From 8e0eaf2427a99f093a35d686532214534c1bb043 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 24 Aug 2016 22:19:10 -0400 Subject: [PATCH 01/27] Add biojs multiple sequence viewer --- .../visualizations/charts/config/charts.xml | 3 ++- .../charts/static/charts/biojs/msa/config.js | 9 ++++++++ .../charts/static/charts/biojs/msa/logo.png | Bin 0 -> 28113 bytes .../charts/static/charts/biojs/msa/wrapper.js | 18 +++++++++++++++ .../charts/static/charts/overview.js | 3 +++ .../charts/static/charts/types.js | 9 +++++--- .../charts/static/plugins/biojs/biojs.msa.js | 21 ++++++++++++++++++ .../charts/static/views/editor.js | 2 +- .../charts/static/views/groups.js | 2 +- .../charts/static/views/settings.js | 4 +++- .../charts/static/views/viewport.js | 9 +++++++- .../charts/templates/charts.mako | 3 +++ 12 files changed, 75 insertions(+), 8 deletions(-) create mode 100644 config/plugins/visualizations/charts/static/charts/biojs/msa/config.js create mode 100644 config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png create mode 100644 config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js create mode 100755 config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js diff --git a/config/plugins/visualizations/charts/config/charts.xml b/config/plugins/visualizations/charts/config/charts.xml index 8356fc32d5f2..caae65f8a12d 100644 --- a/config/plugins/visualizations/charts/config/charts.xml +++ b/config/plugins/visualizations/charts/config/charts.xml @@ -6,6 +6,7 @@ HistoryDatasetAssociation tabular.Tabular tabular.CSV + data.Text dataset_id @@ -13,4 +14,4 @@ dataset_id charts.mako - + \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/biojs/msa/config.js b/config/plugins/visualizations/charts/static/charts/biojs/msa/config.js new file mode 100644 index 000000000000..ca99220105a5 --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/biojs/msa/config.js @@ -0,0 +1,9 @@ +define( [], function() { + return { + title : 'Multiple Sequence Alignment', + category : 'Sequence', + library : 'BioJS', + datatype : 'txt', + keywords : 'biojs' + } +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png b/config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png new file mode 100644 index 0000000000000000000000000000000000000000..ad87f32b3b47982acf1feca24e72e3270ae307a4 GIT binary patch literal 28113 zcmZ^K1ymgGvL^)h;4Z=4b+918-QC?~a1Rg|G`K@>cXxMpcY?b+%l+T`-rL=?JLk+y zebwdNr@!g?)qoV_#F60f;K9JakR&BUl|H{OKi@;J(4U_R-Zq~ML`+K&5d}#R5fTL_ zdoxQLQ!p?IP(l)nO58Bk-~k;?P!LwAfBaM$NxRg=kMDpbSV?~cVOU5^FHIE(hN4h| zAL`$2tieqbQ59{%4KA2Mi^|Hvq3Da+B)=RwZ)Un}?2RSqpRaix2*#ycjDh{Jm_&oE zQJ?^;d3x$8`c7;nY=jm^4h{QS^u^R*)aU@Njf||fOE58ebqYHXKQUJ4cz3kAbK?Ows6my~z*+ 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b/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js @@ -0,0 +1,18 @@ +define( [ 'utils/utils' ], function( Utils ) { + return Backbone.Model.extend({ + initialize: function( app, options ) { + var chart = app.chart; + var m = new msa.msa({ + el: $( '#' + options.canvas_list[ 0 ] ), + vis: { conserv: false, overviewbox: false }, + menu: 'small', + bootstrapMenu: true + }); + m.u.file.importURL( options.dataset.download_url, function() { + m.render(); + app.chart.state( 'ok', 'Chart drawn.' ); + options.process.resolve(); + }); + } + }); +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/overview.js b/config/plugins/visualizations/charts/static/charts/overview.js index df07c21ca70d..fd2fac444920 100644 --- a/config/plugins/visualizations/charts/static/charts/overview.js +++ b/config/plugins/visualizations/charts/static/charts/overview.js @@ -8,6 +8,9 @@ define( [], function() { help : 'jqPlot is a canvas-based library hosted at www.jqplot.com. It is a plotting and charting plugin for the jQuery Javascript framework. Since based on canvas it is capable of rendering many thousand data points without adverse effects.' }, { label : 'Others', value: 'others', help : 'These visualizations were developed by the Galaxy team.' + }, + { label : 'BioJS', value: 'biojs', + help : 'BioJS plugins.' } ]; }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/types.js b/config/plugins/visualizations/charts/static/charts/types.js index 07b17cc443aa..55f1ca1b5543 100644 --- a/config/plugins/visualizations/charts/static/charts/types.js +++ b/config/plugins/visualizations/charts/static/charts/types.js @@ -18,7 +18,8 @@ define(['plugin/charts/nvd3/bar/config', 'plugin/charts/jqplot/histogram_discrete/config', 'plugin/charts/others/heatmap/config', 'plugin/charts/others/heatmap_cluster/config', - 'plugin/charts/others/example/config' ], + 'plugin/charts/others/example/config', + 'plugin/charts/biojs/msa/config' ], function(nvd3_bar, nvd3_bar_stacked, nvd3_bar_horizontal, @@ -39,7 +40,8 @@ define(['plugin/charts/nvd3/bar/config', jqplot_histogram_discrete, others_heatmap, others_heatmap_cluster, - others_example) { + others_example, + biojs_msa) { return { 'nvd3_bar' : nvd3_bar, 'nvd3_bar_stacked' : nvd3_bar_stacked, @@ -61,6 +63,7 @@ define(['plugin/charts/nvd3/bar/config', 'jqplot_boxplot' : jqplot_boxplot, 'others_heatmap' : others_heatmap, 'others_heatmap_cluster' : others_heatmap_cluster, - 'others_example' : others_example + 'others_example' : others_example, + 'biojs_msa' : biojs_msa } }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js b/config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js new file mode 100755 index 000000000000..e44545e56d0f --- /dev/null +++ b/config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js @@ -0,0 +1,21 @@ +!function(t){function e(r){if(n[r])return n[r].exports;var i=n[r]={exports:{},id:r,loaded:!1};return 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t.mousedown="_onmousedown",t.touchstart="_ontouchstart",this.g.config.get("registerMouseClicks")&&(t.dblclick="_onclick"),this.g.config.get("registerMouseHover")&&(t.mousein="_onmousein",t.mouseout="_onmouseout"),t.mousewheel="_onmousewheel",t.DOMMouseScroll="_onmousewheel",this.delegateEvents(t),this.listenTo(this.g.config,"change:registerMouseHover",this.manageEvents),this.listenTo(this.g.config,"change:registerMouseClick",this.manageEvents),this.dragStart=[]},_setColor:function(){return this.color=this.g.colorscheme.getSelectedScheme()},draw:function(){if(this.el.width=this.el.width,null!=this.seqDrawer&&this.model.length>0)return this.seqDrawer.drawLetters(),this.seqDrawer.drawRows(this.sel._appendSelection,this.sel),this.seqDrawer.drawRows(this.drawFeatures,this)},drawFeatures:function(t){var e=this,n=this.g.zoomer.get("columnWidth"),r=this.g.zoomer.get("rowHeight");if(t.model.attributes.height>1){var i=function(){var i=e.ctx;return t.model.attributes.features.each(function(e){i.fillStyle=e.attributes.fillColor||"red";var o=e.attributes.xEnd-e.attributes.xStart+1,s=(e.attributes.row+1)*r;return i.fillRect(e.attributes.xStart*n+t.xZero,s+t.yZero,n*o,r)}),i.fillStyle="black",i.font=e.g.zoomer.get("residueFont")+"px mono",i.textBaseline="middle",i.textAlign="center",{v:t.model.attributes.features.each(function(e){var o=e.attributes.xEnd-e.attributes.xStart+1,s=(e.attributes.row+1)*r;return i.fillText(e.attributes.text,t.xZero+e.attributes.xStart*n+o/2*n,t.yZero+.5*r+s)})}}();if("object"===("undefined"==typeof i?"undefined":o(i)))return i.v}},render:function(){return this.el.setAttribute("height",this.g.zoomer.get("alignmentHeight")+"px"),this.el.setAttribute("width",this.g.zoomer.getAlignmentWidth()+"px"),this.g.zoomer._checkScrolling(this._checkScrolling([this.g.zoomer.get("_alignmentScrollLeft"),this.g.zoomer.get("_alignmentScrollTop")]),{header:"canvasseq"}),this._setColor(),this.seqDrawer=new 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this.dragStart=v.abs(t),this.dragStartScroll=[this.g.zoomer.get("_alignmentScrollLeft"),this.g.zoomer.get("_alignmentScrollTop")],m(document.body).on("mousemove.overmove",function(t){return e._onmousemove(t)}),m(document.body).on("mouseup.overup",function(){return e._cleanup()}),t.preventDefault()},_ontouchstart:function(t){var e=this;return this.dragStart=v.abs(t.changedTouches[0]),this.dragStartScroll=[this.g.zoomer.get("_alignmentScrollLeft"),this.g.zoomer.get("_alignmentScrollTop")],m(document.body).on("touchmove.overtmove",function(t){return e._ontouchmove(t)}),m(document.body).on("touchend.overtend touchleave.overtleave touchcancel.overtcanel",function(t){return e._touchCleanup(t)})},_onmousewinout:function(t){if(t.toElement===document.body.parentNode)return this._cleanup()},_cleanup:function(){return this.dragStart=[],m(document.body).off(".overmove"),m(document.body).off(".overup"),m(document.body).off(".overout")},_touchCleanup:function(t){return t.changedTouches.length>0&&this._onmousemove(t.changedTouches[0],!0),this.dragStart=[],m(document.body).off(".overtmove"),m(document.body).off(".overtend"),m(document.body).off(".overtleave"),m(document.body).off(".overtcancel")},_onmousewheel:function(t){var e=v.wheelDelta(t);return this.g.zoomer.set("_alignmentScrollLeft",this.g.zoomer.get("_alignmentScrollLeft")+e[0]),this.g.zoomer.set("_alignmentScrollTop",this.g.zoomer.get("_alignmentScrollTop")+e[1]),t.preventDefault()},_onclick:function(t){var e=this._getClickPos(t);return"undefined"!=typeof e&&null!==e&&(null!=e.feature?this.g.trigger("feature:click",e):this.g.trigger("residue:click",e)),this.throttledDraw()},_onmousein:function(t){var e=this._getClickPos(t);return"undefined"!=typeof e&&null!==e&&(null!=e.feature?this.g.trigger("feature:mousein",e):this.g.trigger("residue:mousein",e)),this.throttledDraw()},_onmouseout:function(t){var e=this._getClickPos(t);return"undefined"!