layout.data.chrom === chrom; }); // Add new data path and apply preferences. @@ -668,7 +668,7 @@ .attr('id', function(d) { return 'label-' + d.data.chrom; }); chrom_arcs.append("svg:text") - .filter(function(d) { + .filter(function(d) { return d.endAngle - d.startAngle > self.min_arc_len; }) .attr('text-anchor', 'middle') @@ -676,7 +676,7 @@ .attr("xlink:href", function(d) { return "#label-" + d.data.chrom; }) .attr('startOffset', '25%') .attr('font-weight', 'bold') - .text(function(d) { + .text(function(d) { return d.data.chrom; }); @@ -944,9 +944,9 @@ }); // Return angle at position. - return chrom_angle_data.endAngle - - ( - (chrom_angle_data.endAngle - chrom_angle_data.startAngle) * + return chrom_angle_data.endAngle - + ( + (chrom_angle_data.endAngle - chrom_angle_data.startAngle) * (chrom_angle_data.data.len - position) / chrom_angle_data.data.len ); } @@ -1021,7 +1021,7 @@ Galaxy.modal.show({ title : "Could Not Save", body : "Could not save visualization. Please try again later.", - buttons : { "Cancel": function() { Galaxy.modal.hide() } } + buttons : { "Cancel": function() { Galaxy.modal.hide(); } } }); }); } https://bitbucket.org/galaxy/galaxy-central/commits/cad75a868821/ Changeset: cad75a868821 User: jeremy goecks Date: 2014-01-22 01:50:13 Summary: Circster fixes for f4832c4 Affected #: 1 file diff -r e184e48b8e2d6f723ea55e351ab3820a8735c03e -r cad75a8688211b5fdf4c57d338fee009febfd230 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -875,7 +875,7 @@ var BackboneTrack = Backbone.Model.extend({ initialize: function(options) { - this.set('dataset', new data_mod.Dataset('dataset')); + this.set('dataset', new data_mod.Dataset(options.dataset)); // -- Set up config settings. -- @@ -902,7 +902,7 @@ } }); -var BackboneTrackCollection = new Backbone.Collection.extend({ +var BackboneTrackCollection = Backbone.Collection.extend({ model: BackboneTrack }); https://bitbucket.org/galaxy/galaxy-central/commits/6c3c24b83d97/ Changeset: 6c3c24b83d97 User: jeremy goecks Date: 2014-01-22 01:51:10 Summary: Automated merge of local changesets with default branch. Affected #: 12 files diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -37,17 +37,27 @@ this.chart_view = new ChartView(this); this.viewport_view = new ViewportView(this); - // portlet - this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'}); + // append view port to charts viewer + this.charts_view.append(this.viewport_view.$el); + + // create portlet + if (!this.options.config.widget) { + this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'}); + } else { + this.portlet = $('<div></div>'); + } + + // append views this.portlet.append(this.charts_view.$el); this.portlet.append(this.group_view.$el); this.portlet.append(this.chart_view.$el); - // append main - this.charts_view.append(this.viewport_view.$el); - - // set elements - this.setElement(this.portlet.$el); + // set element + if (!this.options.config.widget) { + this.setElement(this.portlet.$el); + } else { + this.setElement(this.portlet); + } // hide views this.group_view.$el.hide(); diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 config/plugins/visualizations/charts/static/library/portlet.js --- a/config/plugins/visualizations/charts/static/library/portlet.js +++ b/config/plugins/visualizations/charts/static/library/portlet.js @@ -116,21 +116,38 @@ showOperation: function(id) { this.$operations.find('#' + id).show(); }, - + + // set operation + setOperation: function(id, callback) { + var $el = this.$operations.find('#' + id); + $el.off('click'); + $el.on('click', callback); + }, + + // label + label: function(new_label) { + var $el = this.$el.find('#label'); + if (new_label) { + $el.html(new_label); + } + return $el.html(); + }, + // fill regular modal template template: function(options) { var tmpl = '<div class="toolForm">'; - if (options.label) { - tmpl += '<div id="title" class="toolFormTitle" style="padding-bottom: 7px;">' + + if (options.label || options.icon) { + tmpl += '<div id="title" class="toolFormTitle" style="overflow:hidden;">' + '<div id="operations" style="float: right;"></div>' + - '<div>'; + '<div style="overflow: hidden">'; if (options.icon) - tmpl += '<i style="font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>'; + tmpl += '<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>'; - tmpl += options.label + - '</div>' + + tmpl += '<div id="label" style="padding-top: 