[galaxy-commits] commit/galaxy-central: carlfeberhard: Added history.js templates: icon-button partial, hdaSummary, titleLink; packed scripts

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/802b87d64910/ changeset: 802b87d64910 user: carlfeberhard date: 2012-09-13 17:58:14 summary: Added history.js templates: icon-button partial, hdaSummary, titleLink; packed scripts affected #: 25 files diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -124,8 +124,12 @@ }, isEditable : function(){ - // roughly can_edit from history_common.mako - return ( !( this.get( 'deleted' ) || this.get( 'purged' ) ) ); + // roughly can_edit from history_common.mako - not deleted or purged = editable + return ( + //this.get( 'for_editing' ) + //&& !( this.get( 'deleted' ) || this.get( 'purged' ) ) + !( this.get( 'deleted' ) || this.get( 'purged' ) ) + ); }, hasData : function(){ @@ -159,10 +163,11 @@ //============================================================================== var HistoryItemView = BaseView.extend( LoggableMixin ).extend({ + //??TODO: add alias in initialize this.hda = this.model? // view for HistoryItem model above // uncomment this out see log messages - //logger : console, + logger : console, tagName : "div", className : "historyItemContainer", @@ -179,6 +184,7 @@ this.log( this + '.model:', this.model ); var id = this.model.get( 'id' ), state = this.model.get( 'state' ); + this.clearReferences(); this.$el.attr( 'id', 'historyItemContainer-' + id ); @@ -191,7 +197,7 @@ this.body = $( this._render_body() ); itemWrapper.append( this.body ); - // set up canned behavior (bootstrap, popupmenus, editable_text, etc.) + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); //TODO: broken @@ -206,6 +212,14 @@ return this.$el.append( itemWrapper ); }, + clearReferences : function(){ + //??TODO: best way? + this.displayButton = null; + this.editButton = null; + this.deleteButton = null; + this.errButton = null; + }, + // ................................................................................ RENDER WARNINGS _render_warnings : function(){ // jQ errs on building dom with whitespace - if there are no messages, trim -> '' @@ -224,16 +238,10 @@ // ................................................................................ DISPLAY, EDIT ATTR, DELETE _render_titleButtons : function(){ // render the display, edit attr and delete icon-buttons - var buttonDiv = $( '<div class="historyItemButtons"></div>' ), - for_editing = this.model.get( 'for_editing' ); - - // don't show display, edit while uploading - if( this.model.get( 'state' ) !== HistoryItem.STATES.UPLOAD ){ - buttonDiv.append( this._render_displayButton() ); - - if( for_editing ){ buttonDiv.append( this._render_editButton() ); } - } - if( for_editing ){ buttonDiv.append( this._render_deleteButton() ); } + var buttonDiv = $( '<div class="historyItemButtons"></div>' ); + buttonDiv.append( this._render_displayButton() ); + buttonDiv.append( this._render_editButton() ); + buttonDiv.append( this._render_deleteButton() ); return buttonDiv; }, @@ -241,15 +249,19 @@ //TODO: move other data (non-href) into {} in view definition, cycle over those keys in _titlebuttons //TODO: move disabled span data into view def, move logic into _titlebuttons _render_displayButton : function(){ + + // don't show display while uploading + if( this.model.get( 'state' ) === HistoryItem.STATES.UPLOAD ){ return null; } + + // show a disabled display if the data's been purged displayBtnData = ( this.model.get( 'purged' ) )?({ - // show a disabled display if the data's been purged title : 'Cannot display datasets removed from disk', + enabled : false, icon_class : 'display', - enabled : false, + + // if not, render the display icon-button with href }):({ - // if not, render the display icon-button with href title : 'Display data in browser', - //TODO: need generated url here href : this.model.get( 'display_url' ), target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( null ), icon_class : 'display', @@ -259,32 +271,39 @@ }, _render_editButton : function(){ - // render the edit attr icon-button - var id = this.model.get( 'id' ), - purged = this.model.get( 'purged' ), - deleted = this.model.get( 'deleted' ); + + // don't show edit while uploading, or if editable + if( ( this.model.get( 'state' ) === HistoryItem.STATES.UPLOAD ) + || ( !this.model.get( 'for_editing' ) ) ){ + return null; + } + + var purged = this.model.get( 'purged' ), + deleted = this.model.get( 'deleted' ), + editBtnData = { + title : 'Edit attributes', + href : this.model.get( 'edit_url' ), + target : 'galaxy_main', + icon_class : 'edit' + }; - var editBtnData = { - title : 'Edit attributes', - href : this.model.get( 'edit_url' ), - target : 'galaxy_main', - icon_class : 'edit' - } // disable if purged or deleted and explain why in the tooltip //TODO: if for_editing if( deleted || purged ){ - editBtnData = { - enabled : false, - icon_class : 'edit' - }; - editBtnData.title = ( !purged )?( 'Undelete dataset to edit attributes' ): - ( 'Cannot edit attributes of datasets removed from disk' ); + editBtnData.enabled = false; } + if( deleted ){ + editBtnData.title = 'Undelete dataset to edit attributes'; + } else if( purged ){ + editBtnData.title = 'Cannot edit attributes of datasets removed from disk'; + } + this.editButton = new IconButtonView({ model : new IconButton( editBtnData ) }); return this.editButton.render().$el; }, _render_deleteButton : function(){ + // don't show delete if not editable if( !this.model.get( 'for_editing' ) ){ return null; } var deleteBtnData = ( this.model.get( 'delete_url' ) )?({ @@ -303,14 +322,8 @@ }, _render_titleLink : function(){ - // render the title (hda name) - var h_name = this.model.get( 'name' ), - hid = this.model.get( 'hid' ); - title = ( hid + ': ' + h_name ); - return $( linkHTMLTemplate({ - href : 'javascript:void(0);', - text : '<span class="historyItemTitle">' + title + '</span>' - })); + this.log( 'model:', this.model.toJSON() ); + return $( jQuery.trim( HistoryItemView.templates.titleLink( this.model.toJSON() ) ) ); }, // ................................................................................ RENDER BODY @@ -344,12 +357,14 @@ // bug report button //NOTE: these are shown _before_ info, rerun so use _prepend_ if( this.model.get( 'for_editing' ) ){ - actionBtnDiv.prepend( $( linkHTMLTemplate({ + //TODO??: save to view 'this.errButton' + this.errButton = new IconButtonView({ model : new IconButton({ title : 'View or report this error', - href : this.model.get( 'report_errors_url' ), + href : this.model.get( 'report_error_url' ), target : 'galaxy_main', - classes : [ 'icon-button', 'tooltip', 'bug' ] - }))); + icon_class : 'bug' + })}); + actionBtnDiv.prepend( this.errButton.render().$el ); } if( this.model.hasData() ){ //TODO: render_download_links( data, dataset_id ) @@ -568,37 +583,35 @@ }, _render_hdaSummary : function(){ - // default span rendering - var dbkeyHTML = _.template( '<span class="<%= dbkey %>"><%= dbkey %></span>', - { dbkey: this.model.get( 'metadata_dbkey' ) } ); - // if there's no dbkey and it's editable : render a link to editing in the '?' - if( this.model.get( 'metadata_dbkey' ) === '?' && this.model.isEditable() ){ - dbkeyHTML = linkHTMLTemplate({ - text : this.model.get( 'metadata_dbkey' ), - href : this.model.get( 'edit_url' ), - target : 'galaxy_main' - }); + var modelData = this.model.toJSON(); + + // if there's no dbkey and it's editable : pass a flag to the template to render a link to editing in the '?' + if( this.model.get( 'metadata_dbkey' ) === '?' + && this.model.isEditable() ){ + _.extend( modelData, { dbkey_unknown_and_editable : true }); } - return ( HistoryItemView.TEMPLATES.hdaSummary( - _.extend({ dbkeyHTML: dbkeyHTML }, this.model.attributes ) ) ); + return HistoryItemView.templates.hdaSummary( modelData ); }, _render_showParamsAndRerun : function(){ //TODO??: generalize to _render_actionButtons, pass in list of 'buttons' to render, default to these two var actionBtnDiv = $( '<div/>' ); - actionBtnDiv.append( $( linkHTMLTemplate({ + + this.showParamsButton = new IconButtonView({ model : new IconButton({ title : 'View details', href : this.model.get( 'show_params_url' ), target : 'galaxy_main', - classes : [ 'icon-button', 'tooltip', 'information' ] - }))); + icon_class : 'information' + }) }); + actionBtnDiv.append( this.showParamsButton.render().$el ); + if( this.model.get( 'for_editing' ) ){ - actionBtnDiv.append( $( linkHTMLTemplate({ + this.rerunButton = new IconButtonView({ model : new IconButton({ title : 'Run this job again', href : this.model.get( 'rerun_url' ), target : 'galaxy_main', - classes : [ 'icon-button', 'tooltip', 'arrow-circle' ] - }))); + icon_class : 'arrow-circle' + }) }); } return actionBtnDiv; }, @@ -748,24 +761,14 @@ return 'HistoryItemView(' + modelString + ')'; } }); -HistoryItemView.TEMPLATES = {}; - -//TODO: contains localized strings -HistoryItemView.TEMPLATES.hdaSummary = _.template([ - '<%= misc_blurb %><br />', - 'format: <span class="<%= data_type %>"><%= data_type %></span>, ', - 'database: <%= dbkeyHTML %>' -].join( '' )); //============================================================================== //HistoryItemView.templates = InDomTemplateLoader.getTemplates({ HistoryItemView.templates = CompiledTemplateLoader.getTemplates({ - 'common-templates.html' : { - warningMsg : 'template-warningmessagesmall', - }, 'history-templates.html' : { - messages : 'template-history-warning-messages2', + messages : 'template-history-warning-messages', + titleLink : 'template-history-titleLink', hdaSummary : 'template-history-hdaSummary' } }); @@ -1039,7 +1042,8 @@ { state : HistoryItem.STATES.EMPTY }), error : _.extend( _.clone( mockHistory.data.template ), - { state : HistoryItem.STATES.ERROR }), + { state : HistoryItem.STATES.ERROR, + report_error_url: 'example.com/report_err' }), discarded : _.extend( _.clone( mockHistory.data.template ), { state : HistoryItem.STATES.DISCARDED }), diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 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t}if(F){l=l.slice(0,-1*F*2);G=G.slice(0,-1*F);s=s.slice(0,-1*F)}l.push(this.productions_[C[1]][0]);G.push(B.$);s.push(B._$);g=H[l[l.length-2]][l[l.length-1]];l.push(g);break;case 3:return true}}return true}};var a=(function(){var j=({EOF:1,parseError:function l(o,n){if(this.yy.parseError){this.yy.parseError(o,n)}else{throw new Error(o)}},setInput:function(n){this._input=n;this._more=this._less=this.done=false;this.yylineno=this.yyleng=0;this.yytext=this.matched=this.match="";this.conditionStack=["INITIAL"];this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0};return this},input:function(){var o=this._input[0];this.yytext+=o;this.yyleng++;this.match+=o;this.matched+=o;var n=o.match(/\n/);if(n){this.yylineno++}this._input=this._input.slice(1);return o},unput:function(n){this._input=n+this._input;return this},more:function(){this._more=true;return this},pastInput:function(){var n=this.matched.substr(0,this.matched.length-this.match.length);return(n.length>20?"...":"")+n.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var n=this.match;if(n.length<20){n+=this._input.substr(0,20-n.length)}return(n.substr(0,20)+(n.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var n=this.pastInput();var o=new Array(n.length+1).join("-");return n+this.upcomingInput()+"\n"+o+"^"},next:function(){if(this.done){return this.EOF}if(!this._input){this.done=true}var r,p,o,n;if(!this._more){this.yytext="";this.match=""}var s=this._currentRules();for(var q=0;q<s.length;q++){p=this._input.match(this.rules[s[q]]);if(p){n=p[0].match(/\n.