=typeof 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this.drawSeqs(function(n){return this.drawRow(n,t,e)})},drawRow:function(t,e,n){var r=this.g.zoomer.get("columnWidth"),i=Math.max(0,Math.abs(Math.ceil(-this.g.zoomer.get("_alignmentScrollLeft")/r))),o=-Math.abs(-this.g.zoomer.get("_alignmentScrollLeft")%r),s=o-i*r,u=t.yPos;return e.call(n,{model:t.model,xZero:s,yZero:u,hidden:t.hidden})},getStartSeq:function(){for(var t=Math.max(0,Math.floor(this.g.zoomer.get("_alignmentScrollTop")/this.rectHeight))+1,e=0,n=0;el))break}},_drawRect:function(t,e){var n=t.color.getColor(e.c,{pos:e.x,y:e.y});if("undefined"!=typeof n&&null!==n)return t.ctx.fillStyle=n,t.ctx.fillRect(e.xPos,e.yPos,e.rectWidth,e.rectHeight)},_drawLetter:function(t,e){return t.ctx.drawImage(t.cache.getFontTile(e.c,e.rectWidth,e.rectHeight),e.xPos,e.yPos,e.rectWidth,e.rectHeight)}},s=function(t,e,n,r){return this.g=t,this.ctx=e,this.model=n,this.width=r.width,this.height=r.height,this.color=r.color,this.cache=r.cache,this.rectHeight=this.g.zoomer.get("rowHeight"),this.rectWidth=this.g.zoomer.get("columnWidth"),this};(0,i.extend)(s.prototype,o),e["default"]=s},function(t,e,n){"use strict";function r(t){if(t&&t.__esModule)return t;var e={};if(null!=t)for(var n in t)Object.prototype.hasOwnProperty.call(t,n)&&(e[n]=t[n]);return e["default"]=t,e}Object.defineProperty(e,"__esModule",{value:!0});var i="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol?"symbol":typeof t},o=n(12),s=r(o),u=n(2),a=n(7),l=u.extend({className:"biojs_msa_conserv",initialize:function(t){this.g=t.g,this.listenTo(this.g.zoomer,"change:stepSize change:labelWidth change:columnWidth",this.render),this.listenTo(this.g.vis,"change:labels 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this.el.appendChild(o),this},markerHidden:function(t,e,n){for(var r=this,i=this.g.columns.get("hidden").slice(0),s=Math.max(0,e-n),u=!0,l=s;s=e;s=0;if(!u){for(var c=this.model.getMaxLength(),f=0,h=-1,e=e;(e=c)&&(h>=0||(h=i.indexOf(e)),i.indexOf(e)>=0);e0?this.el.style.fontWeight="bold":this.el.style.fontWeight="normal"}});e["default"]=l},function(t,e,n){"use strict";Object.defineProperty(e,"__esModule",{value:!0});var r=n(2),i=n(7),o=r.extend({initialize:function(t){return this.seq=t.seq,this.g=t.g,this.manageEvents()},manageEvents:function(){var t={};return this.g.config.get("registerMouseClicks")&&(t.click="_onclick"),this.g.config.get("registerMouseHover")&&(t.mousein="_onmousein",t.mouseout="_onmouseout"),this.delegateEvents(t),this.listenTo(this.g.config,"change:registerMouseHover",this.manageEvents),this.listenTo(this.g.config,"change:registerMouseClick",this.manageEvents),this.listenTo(this.g.vis,"change:labelName change:labelId change:labelPartition 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r=document.createElement("span");r.style.width=this.g.zoomer.get("labelPartLength")+"px",r.textContent=this.model.get("partition"),r.style.display="inline-block",this.el.appendChild(e),this.el.appendChild(r)}if(this.g.vis.get("labelName")){var o=document.createElement("span");o.textContent=this.model.get("name"),this.model.get("ref")&&this.g.config.get("hasRef")&&(o.style.fontWeight="bold"),o.style.width=this.g.zoomer.get("labelNameLength")+"px",this.el.appendChild(o)}return this.el.style.overflow=scroll,this.el.style.fontSize=this.g.zoomer.get("labelFontsize")+"px",this},_onclick:function(t){var e=this.model.get("id");return this.g.trigger("row:click",{seqId:e,evt:t})},_onmousein:function(t){var e=this.model.get("id");return this.g.trigger("row:mouseout",{seqId:e,evt:t})},_onmouseout:function(t){var e=this.model.get("id");return this.g.trigger("row:mouseout",{seqId:e,evt:t})}});e["default"]=o},function(t,e,n){"use strict";function r(t){return 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o=this.g.stats.identity()[this.model.id],a=document.createElement("span");this.model.get("ref")&&this.g.config.get("hasRef")?a.textContent="ref.":"undefined"!=typeof o&&null!==o&&(a.textContent=o.toFixed(2)),a.style.display="inline-block",a.style.width=40,this.el.appendChild(a)}if(this.g.vis.get("metaLinks")&&this.model.attributes.ids){var c=i.seqs.buildLinks(this.model.attributes.ids);if(Object.keys(c).length>0){var f=new s["default"]({name:"↗"});c.forEach(function(t,e){return f.addNode(e,function(e){return window.open(t)})});var h=f.buildDOM();return h.style.cursor="pointer",this.el.appendChild(h)}}},_onclick:function(t){return this.g.trigger("meta:click",{seqId:this.model.get("id",{evt:t})})},_onmousein:function(t){return this.g.trigger("meta:mousein",{seqId:this.model.get("id",{evt:t})})},_onmouseout:function(t){return this.g.trigger("meta:mouseout",{seqId:this.model.get("id",{evt:t})})}});e["default"]=c},function(t,e){(function(e){"use strict";"undefined"!=typeof window?t.exports=window:"undefined"!=typeof e?t.exports=e:"undefined"!=typeof self?t.exports=self:t.exports={}}).call(e,function(){return this}())},function(t,e,n){"use strict";function r(t,e,n){if(!u(e))throw new TypeError("iterator must be a function");arguments.length<3&&(n=this),"[object Array]"===a.call(t)?i(t,e,n):"string"==typeof t?o(t,e,n):s(t,e,n)}function i(t,e,n){for(var r=0,i=t.length;r=0&&_.splice(e,1)}function u(t){var e=document.createElement("style");return e.type="text/css",o(t,e),e}function a(t){var e=document.createElement("link");return e.rel="stylesheet",o(t,e),e}function l(t,e){var n,r,i;if(e.singleton){var o=y++;n=m||(m=u(e)),r=c.bind(null,n,o,!1),i=c.bind(null,n,o,!0)}else t.sourceMap&&"function"==typeof URL&&"function"==typeof URL.createObjectURL&&"function"==typeof URL.revokeObjectURL&&"function"==typeof Blob&&"function"==typeof btoa?(n=a(e),r=h.bind(null,n),i=function(){s(n),n.href&&URL.revokeObjectURL(n.href)}):(n=u(e),r=f.bind(null,n),i=function(){s(n)});return r(t),function(e){if(e){if(e.css===t.css&&e.media===t.media&&e.sourceMap===t.sourceMap)return;r(t=e)}else i()}}function c(t,e,n,r){var i=n?"":r.css;if(t.styleSheet)t.styleSheet.cssText=b(e,i);else{var o=document.createTextNode(i),s=t.childNodes;s[e]&&t.removeChild(s[e]),s.length?t.insertBefore(o,s[e]):t.appendChild(o)}}function f(t,e){var n=e.css,r=e.media;if(r&&t.setAttribute("media",r),t.styleSheet)t.styleSheet.cssText=n;else{for(;t.firstChild;)t.removeChild(t.firstChild);t.appendChild(document.createTextNode(n))}}function h(t,e){var n=e.css,r=e.sourceMap;r&&(n+="\n/*# sourceMappingURL=data:application/json;base64,"+btoa(unescape(encodeURIComponent(JSON.stringify(r))))+" */");var i=new Blob([n],{type:"text/css"}),o=t.href;t.href=URL.createObjectURL(i),o&&URL.revokeObjectURL(o)}var d={},p=function(t){var e;return function(){return"undefined"==typeof e&&(e=t.apply(this,arguments)),e}},g=p(function(){return/msie [6-9]\b/.test(window.navigator.userAgent.toLowerCase())}),v=p(function(){return document.head||document.getElementsByTagName("head")[0]}),m=null,y=0,_=[];t.exports=function(t,e){e=e||{},"undefined"==typeof e.singleton&&(e.singleton=g()),"undefined"==typeof e.insertAt&&(e.insertAt="bottom");var n=i(t);return r(n,e),function(t){for(var o=[],s=0;s' ).append( this.description.$el ).append( this.message.$el ).append( this.$form = $( '
' ) ) ); + this.setElement( $( '
' ).append( this.description.$el ) + .append( this.message.$el.addClass( 'ui-margin-bottom' ) ) + .append( this.$form = $( '
' ).addClass( 'ui-margin-bottom' ) ) ); this.listenTo( this.chart, 'change', function() { self.render() } ); }, render: function() { diff --git a/config/plugins/visualizations/charts/static/views/viewport.js b/config/plugins/visualizations/charts/static/views/viewport.js index 9bf1245899a1..32ed1f618bb7 100644 --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -86,6 +86,7 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port /** A chart may contain multiple sub charts/containers which are created here */ _createContainer: function( tag, n ) { + tag = tag || 'div'; n = n || 1; for ( var i in this.container_list ) { this.container_list[ i ].remove(); @@ -111,7 +112,13 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port this._createContainer( chart.definition.tag, n_panels ); chart.state( 'wait', 'Please wait...' ); require( [ 'plugin/charts/' + this.app.split( chart.get( 'type' ) ) + '/wrapper' ], function( ChartView ) { - new ChartView( self.app, { process : process, chart : chart, canvas_list : self.canvas_list } ); + Utils.get({ + url : Galaxy.root + 'api/datasets/' + chart.get( 'dataset_id' ), + cache : true, + success : function( dataset ) { + new ChartView( self.app, { process: process, canvas_list: self.canvas_list, dataset: dataset } ); + } + }); }); } }); diff --git a/config/plugins/visualizations/charts/templates/charts.mako b/config/plugins/visualizations/charts/templates/charts.mako index 9d3108990981..44021108cdc7 100644 --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -30,6 +30,9 @@ ${h.javascript_link( app_root + "plugins/canvg/rgbcolor.js" )} ${h.javascript_link( app_root + "plugins/canvg/canvg.js" )} + ## biojs + ${h.javascript_link( app_root + "plugins/biojs/biojs.msa.js" )} + ## nvd3 ${h.stylesheet_link( app_root + "plugins/nvd3/nv.d3.css" )} From 97519231e536ab689d5285ce328c46e19fa2566b Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 24 Aug 2016 22:25:06 -0400 Subject: [PATCH 02/27] Fix style --- config/plugins/visualizations/charts/static/app.css | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/config/plugins/visualizations/charts/static/app.css b/config/plugins/visualizations/charts/static/app.css index 483fd737a30b..19e85e5210c2 100644 --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -1,3 +1,7 @@ +.charts-viewer { + overflow: hidden; +} + .charts-viewer .ui-message { position: absolute; width: calc(100% - 20px); From 6a450b9a06a81a58875297af7832f1d5a2cab8a5 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 24 Aug 2016 22:42:07 -0400 Subject: [PATCH 03/27] Add basic options to configure msa viewer --- .../charts/static/charts/biojs/msa/config.js | 7 ++++++- .../charts/static/charts/biojs/msa/wrapper.js | 6 ++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/config/plugins/visualizations/charts/static/charts/biojs/msa/config.js b/config/plugins/visualizations/charts/static/charts/biojs/msa/config.js index ca99220105a5..dcae41733e66 100644 --- a/config/plugins/visualizations/charts/static/charts/biojs/msa/config.js +++ b/config/plugins/visualizations/charts/static/charts/biojs/msa/config.js @@ -4,6 +4,11 @@ define( [], function() { category : 'Sequence', library : 'BioJS', datatype : 'txt', - keywords : 'biojs' + keywords : 'biojs', + settings : { + conserv: { label :'Show conservation', help : 'Do you want to display a bar diagram indicating sequence conservation?', type : 'boolean', value: 'true' }, + overviewbox: { label :'Show overview box', help : 'Do you want to display the overview box below the sequence alignments?', type : 'boolean', value: 'true' }, + menu: { label :'Show interactive menu', help : 'Do you want to show a menu for interactive configuration?', type : 'boolean', value: 'true' } + } } }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js b/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js index 15998703aef8..0e9a7b6632cb 100644 --- a/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js @@ -2,11 +2,13 @@ define( [ 'utils/utils' ], function( Utils ) { return Backbone.Model.extend({ initialize: function( app, options ) { var chart = app.chart; + var settings = chart.settings; var m = new msa.msa({ el: $( '#' + options.canvas_list[ 0 ] ), - vis: { conserv: false, overviewbox: false }, + vis: { conserv: settings.get( 'conserv' ) == 'true', + overviewbox: settings.get( 'overviewbox' ) == 'true' }, menu: 'small', - bootstrapMenu: true + bootstrapMenu: settings.get( 'menu' ) == 'true' }); m.u.file.importURL( options.dataset.download_url, function() { m.render(); From 72ea2b030242cf448829f82d02e77a10ef7ce75d Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 04:49:47 -0400 Subject: [PATCH 04/27] Avoid parsing app to chart wrappers --- .../visualizations/charts/static/app.js | 18 +++++- .../charts/static/charts/biojs/msa/wrapper.js | 9 +-- .../static/charts/jqplot/bar/wrapper.js | 4 +- .../static/charts/jqplot/boxplot/wrapper.js | 8 +-- .../static/charts/jqplot/common/wrapper.js | 2 +- .../jqplot/histogram_discrete/wrapper.js | 8 +-- .../static/charts/jqplot/line/wrapper.js | 4 +- .../static/charts/jqplot/scatter/wrapper.js | 4 +- .../charts/static/charts/nvd3/bar/wrapper.js | 4 +- .../charts/nvd3/bar_horizontal/wrapper.js | 4 +- .../nvd3/bar_horizontal_stacked/wrapper.js | 4 +- .../static/charts/nvd3/bar_stacked/wrapper.js | 4 +- .../static/charts/nvd3/common/wrapper.js | 2 +- .../static/charts/nvd3/histogram/wrapper.js | 8 +-- .../charts/nvd3/histogram_discrete/wrapper.js | 8 +-- .../charts/static/charts/nvd3/line/wrapper.js | 4 +- .../static/charts/nvd3/line_focus/wrapper.js | 4 +- .../charts/static/charts/nvd3/pie/wrapper.js | 6 +- .../static/charts/nvd3/scatter/wrapper.js | 4 +- .../static/charts/nvd3/stackedarea/wrapper.js | 4 +- .../charts/nvd3/stackedarea_full/wrapper.js | 4 +- .../charts/nvd3/stackedarea_stream/wrapper.js | 4 +- .../charts/others/heatmap/heatmap-plugin.js | 3 +- .../static/charts/others/heatmap/wrapper.js | 4 +- .../charts/others/heatmap_cluster/wrapper.js | 8 +-- .../charts/static/components/jobs.js | 4 +- .../charts/static/components/model.js | 10 ++-- .../charts/static/views/types.js | 55 +++++++++++-------- .../charts/static/views/viewport.js | 8 +-- 29 files changed, 114 insertions(+), 99 deletions(-) diff --git a/config/plugins/visualizations/charts/static/app.js b/config/plugins/visualizations/charts/static/app.js index be38bf36b1c4..e00f8ce5926e 100644 --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -4,7 +4,19 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils', 'plugin/components/storage', 'plugin/components/model', 'utils/deferred', 'plugin/views/viewer', 'plugin/views/editor', 'plugin/charts/types' ], function( Modal, Portlet, Ui, Utils, Storage, Chart, Deferred, Viewer, Editor, Types ) { return Backbone.View.extend({ - initialize: function(options){ + initialize: function( options ){ + var self = this; + Utils.get({ + url : Galaxy.root + 'api/datasets/' + options.config.dataset_id, + cache : true, + success : function( dataset ) { + self.dataset = dataset; + self._build( options ); + } + }); + }, + + _build: function( options ){ this.options = options; this.modal = parent.Galaxy && parent.Galaxy.modal || new Modal.View(); this.types = Types; @@ -18,13 +30,15 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils this.$el.append( this.viewer.$el ); this.$el.append( this.editor.$el ); - // pick start screen + // load dataset and pick start screen if ( !this.storage.load() ) { this.go( 'editor' ); } else { this.go( 'viewer' ); this.chart.trigger( 'redraw' ); } + var self = this; + this.chart.on( 'change:dataset_id_job', function() { self.storage.save() } ); }, /** Loads a view and makes sure that all others are hidden */ diff --git a/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js b/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js index 0e9a7b6632cb..b61c5835e156 100644 --- a/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js @@ -1,7 +1,8 @@ define( [ 'utils/utils' ], function( Utils ) { return Backbone.Model.extend({ - initialize: function( app, options ) { - var chart = app.chart; + initialize: function( options ) { + var chart = options.chart; + var dataset = options.dataset; var settings = chart.settings; var m = new msa.msa({ el: $( '#' + options.canvas_list[ 0 ] ), @@ -10,9 +11,9 @@ define( [ 'utils/utils' ], function( Utils ) { menu: 'small', bootstrapMenu: settings.get( 'menu' ) == 'true' }); - m.u.file.importURL( options.dataset.download_url, function() { + m.u.file.importURL( dataset.download_url, function() { m.render(); - app.chart.state( 'ok', 'Chart drawn.' ); + chart.state( 'ok', 'Chart drawn.' ); options.process.resolve(); }); } diff --git a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js index 55c8dc3f8da8..bf1d0525fff8 100644 --- a/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js @@ -1,6 +1,6 @@ define( [ 'plugin/charts/jqplot/common/wrapper' ], function( Plot ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.makeConfig = function( groups, plot_config ){ $.extend( true, plot_config, { seriesDefaults: { @@ -16,7 +16,7 @@ define( [ 'plugin/charts/jqplot/common/wrapper' ], function( Plot ) { } }); }; - new Plot( app, options ); + new Plot( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js index df096f88dc0b..dce642c87dc4 100644 --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -1,14 +1,14 @@ define( [ 'plugin/charts/jqplot/common/wrapper', 'plugin/components/jobs', 'plugin/charts/utilities/tabular-utilities' ], function( Plot, Jobs, Utilities ) { return Backbone.View.extend({ - initialize: function( app, options ) { - Jobs.request( app, Utilities.buildJobDictionary( 'boxplot', app.chart ), function( dataset ) { - var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id ); + initialize: function( options ) { + Jobs.request( options.chart, Utilities.buildJobDictionary( 'boxplot', options.chart ), function( dataset ) { + var request_dictionary = Utilities.buildRequestDictionary( options.chart, dataset.id ); var chart = options.chart; var index = 0; _.each( request_dictionary.groups, function( group ) { group.columns = { x: { index : index++ } }; }); - var plot = new Plot( app, { + var plot = new Plot( { process : options.process, chart : options.chart, request_dictionary : request_dictionary, diff --git a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js index 7e0bf6b71b4b..8f787ef9df50 100644 --- a/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js @@ -1,7 +1,7 @@ /** This is the common wrapper for jqplot based visualizations. */ define( [ 'plugin/charts/jqplot/common/plot-config', 'plugin/charts/utilities/tabular-utilities' ], function( configmaker, Utilities ) { return Backbone.View.extend({ - initialize: function( app, options ) { + initialize: function( options ) { this.options = options; var self = this; options.render = function( canvas_id, groups ) { diff --git a/config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js b/config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js index 2e6c6c7a6fa2..6678f7c0b799 100644 --- a/config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/jqplot/common/wrapper' ], function( Utilities, Jobs, Plot ) { return Backbone.Model.extend({ - initialize: function( app, options ) { - Jobs.request( app, Utilities.buildJobDictionary( 'histogramdiscrete', app.chart ), function( dataset ) { - var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id ); + initialize: function( options ) { + Jobs.request( options.chart, Utilities.buildJobDictionary( 'histogramdiscrete', options.chart ), function( dataset ) { + var request_dictionary = Utilities.buildRequestDictionary( options.chart, dataset.id ); var index = 1; var tmp_dict = { id : request_dictionary.id, groups : [] }; _.each( request_dictionary.groups, function( group ) { @@ -18,7 +18,7 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', axes: { xaxis: { min : -1 }, yaxis: { pad : 1.2 } } }); }; - new