September 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dannon: Pack scripts.
by Bitbucket 12 Sep '12

12 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/72f1dcdf1c54/ changeset: 72f1dcdf1c54 user: dannon date: 2012-09-12 19:05:15 summary: Pack scripts. affected #: 4 files diff -r 8b301f6af8340f8cd01022035d5765cf0aba3ede -r 72f1dcdf1c542e6d4689305f5de2077c0bfb4035 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var 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a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".tooltip").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r 8b301f6af8340f8cd01022035d5765cf0aba3ede -r 72f1dcdf1c542e6d4689305f5de2077c0bfb4035 static/scripts/packed/mvc/history.js --- a/static/scripts/packed/mvc/history.js +++ b/static/scripts/packed/mvc/history.js @@ -1,1 +1,1 @@ -_=_;var Loggable={logger:null,log:function(){return(this.logger)?(this.logger.debug.apply(this,arguments)):(undefined)}};var LoggingModel=BaseModel.extend(Loggable);var LoggingView=BaseView.extend(Loggable);var Localizable={localizedStrings:{},setLocalizedString:function(b,a){this.localizedStrings[b]=a},localize:function(a){if(a in this.localizedStrings){return this.localizedStrings[a]}return a}};var LocalizableView=LoggingView.extend(Localizable);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=LoggingModel.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(){return"HistoryItem("+(this.get("name")||this.get("id")||"")+")"}});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=LoggingView.extend({logger:console,tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model);return this},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_purgedWarning());a.append(this._render_deletionWarning());a.append(this._render_visibleWarning());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_purgedWarning:function(){var a=null;if(this.model.get("purged")){a=$(HistoryItemView.STRINGS.purgedMsg)}return a},_render_deletionWarning:function(){var b=null;if(this.model.get("deleted")){var a="";if(this.model.get("undelete_url")){a+=HistoryItemView.TEMPLATES.undeleteLink(this.model.attributes)}if(this.model.get("purge_url")){a+=HistoryItemView.TEMPLATES.purgeLink(this.model.attributes)}b=$(HistoryItemView.TEMPLATES.warningMsg({warning:a}))}return b},_render_visibleWarning:function(){var b=null;if(!this.model.get("visible")&&this.model.get("unhide_url")){var a=HistoryItemView.TEMPLATES.hiddenMsg(this.model.attributes);b=$(HistoryItemView.TEMPLATES.warningMsg({warning:a}))}return b},_render_titleBar:function(){var a=$('<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(){if(this.model.get("purged")){return $('<span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span>')}var b=this.model.get("id"),a={title:"Display data in browser",href:"/datasets/"+b+"/display/?preview=True",target:(this.model.get("for_editing"))?("galaxy_main"):(""),classes:["icon-button","tooltip","display"],dataset_id:b};return $(linkHTMLTemplate(a))},_render_editButton:function(){var c=this.model.get("id"),b=this.model.get("purged"),a=this.model.get("deleted");if(a||b){if(!b){return $('<span class="icon-button edit_disabled tooltip" title="Undelete dataset to edit attributes"></span>')}else{return $('<span class="icon-button edit_disabled tooltip" title="Cannot edit attributes of datasets removed from disk"></span>')}}return $(linkHTMLTemplate({title:"Edit attributes",href:"/datasets/"+c+"/edit",target:"galaxy_main",classes:["icon-button","tooltip","edit"]}))},_render_deleteButton:function(){var c=this.model.get("id"),b=this.model.get("purged"),a=this.model.get("deleted");if(b||a){return $('<span title="Dataset is already deleted" class="icon-button delete_disabled tooltip"></span>')}return $(linkHTMLTemplate({title:"Delete",href:"/datasets/"+c+"/delete?show_deleted_on_refresh=False",target:"galaxy_main",id:"historyItemDeleter-"+c,classes:["icon-button","tooltip","delete"]}))},_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($(HistoryItemView.TEMPLATES.warningMsg({warning:c})));this._render_body_ok(b)},_render_body_ok:function(i){i.append(this._render_hdaSummary());if(this.model.get("misc_info")){i.append($('<div class="info">Info: '+this.model.get("misc_info")+"</div>"))}if(this.model.hasData()){var d=$("<div/>");d.append(this._render_downloadLinks());d.append($(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")){d.append($(linkHTMLTemplate({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",classes:["icon-button","tooltip","arrow-circle"]})));if(this.model.get("trackster_urls")){var