2px; float: left;">' + options.label + '</div>'; + + tmpl += '</div>' + '</div>'; } tmpl += '<div id="body" class="toolFormBody">'; diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 config/plugins/visualizations/charts/static/models/datasets.js --- a/config/plugins/visualizations/charts/static/models/datasets.js +++ b/config/plugins/visualizations/charts/static/models/datasets.js @@ -6,9 +6,9 @@ { // options optionsDefault : { - limit : 20, + limit : 500, pace : 1000, - max : 5 + max : 2 }, // list diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 config/plugins/visualizations/charts/static/views/charts.js --- a/config/plugins/visualizations/charts/static/views/charts.js +++ b/config/plugins/visualizations/charts/static/views/charts.js @@ -45,25 +45,6 @@ self.app.chart_view.$el.show(); } }), - 'edit' : new Ui.ButtonIcon({ - icon : 'fa-pencil', - tooltip: 'Edit', - onclick: function() { - // check if element has been selected - var chart_id = self.table.value(); - if (!chart_id) { - return; - } - - // get chart - var chart = self.app.charts.get(chart_id); - self.app.chart.copy(chart); - - // show edit - self.$el.hide(); - self.app.chart_view.$el.show(); - } - }), 'delete' : new Ui.ButtonIcon({ icon : 'fa-minus', tooltip: 'Delete', @@ -100,7 +81,9 @@ this.portlet.append(this.table.$el); // append to main - this.$el.append(this.portlet.$el); + if (!this.app.options.config.widget) { + this.$el.append(this.portlet.$el); + } // events var self = this; diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 config/plugins/visualizations/charts/static/views/viewport.js --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -25,8 +25,16 @@ // add table to portlet this.portlet = new Portlet({ + label : '', + icon : 'fa-signal', height : this.options.height, - overflow : 'hidden' + overflow : 'hidden', + operations : { + 'edit' : new Ui.ButtonIcon({ + icon : 'fa-gear', + tooltip : 'Configure' + }) + } }); // set this element @@ -69,6 +77,24 @@ // add _addChart: function(chart) { + // link this + var self = this; + + // backup chart details + var chart_id = chart.id; + + // update portlet + this.portlet.label(chart.get('title')); + this.portlet.setOperation('edit', function() { + // get chart + var chart = self.app.charts.get(chart_id); + self.app.chart.copy(chart); + + // show edit + self.app.charts_view.$el.hide(); + self.app.chart_view.$el.show(); + }); + // make sure that svg does not exist already this._removeChart(chart.id); diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -361,6 +361,7 @@ 'filename' : os.path.basename( ftp_file ) } file_bunch = get_data_file_filename( ftp_data_file, override_name = name, override_info = info ) if file_bunch.path: + file_bunch.to_posix_lines = to_posix_lines file_bunch.space_to_tab = space_to_tab rval.append( file_bunch ) return rval diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -173,8 +173,7 @@ title: '', content: null, target: '', - type: null, - scratchbook: false + type: null } // read in defaults @@ -1096,8 +1095,14 @@ title = ''; // identify content type - if (type == 'url') - content = '<iframe scrolling="auto" class="f-iframe" src="' + content + '"></iframe>'; + if (type == 'url') { + if (content.indexOf('?') == -1) + content += '?'; + else + content += '&'; + content += 'widget=True'; + content = '<iframe scrolling="auto" class="f-iframe" src="' + content + '"></iframe>'; + } // load template return '<div id="' + id + '" class="frame corner">' + diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -425,8 +425,7 @@ title : "Scatterplot", type : "url", content : url + '/scatterplot?' + $.param(params), - target : target, - scratchbook : true + target : target }); //TODO: this needs to go away @@ -487,8 +486,7 @@ parent.Galaxy.frame.add({ title : "Trackster", type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params), - scratchbook : true + content : vis_url + "/trackster?" + $.param(dataset_params) }); }); } @@ -505,8 +503,7 @@ parent.Galaxy.frame.add({ title : "Trackster", type : "url", - content : url, - scratchbook : true + content : url }); } } diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 static/scripts/packed/galaxy.frame.js --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(f){c._event_panel_active(f)},onunload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){c._event_panel_load(f)},with_number:true});Galaxy.masthead.