Plot( app, options ); + new Plot( options ); }); } }); diff --git a/config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js b/config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js index 669b6529898d..881f2faa07f7 100644 --- a/config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js @@ -1,7 +1,7 @@ define( [ 'plugin/charts/jqplot/common/wrapper' ], function( Plot ) { return Backbone.Model.extend({ - initialize: function( app, options ) { - new Plot( app, options ); + initialize: function( options ) { + new Plot( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js b/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js index effb9ead43e6..1a9204ba55b6 100644 --- a/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js @@ -1,6 +1,6 @@ define( [ 'plugin/charts/jqplot/common/wrapper' ], function( Plot ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.makeConfig = function( groups, plot_config ) { $.extend( true, plot_config, { seriesDefaults: { @@ -12,7 +12,7 @@ define( [ 'plugin/charts/jqplot/common/wrapper' ], function( Plot ) { } }); }; - new Plot( app, options ); + new Plot( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js index 9b6a1f17222f..34d275daab49 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'multiBarChart'; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js index 5e6f4e154614..081796c7899e 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'multiBarHorizontalChart'; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js index 47218c8a27ca..3dfb6cb24f53 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js @@ -1,11 +1,11 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'multiBarHorizontalChart'; options.makeConfig = function( nvd3_model ) { nvd3_model.stacked( true ); }; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js index 876ce8fe3a40..dee4d151d7c1 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js @@ -1,11 +1,11 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'multiBarChart'; options.makeConfig = function( nvd3_model ) { nvd3_model.stacked( true ); }; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js index 28e47f8c86c3..e0d35bcd8dd0 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js @@ -1,7 +1,7 @@ /** This is the common wrapper for nvd3 based visualizations. */ define( [ 'plugin/charts/utilities/tabular-utilities' ], function( Utilities ) { return Backbone.View.extend({ - initialize: function( app, options ) { + initialize: function( options ) { var self = this; this.options = options; options.render = function( canvas_id, groups ) { diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js index 7faf9a07adc8..5a908f231171 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/nvd3/common/wrapper' ], function( Utilities, Jobs, NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { - Jobs.request( app, Utilities.buildJobDictionary( 'histogram', app.chart ), function( dataset ) { - options.request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id ); + initialize: function( options ) { + Jobs.request( options.chart, Utilities.buildJobDictionary( 'histogram', options.chart ), function( dataset ) { + options.request_dictionary = Utilities.buildRequestDictionary( options.chart, dataset.id ); var index = 1; _.each( options.request_dictionary.groups, function( group ) { group.columns = { x : { index : 0, is_numeric : true }, y : { index : index++ } } @@ -11,7 +11,7 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', options.makeConfig = function( nvd3_model ) { nvd3_model.options( { showControls: true } ); }; - new NVD3( app, options ); + new NVD3( options ); }, function() { options.process.reject() } ); } }); diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js index 6230c97c3e36..28c8f968195d 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/nvd3/common/wrapper' ], function( Utilities, Jobs, NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { - Jobs.request( app, Utilities.buildJobDictionary( 'histogramdiscrete', app.chart ), function( dataset ) { - var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id ); + initialize: function( options ) { + Jobs.request( options.chart, Utilities.buildJobDictionary( 'histogramdiscrete', options.chart ), function( dataset ) { + var request_dictionary = Utilities.buildRequestDictionary( options.chart, dataset.id ); var index = 1; var tmp_dict = { id : request_dictionary.id, groups : [] }; _.each( request_dictionary.groups, function( group ) { @@ -16,7 +16,7 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', options.makeConfig = function( nvd3_model ) { nvd3_model.options( { showControls: true } ); }; - new NVD3( app, options ); + new NVD3( options ); }, function() { options.process.reject() } ); } }); diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js index 060a01b9ba80..bc612ab19e14 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'lineChart'; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js index 66d89e5de813..6649e1ccf38b 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'lineWithFocusChart'; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js index 7a93a525213c..cff9e6ff4235 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js @@ -1,10 +1,10 @@ /** Pie chart wrapper */ define( [ 'utils/utils', 'plugin/charts/utilities/tabular-utilities', 'plugin/charts/utilities/tabular-datasets' ], function( Utils, Utilities, Datasets ) { return Backbone.View.extend({ - initialize: function( app, options ) { + initialize: function( options ) { var self = this; - var chart = app.chart; - var request_dictionary = Utilities.buildRequestDictionary( app.chart ); + var chart = options.chart; + var request_dictionary = Utilities.buildRequestDictionary( chart ); var canvas_list = options.canvas_list; var process = options.process; request_dictionary.success = function( result ) { diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js index 73a7e1ccc736..b9ab9a9eaa6e 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js @@ -1,13 +1,13 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'scatterChart'; options.makeConfig = function( nvd3_model ) { nvd3_model.showDistX( true ) .showDistY( true ) .color( d3.scale.category10().range() ); }; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js index 3a609b919bfb..1bbccba6964f 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'stackedAreaChart'; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js index b7c8147cc896..432e68dc59a9 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js @@ -1,11 +1,11 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'stackedAreaChart'; options.makeConfig = function( nvd3_model ) { nvd3_model.style( 'expand' ); }; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js index 29a1e70ea2ea..4f456b3ec997 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js @@ -1,11 +1,11 @@ define( [ 'plugin/charts/nvd3/common/wrapper' ], function( NVD3 ) { return Backbone.Model.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.type = 'stackedAreaChart'; options.makeConfig = function( nvd3_model ) { nvd3_model.style( 'stream' ) }; - new NVD3( app, options ); + new NVD3( options ); } }); }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js index b039e5ed1453..e96ba4ff768d 100644 --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js @@ -26,9 +26,8 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'utils/utils', 'plugin/ch debug_color : '#FFFFFF' }, - initialize: function( app, options ) { + initialize: function( options ) { var self = this; - this.app = app; this.chart = options.chart; this.canvas_id = options.canvas_id; this.group = options.groups[ 0 ]; diff --git a/config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js b/config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js index 5179271ccc89..38471a8bbb8d 100644 --- a/config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/charts/others/heatmap/heatmap-plugin' ], function( Utilities, HeatMap ) { return Backbone.View.extend({ - initialize: function( app, options ) { + initialize: function( options ) { options.render = function( canvas_id, groups ) { - new HeatMap( app, { + new HeatMap({ chart : options.chart, canvas_id : canvas_id, groups : groups diff --git a/config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js b/config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js index 79d6c97fe3ae..388a5eea5741 100644 --- a/config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js @@ -1,8 +1,8 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', 'plugin/charts/others/heatmap/heatmap-plugin' ], function( Utilities, Jobs, HeatMap ) { return Backbone.View.extend({ - initialize: function(app, options) { - Jobs.request( app, Utilities.buildJobDictionary( 'heatmap', app.chart ), function( dataset ) { - var request_dictionary = Utilities.buildRequestDictionary( app.chart, dataset.id ); + initialize: function( options ) { + Jobs.request( options.chart, Utilities.buildJobDictionary( 'heatmap', options.chart ), function( dataset ) { + var request_dictionary = Utilities.buildRequestDictionary( options.chart, dataset.id ); var index = 0; var tmp_dict = { id : request_dictionary.id, groups : [] }; for ( var group_index in request_dictionary.groups ) { @@ -26,7 +26,7 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/components/jobs', } options.request_dictionary = tmp_dict; options.render = function( canvas_id, groups ) { - new HeatMap( app, { + new HeatMap({ chart : options.chart, canvas_id : canvas_id, groups : groups diff --git a/config/plugins/visualizations/charts/static/components/jobs.js