*/g);if(n){this.yylineno+=n.length}this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:n?n[n.length-1].length-1:this.yylloc.last_column+p[0].length};this.yytext+=p[0];this.match+=p[0];this.matches=p;this.yyleng=this.yytext.length;this._more=false;this._input=this._input.slice(p[0].length);this.matched+=p[0];r=this.performAction.call(this,this.yy,this,s[q],this.conditionStack[this.conditionStack.length-1]);if(r){return r}else{return}}}if(this._input===""){return this.EOF}else{this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})}},lex:function g(){var n=this.next();if(typeof n!=="undefined"){return n}else{return this.lex()}},begin:function h(n){this.conditionStack.push(n)},popState:function m(){return this.conditionStack.pop()},_currentRules:function k(){return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules},topState:function(){return this.conditionStack[this.conditionStack.length-2]},pushState:function h(n){this.begin(n)}});j.performAction=function i(r,o,q,n){var p=n;switch(q){case 0:if(o.yytext.slice(-1)!=="\\"){this.begin("mu")}if(o.yytext.slice(-1)==="\\"){o.yytext=o.yytext.substr(0,o.yyleng-1),this.begin("emu")}if(o.yytext){return 14}break;case 1:return 14;break;case 2:this.popState();return 14;break;case 3:return 24;break;case 4:return 16;break;case 5:return 20;break;case 6:return 19;break;case 7:return 19;break;case 8:return 23;break;case 9:return 23;break;case 10:o.yytext=o.yytext.substr(3,o.yyleng-5);this.popState();return 15;break;case 11:return 22;break;case 12:return 34;break;case 13:return 33;break;case 14:return 33;break;case 15:return 36;break;case 16:break;case 17:this.popState();return 18;break;case 18:this.popState();return 18;break;case 19:o.yytext=o.yytext.substr(1,o.yyleng-2).replace(/\\"/g,'"');return 28;break;case 20:return 30;break;case 21:return 30;break;case 22:return 29;break;case 23:return 33;break;case 24:o.yytext=o.yytext.substr(1,o.yyleng-2);return 33;break;case 25:return"INVALID";break;case 26:return 5;break}};j.rules=[/^[^\x00]*?(?=(\{\{))/,/^[^\x00]+/,/^[^\x00]{2,}?(?=(\{\{))/,/^\{\{>/,/^\{\{#/,/^\{\{\//,/^\{\{\^/,/^\{\{\s*else\b/,/^\{\{\{/,/^\{\{&/,/^\{\{![\s\S]*?\}\}/,/^\{\{/,/^=/,/^\.(?=[} ])/,/^\.\./,/^[\/.]/,/^\s+/,/^\}\}\}/,/^\}\}/,/^"(\\["]|[^"])*"/,/^true(?=[}\s])/,/^false(?=[}\s])/,/^[0-9]+(?=[}\s])/,/^[a-zA-Z0-9_$-]+(?=[=}\s\/.])/,/^\[[^\]]*\]/,/^./,/^$/];j.conditions={mu:{rules:[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26],inclusive:false},emu:{rules:[2],inclusive:false},INITIAL:{rules:[0,1,26],inclusive:true}};return j})();f.lexer=a;return f})();if(typeof require!=="undefined"&&typeof exports!=="undefined"){exports.parser=handlebars;exports.parse=function(){return handlebars.parse.apply(handlebars,arguments)};exports.main=function commonjsMain(a){if(!a[1]){throw new Error("Usage: "+a[0]+" FILE")}if(typeof process!=="undefined"){var c=require("fs").readFileSync(require("path").join(process.cwd(),a[1]),"utf8")}else{var b=require("file").path(require("file").cwd());var c=b.join(a[1]).read({charset:"utf-8"})}return exports.parser.parse(c)};if(typeof module!=="undefined"&&require.main===module){exports.main(typeof process!=="undefined"?process.argv.slice(1):require("system").args)}}Handlebars.Parser=handlebars;Handlebars.parse=function(a){Handlebars.Parser.yy=Handlebars.AST;return Handlebars.Parser.parse(a)};Handlebars.print=function(a){return new Handlebars.PrintVisitor().accept(a)};Handlebars.logger={DEBUG:0,INFO:1,WARN:2,ERROR:3,level:3,log:function(b,a){}};Handlebars.log=function(b,a){Handlebars.logger.log(b,a)};(function(){Handlebars.AST={};Handlebars.AST.ProgramNode=function(c,b){this.type="program";this.statements=c;if(b){this.inverse=new Handlebars.AST.ProgramNode(b)}};Handlebars.AST.MustacheNode=function(d,c,b){this.type="mustache";this.id=d[0];this.params=d.slice(1);this.hash=c;this.escaped=!b};Handlebars.AST.PartialNode=function(c,b){this.type="partial";this.id=c;this.context=b};var a=function(b,c){if(b.original!==c.original){throw new Handlebars.Exception(b.original+" doesn't match "+c.original)}};Handlebars.AST.BlockNode=function(c,b,d){a(c.id,d);this.type="block";this.mustache=c;this.program=b};Handlebars.AST.InverseNode=function(c,b,d){a(c.id,d);this.type="inverse";this.mustache=c;this.program=b};Handlebars.AST.ContentNode=function(b){this.type="content";this.string=b};Handlebars.AST.HashNode=function(b){this.type="hash";this.pairs=b};Handlebars.AST.IdNode=function(f){this.type="ID";this.original=f.join(".");var d=[],g=0;for(var e=0,b=f.length;e<b;e++){var c=f[e];if(c===".."){g++}else{if(c==="."||c==="this"){this.isScoped=true}else{d.push(c)}}}this.parts=d;this.string=d.join(".");this.depth=g;this.isSimple=(d.length===1)&&(g===0)};Handlebars.AST.StringNode=function(b){this.type="STRING";this.string=b};Handlebars.AST.IntegerNode=function(b){this.type="INTEGER";this.integer=b};Handlebars.AST.BooleanNode=function(b){this.type="BOOLEAN";this.bool=b};Handlebars.AST.CommentNode=function(b){this.type="comment";this.comment=b}})();Handlebars.Exception=function(b){var a=Error.prototype.constructor.apply(this,arguments);for(var c in a){if(a.hasOwnProperty(c)){this[c]=a[c]}}this.message=a.message};Handlebars.Exception.prototype=new Error;Handlebars.SafeString=function(a){this.string=a};Handlebars.SafeString.prototype.toString=function(){return this.string.toString()};(function(){var c={"<":"<",">":">",'"':""","'":"'","`":"`"};var d=/&(?!\w+;)|[<>"'`]/g;var b=/[&<>"'`]/;var a=function(e){return c[e]||"&"};Handlebars.Utils={escapeExpression:function(e){if(e instanceof Handlebars.SafeString){return e.toString()}else{if(e==null||e===false){return""}}if(!b.test(e)){return e}return e.replace(d,a)},isEmpty:function(e){if(typeof e==="undefined"){return true}else{if(e===null){return true}else{if(e===false){return true}else{if(Object.prototype.toString.call(e)==="[object Array]"&&e.length===0){return true}else{return false}}}}}}})();Handlebars.Compiler=function(){};Handlebars.JavaScriptCompiler=function(){};(function(f,e){f.OPCODE_MAP={appendContent:1,getContext:2,lookupWithHelpers:3,lookup:4,append:5,invokeMustache:6,appendEscaped:7,pushString:8,truthyOrFallback:9,functionOrFallback:10,invokeProgram:11,invokePartial:12,push:13,assignToHash:15,pushStringParam:16};f.MULTI_PARAM_OPCODES={appendContent:1,getContext:1,lookupWithHelpers:2,lookup:1,invokeMustache:3,pushString:1,truthyOrFallback:1,functionOrFallback:1,invokeProgram:3,invokePartial:1,push:1,assignToHash:1,pushStringParam:1};f.DISASSEMBLE_MAP={};for(var h in f.OPCODE_MAP){var g=f.OPCODE_MAP[h];f.DISASSEMBLE_MAP[g]=h}f.multiParamSize=function(i){return f.MULTI_PARAM_OPCODES[f.DISASSEMBLE_MAP[i]]};f.prototype={compiler:f,disassemble:function(){var t=this.opcodes,r,n;var q=[],v,m,w;for(var s=0,o=t.length;s<o;s++){r=t[s];if(r==="DECLARE"){m=t[++s];w=t[++s];q.push("DECLARE "+m+" = "+w)}else{v=f.DISASSEMBLE_MAP[r];var u=f.multiParamSize(r);var k=[];for(var p=0;p<u;p++){n=t[++s];if(typeof n==="string"){n='"'+n.replace("\n","\\n")+'"'}k.push(n)}v=v+" "+k.join(" ");q.push(v)}}return q.join("\n")},guid:0,compile:function(i,k){this.children=[];this.depths={list:[]};this.options=k;var l=this.options.knownHelpers;this.options.knownHelpers={helperMissing:true,blockHelperMissing:true,each:true,"if":true,unless:true,"with":true,log:true};if(l){for(var j in l){this.options.knownHelpers[j]=l[j]}}return this.program(i)},accept:function(i){return this[i.type](i)},program:function(m){var k=m.statements,o;this.opcodes=[];for(var n=0,j=k.length;n<j;n++){o=k[n];this[o.type](o)}this.isSimple=j===1;this.depths.list=this.depths.list.sort(function(l,i){return l-i});return this},compileProgram:function(m){var j=new this.compiler().compile(m,this.options);var n=this.guid++;this.usePartial=this.usePartial||j.usePartial;this.children[n]=j;for(var o=0,k=j.depths.list.length;o<k;o++){depth=j.depths.list[o];if(depth<2){continue}else{this.addDepth(depth-1)}}return n},block:function(o){var l=o.mustache;var n,p,j,k;var m=this.setupStackForMustache(l);var i=this.compileProgram(o.program);if(o.program.inverse){k=this.compileProgram(o.program.inverse);this.declare("inverse",k)}this.opcode("invokeProgram",i,m.length,!!l.hash);this.declare("inverse",null);this.opcode("append")},inverse:function(k){var j=this.setupStackForMustache(k.mustache);var i=this.compileProgram(k.program);this.declare("inverse",i);this.opcode("invokeProgram",null,j.length,!!k.mustache.hash);this.declare("inverse",null);this.opcode("append")},hash:function(n){var m=n.pairs,p,o;this.opcode("push","{}");for(var k=0,j=m.length;k<j;k++){p=m[k];o=p[1];this.accept(o);this.opcode("assignToHash",p[0])}},partial:function(i){var j=i.id;this.usePartial=true;if(i.context){this.ID(i.context)}else{this.opcode("push","depth0")}this.opcode("invokePartial",j.original);this.opcode("append")},content:function(i){this.opcode("appendContent",i.string)},mustache:function(i){var j=this.setupStackForMustache(i);this.opcode("invokeMustache",j.length,i.id.original,!!i.hash);if(i.escaped&&!this.options.noEscape){this.opcode("appendEscaped")}else{this.opcode("append")}},ID:function(m){this.addDepth(m.depth);this.opcode("getContext",m.depth);this.opcode("lookupWithHelpers",m.parts[0]||null,m.isScoped||false);for(var k=1,j=m.parts.length;k<j;k++){this.opcode("lookup",m.parts[k])}},STRING:function(i){this.opcode("pushString",i.string)},INTEGER:function(i){this.opcode("push",i.integer)},BOOLEAN:function(i){this.opcode("push",i.bool)},comment:function(){},pushParams:function(l){var j=l.length,k;while(j--){k=l[j];if(this.options.stringParams){if(k.depth){this.addDepth(k.depth)}this.opcode("getContext",k.depth||0);this.opcode("pushStringParam",k.string)}else{this[k.type](k)}}},opcode:function(i,l,k,j){this.opcodes.push(f.OPCODE_MAP[i]);if(l!==undefined){this.opcodes.push(l)}if(k!==undefined){this.opcodes.push(k)}if(j!==undefined){this.opcodes.push(j)}},declare:function(i,j){this.opcodes.push("DECLARE");this.opcodes.push(i);this.opcodes.push(j)},addDepth:function(i){if(i===0){return}if(!this.depths[i]){this.depths[i]=true;this.depths.list.push(i)}},setupStackForMustache:function(i){var j=i.params;this.pushParams(j);if(i.hash){this.hash(i.hash)}this.ID(i.id);return j}};e.prototype={nameLookup:function(k,i,j){if(/^[0-9]+$/.test(i)){return k+"["+i+"]"}else{if(e.isValidJavaScriptVariableName(i)){return k+"."+i}else{return k+"['"+i+"']"}}},appendToBuffer:function(i){if(this.environment.isSimple){return"return "+i+";"}else{return"buffer += "+i+";"}},initializeBuffer:function(){return this.quotedString("")},namespace:"Handlebars",compile:function(i,j,l,k){this.environment=i;this.options=j||{};this.name=this.environment.name;this.isChild=!!l;this.context=l||{programs:[],aliases:{self:"this"},registers:{list:[]}};this.preamble();this.stackSlot=0;this.stackVars=[];this.compileChildren(i,j);var n=i.opcodes,m;this.i=0;for(b=n.length;this.i<b;this.i++){m=this.nextOpcode(0);if(m[0]==="DECLARE"){this.i=this.i+2;this[m[1]]=m[2]}else{this.i=this.i+m[1].length;this[m[0]].apply(this,m[1])}}return this.createFunctionContext(k)},nextOpcode:function(r){var o=this.environment.opcodes,m=o[this.i+r],l,p;var q,i;if(m==="DECLARE"){l=o[this.i+1];p=o[this.i+2];return["DECLARE",l,p]}else{l=f.DISASSEMBLE_MAP[m];q=f.multiParamSize(m);i=[];for(var k=0;k<q;k++){i.push(o[this.i+k+1+r])}return[l,i]}},eat:function(i){this.i=this.i+i.length},preamble:function(){var i=[];this.useRegister("foundHelper");if(!this.isChild){var j=this.namespace;var k="helpers = helpers || "+j+".helpers;";if(this.environment.usePartial){k=k+" partials = partials || "+j+".partials;"}i.push(k)}else{i.push("")}if(!this.environment.isSimple){i.push(", buffer = "+this.initializeBuffer())}else{i.push("")}this.lastContext=0;this.source=i},createFunctionContext:function(p){var q=this.stackVars;if(!this.isChild){q=q.concat(this.context.registers.list)}if(q.length>0){this.source[1]=this.source[1]+", "+q.join(", ")}if(!this.isChild){var k=[];for(var o in this.context.aliases){this.source[1]=this.source[1]+", "+o+"="+this.context.aliases[o]}}if(this.source[1]){this.source[1]="var "+this.source[1].substring(2)+";"}if(!this.isChild){this.source[1]+="\n"+this.context.programs.join("\n")+"\n"}if(!this.environment.isSimple){this.source.push("return buffer;")}var r=this.isChild?