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},add:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},_location_rank:function(c){return(c.top*this.cols)+c.left},_menu_refresh:function(){this.button_load.number(this.frame_counter);if(this.frame_counter==0){this.button_load.hide()}else{this.button_load.show()}if(this.top==this.options.top_min){$(".frame-scroll-up").hide()}else{$(".frame-scroll-up").show()}if(this.top==this.top_max){$(".frame-scroll-down").hide()}else{$(".frame-scroll-down").show()}},_panel_animation_complete:function(){var c=this;$(".frame").promise().done(function(){c._panel_scroll(0,true)})},_panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this._frame_insert(null,null,c)},_panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this._frame_offset(g,f,c)}}this.top=e}this._menu_refresh()},_panel_show_hide:function(){if(this.visible){this.visible=false;$(".frame").fadeOut("fast");this.button_load.icon("fa-eye-slash");this.button_load.untoggle();$(".frame-background").hide();$(".frame-menu").hide()}else{this.visible=true;$(".frame").fadeIn("fast");this.button_load.icon("fa-eye");this.button_load.toggle();$(this.frame_shadow.id).hide();$(".frame-background").show();this._panel_refresh()}},_panel_active_disable:function(){if(this.active){this.active=false;this.button_active.untoggle();if(this.visible){this._panel_show_hide()}}else{this.active=true;this.button_active.toggle()}},_frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this._location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this._frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this._menu_refresh()},_frame_place:function(k,d){k.grid_location=null;var h=this._to_grid(this._frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this._is_collision(h)){c=true;break}}if(c){break}}if(c){this._frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},_frame_focus:function(e,c){var d=this.frame_z+(c?1:0);$(e.id).css("z-index",d)},_frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this._frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c._frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},_frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},_frame_grid:function(e,c,d){e.grid_location=c;this._frame_offset(e,this._to_pixel(c),d);e.grid_rank=this._location_rank(c)},_frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},_template:function(){return'<div class="galaxy-frame"></div>'},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="frame corner"><div class="f-header corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa fa-thumb-tack"></span><span class="f-icon f-close fa fa-trash-o"></span></div><div class="f-content">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon corner fa fa-resize-full"></span></div>'},_template_shadow:function(c){return'<div id="'+c+'" class="frame-shadow corner"></div>'},_template_background:function(){return'<div class="frame-background"></div>'},_template_menu:function(){return'<div class="frame-scroll-up frame-menu fa fa-chevron-up fa-2x"></div><div class="frame-scroll-down frame-menu fa fa-chevron-down fa-2x"></div>'}});return{GalaxyFrame:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(f){c._event_panel_active(f)},onunload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){c._event_panel_load(f)},with_number:true});Galaxy.masthead.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},add:function(d){var g={title:"",content:null,target:"",type:null};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},_location_rank:function(c){return(c.top*this.cols)+c.left},_menu_refresh:function(){this.button_load.number(this.frame_counter);if(this.frame_counter==0){this.button_load.hide()}else{this.button_load.show()}if(this.top==this.options.top_min){$(".frame-scroll-up").hide()}else{$(".frame-scroll-up").show()}if(this.top==this.top_max){$(".frame-scroll-down").hide()}else{$(".frame-scroll-down").show()}},_panel_animation_complete:function(){var