b/config/plugins/visualizations/charts/static/components/jobs.js index 4a316004900e..82a056d7330b 100644 --- a/config/plugins/visualizations/charts/static/components/jobs.js +++ b/config/plugins/visualizations/charts/static/components/jobs.js @@ -5,8 +5,7 @@ define( [ 'utils/utils' ], function( Utils ) { var WAITTIME = 1000; /** Submit job request to charts tool */ - var request = function( app, parameters, success, error ) { - var chart = app.chart; + var request = function( chart, parameters, success, error ) { chart.state( 'wait', 'Requesting job results...' ); if ( chart.get( 'modified' ) ) { cleanup( chart ); @@ -33,7 +32,6 @@ define( [ 'utils/utils' ], function( Utils ) { var job = response.outputs[0]; chart.state( 'wait', 'Your job has been queued. You may close the browser window. The job will run in the background.' ); chart.set( 'dataset_id_job', job.id ); - self.app.storage.save(); wait( chart, success, error ); } }, diff --git a/config/plugins/visualizations/charts/static/components/model.js b/config/plugins/visualizations/charts/static/components/model.js index b0b782aa283f..0b72da8a90a4 100644 --- a/config/plugins/visualizations/charts/static/components/model.js +++ b/config/plugins/visualizations/charts/static/components/model.js @@ -20,10 +20,10 @@ define( [ 'utils/utils' ], function( Utils ) { reset: function( options ) { this.set({ - 'id' : Utils.uid(), - 'type' : 'nvd3_bar', - 'dataset_id' : options.config.dataset_id, - 'title' : 'New Chart' + id : Utils.uid(), + type : '__first', + dataset_id : options.config.dataset_id, + title : 'New Chart' }); this.settings.clear(); this.groups.reset(); @@ -31,7 +31,7 @@ define( [ 'utils/utils' ], function( Utils ) { }, state: function( value, info ) { - this.set( { 'state': value, 'state_info': info } ); + this.set( { state : value, state_info : info } ); this.trigger( 'set:state' ); console.debug( 'Chart:state() - ' + info + ' (' + value + ')' ); } diff --git a/config/plugins/visualizations/charts/static/views/types.js b/config/plugins/visualizations/charts/static/views/types.js index 26500bd0ed9a..ae71cd0f6f53 100644 --- a/config/plugins/visualizations/charts/static/views/types.js +++ b/config/plugins/visualizations/charts/static/views/types.js @@ -18,40 +18,49 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'plugin/charts/over render: function() { var self = this; this.index = {}; + this.first = null; _.each( this.app.types, function( type, type_id ) { - _.each( type.keywords.split( ' ' ), function( keyword ) { - self.index[ keyword ] = self.index[ keyword ] || {}; - self.index[ keyword ][ type.category ] = self.index[ keyword ][ type.category ] || {}; - self.index[ keyword ][ type.category ][ type_id ] = type; - }); + if ( self.app.dataset.file_ext === type.datatype ) { + _.each( type.keywords.split( ' ' ), function( keyword ) { + self.index[ keyword ] = self.index[ keyword ] || {}; + self.index[ keyword ][ type.category ] = self.index[ keyword ][ type.category ] || {}; + self.index[ keyword ][ type.category ][ type_id ] = type; + self.first = self.first || type_id; + }); + } }); this.tabs.delAll(); _.each( Overview, function( d, i ) { var keyword = d.value; var categories = self.index[ keyword ]; - var $help = $( '

' ).addClass( 'ui-form-info' ).html( d.help ) ; - var $el = $( '

' ).addClass( 'charts-grid' ).append( $help ); - _.each( categories, function( category, category_header ) { - var $category = self._templateHeader( { title: category_header } ); - $el.append( $category ); - _.each( category, function( type, type_id ) { - $el.append( self._templateType({ - id : type_id, - title : ( type.zoomable ? '' : '' ) + type.title + ' (' + type.library + ')', - url : app_root + 'charts/' + self.app.split( type_id ) + '/logo.png' - })); + if ( _.size( categories ) > 0 ) { + var $help = $( '

' ).addClass( 'ui-form-info' ).html( d.help ) ; + var $el = $( '

' ).addClass( 'charts-grid' ).append( $help ); + _.each( categories, function( category, category_header ) { + var $category = self._templateHeader( { title: category_header } ); + $el.append( $category ); + _.each( category, function( type, type_id ) { + $el.append( self._templateType({ + id : type_id, + title : ( type.zoomable ? '' : '' ) + type.title + ' (' + type.library + ')', + url : app_root + 'charts/' + self.app.split( type_id ) + '/logo.png' + })); + }); + }); + self.tabs.add({ + id : Utils.uid(), + title : d.label, + $el : $el }); - }); - self.tabs.add({ - id : Utils.uid(), - title : d.label, - $el : $el - }); + } }); }, /** Set/Get selected chart type */ value: function( new_value ) { + if ( new_value == '__first' ) { + new_value = this.first; + } var before = this.$( '.current' ).attr( 'chart_id' ); if ( new_value !== undefined ) { this.$( '.current' ).removeClass( 'current' ); @@ -60,7 +69,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'plugin/charts/over var after = this.$( '.current' ).attr( 'chart_id' ); if( after !== undefined ) { if ( after != before && this.options.onchange ) { - this.options.onchange( new_value ); + this.options.onchange( after ); } return after; } diff --git a/config/plugins/visualizations/charts/static/views/viewport.js b/config/plugins/visualizations/charts/static/views/viewport.js index 32ed1f618bb7..3ac31b9bce5e 100644 --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -112,13 +112,7 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port this._createContainer( chart.definition.tag, n_panels ); chart.state( 'wait', 'Please wait...' ); require( [ 'plugin/charts/' + this.app.split( chart.get( 'type' ) ) + '/wrapper' ], function( ChartView ) { - Utils.get({ - url : Galaxy.root + 'api/datasets/' + chart.get( 'dataset_id' ), - cache : true, - success : function( dataset ) { - new ChartView( self.app, { process: process, canvas_list: self.canvas_list, dataset: dataset } ); - } - }); + new ChartView( { process: process, chart: chart, dataset: self.app.dataset, canvas_list: self.canvas_list } ); }); } }); From e02eb60296eac4339aa2265313a38d4dc36aa415 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 05:02:26 -0400 Subject: [PATCH 05/27] Decouple storage, parse parameters explicitly --- .../visualizations/charts/static/app.js | 25 ++++++------------- .../charts/static/components/storage.js | 19 +++++++------- 2 files changed, 17 insertions(+), 27 deletions(-) diff --git a/config/plugins/visualizations/charts/static/app.js b/config/plugins/visualizations/charts/static/app.js index e00f8ce5926e..81b0622f63a0 100644 --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -4,8 +4,13 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils', 'plugin/components/storage', 'plugin/components/model', 'utils/deferred', 'plugin/views/viewer', 'plugin/views/editor', 'plugin/charts/types' ], function( Modal, Portlet, Ui, Utils, Storage, Chart, Deferred, Viewer, Editor, Types ) { return Backbone.View.extend({ - initialize: function( options ){ + initialize: function( options ) { var self = this; + this.options = options; + this.chart = new Chart(); + this.types = Types; + this.storage = new Storage( this.chart, this.types, options ); + this.deferred = new Deferred(); Utils.get({ url : Galaxy.root + 'api/datasets/' + options.config.dataset_id, cache : true, @@ -16,21 +21,11 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils }); }, - _build: function( options ){ - this.options = options; - this.modal = parent.Galaxy && parent.Galaxy.modal || new Modal.View(); - this.types = Types; - this.chart = new Chart(); - this.storage = new Storage( this ); - this.deferred = new Deferred(); - - // views + _build: function( options ) { this.viewer = new Viewer( this ); this.editor = new Editor( this ); this.$el.append( this.viewer.$el ); this.$el.append( this.editor.$el ); - - // load dataset and pick start screen if ( !this.storage.load() ) { this.go( 'editor' ); } else { @@ -49,12 +44,6 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils this[ view_id ].show(); }, - /** Message */ - showModal: function( title, body ) { - var self = this; - this.modal.show( { title: title, body: body, buttons: { 'Close': function() { self.modal.hide() } } } ); - }, - /** Split chart type into path components */ split: function( chart_type ) { var path = chart_type.split( /_(.