["depth0","data"]:["Handlebars","depth0","helpers","partials","data"];for(var n=0,j=this.environment.depths.list.length;n<j;n++){r.push("depth"+this.environment.depths.list[n])}if(p){r.push(this.source.join("\n "));return Function.apply(this,r)}else{var m="function "+(this.name||"")+"("+r.join(",")+") {\n "+this.source.join("\n ")+"}";Handlebars.log(Handlebars.logger.DEBUG,m+"\n\n");return m}},appendContent:function(i){this.source.push(this.appendToBuffer(this.quotedString(i)))},append:function(){var i=this.popStack();this.source.push("if("+i+" || "+i+" === 0) { "+this.appendToBuffer(i)+" }");if(this.environment.isSimple){this.source.push("else { "+this.appendToBuffer("''")+" }")}},appendEscaped:function(){var j=this.nextOpcode(1),i="";this.context.aliases.escapeExpression="this.escapeExpression";if(j[0]==="appendContent"){i=" + "+this.quotedString(j[1][0]);this.eat(j)}this.source.push(this.appendToBuffer("escapeExpression("+this.popStack()+")"+i))},getContext:function(i){if(this.lastContext!==i){this.lastContext=i}},lookupWithHelpers:function(k,l){if(k){var i=this.nextStack();this.usingKnownHelper=false;var j;if(!l&&this.options.knownHelpers[k]){j=i+" = "+this.nameLookup("helpers",k,"helper");this.usingKnownHelper=true}else{if(l||this.options.knownHelpersOnly){j=i+" = "+this.nameLookup("depth"+this.lastContext,k,"context")}else{this.register("foundHelper",this.nameLookup("helpers",k,"helper"));j=i+" = foundHelper || "+this.nameLookup("depth"+this.lastContext,k,"context")}}j+=";";this.source.push(j)}else{this.pushStack("depth"+this.lastContext)}},lookup:function(j){var i=this.topStack();this.source.push(i+" = ("+i+" === null || "+i+" === undefined || "+i+" === false ? "+i+" : "+this.nameLookup(i,j,"context")+");")},pushStringParam:function(i){this.pushStack("depth"+this.lastContext);this.pushString(i)},pushString:function(i){this.pushStack(this.quotedString(i))},push:function(i){this.pushStack(i)},invokeMustache:function(k,j,i){this.populateParams(k,this.quotedString(j),"{}",null,i,function(l,n,m){if(!this.usingKnownHelper){this.context.aliases.helperMissing="helpers.helperMissing";this.context.aliases.undef="void 0";this.source.push("else if("+m+"=== undef) { "+l+" = helperMissing.call("+n+"); }");if(l!==m){this.source.push("else { "+l+" = "+m+"; }")}}})},invokeProgram:function(k,l,j){var i=this.programExpression(this.inverse);var m=this.programExpression(k);this.populateParams(l,null,m,i,j,function(n,p,o){if(!this.usingKnownHelper){this.context.aliases.blockHelperMissing="helpers.blockHelperMissing";this.source.push("else { "+n+" = blockHelperMissing.call("+p+"); }")}})},populateParams:function(p,k,t,q,x,w){var l=x||this.options.stringParams||q||this.options.data;var j=this.popStack(),v;var n=[],m,o,u;if(l){this.register("tmp1",t);u="tmp1"}else{u="{ hash: {} }"}if(l){var s=(x?this.popStack():"{}");this.source.push("tmp1.hash = "+s+";")}if(this.options.stringParams){this.source.push("tmp1.contexts = [];")}for(var r=0;r<p;r++){m=this.popStack();n.push(m);if(this.options.stringParams){this.source.push("tmp1.contexts.push("+this.popStack()+");")}}if(q){this.source.push("tmp1.fn = tmp1;");this.source.push("tmp1.inverse = "+q+";")}if(this.options.data){this.source.push("tmp1.data = data;")}n.push(u);this.populateCall(n,j,k||j,w,t!=="{}")},populateCall:function(n,j,k,q,o){var m=["depth0"].concat(n).join(", ");var i=["depth0"].concat(k).concat(n).join(", ");var p=this.nextStack();if(this.usingKnownHelper){this.source.push(p+" = "+j+".call("+m+");")}else{this.context.aliases.functionType='"function"';var l=o?"foundHelper && ":"";this.source.push("if("+l+"typeof "+j+" === functionType) { "+p+" = "+j+".call("+m+"); 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\ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/mvc/annotations.js --- /dev/null +++ b/static/scripts/packed/mvc/annotations.js @@ -0,0 +1,1 @@ +var Annotation=BaseModel.extend(LoggableMixin).extend({logger:console,toString:function(){return"Annotation()"}});var AnnotationView=BaseView.extend(LoggableMixin).extend({logger:console,toString:function(){return"AnnotationView()"}}); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/mvc/base-mvc.js --- /dev/null +++ b/static/scripts/packed/mvc/base-mvc.js @@ -0,0 +1,1 @@ +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){return(this.logger)?(this.logger.log.apply(this,arguments)):(undefined)}};var TemplateLoader=_.extend({},LoggableMixin,{getTemplateLoadFn:function(){throw ("There is no templateLoadFn. Make sure you're using a subclass of TemplateLoader")},getTemplates:function(d,e){e=e||false;this.log(this,"getTemplates:",d,", forceReload:",e);var c={},a=this,b=this.getTemplateLoadFn();if(!d){return c}jQuery.each(d,function(f,g){jQuery.each(g,function(h,i){a.log(a+", templateFile:",f,"templateName:",h,", templateID:",i);c[h]=b.call(a,f,h,i)})});return c}});var CompiledTemplateLoader=_.extend({},TemplateLoader,{getTemplateLoadFn:function(){return this.loadCompiledHandlebarsTemplate},loadCompiledHandlebarsTemplate:function(b,a,c){this.log("getInDomTemplates, templateFile:",b,"templateName:",a,", templateID:",c);if(!Handlebars.templates||!Handlebars.templates[c]){throw ("Template not found: Handlebars."+c+". Check your h.templates() call in the mako file that rendered this page")}this.log("found template function:",c);return Handlebars.templates[c]}});var InDomTemplateLoader=_.extend({},TemplateLoader,{compileTemplate:function(a){if(!Handlebars||!Handlebars.compile){throw ("No Handlebars.compile found. You may only have Handlebars.runtime loaded.Include handlebars.full for this to work")}this.log("compiling template:",a);return Handlebars.compile(a)},findTemplateInDom:function(b,a,c){return $("script#"+c).last()},getTemplateLoadFn:function(){return this.loadInDomTemplate},loadInDomTemplate:function(b,a,c){this.log("getInDomTemplate, templateFile:",b,"templateName:",a,", templateID:",c);var d=this.findTemplateInDom(b,a,c);if(!d||!d.length){throw ("Template not found within the DOM: "+c+". Check that this template has been included in the page")}this.log("found template in dom:",d.html());return this.compileTemplate(d.html())}});var RemoteTemplateLoader=_.extend({},InDomTemplateLoader,{templateBaseURL:"static/scripts/templates/",getTemplateLoadFn:function(){return this.loadViaHttpGet},loadViaHttpGet:function(d,c,f){var b="static/scripts/templates/";this.log("loadViaHttpGet, templateFile:",d,"templateName:",c,", templateID:",f,"templateBaseURL:",this.templateBaseURL);var h=null;try{h=this.loadInDomTemplate(d,c,f)}catch(g){this.log("getInDomTemplate exception:"+g);if(!Handlebars.compile){throw (g)}this.log("Couldn't locate template in DOM: "+f);var a=this;var e=b+d;jQuery.ajax(e,{method:"GET",async:false,success:function(i){a.log(d+" loaded via GET. Attempting compile...");$("body").append(i);h=a.loadInDomTemplate(d,c,f)},error:function(j,i,k){throw ("Failed to fetch "+e+":"+i)}})}if(!h){throw ("Couldn't load or fetch template: "+f)}return h}}); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/mvc/history.js --- a/static/scripts/packed/mvc/history.js +++ b/static/scripts/packed/mvc/history.js @@ -1,1 +1,1 @@ -function linkHTMLTemplate(b,a){if(!b){return"<a></a>"}a=a||"a";var c=["<"+a];for(key in b){var d=b[key];if(d===""){continue}switch(key){case"text":continue;case"classes":key="class";d=(b.classes.join)?(b.classes.join(" ")):(b.classes);default:c.push([" ",key,'="',d,'"'].join(""))}}c.push(">");if("text" in b){c.push(b.text)}c.push("</"+a+">");return c.join("")}var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"))},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){this.log(this+".model:",this.model);var d=this.model.get("id"),c=this.model.get("state");this.$el.attr("id","historyItemContainer-"+d);var a=$("<div/>").attr("id","historyItem-"+d).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});var b=a.find("[popupmenu]");b.each(function(e,f){f=$(f);make_popupmenu(f)});this.$el.children().remove();return this.$el.append(a)},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>'),b=this.model.get("for_editing");if(this.model.get("state")!==HistoryItem.STATES.UPLOAD){a.append(this._render_displayButton());if(b){a.append(this._render_editButton())}}if(b){a.append(this._render_deleteButton())}return a},_render_displayButton:function(){displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",icon_class:"display",enabled:false,}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display",});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){var d=this.model.get("id"),c=this.model.get("purged"),a=this.model.get("deleted");var b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b={enabled:false,icon_class:"edit"};b.title=(!c)?("Undelete dataset to edit attributes"):("Cannot edit attributes of datasets removed from disk")}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a=(this.model.get("delete_url"))?({title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"}):({title:"Dataset is already deleted",icon_class:"delete",enabled:false});this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){var b=this.model.get("name"),a=this.model.get("hid");title=(a+": "+b);return $(linkHTMLTemplate({href:"javascript:void(0);",text:'<span class="historyItemTitle">'+title+"</span>"}))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_showParamsAndRerun())},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_showParamsAndRerun())},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));var b=$(this._render_showParamsAndRerun());if(this.model.get("for_editing")){b.prepend($(linkHTMLTemplate({title:"View or report this error",href:this.model.get("report_errors_url"),target:"galaxy_main",classes:["icon-button","tooltip","bug"]})))}if(this.model.hasData()){b.prepend(this._render_downloadLinks())}a.append(b)},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_showParamsAndRerun())},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_showParamsAndRerun())},_render_body_failed_metadata:function(b){var c="An error occurred setting the metadata for this dataset.";if(this.model.isEditable()){var a=linkHTMLTemplate({text:"set it manually or retry auto-detection",href:this.model.get("edit_url"),target:"galaxy_main"});c+="You may be able to "+a+"."