c=this;$(".frame").promise().done(function(){c._panel_scroll(0,true)})},_panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this._frame_insert(null,null,c)},_panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this._frame_offset(g,f,c)}}this.top=e}this._menu_refresh()},_panel_show_hide:function(){if(this.visible){this.visible=false;$(".frame").fadeOut("fast");this.button_load.icon("fa-eye-slash");this.button_load.untoggle();$(".frame-background").hide();$(".frame-menu").hide()}else{this.visible=true;$(".frame").fadeIn("fast");this.button_load.icon("fa-eye");this.button_load.toggle();$(this.frame_shadow.id).hide();$(".frame-background").show();this._panel_refresh()}},_panel_active_disable:function(){if(this.active){this.active=false;this.button_active.untoggle();if(this.visible){this._panel_show_hide()}}else{this.active=true;this.button_active.toggle()}},_frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this._location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this._frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this._menu_refresh()},_frame_place:function(k,d){k.grid_location=null;var h=this._to_grid(this._frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this._is_collision(h)){c=true;break}}if(c){break}}if(c){this._frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},_frame_focus:function(e,c){var d=this.frame_z+(c?1:0);$(e.id).css("z-index",d)},_frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this._frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c._frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},_frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},_frame_grid:function(e,c,d){e.grid_location=c;this._frame_offset(e,this._to_pixel(c),d);e.grid_rank=this._location_rank(c)},_frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},_template:function(){return'<div class="galaxy-frame"></div>'},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){if(d.indexOf("?")==-1){d+="?"}else{d+="&"}d+="widget=True";d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="frame corner"><div class="f-header corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa fa-thumb-tack"></span><span class="f-icon f-close fa fa-trash-o"></span></div><div class="f-content">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon corner fa fa-resize-full"></span></div>'},_template_shadow:function(c){return'<div id="'+c+'" class="frame-shadow corner"></div>'},_template_background:function(){return'<div class="frame-background"></div>'},_template_menu:function(){return'<div class="frame-scroll-up frame-menu fa fa-chevron-up fa-2x"></div><div class="frame-scroll-down frame-menu fa fa-chevron-down fa-2x"></div>'}});return{GalaxyFrame:a}}); \ No newline at end of file diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(g.length===1){var h=g[0];i.attr("data-original-title",_l("Visualize in ")+h.html);i.attr("href",h.href)}else{var j=[];_.each(g,function(k){k.func=function(){if(Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:k.href});return false}return true};j.push(k);return false});PopupMenu.create(i,j)}return i},_buildNewRender:function(){var g=a.HDABaseView.prototype._buildNewRender.call(this);g.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));g.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return g},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(h){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var g=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);h.find(".dataset-dbkey .value").replaceWith(g)}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h,scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton];this.tagsEditorShown=g.tagsEditorShown||false;this.annotationEditorShown=g.annotationEditorShown||false},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit attributes"),href:this.urls.edit,target:this.linkTarget,classes:"dataset-edit"};if(g||i){h.disabled=true;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h={title:_l("Delete"),classes:"dataset-delete",onclick:function(){g.$el.find(".icon-btn.dataset-delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){h={title:_l("Dataset is already deleted"),disabled:true}}h.faIcon="fa-times";return faIconButton(h)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,classes:"dataset-report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,classes:"dataset-rerun-btn",target:this.linkTarget,faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var n=this.model.get("visualizations");if((!this.hasUser)||(!this.model.hasData())||(_.isEmpty(n))){return null}if(_.isObject(n[0])){return this._render_visualizationsFrameworkButton(n)}if(!this.urls.visualization){return null}var k=this.model.get("dbkey"),g=this.urls.visualization,j={},h={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(k){h.dbkey=k}var l=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});var m=this;function i(p){switch(p){case"trackster":return b(g,h,k);case"scatterplot":return e(g,h,m.linkTarget);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:g+"/"+p+"?"