+)/ ); diff --git a/config/plugins/visualizations/charts/static/components/storage.js b/config/plugins/visualizations/charts/static/components/storage.js index 5ef3abdc58e4..e2a696a1bd99 100644 --- a/config/plugins/visualizations/charts/static/components/storage.js +++ b/config/plugins/visualizations/charts/static/components/storage.js @@ -1,12 +1,13 @@ /** This class saves and loads a chart through the api. */ -define( [ 'utils/utils', 'plugin/components/model', 'mvc/visualization/visualization-model' ], function( Utils, Chart ) { +define( [ 'utils/utils', 'mvc/ui/ui-modal', 'plugin/components/model', 'mvc/visualization/visualization-model' ], function( Utils, Modal, Chart ) { return Backbone.Model.extend({ - initialize: function( app ) { - this.app = app; - this.chart = this.app.chart; - this.options = this.app.options; - this.id = this.options.id; + initialize: function( chart, types, options ) { + this.chart = chart; + this.options = options; + this.id = options.id; + this.types = types; + this.modal = parent.Galaxy && parent.Galaxy.modal || new Modal.View(); this.vis = new Visualization({ id : this.id, type : 'charts', @@ -24,7 +25,7 @@ define( [ 'utils/utils', 'plugin/components/model', 'mvc/visualization/visualiza /** Pack and save nested chart model */ save: function() { var self = this; - var chart = this.app.chart; + var chart = this.chart; var chart_dict = { attributes : chart.attributes, settings : chart.settings.attributes, @@ -37,7 +38,7 @@ define( [ 'utils/utils', 'plugin/components/model', 'mvc/visualization/visualiza this.vis.get( 'config' ).chart_dict = chart_dict; this.vis.save() .fail(function( xhr, status, message ) { - self.app.showModal( 'Saving failed.', 'An attempt to save this chart to the server failed. Please try again and contact the administrator.' ); + this.modal.show( { title: 'Saving failed.', body: 'An attempt to save this chart to the server failed. Please try again and contact the administrator.', buttons: { 'Close': function() { self.modal.hide() } } } ); }) .then( function( response ) { if ( response && response.id ) { @@ -60,7 +61,7 @@ define( [ 'utils/utils', 'plugin/components/model', 'mvc/visualization/visualiza console.debug( 'Storage::load() - Chart type not provided. Invalid format.' ); return false; } - var chart_definition = this.app.types[ chart_type ]; + var chart_definition = this.types[ chart_type ]; if ( !chart_definition ) { console.debug( 'Storage::load() - Chart type not supported. Please re-configure the chart.' ); return false; From 37c1e316a74348ad1023bd071f19e4396758540a Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 05:33:33 -0400 Subject: [PATCH 06/27] Move chart listener into storage --- config/plugins/visualizations/charts/static/app.js | 12 +++++------- .../charts/static/components/storage.js | 2 ++ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/config/plugins/visualizations/charts/static/app.js b/config/plugins/visualizations/charts/static/app.js index 81b0622f63a0..bd78fdb1f7a5 100644 --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -6,11 +6,6 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils return Backbone.View.extend({ initialize: function( options ) { var self = this; - this.options = options; - this.chart = new Chart(); - this.types = Types; - this.storage = new Storage( this.chart, this.types, options ); - this.deferred = new Deferred(); Utils.get({ url : Galaxy.root + 'api/datasets/' + options.config.dataset_id, cache : true, @@ -22,6 +17,11 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils }, _build: function( options ) { + this.options = options; + this.chart = new Chart(); + this.types = Types; + this.storage = new Storage( this.chart, this.types, options ); + this.deferred = new Deferred(); this.viewer = new Viewer( this ); this.editor = new Editor( this ); this.$el.append( this.viewer.$el ); @@ -32,8 +32,6 @@ define( [ 'mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils this.go( 'viewer' ); this.chart.trigger( 'redraw' ); } - var self = this; - this.chart.on( 'change:dataset_id_job', function() { self.storage.save() } ); }, /** Loads a view and makes sure that all others are hidden */ diff --git a/config/plugins/visualizations/charts/static/components/storage.js b/config/plugins/visualizations/charts/static/components/storage.js index e2a696a1bd99..4369821b9f92 100644 --- a/config/plugins/visualizations/charts/static/components/storage.js +++ b/config/plugins/visualizations/charts/static/components/storage.js @@ -3,6 +3,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-modal', 'plugin/components/model', 'mvc/visu return Backbone.Model.extend({ initialize: function( chart, types, options ) { + var self = this; this.chart = chart; this.options = options; this.id = options.id; @@ -20,6 +21,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-modal', 'plugin/components/model', 'mvc/visu if ( chart_dict ) { this.vis.get( 'config' ).chart_dict = chart_dict; } + this.chart.on( 'change:dataset_id_job', function() { self.save() } ); }, /** Pack and save nested chart model */ From 48ff0790bf9b2115d891ca4c1a375f7f266b3399 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 05:34:42 -0400 Subject: [PATCH 07/27] Fix save failed message --- .../plugins/visualizations/charts/static/components/storage.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/components/storage.js b/config/plugins/visualizations/charts/static/components/storage.js index 4369821b9f92..02c227110d19 100644 --- a/config/plugins/visualizations/charts/static/components/storage.js +++ b/config/plugins/visualizations/charts/static/components/storage.js @@ -40,7 +40,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-modal', 'plugin/components/model', 'mvc/visu this.vis.get( 'config' ).chart_dict = chart_dict; this.vis.save() .fail(function( xhr, status, message ) { - this.modal.show( { title: 'Saving failed.', body: 'An attempt to save this chart to the server failed. Please try again and contact the administrator.', buttons: { 'Close': function() { self.modal.hide() } } } ); + self.modal.show( { title: 'Saving failed.', body: 'An attempt to save this chart to the server failed. Please try again and contact the administrator.', buttons: { 'Close': function() { self.modal.hide() } } } ); }) .then( function( response ) { if ( response && response.id ) { From 3048b56006cc1ee0877e24767e2535ccbe5164b7 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 05:47:11 -0400 Subject: [PATCH 08/27] Remove unused container list --- .../charts/static/charts/biojs/msa/wrapper.js | 2 +- .../charts/static/charts/jqplot/boxplot/wrapper.js | 2 +- .../charts/static/charts/nvd3/pie/wrapper.js | 4 ++-- .../charts/static/charts/others/example/wrapper.js | 2 +- .../static/charts/utilities/tabular-utilities.js | 6 +++--- .../visualizations/charts/static/views/viewport.js | 12 ++++-------- 6 files changed, 12 insertions(+), 16 deletions(-) diff --git a/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js b/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js index b61c5835e156..f49439dbfb7f 100644 --- a/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js @@ -5,7 +5,7 @@ define( [ 'utils/utils' ], function( Utils ) { var dataset = options.dataset; var settings = chart.settings; var m = new msa.msa({ - el: $( '#' + options.canvas_list[ 0 ] ), + el: $( '#' + options.targets[ 0 ] ), vis: { conserv: settings.get( 'conserv' ) == 'true', overviewbox: settings.get( 'overviewbox' ) == 'true' }, menu: 'small', diff --git a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js index dce642c87dc4..eb0628232707 100644 --- a/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js @@ -12,7 +12,7 @@ define( [ 'plugin/charts/jqplot/common/wrapper', 'plugin/components/jobs', 'plug process : options.process, chart : options.chart, request_dictionary : request_dictionary, - canvas_list : options.canvas_list, + targets : options.targets, makeConfig : function( groups, plot_config ){ var boundary = Utilities.getDomains( groups, 'x' ); $.extend( true, plot_config, { diff --git a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js index cff9e6ff4235..591a017c4f19 100644 --- a/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js @@ -5,12 +5,12 @@ define( [ 'utils/utils', 'plugin/charts/utilities/tabular-utilities', 'plugin/ch var self = this; var chart = options.chart; var request_dictionary = Utilities.buildRequestDictionary( chart ); - var canvas_list = options.canvas_list; + var targets = options.targets; var process = options.process; request_dictionary.success = function( result ) { for ( var group_index in result.groups ) { var group = result.groups[ group_index ]; - self._drawGroup( chart, group, canvas_list[ group_index ] ); + self._drawGroup( chart, group, targets[ group_index ] ); } chart.state('ok', 'Pie chart has been drawn.'); process.resolve(); diff --git a/config/plugins/visualizations/charts/static/charts/others/example/wrapper.js b/config/plugins/visualizations/charts/static/charts/others/example/wrapper.js index 7f86ebc872ae..7473b664a78b 100755 --- a/config/plugins/visualizations/charts/static/charts/others/example/wrapper.js +++ b/config/plugins/visualizations/charts/static/charts/others/example/wrapper.js @@ -8,7 +8,7 @@ define( [ 'plugin/charts/utilities/tabular-utilities', 'plugin/charts/utilities/ var colors = d3.scale.category20(); _.each( result.groups, function( group, group_index ) { try { - var svg = d3.select( '#' + ( options.canvas_list[ group_index ] || options.canvas_list[ 0 ] ) ); + var svg = d3.select( '#' + ( options.targets[ group_index ] || options.targets[ 0 ] ) ); var height = parseInt( svg.style( 'height' ) ); var width = parseInt( svg.style( 'width' ) ); var maxValue = d3.max( group.values, function( d ) { return Math.max( d.x, d.y ) } ); diff --git a/config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js b/config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js index dec6f2a79c57..ddaa8a699968 100644 --- a/config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js +++ b/config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js @@ -55,14 +55,14 @@ define( [ 'utils/utils', 'plugin/charts/utilities/tabular-datasets' ], function( var chart = options.chart; var request_dictionary = options.request_dictionary || buildRequestDictionary( chart ); var render = options.render; - var canvas_list = options.canvas_list; + var targets = options.targets; request_dictionary.success = function( result ) { try { if ( chart.settings.get( 'use_panels' ) === 'true' ) { var valid = true; for ( var group_index in result.groups ) { var group = result.groups[ group_index ]; - if (!render( canvas_list[ group_index ], [ group ] ) ) { + if (!render( targets[ group_index ], [ group ] ) ) { valid = false; break; } @@ -71,7 +71,7 @@ define( [ 'utils/utils', 'plugin/charts/utilities/tabular-datasets' ], function( chart.state( 'ok', 'Multi-panel chart drawn.' ); } } else { - if ( render( canvas_list[ 0 ], result.groups ) ) { + if ( render( targets[ 0 ], result.groups ) ) { chart.state( 'ok', 'Chart drawn.' ); } } diff --git a/config/plugins/visualizations/charts/static/views/viewport.js b/config/plugins/visualizations/charts/static/views/viewport.js index 3ac31b9bce5e..240be5a06552 100644 --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -88,11 +88,8 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port _createContainer: function( tag, n ) { tag = tag || 'div'; n = n || 1; - for ( var i in this.container_list ) { - this.container_list[ i ].remove(); - } - this.container_list = []; - this.canvas_list = []; + this.$( '.charts-viewport-container' ).remove(); + this.targets = []; for ( var i = 0; i < n; i++ ) { var container_id = Utils.uid(); var container_el = $( '