}b.append($(HistoryItemView.templates.warningMsg({warning:c})));this._render_body_ok(b)},_render_body_ok:function(h){h.append(this._render_hdaSummary());if(this.model.get("misc_info")){h.append($('<div class="info">Info: '+this.model.get("misc_info")+"</div>"))}if(this.model.hasData()){var c=$("<div/>");c.append(this._render_downloadLinks());c.append($(linkHTMLTemplate({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",classes:["icon-button","tooltip","information"]})));if(this.model.get("for_editing")){c.append($(linkHTMLTemplate({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",classes:["icon-button","tooltip","arrow-circle"]})));if(this.model.get("trackster_urls")){var a=this.model.get("trackster_urls");c.append($(linkHTMLTemplate({title:"View in 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none">'));this.annotationArea=e;e.append("<strong>Annotation:</strong>");this.annotationElem=$('<div id="'+this.model.get("id")+'-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" title="Edit dataset annotation"></div>');e.append(this.annotationElem);c.append(e)}}c.append('<div style="clear: both;"></div>');h.append(c);var i=$("<div/>");if(this.model.get("display_apps")){var j=this.model.get("display_apps"),b=$("<span/>");for(app_name in j){var g=j[app_name],f=app_name+" ";for(location_name in g){f+=linkHTMLTemplate({text:location_name,href:g[location_name].url,target:g[location_name].target})+" "}b.append(f)}i.append(b)}h.append(i)}else{if(this.model.get("for_editing")){h.append(this._render_showParamsAndRerun())}}h.append(this._render_peek())},_render_body:function(){var b=this.model.get("state"),c=this.model.get("for_editing");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},_render_hdaSummary:function(){var a=_.template('<span class="<%= dbkey %>"><%= dbkey %></span>',{dbkey:this.model.get("metadata_dbkey")});if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){a=linkHTMLTemplate({text:this.model.get("metadata_dbkey"),href:this.model.get("edit_url"),target:"galaxy_main"})}return(HistoryItemView.TEMPLATES.hdaSummary(_.extend({dbkeyHTML:a},this.model.attributes)))},_render_showParamsAndRerun:function(){var a=$("<div/>");a.append($(linkHTMLTemplate({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",classes:["icon-button","tooltip","information"]})));if(this.model.get("for_editing")){a.append($(linkHTMLTemplate({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",classes:["icon-button","tooltip","arrow-circle"]})))}return a},_render_downloadLinks:function(){if(this.model.get("purged")){return null}var a=linkHTMLTemplate({title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]});var d=this.model.get("download_meta_urls");if(!d){return a}var c=$('<div popupmenu="dataset-'+this.model.get("id")+'-popup"></div>');c.append(linkHTMLTemplate({text:"Download Dataset",title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]}));c.append("<a>Additional Files</a>");for(file_type in d){c.append(linkHTMLTemplate({text:"Download "+file_type,href:d[file_type],classes:["action-button"]}))}var b=$(('<div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"></div>'));b.append(a);c.append(b);return c},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this,".loadAndDisplayTags",b);var c=this.tagArea;var a=this.tagElt;if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){this.log("tag_elt_html:",d);a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this,".loadAndDisplayAnnotation",b);var d=this.annotationArea,c=this.annotationElem,a=this.model.get("ajax_set_annotation_url");this.log("annotationArea hidden:",d.is(":hidden"));this.log("annotationElem html:",c.html());if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.TEMPLATES={};HistoryItemView.TEMPLATES.hdaSummary=_.template(["<%= misc_blurb %><br />",'format: <span class="<%= data_type %>"><%= data_type %></span>, ',"database: <%= dbkeyHTML %>"].join(""));HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall",},"history-templates.html":{messages:"template-history-warning-messages2",hdaSummary:"template-history-hdaSummary"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("<div/>");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});function createMockHistoryData(){mockHistory={};mockHistory.data={template:{id:"a799d38679e985db",name:"template",data_type:"fastq",file_size:226297533,genome_build:"?",metadata_data_lines:0,metadata_dbkey:"?",metadata_sequences:0,misc_blurb:"215.8 MB",misc_info:"uploaded fastq file",model_class:"HistoryDatasetAssociation",download_url:"",state:"ok",visible:true,deleted:false,purged:false,hid:0,for_editing:true,undelete_url:"example.com/undelete",purge_url:"example.com/purge",unhide_url:"example.com/unhide",display_url:"example.com/display",edit_url:"example.com/edit",delete_url:"example.com/delete",show_params_url:"example.com/show_params",rerun_url:"example.com/rerun",retag_url:"example.com/retag",annotate_url:"example.com/annotate",peek:['<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>','<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>','<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>','<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>','<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>',"</table>"].join("")}};_.extend(mockHistory.data,{deleted:_.extend(_.clone(mockHistory.data.template),{deleted:true}),purgedNotDeleted:_.extend(_.clone(mockHistory.data.template),{purged:true}),notvisible:_.extend(_.clone(mockHistory.data.template),{visible:false}),hasDisplayApps:_.extend(_.clone(mockHistory.data.template),{display_apps:{"display in IGB":{Web:"/display_application/63cd3858d057a6d1/igb_bam/Web",Local:"/display_application/63cd3858d057a6d1/igb_bam/Local"}}}),canTrackster:_.extend(_.clone(mockHistory.data.template),{trackster_urls:{"data-url":"example.com/trackster-data","action-url":"example.com/trackster-action","new-url":"example.com/trackster-new"}}),zeroSize:_.extend(_.clone(mockHistory.data.template),{file_size:0}),hasMetafiles:_.extend(_.clone(mockHistory.data.template),{download_meta_urls:{bam_index:"example.com/bam-index"}}),upload:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.UPLOAD}),queued:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.QUEUED}),running:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.RUNNING}),empty:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.EMPTY}),error:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.ERROR}),discarded:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.DISCARDED}),setting_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.SETTING_METADATA}),failed_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.FAILED_METADATA})});$(document).ready(function(){mockHistory.items={};mockHistory.views={};for(key in mockHistory.data){mockHistory.items[key]=new HistoryItem(mockHistory.data[key]);mockHistory.items[key].set("name",key);mockHistory.views[key]=new HistoryItemView({model:mockHistory.items[key]});$("body").append(mockHistory.views[key].render())}})}; \ No newline at end of file +function linkHTMLTemplate(b,a){if(!b){return"<a></a>"}a=a||"a";var c=["<"+a];for(key in b){var d=b[key];if(d===""){continue}switch(key){case"text":continue;case"classes":key="class";d=(b.classes.join)?(b.classes.join(" ")):(b.classes);default:c.push([" ",key,'="',d,'"'].join(""))}}c.push(">");if("text" in b){c.push(b.text)}c.push("</"+a+">");return c.join("")}var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"))},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({logger:console,tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){this.log(this+".model:",this.model);var d=this.model.get("id"),c=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+d);var a=$("<div/>").attr("id","historyItem-"+d).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});var b=a.find("[popupmenu]");b.each(function(e,f){f=$(f);make_popupmenu(f)});this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display",}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display",});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a=(this.model.get("delete_url"))?({title:"Delete",href:this.model.get("delete_url"),target:"galaxy_main",id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"}):({title:"Dataset is already deleted",icon_class:"delete",enabled:false});this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){this.log("model:",this.model.toJSON());return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_showParamsAndRerun())},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_showParamsAndRerun())},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));var b=$(this._render_showParamsAndRerun());if(this.model.get("for_editing")){this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});b.prepend(this.errButton.render().$el)}if(this.model.hasData()){b.prepend(this._render_downloadLinks())}a.append(b)},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_showParamsAndRerun())},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_showParamsAndRerun())},_render_body_failed_metadata:function(b){var c="An error occurred setting the metadata for this dataset.";if(this.model.isEditable()){var a=linkHTMLTemplate({text:"set it manually or retry auto-detection",href:this.model.get("edit_url"),target:"galaxy_main"});c+="You may be able to "+a+"."}b.append($(HistoryItemView.templates.warningMsg({warning:c})));this._render_body_ok(b)},_render_body_ok:function(h){h.append(this._render_hdaSummary());if(this.model.get("misc_info")){h.append($('<div class="info">Info: '+this.model.get("misc_info")+"</div>"))}if(this.model.hasData()){var c=$("<div/>");c.append(this._render_downloadLinks());c.append($(linkHTMLTemplate({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",classes:["icon-button","tooltip","information"]})));if(this.model.get("for_editing")){c.append($(linkHTMLTemplate({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",classes:["icon-button","tooltip","arrow-circle"]})));if(this.model.get("trackster_urls")){var a=this.model.get("trackster_urls");c.append($(linkHTMLTemplate({title:"View in Trackster",href:"javascript:void(0)",classes:["icon-button","tooltip","chart_curve","trackster-add"],"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]})))}if(this.model.get("retag_url")&&this.model.get("annotate_url")){var d=$('<div style="float: right;"></div>');d.append($(linkHTMLTemplate({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),classes:["icon-button","tooltip","tags"]})));d.append($(linkHTMLTemplate({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotation_url"),classes:["icon-button","tooltip","annotate"]})));c.append(d);c.append('<div style="clear: both"></div>');this.tagArea=$('<div class="tag-area" style="display: none">');this.tagArea.append("<strong>Tags:</strong>");this.tagElt=$('<div class="tag-elt"></div>');c.append(this.tagArea.append(this.tagElt));var e=$(('<div id="${dataset_id}-annotation-area" class="annotation-area" style="display: none">'));this.annotationArea=e;e.append("<strong>Annotation:</strong>");this.annotationElem=$('<div id="'+this.model.get("id")+'-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" title="Edit dataset annotation"></div>');e.append(this.annotationElem);c.append(e)}}c.append('<div style="clear: both;"></div>');h.append(c);var i=$("<div/>");if(this.model.get("display_apps")){var j=this.model.get("display_apps"),b=$("<span/>");for(app_name in j){var g=j[app_name],f=app_name+" ";for(location_name in g){f+=linkHTMLTemplate({text:location_name,href:g[location_name].url,target:g[location_name].target})+" "}b.append(f)}i.append(b)}h.append(i)}else{if(this.model.get("for_editing")){h.append(this._render_showParamsAndRerun())}}h.append(this._render_peek())},_render_body:function(){var b=this.model.get("state"),c=this.model.get("for_editing");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_showParamsAndRerun:function(){var a=$("<div/>");this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});a.append(this.showParamsButton.render().