+$.param(h)})}}}function o(p){return p.charAt(0).toUpperCase()+p.slice(1)}if(n.length===1){l.attr("data-original-title",_l("Visualize in ")+_l(o(n[0])));l.click(i(n[0]))}else{_.each(n,function(p){j[_l(o(p))]=i(p)});make_popupmenu(l,j)}return l},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),classes:"dataset-visualize-btn",faIcon:"fa-bar-chart-o"});if(g.length===1){var h=g[0];i.attr("data-original-title",_l("Visualize in ")+h.html);i.attr("href",h.href)}else{var j=[];_.each(g,function(k){k.func=function(){if(Galaxy.frame.active){Galaxy.frame.add({title:"Visualization",type:"url",content:k.href});return false}return true};j.push(k);return false});PopupMenu.create(i,j)}return i},_buildNewRender:function(){var g=a.HDABaseView.prototype._buildNewRender.call(this);g.find(".dataset-deleted-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-undelete">here</a> to undelete it or <a href="javascript:void(0);" class="dataset-purge">here</a> to immediately remove it from disk'));g.find(".dataset-hidden-msg").append(_l('Click <a href="javascript:void(0);" class="dataset-unhide">here</a> to unhide it'));return g},_render_body_failed_metadata:function(){var h=$("<a/>").attr({href:this.urls.edit,target:this.linkTarget}).text(_l("set it manually or retry auto-detection")),g=$("<span/>").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){var h=this;this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.tagsEditorShown=true},onhide:function(){h.tagsEditorShown=false},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))});if(this.tagsEditorShown){this.tagsEditor.toggle(true)}},_renderAnnotation:function(g){var h=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){h.annotationEditorShown=true},onhide:function(){h.annotationEditorShown=false},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))});if(this.annotationEditorShown){this.annotationEditor.toggle(true)}},makeDbkeyEditLink:function(h){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){var g=$('<a class="value">?</a>').attr("href",this.urls.edit).attr("target",this.linkTarget);h.find(".dataset-dbkey .value").replaceWith(g)}},events:_.extend(_.clone(a.HDABaseView.prototype.events),{"click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"}),confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,i,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(i),target:h});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i)})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff -r cad75a8688211b5fdf4c57d338fee009febfd230 -r 6c3c24b83d97adc4b946f01321c540fc48e6bb21 templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -3,6 +3,9 @@ <%def name="javascripts()"> ${parent.javascripts()} <script type="text/javascript"> + $.fn.outerHTML = function(s) { + return s ? this.before(s).remove() : jQuery("<p>").append(this.eq(0).clone()).html(); + }; $( function() { function show_tool_body(title){ title.parent().show().css('border-bottom-width', '1px'); @@ -57,7 +60,7 @@ } else { // Collapse non-interactive run-workflow panels by default. - $("div.toolFormBody:not(:has(select, textarea, input[type!=hidden], .wfpspan))").hide().parent().css('border-bottom-width', '0px'); + $("div.toolFormBody:not(:has(.runtime-form-row))").hide().parent().css('border-bottom-width', '0px'); } $("#show_all_tool_body").click(function(){ $("div.toolFormTitle").each(function(){ @@ -129,6 +132,55 @@ select.after(filter); select.width(new_width); }); + // Editable Workflow + + var readyParameter = function(icon) { + icon.attr("name", "edit"); + icon.attr('title', "Modify default value for this workflow parameter."); + icon.removeClass("workflow-edit-button-editing"); + icon.addClass("workflow-edit-button-ready"); + icon.addClass("fa-edit"); + icon.removeClass("fa-undo"); + }; + + var editingParameter = function(icon) { + icon.attr("name", "revert"); + icon.attr('title', "Restore workflow default value for this parameter."); + icon.addClass("workflow-edit-button-editing"); + icon.removeClass("workflow-edit-button-ready"); + icon.removeClass("fa-edit"); + icon.addClass("fa-undo"); + }; + + $(".workflow-edit-button").on("click",function(){ + var state = $(this).attr("name"); + var stepToolBox = $(this).parent().find('input:not([class]), select:not([class])'); + var split_name=stepToolBox.attr("name").split("|"); + var step_id = split_name[0]; + var step_name = split_name[split_name.length-1]; + hidden_html = "<input type='hidden' name='"+step_id+"|__runtime__"+step_name+"' value='true' />"; + if (state === "edit"){ + stepToolBoxClone = stepToolBox.clone(); + stepToolBoxClone.attr({"name":step_id+"|"+step_name}); + stepToolBoxClone.show() + $(this).parent().find(".editable").show(); + $(this).parent().parent().find(".uneditable_field").hide(); + $(this).parent().find(".editable").html(stepToolBoxClone.outerHTML()+hidden_html); + editingParameter($(this)); + } + else{ + $(this).parent().find(".editable").hide(); + $(this).parent().parent().find(".uneditable_field").show(); + $(this).attr("name", "edit"); + stepToolBox.hide(); + readyParameter($(this)); + } + }).each(function(i, icon) { + var conditionalStart = $(this).closest(".form-row").prev().hasClass("conditional-start"); + if(! conditionalStart ) { + readyParameter($(icon)); + } + }); // Augment hidden fields with icons. // http://stackoverflow.com/a/2088430 @@ -217,6 +269,22 @@ .workflow-annotation { margin-bottom: 1em; } + .editable { + display: none; + } + + .workflow-edit-button-editing { + color: black; + } + + .workflow-edit-button-default { + color: Gray; + } + + .workflow-edit-button:hover { + color: green; // TODO: Use a history panel green. + } + </style></%def> @@ -273,6 +341,7 @@ <% current_case = group_values['__current_case__'] %><% new_prefix = prefix + input.name + "|" %><% group_errors = errors.get( input.name, {} ) %> + <span class="conditional-start"></span> ${row_for_param( input.test_param, group_values[ input.test_param.name ], other_values, group_errors, prefix, step, already_used )} ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, new_prefix, step, other_values, already_used )} %else: @@ -310,12 +379,16 @@ %> %if step.type == 'data_input': ##Input Dataset Step, wrap for multiinput. - <span class='multiinput_wrap'> - <input class="multi-mode" type="hidden" name="${str(step.id)}|multi_mode" id="${str(step.id)}|multi_mode" value="matched" /> - ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + <span class="runtime-form-row"> + <span class='multiinput_wrap'> + <input class="multi-mode" type="hidden" name="${str(step.id)}|multi_mode" id="${str(step.id)}|multi_mode" value="matched" /> + ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + </span></span> %else: - ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + <span class="runtime-form-row"> + ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + </span> %endif <input type="hidden" name="${step.id}|__force_update__${prefix}${param.name}" value="true" /> @@ -335,8 +408,10 @@ if not enable_unique_defaults: del already_used[:] %> - ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} - <input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" /> + <span class="runtime-form-row"> + ${param.get_html_field( t, value, other_values ).get_html( str(step.id) + "|" + prefix )} + <input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" /> + </span> %else: <% p_text = param.value_to_display_text( value, app ) @@ -344,7 +419,7 @@ if isinstance(p_text, basestring): for rematch in re.findall('\$\{.+?\}', p_text): replacements.append('wf_parm__%s' % rematch[2:-1]) - p_text = p_text.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1])) + p_text = p_text.replace(rematch, '<span style="background-color:%s" class="runtime-form-row wfpspan wf_parm__%s">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1])) %> %if replacements: <span style="display:none" class="parm_wrap ${' '.join(replacements)}"> @@ -353,7 +428,18 @@ <span class="p_text_wrapper">${p_text}</span><input type="hidden" name="${step.id}|__runtime__${prefix}${param.name}" value="true" /> %else: - ${param.value_to_display_text( value, app )} + <span class="workflow_parameters"> + <span class="uneditable_field"> + ${param.value_to_display_text( value, app )} + </span> + <span class="editable_field"> + <span class="editable"> + ${param.get_html_field( t, value, other_values).get_html( str(step.id) + "|" + "editable" + "|"+ prefix )} + </span> + + <i class="fa workflow-edit-button"></i> + </span> + </span> %endif %endif </div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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