' ).addClass( 'charts-viewport-container' ) @@ -100,8 +97,7 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port .append( $( '
' ).attr( 'id', 'menu' ) ) .append( $( '<' + tag + ' class="charts-viewport-canvas" />' ).attr( 'id', container_id ) ); this.$el.append( container_el ); - this.container_list[ i ] = container_el; - this.canvas_list[ i ] = container_id; + this.targets.push( container_id ); } }, @@ -112,7 +108,7 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port this._createContainer( chart.definition.tag, n_panels ); chart.state( 'wait', 'Please wait...' ); require( [ 'plugin/charts/' + this.app.split( chart.get( 'type' ) ) + '/wrapper' ], function( ChartView ) { - new ChartView( { process: process, chart: chart, dataset: self.app.dataset, canvas_list: self.canvas_list } ); + new ChartView( { process: process, chart: chart, dataset: self.app.dataset, targets: self.targets } ); }); } }); From a63b07795c23a7412592d8aa7e395ff6394625ae Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 05:59:13 -0400 Subject: [PATCH 09/27] Fix scrolling behavior --- .../visualizations/charts/static/app.css | 2 +- .../charts/static/views/viewport.js | 17 ----------------- 2 files changed, 1 insertion(+), 18 deletions(-) diff --git a/config/plugins/visualizations/charts/static/app.css b/config/plugins/visualizations/charts/static/app.css index 19e85e5210c2..5952e6c25fb7 100644 --- a/config/plugins/visualizations/charts/static/app.css +++ b/config/plugins/visualizations/charts/static/app.css @@ -1,5 +1,5 @@ .charts-viewer { - overflow: hidden; + overflow: auto; } .charts-viewer .ui-message { diff --git a/config/plugins/visualizations/charts/static/views/viewport.js b/config/plugins/visualizations/charts/static/views/viewport.js index 240be5a06552..c3ef594263f9 100644 --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -17,30 +17,13 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port this.$info = this.$( '.info' ); this.$icon = this.$( '.icon' ); this.$text = this.$( '.text' ); - - // use full screen for viewer this._fullscreen( this.$el, 55 ); - - // prevent window scrolling - var initial_overflow = $( 'body' ).css( 'overflow' ); - this.$el.on( 'mouseover', function() { - $( 'body' ).css( 'overflow', 'hidden' ); - }).on('mouseout', function() { - $( 'body' ).css( 'overflow', initial_overflow ); - }); - - // create container element this._createContainer( 'div' ); - - // link redraw trigger - var self = this; this.chart.on( 'redraw', function() { self.app.deferred.execute( function( process ) { self._draw( process, self.chart ); }); }); - - // link status handler this.chart.on( 'set:state', function() { var $container = self.$el.find( '.charts-viewport-container' ); var $info = self.$info; From f2c1e23409f407b773913629714c697a04fb0740 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 07:57:20 -0400 Subject: [PATCH 10/27] Add description for biojs --- .../plugins/visualizations/charts/static/charts/overview.js | 2 +- config/plugins/visualizations/charts/static/views/viewer.js | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/plugins/visualizations/charts/static/charts/overview.js b/config/plugins/visualizations/charts/static/charts/overview.js index fd2fac444920..1c406b5e9298 100644 --- a/config/plugins/visualizations/charts/static/charts/overview.js +++ b/config/plugins/visualizations/charts/static/charts/overview.js @@ -10,7 +10,7 @@ define( [], function() { help : 'These visualizations were developed by the Galaxy team.' }, { label : 'BioJS', value: 'biojs', - help : 'BioJS plugins.' + help : 'BioJS is hosted at http://biojs.net. It is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.' } ]; }); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/views/viewer.js b/config/plugins/visualizations/charts/static/views/viewer.js index bbe9c757296e..a5bf09ecebaf 100644 --- a/config/plugins/visualizations/charts/static/views/viewer.js +++ b/config/plugins/visualizations/charts/static/views/viewer.js @@ -106,7 +106,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'plugin/views/vi this.setElement( this.portlet.$el ); // events - this.chart.on( 'change:title', function() { self._refreshTitle() } ); + this.listenTo( this.chart, 'change', function() { self.render() } ); }, /** Show and refresh viewer */ @@ -121,7 +121,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'plugin/views/vi }, /** Change title */ - _refreshTitle: function() { + render: function() { var title = this.chart.get( 'title' ); this.portlet.title( title ); }, From 7107705b9c821c20a07ae3275c50eac517b44a37 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 08:23:01 -0400 Subject: [PATCH 11/27] Remove unused menu div --- config/plugins/visualizations/charts/static/views/viewport.js | 1 - 1 file changed, 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/views/viewport.js b/config/plugins/visualizations/charts/static/views/viewport.js index c3ef594263f9..f127520d7bf1 100644 --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -77,7 +77,6 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port var container_id = Utils.uid(); var container_el = $( '
' ).addClass( 'charts-viewport-container' ) .width( parseInt( 100 / n ) + '%' ) - .append( $( '
' ).attr( 'id', 'menu' ) ) .append( $( '<' + tag + ' class="charts-viewport-canvas" />' ).attr( 'id', container_id ) ); this.$el.append( container_el ); this.targets.push( container_id ); From 5f642113156435b34d3ff6de01144069d2e370c1 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 08:27:14 -0400 Subject: [PATCH 12/27] Use shorter dom query command --- config/plugins/visualizations/charts/static/views/viewport.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/views/viewport.js b/config/plugins/visualizations/charts/static/views/viewport.js index f127520d7bf1..5363f0726605 100644 --- a/config/plugins/visualizations/charts/static/views/viewport.js +++ b/config/plugins/visualizations/charts/static/views/viewport.js @@ -25,7 +25,7 @@ define( [ 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'utils/utils' ], function( Port }); }); this.chart.on( 'set:state', function() { - var $container = self.$el.find( '.charts-viewport-container' ); + var $container = self.$( '.charts-viewport-container' ); var $info = self.$info; var $icon = self.$icon; var $text = self.$text; From ebd0dab936b4fbb82dbb21218851ca7579197bf7 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 08:35:53 -0400 Subject: [PATCH 13/27] Change draw label to indicate that the chart will be saved too --- config/plugins/visualizations/charts/static/views/editor.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/views/editor.js b/config/plugins/visualizations/charts/static/views/editor.js index c4fd1f3aeb9c..4ea90fa0ba0e 100644 --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -17,7 +17,7 @@ define( [ 'mvc/ui/ui-tabs', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'utils/utils' 'save' : new Ui.ButtonIcon({ icon : 'fa-save', tooltip : 'Draw Chart', - title : 'Draw', + title : 'Save and Draw', onclick : function() { self._saveChart(); } From 30bd72310e4d51f49e9fe020b119c02642ffe854 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 08:36:43 -0400 Subject: [PATCH 14/27] Fix tooltip --- config/plugins/visualizations/charts/static/views/editor.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/views/editor.js b/config/plugins/visualizations/charts/static/views/editor.js index 4ea90fa0ba0e..4086a16da819 100644 --- a/config/plugins/visualizations/charts/static/views/editor.js +++ b/config/plugins/visualizations/charts/static/views/editor.js @@ -16,7 +16,7 @@ define( [ 'mvc/ui/ui-tabs', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'utils/utils' operations : { 'save' : new Ui.ButtonIcon({ icon : 'fa-save', - tooltip : 'Draw Chart', + tooltip : 'Save and Draw Chart', title : 'Save and Draw', onclick : function() { self._saveChart(); From 9481939154269253e59a2d9ffafe506947287dc1 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 08:57:17 -0400 Subject: [PATCH 15/27] Remove separated tabular input element --- .../static/charts/utilities/tabular-form.js | 69 +++++++++++++++++-- .../static/charts/utilities/tabular-inputs.js | 65 ----------------- .../charts/static/views/settings.js | 5 +- 3 files changed, 66 insertions(+), 73 deletions(-) delete mode 100644 config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js diff --git a/config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js b/config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js index b7c22827d579..2b540bccc362 100644 --- a/config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js +++ b/config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js @@ -1,4 +1,59 @@ -define( [ 'plugin/charts/utilities/tabular-inputs' ], function( Inputs ) { +define( [], function() { + var