$el);if(this.model.get("for_editing")){this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})})}return a},_render_downloadLinks:function(){if(this.model.get("purged")){return null}var a=linkHTMLTemplate({title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]});var d=this.model.get("download_meta_urls");if(!d){return a}var c=$('<div popupmenu="dataset-'+this.model.get("id")+'-popup"></div>');c.append(linkHTMLTemplate({text:"Download Dataset",title:"Download",href:this.model.get("download_url"),classes:["icon-button","tooltip","disk"]}));c.append("<a>Additional Files</a>");for(file_type in d){c.append(linkHTMLTemplate({text:"Download "+file_type,href:d[file_type],classes:["action-button"]}))}var b=$(('<div style="float:left;" class="menubutton split popup" id="dataset-${dataset_id}-popup"></div>'));b.append(a);c.append(b);return c},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this,".loadAndDisplayTags",b);var c=this.tagArea;var a=this.tagElt;if(c.is(":hidden")){if(!a.html()){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){this.log("tag_elt_html:",d);a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this,".loadAndDisplayAnnotation",b);var d=this.annotationArea,c=this.annotationElem,a=this.model.get("ajax_set_annotation_url");this.log("annotationArea hidden:",d.is(":hidden"));this.log("annotationElem html:",c.html());if(d.is(":hidden")){if(!c.html()){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0}},initialize:function(b,a){this.log(this+".initialize",b,a);this.items=new HistoryCollection()},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){a.log("loading dataset: ",f,e);var h=new HistoryItem(_.extend(f,{history_id:b}));a.log("as History:",h);a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize");this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.log(this+".render");var a=$("<div/>");_.each(this.itemViews,function(b){a.prepend(b.render())});this.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});function createMockHistoryData(){mockHistory={};mockHistory.data={template:{id:"a799d38679e985db",name:"template",data_type:"fastq",file_size:226297533,genome_build:"?",metadata_data_lines:0,metadata_dbkey:"?",metadata_sequences:0,misc_blurb:"215.8 MB",misc_info:"uploaded fastq file",model_class:"HistoryDatasetAssociation",download_url:"",state:"ok",visible:true,deleted:false,purged:false,hid:0,for_editing:true,undelete_url:"example.com/undelete",purge_url:"example.com/purge",unhide_url:"example.com/unhide",display_url:"example.com/display",edit_url:"example.com/edit",delete_url:"example.com/delete",show_params_url:"example.com/show_params",rerun_url:"example.com/rerun",retag_url:"example.com/retag",annotate_url:"example.com/annotate",peek:['<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>','<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>','<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>','<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0A100</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 133 gi|87159884|ref|NC_007793.1| 2720169 0 * = 2720169 0 NAAACTGTGGCTTCGTTNNNNNNNNNNNNNNNGTGANNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNCNAANNNNNNNNNNNNNNNNNNNNN !!!!!!!!!!!!$!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>','<tr><td colspan="100%">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</td></tr>',"</table>"].join("")}};_.extend(mockHistory.data,{deleted:_.extend(_.clone(mockHistory.data.template),{deleted:true}),purgedNotDeleted:_.extend(_.clone(mockHistory.data.template),{purged:true}),notvisible:_.extend(_.clone(mockHistory.data.template),{visible:false}),hasDisplayApps:_.extend(_.clone(mockHistory.data.template),{display_apps:{"display in IGB":{Web:"/display_application/63cd3858d057a6d1/igb_bam/Web",Local:"/display_application/63cd3858d057a6d1/igb_bam/Local"}}}),canTrackster:_.extend(_.clone(mockHistory.data.template),{trackster_urls:{"data-url":"example.com/trackster-data","action-url":"example.com/trackster-action","new-url":"example.com/trackster-new"}}),zeroSize:_.extend(_.clone(mockHistory.data.template),{file_size:0}),hasMetafiles:_.extend(_.clone(mockHistory.data.template),{download_meta_urls:{bam_index:"example.com/bam-index"}}),upload:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.UPLOAD}),queued:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.QUEUED}),running:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.RUNNING}),empty:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.EMPTY}),error:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.ERROR,report_error_url:"example.com/report_err"}),discarded:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.DISCARDED}),setting_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.SETTING_METADATA}),failed_metadata:_.extend(_.clone(mockHistory.data.template),{state:HistoryItem.STATES.FAILED_METADATA})});$(document).ready(function(){mockHistory.items={};mockHistory.views={};for(key in mockHistory.data){mockHistory.items[key]=new HistoryItem(mockHistory.data[key]);mockHistory.items[key].set("name",key);mockHistory.views[key]=new HistoryItemView({model:mockHistory.items[key]});$("body").append(mockHistory.views[key].render())}})}; \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/mvc/tags.js --- /dev/null +++ b/static/scripts/packed/mvc/tags.js @@ -0,0 +1,1 @@ +var Tag=BaseModel.extend(LoggableMixin).extend({logger:console,defaults:{id:null,itemClass:null},toString:function(){return"Tag()"}});var TagView=BaseView.extend(LoggableMixin).extend({logger:console,toString:function(){return"TagView()"}});var TagCollection=Backbone.Collection.extend(LoggableMixin).extend({model:Tag,logger:console,toString:function(){return"TagCollection()"}});var TagList=BaseView.extend(LoggableMixin).extend({logger:console,toString:function(){return"TagList()"}}); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/templates/compiled/helpers-common-templates.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/helpers-common-templates.js @@ -0,0 +1,1 @@ +Handlebars.registerPartial("clearFloatDiv",function(a){return'<div class="clear"></div>'});Handlebars.registerPartial("iconButton",function(c,b){var a="";a+=(c.enabled)?("<a"):("<span");if(c.title){c.buffer+=' title="'+c.title+'"'}a+=' class="icon-button';if(c.isMenuButton){a+=" menu-button"}if(c.title){a+=" tooltip"}a+=" "+c.icon_class;if(!c.enabled){a+="_disabled"}a+='"';if(c.id){a+=' id="'+c.id+'"'}a+=' href="'+((c.href)?(c.href):("javascript:void(0);"))+'"';if(c.target){a+=' target="'+c.target+'"'}if(!c.visible){a+=' style="display: none;"'}a+=">Bler"+((c.enabled)?("</a>"):("</span>"));return a});Handlebars.registerHelper("warningmessagesmall",function(a){return'<div class="warningmessagesmall"><strong>'+a.fn(this)+"</strong></div>"}); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/templates/compiled/template-history-hdaSummary.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-history-hdaSummary.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-hdaSummary"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,o=this;function e(t,s){var q="",r,p;q+='\n <a href="';p=f.edit_url;if(p){r=p.call(t,{hash:{}})}else{r=t.edit_url;r=typeof r===h?r():r}q+=k(r)+'" target="galaxy_main">';p=f.metadata_dbkey;if(p){r=p.call(t,{hash:{}})}else{r=t.metadata_dbkey;r=typeof r===h?r():r}q+=k(r)+"</a>\n";return q}function c(t,s){var q="",r,p;q+='\n <span class="';p=f.metadata_dbkey;if(p){r=p.call(t,{hash:{}})}else{r=t.metadata_dbkey;r=typeof r===h?r():r}q+=k(r)+'">';p=f.metadata_dbkey;if(p){r=p.call(t,{hash:{}})}else{r=t.metadata_dbkey;r=typeof r===h?r():r}q+=k(r)+"</span>\n";return q}i=f.misc_blurb;if(i){d=i.call(n,{hash:{}})}else{d=n.misc_blurb;d=typeof d===h?d():d}j+=k(d)+'<br />\nformat: <span class="';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+'">';i=f.data_type;if(i){d=i.call(n,{hash:{}})}else{d=n.data_type;d=typeof d===h?d():d}j+=k(d)+"</span>,\ndatabase:\n";d=n.dbkey_unknown_and_editable;d=f["if"].call(n,d,{hash:{},inverse:o.program(3,c,l),fn:o.program(1,e,l)});if(d||d===0){j+=d}return j})})(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/templates/compiled/template-history-titleLink.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-history-titleLink.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-titleLink"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+='<a href="javascript:void(0);"><span class="historyItemTitle">';g=d.hid;if(g){c=g.call(l,{hash:{}})}else{c=l.hid;c=typeof c===f?c():c}h+=i(c)+": ";g=d.name;if(g){c=g.call(l,{hash:{}})}else{c=l.name;c=typeof c===f?c():c}h+=i(c)+"</span></a>";return h})})(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/templates/compiled/template-history-warning-messages.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-history-warning-messages.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-warning-messages"]=b(function(g,s,q,k,v){q=q||g.helpers;var r="",h,e="function",d=this.escapeExpression,p=this,c=q.blockHelperMissing;function o(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(2,n,y)})}if(x||x===0){return x}else{return""}}function n(z,y){var w="",x;w+="\n This dataset has been deleted.\n ";x=z.undelete_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(3,m,y)});if(x||x===0){w+=x}w+="\n";return w}function m(A,z){var x="",y,w;x+='\n Click <a href="';w=q.undelete_url;if(w){y=w.call(A,{hash:{}})}else{y=A.undelete_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUndelete" id="historyItemUndeleter-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to undelete it\n ';y=A.purge_url;y=q["if"].call(A,y,{hash:{},inverse:p.noop,fn:p.program(4,l,z)});if(y||y===0){x+=y}x+="\n ";return x}function l(A,z){var x="",y,w;x+='\n or <a href="';w=q.purge_url;if(w){y=w.call(A,{hash:{}})}else{y=A.purge_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemPurge" id="historyItemPurger-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to immediately remove it from disk\n ';return x}function j(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(7,i,y)})}if(x||x===0){return x}else{return""}}function i(x,w){return"\n This dataset has been deleted and removed from disk.\n"}function f(z,y){var x,w;w=q.warningmessagesmall;if(w){x=w.call(z,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}else{x=z.warningmessagesmall;x=typeof x===e?x():x}if(!q.warningmessagesmall){x=c.call(z,x,{hash:{},inverse:p.noop,fn:p.program(10,u,y)})}if(x||x===0){return x}else{return""}}function u(z,y){var w="",x;w+="\n This dataset has been hidden.\n ";x=z.undelete_url;x=q["if"].call(z,x,{hash:{},inverse:p.noop,fn:p.program(11,t,y)});if(x||x===0){w+=x}w+="\n";return w}function t(A,z){var x="",y,w;x+='\n Click <a href="';w=q.unhide_url;if(w){y=w.call(A,{hash:{}})}else{y=A.unhide_url;y=typeof y===e?y():y}x+=d(y)+'" class="historyItemUnhide" id="historyItemUnhider-';w=q.id;if(w){y=w.call(A,{hash:{}})}else{y=A.id;y=typeof y===e?y():y}x+=d(y)+'"\n target="galaxy_history">here</a> to unhide it\n ';return x}h=s.deleted;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(1,o,v)});if(h||h===0){r+=h}r+="\n\n";h=s.purged;h=q["if"].call(s,h,{hash:{},inverse:p.noop,fn:p.program(6,j,v)});if(h||h===0){r+=h}r+="\n\n";h=s.visible;h=q.unless.call(s,h,{hash:{},inverse:p.noop,fn:p.program(9,f,v)});if(h||h===0){r+=h}return r})})(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/templates/compiled/template-warningmessagesmall.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-warningmessagesmall.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-warningmessagesmall"]=b(function(e,l,d,k,j){d=d||e.helpers;var h="",c,g,f="function",i=this.escapeExpression;h+=' \n <div class="warningmessagesmall"><strong>';g=d.warning;if(g){c=g.call(l,{hash:{}})}else{c=l.warning;c=typeof c===f?c():c}h+=i(c)+"</strong></div>";return h})})(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["libs/d3","viz/visualization"],function(d,e){var c=function(){this.initialize&&this.initialize.apply(this,arguments)};c.extend=Backbone.Model.extend;var b=Backbone.View.extend({className:"circster",initialize:function(h){this.total_gap=h.total_gap;this.genome=h.genome;this.dataset_arc_height=h.dataset_arc_height;this.track_gap=5},render:function(){var j=this,l=this.dataset_arc_height,m=j.$el.width(),h=j.$el.height(),k=(Math.min(m,h)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap));var i=d.select(j.$el[0]).append("svg").attr("width",m).attr("height",h).attr("pointer-events","all").append("svg:g").call(d.behavior.zoom().on("zoom",function(){i.attr("transform","translate("+d.event.translate+") scale("+d.event.scale+")")})).attr("transform","translate("+m/2+","+h/2+")").append("svg:g");this.model.get("tracks").each(function(n,p){var q=n.get("genome_wide_data"),r=k+p*(l+j.track_gap),o=(q instanceof e.GenomeWideBigWigData?f:CircsterSummaryTreeTrackRenderer);track_renderer=new o({track:n,radius_start:r,radius_end:r+l,genome:j.genome,total_gap:j.total_gap});track_renderer.render(i)})}});var a=c.extend({initialize:function(h){this.options=h},render:function(i){genome_arcs=this.chroms_layout(),chroms_arcs=this.genome_data_layout();var n=this.options.radius_start,l=this.options.radius_end,o=i.append("g").attr("id","inner-arc"),m=d.svg.arc().innerRadius(n).outerRadius(l),h=o.selectAll("#inner-arc>path").data(genome_arcs).enter().append("path").attr("d",m).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(p){return p.data.chrom});var j=this.options.track.get("prefs"),k=j.block_color;_.each(chroms_arcs,function(p){if(!p){return}var s=i.append("g"),r=d.svg.arc().innerRadius(n),q=s.selectAll("path").data(p).enter();q.append("path").attr("d",r).style("stroke",k)})},chroms_layout:function(){var i=this.options.genome.get_chroms_info(),k=d.layout.pie().value(function(m){return m.len}).sort(null),l=k(i),h=this.options.total_gap/i.length,j=_.map(l,function(o,n){var m=o.endAngle-h;o.endAngle=(m>o.startAngle?m:o.startAngle);return o});return j},chrom_data_layout:function(k,j,i,l,h){},genome_data_layout:function(){var i=this,h=this.chroms_layout(),m=this.options.track.get("genome_wide_data"),l=this.options.radius_start,j=this.options.radius_end,k=_.zip(h,m.get("data")),n=_.map(k,function(p){var q=p[0],o=p[1];return i.chrom_data_layout(q,o,l,j,m.get("min"),m.get("max"))});return n}});var g=a.extend({chrom_data_layout:function(r,i,o,n,k,p){if(!i||typeof i==="string"){return null}var l=i[0],q=i[3],j=d.scale.linear().domain([k,p]).range([o,n]),m=d.layout.pie().value(function(s){return q}).startAngle(r.startAngle).endAngle(r.endAngle),h=m(l);_.each(l,function(s,t){h[t].outerRadius=j(s[1])});return h}});var f=a.extend({chrom_data_layout:function(q,i,o,n,k,p){var l=i.data;if(l.length===0){return}var j=d.scale.linear().domain([k,p]).range([o,n]),m=d.layout.pie().value(function(s,r){if(r+1===l.length){return 0}return l[r+1][0]-l[r][0]}).startAngle(q.startAngle).endAngle(q.endAngle),h=m(l);_.each(l,function(r,s){h[s].outerRadius=j(r[1])});return h}});return{CircsterView:b}}); \ No newline at end of file +define(["libs/d3","viz/visualization"],function(e,f){var d=function(){this.initialize&&this.initialize.apply(this,arguments)};d.extend=Backbone.Model.extend;var c=Backbone.View.extend({className:"circster",initialize:function(h){this.total_gap=h.total_gap;this.genome=h.genome;this.dataset_arc_height=h.dataset_arc_height;this.track_gap=5},render:function(){var j=this,l=this.dataset_arc_height,m=j.$el.width(),h=j.$el.height(),k=(Math.min(m,h)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap));var i=e.select(j.$el[0]).append("svg").attr("width",m).attr("height",h).attr("pointer-events","all").append("svg:g").call(e.behavior.zoom().on("zoom",function(){i.attr("transform","translate("+e.event.translate+") scale("+e.event.scale+")")})).attr("transform","translate("+m/2+","+h/2+")").append("svg:g");this.model.get("tracks").each(function(n,p){var q=n.get("genome_wide_data"),s=k+p*(l+j.track_gap),o=(q instanceof f.GenomeWideBigWigData?g:a);var r=new o({track:n,radius_start:s,radius_end:s+l,genome:j.genome,total_gap:j.total_gap});r.render(i)})}});var b=d.extend({initialize:function(h){this.options=h},render:function(m){var h=this.chroms_layout(),k=this.genome_data_layout();var n=this.options.radius_start,j=this.options.radius_end,p=m.append("g").attr("id","inner-arc"),o=e.svg.arc().innerRadius(n).outerRadius(j),i=p.selectAll("#inner-arc>path").data(h).enter().append("path").attr("d",o).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(r){return r.data.chrom});var q=this.options.track.get("prefs"),l=q.block_color;_.each(k,function(r){if(!r){return}var u=m.append("g"),t=e.svg.arc().innerRadius(n),s=u.selectAll("path").data(r).enter();s.append("path").attr("d",t).style("stroke",l)})},chroms_layout:function(){var i=this.options.genome.get_chroms_info(),k=e.layout.pie().value(function(m){return m.len}).sort(null),l=k(i),h=this.options.total_gap/i.length,j=_.map(l,function(o,n){var m=o.endAngle-h;o.endAngle=(m>o.startAngle?m:o.startAngle);return o});return j},chrom_data_layout:function(k,j,i,l,h){},genome_data_layout:function(){var i=this,h=this.chroms_layout(),m=this.options.track.get("genome_wide_data"),l=this.options.radius_start,j=this.options.radius_end,k=_.zip(h,m.get("data")),n=_.map(k,function(p){var q=p[0],o=p[1];return i.chrom_data_layout(q,o,l,j,m.get("min"),m.get("max"))});return n}});var a=b.extend({chrom_data_layout:function(r,i,o,n,k,p){if(!i||typeof i==="string"){return null}var l=i[0],q=i[3],j=e.scale.linear().domain([k,p]).range([o,n]),m=e.layout.pie().value(function(s){return q}).startAngle(r.startAngle).endAngle(r.endAngle),h=m(l);_.each(l,function(s,t){h[t].outerRadius=j(s[1])});return h}});var g=b.extend({chrom_data_layout:function(q,i,o,n,k,p){var l=i.data;if(l.length===0){return}var j=e.scale.linear().domain([k,p]).range([o,n]),m=e.layout.pie().value(function(s,r){if(r+1===l.length){return 0}return l[r+1][0]-l[r][0]}).startAngle(q.startAngle).endAngle(q.endAngle),h=m(l);_.each(l,function(r,s){h[s].outerRadius=j(r[1])});return h}});return{CircsterView:c}}); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,feature_search_url:null,genome_wide_summary_data:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},search_features:function(a){var b=this.get("dataset"),c={query:a,dataset_id:b.id,hda_ldda:b.get("hda_ldda")};return $.getJSON(this.get("feature_search_url"),c)},load_data:function(j,h,b,g){var d={chrom:j.get("chrom"),low:j.get("start"),high:j.get("end"),mode:h,resolution:b},e=this.get("dataset");if(e){d.dataset_id=e.id;d.hda_ldda=e.get("hda_ldda")}$.extend(d,g);var k=this.get("filters_manager");if(k){var l=[];var a=k.filters;for(var f=0;f<a.length;f++){l.push(a[f].name)}d.filter_cols=JSON.stringify(l)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(j,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var GenomeWideBigWigData=Backbone.Model.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.flatten(_.map(this.get("data"),function(c){if(c.data.length!==0){return _.map(c.data,function(d){return d[1]})}else{return 0}}));this.set("max",_.max(a));this.set("min",_.min(a))}});var GenomeWideSummaryTreeData=Backbone.RelationalModel.extend({defaults:{data:null,min:0,max:0},initialize:function(b){var a=_.max(this.get("data"),function(c){if(!c||typeof c==="string"){return 0}return c[1]});this.attributes.max=(a&&typeof a!=="string"?a[1]:0)}});var BackboneTrack=Dataset.extend({initialize:function(a){this.set("id",a.dataset_id);var c=this.get("genome_wide_data");if(c){var b=(this.get("track_type")==="LineTrack"?GenomeWideBigWigData:GenomeWideSummaryTreeData);this.set("genome_wide_data",new b(c))}}});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:"BackboneTrack"}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var GenomeVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{bookmarks:null,viewport:null})});var TrackConfig=Backbone.Model.extend({});var CircsterDataLayout=Backbone.Model.extend({defaults:{genome:null,dataset:null,total_gap:null},chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(d,c,b,e,a){},genome_data_layout:function(){var b=this,a=this.chroms_layout(),f=this.get("track").get("genome_wide_data"),e=this.get("radius_start"),c=this.get("radius_end"),d=_.zip(a,f.get("data")),g=_.map(d,function(i){var j=i[0],h=i[1];return b.chrom_data_layout(j,h,e,c,f.get("min"),f.get("max"))});return g}});var CircsterSummaryTreeLayout=CircsterDataLayout.extend({chrom_data_layout:function(k,b,h,g,d,i){if(!b||typeof b==="string"){return null}var e=b[0],j=b[3],c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l){return j}).startAngle(k.startAngle).endAngle(k.endAngle),a=f(e);_.each(e,function(l,m){a[m].outerRadius=c(l[1])});return a}});var CircsterBigWigLayout=CircsterDataLayout.extend({chrom_data_layout:function(j,b,h,g,d,i){var e=b.data;if(e.length===0){return}var c=d3.scale.linear().domain([d,i]).range([h,g]),f=d3.layout.pie().value(function(l,k){if(k+1===e.length){return 0}return e[k+1][0]-e[k][0]}).startAngle(j.startAngle).endAngle(j.endAngle),a=f(e);_.each(e,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.total_gap=a.total_gap;this.genome=a.genome;this.dataset_arc_height=a.dataset_arc_height;this.track_gap=5},render:function(){var c=this,e=this.dataset_arc_height,f=c.$el.width(),a=c.$el.height(),d=(Math.min(f,a)/2-this.model.get("tracks").length*(this.dataset_arc_height+this.track_gap));var b=d3.select(c.$el[0]).append("svg").attr("width",f).attr("height",a).attr("pointer-events","all").append("svg:g").call(d3.behavior.zoom().on("zoom",function(){b.attr("transform","translate("+d3.event.translate+") scale("+d3.event.scale+")")})).attr("transform","translate("+f/2+","+a/2+")").append("svg:g");this.model.get("tracks").each(function(i,o){var j=i.get("genome_wide_data"),n=d+o*(e+c.track_gap),k=(j instanceof GenomeWideBigWigData?CircsterBigWigLayout:CircsterSummaryTreeLayout),q=new k({track:i,radius_start:n,radius_end:n+e,genome:c.genome,total_gap:c.total_gap}),g=q.chroms_layout(),l=q.genome_data_layout();var r=b.append("g").attr("id","inner-arc"),p=d3.svg.arc().innerRadius(n).outerRadius(n+e),h=r.selectAll("#inner-arc>path").data(g).enter().append("path").attr("d",p).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(t){return t.data.chrom});var s=i.get("prefs"),m=s.block_color;_.each(l,function(t){if(!t){return}var w=b.append("g"),v=d3.svg.arc().innerRadius(n),u=w.selectAll("path").data(t).enter().append("path").attr("d",v).style("stroke",m).style("fill",m)})})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})}; \ No newline at end of file +(function(){var f=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(t){return true}},go:function(){var w=$.Deferred(),v=this,y=v.get("ajax_settings"),x=v.get("success_fn"),u=v.get("interval"),t=function(){$.ajax(y).success(function(z){if(x(z)){w.resolve(z)}else{setTimeout(t,u)}})};t();return w}});var g=function(t){this.default_font=t!==undefined?t:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(g.prototype,{load_pattern:function(t,x){var u=this.patterns,v=this.dummy_context,w=new Image();w.src=galaxy_paths.attributes.image_path+x;w.onload=function(){u[t]=v.createPattern(w,"repeat")}},get_pattern:function(t){return this.patterns[t]},new_canvas:function(){var t=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(t)}t.manager=this;return t}});var p=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(t){this.clear()},get_elt:function(u){var v=this.attributes.obj_cache,w=this.attributes.key_ary,t=w.indexOf(u);if(t!==-1){if(v[u].stale){w.splice(t,1);delete v[u]}else{this.move_key_to_end(u,t)}}return v[u]},set_elt:function(u,w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=this.attributes.num_elements;if(!x[u]){if(y.length>=v){var t=y.shift();delete x[t]}y.push(u)}x[u]=w;return w},move_key_to_end:function(u,t){this.attributes.key_ary.splice(t,1);this.attributes.key_ary.push(u)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var d=p.extend({defaults:_.extend({},p.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,feature_search_url:null,genome_wide_summary_data:null,data_mode_compatible:function(t,u){return true},can_subset:function(t){return false}}),data_is_ready:function(){var v=this.get("dataset"),u=$.Deferred(),t=new f({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:v.id,hda_ldda:v.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(w){return w!