axisLabel = function( name, options ) { + options = options || {}; + prefix = name.substr( 0, 1 ); + return { + name : name, + label : prefix.toUpperCase() + '-Axis label', + help : 'Provide a label for the axis.', + type : 'text', + value : options.value || prefix.toUpperCase() + '-axis', + placeholder : 'Axis label' + } + } + var axisType = function( name, options ) { + options = options || {}; + prefix = name.substr( 0, 1 ); + var axisPrecision = function() { + return { name : 'precision', + label : 'Axis tick format', + help : 'Select the tick format for the axis.', + type : 'select', + value : options.precision || 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' } ] } + } + return { + name : prefix + '_axis_type', + type : 'conditional', + test_param : { + name : 'type', + label : prefix.toUpperCase() + '-Axis value type', + type : 'select', + value : options.value || 'auto', + help : 'Select the value type of the axis.', + data : [ { value : 'hide', label : '-- Do not show values --' }, + { value : 'auto', label : 'Auto' }, + { value : 'f', label : 'Float' }, + { value : 'd', label : 'Integer' }, + { value : 'e', label : 'Exponent' }, + { value : 'p', label : 'Percent' }, + { value : 's', label : 'SI-prefix' } ] + }, + cases : [ { value : 'hide' }, + { value : 'auto' }, + { value : 'f', inputs: [ axisPrecision() ] }, + { value : 'd' }, + { value : 'e', inputs: [ axisPrecision() ] }, + { value : 'p', inputs: [ axisPrecision() ] }, + { value : 's' } ] + } + } + return { title : '', category : '', @@ -6,13 +61,13 @@ define( [ 'plugin/charts/utilities/tabular-inputs' ], function( Inputs ) { tag : '', keywords : '', datatype : 'tabular', + use_panels : true, settings : { - x_axis_label : Inputs.axisLabel( 'x_axis_label' ), - x_axis_type : Inputs.axisType( 'x_axis_type' ), - y_axis_label : Inputs.axisLabel( 'y_axis_label' ), - y_axis_type : Inputs.axisType( 'y_axis_type' ), - show_legend : Inputs.boolean( 'show_legend', { label: 'Show legend', help: 'Would you like to add a legend?' } ), - use_panels : Inputs.boolean( 'use_panels', { label: 'Use multi-panels', help: 'Would you like to separate your data into individual panels?' } ) + x_axis_label : axisLabel( 'x_axis_label' ), + x_axis_type : axisType( 'x_axis_type' ), + y_axis_label : axisLabel( 'y_axis_label' ), + y_axis_type : axisType( 'y_axis_type' ), + show_legend : { type: 'boolean', label: 'Show legend', help: 'Would you like to add a legend?' } }, groups : { key: { diff --git a/config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js b/config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js deleted file mode 100644 index 742c1517b46b..000000000000 --- a/config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js +++ /dev/null @@ -1,65 +0,0 @@ -define( [], function() { - return { - axisLabel : function( name, options ) { - options = options || {}; - prefix = name.substr( 0, 1 ); - return { - name : name, - label : prefix.toUpperCase() + '-Axis label', - help : 'Provide a label for the axis.', - type : 'text', - value : options.value || prefix.toUpperCase() + '-axis', - placeholder : 'Axis label' - } - }, - axisType : function( name, options ) { - options = options || {}; - prefix = name.substr( 0, 1 ); - var axisPrecision = function() { - return { name : 'precision', - label : 'Axis tick format', - help : 'Select the tick format for the axis.', - type : 'select', - value : options.precision || 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' } ] } - } - return { - name : prefix + '_axis_type', - type : 'conditional', - test_param : { - name : 'type', - label : prefix.toUpperCase() + '-Axis value type', - type : 'select', - value : options.value || 'auto', - help : 'Select the value type of the axis.', - data : [ { value : 'hide', label : '-- Do not show values --' }, - { value : 'auto', label : 'Auto' }, - { value : 'f', label : 'Float' }, - { value : 'd', label : 'Integer' }, - { value : 'e', label : 'Exponent' }, - { value : 'p', label : 'Percent' }, - { value : 's', label : 'SI-prefix' } ] - }, - cases : [ { value : 'hide' }, - { value : 'auto' }, - { value : 'f', inputs: [ axisPrecision() ] }, - { value : 'd' }, - { value : 'e', inputs: [ axisPrecision() ] }, - { value : 'p', inputs: [ axisPrecision() ] }, - { value : 's' } ] - } - }, - boolean : function( name, options ) { - options = options || {}; - return { name : name, - label : options.label, - help : options.help, - type : 'boolean' } - } - } -}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/views/settings.js b/config/plugins/visualizations/charts/static/views/settings.js index 68b437b21f07..d14e95ac20b5 100644 --- a/config/plugins/visualizations/charts/static/views/settings.js +++ b/config/plugins/visualizations/charts/static/views/settings.js @@ -14,7 +14,10 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form- }, render: function() { var self = this; - var inputs = Utils.clone( this.chart.definition.settings ); + var inputs = Utils.clone( this.chart.definition.settings ) || {}; + if ( this.chart.definition.use_panels ) { + inputs[ 'use_panels' ] = { type: 'boolean', label: 'Use multi-panels', help: 'Would you like to separate your data into individual panels?' }; + } if ( _.size( inputs ) > 0 ) { FormData.visitInputs( inputs, function( input, name ) { var model_value = self.chart.settings.get( name ); From 70e68c204b3f250e76032761d796f62552f63d70 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 08:58:07 -0400 Subject: [PATCH 16/27] Fix spacing --- .../plugins/visualizations/charts/static/views/settings.js | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/views/settings.js b/config/plugins/visualizations/charts/static/views/settings.js index d14e95ac20b5..6203d7925058 100644 --- a/config/plugins/visualizations/charts/static/views/settings.js +++ b/config/plugins/visualizations/charts/static/views/settings.js @@ -16,7 +16,11 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form- var self = this; var inputs = Utils.clone( this.chart.definition.settings ) || {}; if ( this.chart.definition.use_panels ) { - inputs[ 'use_panels' ] = { type: 'boolean', label: 'Use multi-panels', help: 'Would you like to separate your data into individual panels?' }; + inputs[ 'use_panels' ] = { + type : 'boolean', + label : 'Use multi-panels', + help : 'Would you like to separate your data into individual panels?' + }; } if ( _.size( inputs ) > 0 ) { FormData.visitInputs( inputs, function( input, name ) { From 77dddc3fa42e28eef9ad14c30d8047b2b2865c09 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 09:03:13 -0400 Subject: [PATCH 17/27] Generalize internal use panels parameter option --- config/plugins/visualizations/charts/static/views/settings.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/views/settings.js b/config/plugins/visualizations/charts/static/views/settings.js index 6203d7925058..089f0a99cfc1 100644 --- a/config/plugins/visualizations/charts/static/views/settings.js +++ b/config/plugins/visualizations/charts/static/views/settings.js @@ -15,7 +15,7 @@ define( [ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form- render: function() { var self = this; var inputs = Utils.clone( this.chart.definition.settings ) || {}; - if ( this.chart.definition.use_panels ) { + if ( this.chart.definition.use_panels && !inputs[ 'use_panels' ]) { inputs[ 'use_panels' ] = { type : 'boolean', label : 'Use multi-panels', From d6f174e487b77862c005b65843af79c53bd560c7 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 25 Aug 2016 09:52:26 -0400 Subject: [PATCH 18/27] Filter exportable datatypes by chart type --- client/galaxy/scripts/mvc/ui/ui-buttons.js | 56 +++++++++++-------- .../visualizations/charts/static/app.js | 15 ++--- .../static/charts/jqplot/common/config.js | 1 + .../static/charts/nvd3/common/config.js | 1 + .../charts/static/views/viewer.js | 36 +++++------- static/maps/mvc/ui/ui-buttons.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 4 +- .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/mvc/ui/ui-buttons.js | 2 +- 10 files changed, 61 insertions(+), 60 deletions(-) diff --git a/client/galaxy/scripts/mvc/ui/ui-buttons.js b/client/galaxy/scripts/mvc/ui/ui-buttons.js index 1a4858324e94..a597d457676f 100644 --- a/client/galaxy/scripts/mvc/ui/ui-buttons.js +++ b/client/galaxy/scripts/mvc/ui/ui-buttons.js @@ -223,9 +223,11 @@ define( [ 'utils/utils' ], function( Utils ) { visible : true, tag : '' }).set( options ); + this.collection = new Backbone.Collection(); this.setElement( $( '
' ).append( this.$root = $( '
' ).append( this.$icon = $( '' ) ) .append( this.$title = $( '' ) ) ) ); this.listenTo( this.model, 'change', this.render, this ); + this.listenTo( this.collection, 'change add remove reset', this.render, this ); this.render(); }, @@ -237,7 +239,7 @@ define( [ 'utils/utils' ], function( Utils ) { .addClass( options.cls ) .attr( 'id', options.id ) .css( { float : options.floating, - display : options.visible ? 'block' : 'none' } ); + display : options.visible && this.collection.where( { visible: true } ).length > 0 ? 'block' : 'none' } ); this.$root.addClass( 'root button dropdown-toggle' ) .attr( 'data-toggle', 'dropdown' ) .tooltip( { title: options.tooltip, placement: 'bottom' } ) @@ -249,11 +251,38 @@ define( [ 'utils/utils' ], function( Utils ) { this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon ); this.$title.removeClass().addClass( 'title' ).html( options.title ); options.icon && options.title && this.$icon.addClass( 'ui-margin-right' ); + this.$menu && this.$menu.remove(); + if ( this.collection.length > 0 ) { + this.$menu = $( '