=="pending"}});$.when(t.go()).then(function(w){u.resolve(w==="ok"||w==="data")});return u},search_features:function(t){var u=this.get("dataset"),v={query:t,dataset_id:u.id,hda_ldda:u.get("hda_ldda")};return $.getJSON(this.get("feature_search_url"),v)},load_data:function(B,A,u,z){var w={chrom:B.get("chrom"),low:B.get("start"),high:B.get("end"),mode:A,resolution:u},x=this.get("dataset");if(x){w.dataset_id=x.id;w.hda_ldda=x.get("hda_ldda")}$.extend(w,z);var C=this.get("filters_manager");if(C){var D=[];var t=C.filters;for(var y=0;y<t.length;y++){D.push(t[y].name)}w.filter_cols=JSON.stringify(D)}var v=this;return $.getJSON(this.get("data_url"),w,function(E){v.set_data(B,E)})},get_data:function(z,y,v,x){var A=this.get_elt(z);if(A&&(is_deferred(A)||this.get("data_mode_compatible")(A,y))){return A}var B=this.get("key_ary"),u=this.get("obj_cache"),C,t;for(var w=0;w<B.length;w++){C=B[w];t=new h({from_str:C});if(t.contains(z)){A=u[C];if(is_deferred(A)||(this.get("data_mode_compatible")(A,y)&&this.get("can_subset")(A))){this.move_key_to_end(C,w);return A}}}A=this.load_data(z,y,v,x);this.set_data(z,A);return A},set_data:function(u,t){this.set_elt(u,t)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(B,A,w,z,x){var D=this.get_elt(B);if(!(D&&this.get("data_mode_compatible")(D,A))){console.log("ERROR: no current data for: ",dataset,B.toString(),A,w,z);return}D.stale=true;var v=B.get("start");if(x===this.DEEP_DATA_REQ){$.extend(z,{start_val:D.data.length+1})}else{if(x===this.BROAD_DATA_REQ){v=(D.max_high?D.max_high:D.data[D.data.length-1][2])+1}}var C=B.copy().set("start",v);var u=this,y=this.load_data(C,A,w,z),t=$.Deferred();this.set_data(B,t);$.when(y).then(function(E){if(E.data){E.data=D.data.concat(E.data);if(E.max_low){E.max_low=D.max_low}if(E.message){E.message=E.message.replace(/[0-9]+/,E.data.length)}}u.set_data(B,E);t.resolve(E)});return t},get_elt:function(t){return p.prototype.get_elt.call(this,t.toString())},set_elt:function(u,t){return p.prototype.set_elt.call(this,u.toString(),t)}});var n=d.extend({load_data:function(t,w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,t,w,x,u,v)}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var h=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(u){if(u.from_str){var w=u.from_str.split(":"),v=w[0],t=w[1].split("-");this.set({chrom:v,start:parseInt(t[0],10),end:parseInt(t[1],10)})}},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(A){var u=this.get("chrom"),z=A.get("chrom"),y=this.get("start"),w=A.get("start"),x=this.get("end"),v=A.get("end"),t;if(u&&z&&u!==z){return this.get("DIF_CHROMS")}if(y<w){if(x<w){t=this.get("BEFORE")}else{if(x<=v){t=this.get("OVERLAP_START")}else{t=this.get("CONTAINS")}}}else{if(y>v){t=this.get("AFTER")}else{if(x<=v){t=this.get("CONTAINED_BY")}else{t=this.get("OVERLAP_END")}}}return t},contains:function(t){return this.compute_overlap(t)===this.get("CONTAINS")},overlaps:function(t){return _.intersection([this.compute_overlap(t)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:h});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:h}]});var q=Backbone.Collection.extend({model:e});var b=Backbone.Model.extend({defaults:{data:null,min:0,max:0},initialize:function(u){var t=_.flatten(_.map(this.get("data"),function(v){if(v.data.length!==0){return _.map(v.data,function(w){return w[1]})}else{return 0}}));this.set("max",_.max(t));this.set("min",_.min(t))}});var m=Backbone.RelationalModel.extend({defaults:{data:null,min:0,max:0},initialize:function(u){var t=_.max(this.get("data"),function(v){if(!v||typeof v==="string"){return 0}return v[1]});this.attributes.max=(t&&typeof t!=="string"?t[1]:0)}});var s=Dataset.extend({initialize:function(t){this.set("id",t.dataset_id);var v=this.get("genome_wide_data");if(v){var u=(this.get("track_type")==="LineTrack"?b:m);this.set("genome_wide_data",new u(v))}}});var o=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:s}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=o.extend({defaults:_.extend({},o.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(u){this.view=u.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var t=this;t.view.on("navigate",function(v){t.navigate(v)})},change_location:function(t){this.view.go_to(t)}});var j=function(t,v,u){$.ajax({url:t,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(w){show_modal("Select datasets for new tracks",w,{Cancel:function(){hide_modal()},Add:function(){var x=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var y,z=$(this).val();if($(this).attr("name")==="id"){y={hda_id:z}}else{y={ldda_id:z}}x[x.length]=$.ajax({url:v,data:y,dataType:"json"})});$.when.apply($,x).then(function(){var y=(arguments[0] instanceof Array?$.map(arguments,function(z){return z[0]}):[arguments[0]]);u(y)});hide_modal()}})}})};var r=(function(){if(typeof module!=="undefined"&&module.exports){return module.exports}else{if(typeof define==="function"&&define.amd){r={};define(function(){return r});return r}else{return window}}})();r.BrowserBookmark=e;r.BrowserBookmarkCollection=q;r.Cache=p;r.CanvasManager=g;r.Genome=c;r.GenomeDataManager=d;r.GenomeRegion=h;r.GenomeRegionCollection=l;r.GenomeVisualization=k;r.GenomeWideBigWigData=b;r.GenomeWideSummaryTreeData=m;r.ReferenceTrackDataManager=n;r.ServerStateDeferred=f;r.TrackBrowserRouter=i;r.TrackConfig=a;r.Visualization=o;r.add_datasets=j}).call(this); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/common-templates.html --- a/static/scripts/templates/common-templates.html +++ b/static/scripts/templates/common-templates.html @@ -1,3 +1,50 @@ +<script type="text/javascript" class="helper-common" id="helper-clearFloatDiv"> +/** Hack div to clear re-enclose float'd elements above it in the parent div + */ +Handlebars.registerPartial( 'clearFloatDiv', function( options ){ + return '<div class="clear"></div>'; +}); +</script> + +<script type="text/javascript" class="helper-common" id="helper-warningmessagesmall"> +/** Renders a warning in a (mostly css) highlighted, iconned warning box + */ +Handlebars.registerHelper( 'warningmessagesmall', function( options ){ + return '<div class="warningmessagesmall"><strong>' + options.fn( this ) + '</strong></div>' +}); +</script> + <script type="text/template" class="template-common" id="template-warningmessagesmall"> - <div class=warningmessagesmall><strong>{{{warning}}}</strong></div> +{{! renders a warning in a (mostly css) highlighted, iconned warning box }} + <div class="warningmessagesmall"><strong>{{ warning }}</strong></div></script> + +<script type="text/javascript" class="helper-common" id="helper-iconButton"> +/** Renders a glx style icon-button (see IconButton in mvc/ui.js) + * can be used in either of the following ways: + * within a template: {{> iconButton buttonData}} + * from js: var templated = ( Handlebars.partials.iconButton( buttonData ) ); + */ +Handlebars.registerPartial( 'iconButton', function( buttonData, options ){ + var buffer = ""; + buffer += ( buttonData.enabled )?( '<a' ):( '<span' ); + + if( buttonData.title ){ buttonData.buffer += ' title="' + buttonData.title + '"'; } + + buffer += ' class="icon-button'; + if( buttonData.isMenuButton ){ buffer += ' menu-button'; } + if( buttonData.title ){ buffer += ' tooltip'; } + buffer += ' ' + buttonData.icon_class; + if( !buttonData.enabled ){ buffer += '_disabled'; } + buffer += '"'; + + if( buttonData.id ){ buffer += ' id="' + buttonData.id + '"'; } + buffer += ' href="' + ( ( buttonData.href )?( buttonData.href ):( 'javascript:void(0);' ) ) + '"'; + if( buttonData.target ){ buffer += ' target="' + buttonData.target + '"'; } + + if( !buttonData.visible ){ buffer += ' style="display: none;"'; } + + buffer += '>Bler' + ( ( buttonData.enabled )?( '</a>' ):( '</span>' ) ); + return buffer; +}); +</script> diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/compiled/helpers-common-templates.js --- /dev/null +++ b/static/scripts/templates/compiled/helpers-common-templates.js @@ -0,0 +1,37 @@ +/** Hack div to clear re-enclose float'd elements above it in the parent div + */ +Handlebars.registerPartial( 'clearFloatDiv', function( options ){ + return '<div class="clear"></div>'; +}); +/** Renders a glx style icon-button (see IconButton in mvc/ui.js) + * can be used in either of the following ways: + * within a template: {{> iconButton buttonData}} + * from js: var templated = ( Handlebars.partials.iconButton( buttonData ) ); + */ +Handlebars.registerPartial( 'iconButton', function( buttonData, options ){ + var buffer = ""; + buffer += ( buttonData.enabled )?( '<a' ):( '<span' ); + + if( buttonData.title ){ buttonData.buffer += ' title="' + buttonData.title + '"'; } + + buffer += ' class="icon-button'; + if( buttonData.isMenuButton ){ buffer += ' menu-button'; } + if( buttonData.title ){ buffer += ' tooltip'; } + buffer += ' ' + buttonData.icon_class; + if( !buttonData.enabled ){ buffer += '_disabled'; } + buffer += '"'; + + if( buttonData.id ){ buffer += ' id="' + buttonData.id + '"'; } + buffer += ' href="' + ( ( buttonData.href )?( buttonData.href ):( 'javascript:void(0);' ) ) + '"'; + if( buttonData.target ){ buffer += ' target="' + buttonData.target + '"'; } + + if( !buttonData.visible ){ buffer += ' style="display: none;"'; } + + buffer += '>Bler' + ( ( buttonData.enabled )?( '</a>' ):( '</span>' ) ); + return buffer; +}); +/** Renders a warning in a (mostly css) highlighted, iconned warning box + */ +Handlebars.registerHelper( 'warningmessagesmall', function( options ){ + return '<div class="warningmessagesmall"><strong>' + options.fn( this ) + '</strong></div>' +}); diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/compiled/template-history-hdaSummary.js --- a/static/scripts/templates/compiled/template-history-hdaSummary.js +++ b/static/scripts/templates/compiled/template-history-hdaSummary.js @@ -2,8 +2,35 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-hdaSummary'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <a href=\""; + foundHelper = helpers.edit_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.edit_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" target=\"galaxy_main\">"; + foundHelper = helpers.metadata_dbkey; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</a>\n"; + return buffer;} + +function program3(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <span class=\""; + foundHelper = helpers.metadata_dbkey; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.metadata_dbkey; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span>\n"; + return buffer;} foundHelper = helpers.misc_blurb; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } @@ -16,10 +43,9 @@ foundHelper = helpers.data_type; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</span>, ',\ndatabase: "; - foundHelper = helpers.dbkeyHTML; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.dbkeyHTML; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1); + buffer += escapeExpression(stack1) + "</span>,\ndatabase:\n"; + stack1 = depth0.dbkey_unknown_and_editable; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } return buffer;}); })(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/compiled/template-history-titleLink.js --- /dev/null +++ b/static/scripts/templates/compiled/template-history-titleLink.js @@ -0,0 +1,18 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-history-titleLink'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; + + + buffer += "<a href=\"javascript:void(0);\"><span class=\"historyItemTitle\">"; + foundHelper = helpers.hid; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + ": "; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span></a>"; + return buffer;}); +})(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/compiled/template-history-warning-messages.js --- a/static/scripts/templates/compiled/template-history-warning-messages.js +++ b/static/scripts/templates/compiled/template-history-warning-messages.js @@ -2,21 +2,30 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-warning-messages'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; function program1(depth0,data) { - var buffer = "", stack1; - buffer += "\n<div class=warningmessagesmall><strong>\nThis dataset has been deleted.\n "; - stack1 = depth0.undelete_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</strong></div>\n"; - return buffer;} + var stack1, foundHelper; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} function program2(depth0,data) { + var buffer = "", stack1; + buffer += "\n This dataset has been deleted.\n "; + stack1 = depth0.undelete_url; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program3(depth0,data) { + var buffer = "", stack1, foundHelper; - buffer += "\n Click <a href=\""; + buffer += "\n Click <a href=\""; foundHelper = helpers.undelete_url; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.undelete_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } @@ -24,16 +33,16 @@ foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to undelete it\n "; stack1 = depth0.purge_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(4, program4, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n "; return buffer;} -function program3(depth0,data) { +function program4(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n or\n <a href=\""; + buffer += "\n or <a href=\""; foundHelper = helpers.purge_url; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.purge_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } @@ -44,24 +53,42 @@ buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to immediately remove it from disk\n "; return buffer;} -function program5(depth0,data) { +function program6(depth0,data) { - - return "\n<div class=warningmessagesmall><strong>\nThis dataset has been deleted and removed from disk.\n</strong></div>\n";} - + var stack1, foundHelper; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} function program7(depth0,data) { + + return "\n This dataset has been deleted and removed from disk.\n";} + +function program9(depth0,data) { + + var stack1, foundHelper; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(10, program10, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} +function program10(depth0,data) { + var buffer = "", stack1; - buffer += "\n<div class=warningmessagesmall><strong>\nThis dataset has been hidden.\n "; + buffer += "\n This dataset has been hidden.\n "; stack1 = depth0.undelete_url; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(11, program11, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n</strong></div>\n"; + buffer += "\n"; return buffer;} -function program8(depth0,data) { +function program11(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n Click <a href=\""; + buffer += "\n Click <a href=\""; foundHelper = helpers.unhide_url; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.unhide_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } @@ -69,7 +96,7 @@ foundHelper = helpers.id; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to unhide it\n "; + buffer += escapeExpression(stack1) + "\"\n target=\"galaxy_history\">here</a> to unhide it\n "; return buffer;} stack1 = depth0.deleted; @@ -77,11 +104,11 @@ if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.purged; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; stack1 = depth0.visible; - stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); + stack1 = helpers.unless.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(9, program9, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } return buffer;}); })(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/compiled/template-warningmessagesmall.js --- a/static/scripts/templates/compiled/template-warningmessagesmall.js +++ b/static/scripts/templates/compiled/template-warningmessagesmall.js @@ -2,14 +2,13 @@ var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-warningmessagesmall'] = template(function (Handlebars,depth0,helpers,partials,data) { helpers = helpers || Handlebars.helpers; - var buffer = "", stack1, foundHelper, functionType="function"; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression; - buffer += "<div class=warningmessagesmall><strong>"; + buffer += " \n <div class=\"warningmessagesmall\"><strong>"; foundHelper = helpers.warning; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.warning; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</strong></div>"; + buffer += escapeExpression(stack1) + "</strong></div>"; return buffer;}); })(); \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -1,38 +1,40 @@ <script type="text/template" class="template-history" id="template-history-warning-messages"> -{{#if deleted}} -<div class=warningmessagesmall><strong> -This dataset has been deleted. +{{#if deleted}}{{#warningmessagesmall}} + This dataset has been deleted. {{#if undelete_url}} - Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" - target="galaxy_history">here</a> to undelete it + Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" + target="galaxy_history">here</a> to undelete it {{#if purge_url}} - or - <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" + or <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" target="galaxy_history">here</a> to immediately remove it from disk {{/if}} {{/if}} -</strong></div> -{{/if}} +{{/warningmessagesmall}}{{/if}} -{{#if purged}} -<div class=warningmessagesmall><strong> -This dataset has been deleted and removed from disk. -</strong></div> -{{/if}} +{{#if purged}}{{#warningmessagesmall}} + This dataset has been deleted and removed from disk. +{{/warningmessagesmall}}{{/if}} -{{#unless visible}} -<div class=warningmessagesmall><strong> -This dataset has been hidden. +{{#unless visible}}{{#warningmessagesmall}} + This dataset has been hidden. {{#if undelete_url}} - Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" - target="galaxy_history">here</a> to unhide it + Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" + target="galaxy_history">here</a> to unhide it {{/if}} -</strong></div> -{{/unless}} +{{/warningmessagesmall}}{{/unless}} +</script> + +<script type="text/template" class="template-history" id="template-history-titleLink"> +<a href="javascript:void(0);"><span class="historyItemTitle">{{ hid }}: {{ name }}</span></a></script><script type="text/template" class="template-history" id="template-history-hdaSummary"> {{ misc_blurb }}<br /> -format: <span class="{{ data_type }}">{{ data_type }}</span>, ', -database: {{ dbkeyHTML }} +format: <span class="{{ data_type }}">{{ data_type }}</span>, +database: +{{#if dbkey_unknown_and_editable }} + <a href="{{ edit_url }}" target="galaxy_main">{{ metadata_dbkey }}</a> +{{else}} + <span class="{{ metadata_dbkey }}">{{ metadata_dbkey }}</span> +{{/if}} </script> diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/template-history-hdaSummary.handlebars --- a/static/scripts/templates/template-history-hdaSummary.handlebars +++ b/static/scripts/templates/template-history-hdaSummary.handlebars @@ -1,3 +1,8 @@ {{ misc_blurb }}<br /> -format: <span class="{{ data_type }}">{{ data_type }}</span>, ', -database: {{ dbkeyHTML }} \ No newline at end of file +format: <span class="{{ data_type }}">{{ data_type }}</span>, +database: +{{#if dbkey_unknown_and_editable }} + <a href="{{ edit_url }}" target="galaxy_main">{{ metadata_dbkey }}</a> +{{else}} + <span class="{{ metadata_dbkey }}">{{ metadata_dbkey }}</span> +{{/if}} \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/template-history-titleLink.handlebars --- /dev/null +++ b/static/scripts/templates/template-history-titleLink.handlebars @@ -0,0 +1,1 @@ +<a href="javascript:void(0);"><span class="historyItemTitle">{{ hid }}: {{ name }}</span></a> \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/template-history-warning-messages.handlebars --- a/static/scripts/templates/template-history-warning-messages.handlebars +++ b/static/scripts/templates/template-history-warning-messages.handlebars @@ -1,30 +1,23 @@ -{{#if deleted}} -<div class=warningmessagesmall><strong> -This dataset has been deleted. +{{#if deleted}}{{#warningmessagesmall}} + This dataset has been deleted. {{#if undelete_url}} - Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" - target="galaxy_history">here</a> to undelete it + Click <a href="{{ undelete_url }}" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" + target="galaxy_history">here</a> to undelete it {{#if purge_url}} - or - <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" + or <a href="{{ purge_url }}" class="historyItemPurge" id="historyItemPurger-{{ id }}" target="galaxy_history">here</a> to immediately remove it from disk {{/if}} {{/if}} -</strong></div> -{{/if}} +{{/warningmessagesmall}}{{/if}} -{{#if purged}} -<div class=warningmessagesmall><strong> -This dataset has been deleted and removed from disk. -</strong></div> -{{/if}} +{{#if purged}}{{#warningmessagesmall}} + This dataset has been deleted and removed from disk. +{{/warningmessagesmall}}{{/if}} -{{#unless visible}} -<div class=warningmessagesmall><strong> -This dataset has been hidden. +{{#unless visible}}{{#warningmessagesmall}} + This dataset has been hidden. {{#if undelete_url}} - Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" - target="galaxy_history">here</a> to unhide it + Click <a href="{{ unhide_url }}" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" + target="galaxy_history">here</a> to unhide it {{/if}} -</strong></div> -{{/unless}} \ No newline at end of file +{{/warningmessagesmall}}{{/unless}} \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 static/scripts/templates/template-warningmessagesmall.handlebars --- a/static/scripts/templates/template-warningmessagesmall.handlebars +++ b/static/scripts/templates/template-warningmessagesmall.handlebars @@ -1,1 +1,2 @@ -<div class=warningmessagesmall><strong>{{{warning}}}</strong></div> \ No newline at end of file +{{! renders a warning in a (mostly css) highlighted, iconned warning box }} + <div class="warningmessagesmall"><strong>{{ warning }}</strong></div> \ No newline at end of file diff -r 6aadac8026cb55844a0e8e49360ad30a9f6d0a25 -r 802b87d6491087f6e82d8490d0d603b7affc3491 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -116,13 +116,17 @@ add_to_data( edit_url=edit_url ) # delete button - if for_editing and not ( dataset_purged or purged ): - add_to_data( delete_url=h.url_for( controller='dataset', action='delete', dataset_id=encoded_data_id ) ) + if for_editing and not ( deleted or dataset_purged or purged ): + add_to_data( delete_url=h.url_for( controller='dataset', action='delete', dataset_id=encoded_data_id, ##TODO: loose end - ##show_deleted_on_refresh=show_deleted_on_refresh ) ) - #show_deleted_on_refresh=False ) ) + show_deleted_on_refresh=show_deleted + )) - #print app + # error report + if for_editing: + #NOTE: no state == 'error' check + add_to_data( report_error_url=h.url_for( h.url_for( controller='dataset', action='errors', id=encoded_data_id ) ) ) + if hda.ext in app.datatypes_registry.get_available_tracks(): # do these need _localized_ dbkeys? trackster_urls = {} @@ -209,7 +213,7 @@ data_dict.update( kwargs ) # trans - add_to_data( non_encoded_id=data.id ) + add_to_data( hid=data.hid ) encoded_data_id = trans.security.encode_id( data.id ) add_to_data( id=encoded_data_id ) @@ -294,9 +298,9 @@ ${h.templates( "helpers-common-templates", - "template-warningmessagesmall", "template-history-warning-messages", + "template-history-titleLink", "template-history-hdaSummary" )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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