a=this.model.get("trackster_urls");d.append($(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 e=$('<div style="float: right;"></div>');e.append($(linkHTMLTemplate({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),classes:["icon-button","tooltip","tags"]})));e.append($(linkHTMLTemplate({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotation_url"),classes:["icon-button","tooltip","annotate"]})));d.append(e);d.append('<div style="clear: both"></div>');var c=$('<div class="tag-area" style="display: none">');c.append("<strong>Tags:</strong>");c.append('<div class="tag-elt"></div>');d.append(c);var f=$(('<div id="${dataset_id}-annotation-area" class="annotation-area" style="display: none">'));f.append("<strong>Annotation:</strong>");f.append(('<div id="${dataset_id}-annotation-elt" style="margin: 1px 0px 1px 0px" class="annotation-elt tooltip editable-text" title="Edit dataset annotation"></div>'));d.append(f)}}d.append('<div style="clear: both;"></div>');i.append(d);var j=$("<div/>");if(this.model.get("display_apps")){var k=this.model.get("display_apps"),b=$("<span/>");for(app_name in k){var h=k[app_name],g=app_name+" ";for(location_name in h){g+=linkHTMLTemplate({text:location_name,href:h[location_name].url,target:h[location_name].target})+" "}b.append(g)}j.append(b)}i.append(j)}else{if(this.model.get("for_editing")){i.append(this._render_showParamsAndRerun())}}i.append(this._render_peek())},_render_body:function(){this.log(this+"_render_body");var b=this.model.get("state"),c=this.model.get("for_editing");this.log("state:",b,"for_editing",c);var a=$("<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"},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.warningMsg=_.template("<div class=warningmessagesmall><strong><%= warning %></strong></div>");HistoryItemView.TEMPLATES.undeleteLink=_.template('This dataset has been deleted. Click <a href="<%= undelete_url %>" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" target="galaxy_history">here</a> to undelete it.');HistoryItemView.TEMPLATES.purgeLink=_.template(' or <a href="<%= purge_url %>" class="historyItemPurge" id="historyItemPurger-{{ id }}" target="galaxy_history">here</a> to immediately remove it from disk.');HistoryItemView.TEMPLATES.hiddenMsg=_.template('This dataset has been hidden. Click <a href="<%= unhide_url %>" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" target="galaxy_history">here</a> to unhide it.');HistoryItemView.TEMPLATES.hdaSummary=_.template(["<%= misc_blurb %><br />",'format: <span class="<%= data_type %>"><%= data_type %></span>, ',"database: <%= dbkeyHTML %>"].join(""));HistoryItemView.STRINGS={};HistoryItemView.STRINGS.purgedMsg=HistoryItemView.TEMPLATES.warningMsg({warning:"This dataset has been deleted and removed from disk."});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=LoggingModel.extend({logger:console,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=LoggingView.extend({logger:console,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.$el.append(a.children());a.remove()},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});if(window.USE_MOCK_DATA){mockHistory={};mockHistory.data={template:{id:"a799d38679e985db",name:"template",data_type:"fastq",file_size:226297533,genome_build:"?",metadata_data_lines:0,metadata_dbkey:"?",metadata_sequences:0,misc_blurb:"215.8 MB",misc_info:"uploaded fastq file",model_class:"HistoryDatasetAssociation",download_url:"",state:"ok",visible:true,deleted:false,purged:false,hid:0,for_editing:true,undelete_url:"example.com/undelete",purge_url:"example.com/purge",unhide_url:"example.com/unhide",display_url:"example.com/display",edit_url:"example.com/edit",delete_url:"example.com/delete",show_params_url:"example.com/show_params",rerun_url:"example.com/rerun",retag_url:"example.com/retag",annotate_url:"example.com/annotate",peek:['<table cellspacing="0" cellpadding="3"><tr><th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th><th>5.MAPQ</th><th>6.CIGAR</th><th>7.MRNM</th><th>8.MPOS</th><th>9.ISIZE</th><th>10.SEQ</th><th>11.QUAL</th><th>12.OPT</th></tr>','<tr><td colspan="100%">@SQ SN:gi|87159884|ref|NC_007793.1| LN:2872769</td></tr>','<tr><td colspan="100%">@PG ID:bwa PN:bwa VN:0.5.9-r16</td></tr>','<tr><td colspan="100%">HWUSI-EAS664L:15:64HOJAAXX:1:1:13280:968 73 gi|87159884|ref|NC_007793.1| 2720169 37 101M = 2720169 0 NAATATGACATTATTTTCAAAACAGCTGAAAATTTAGACGTACCGATTTATCTACATCCCGCGCCAGTTAACAGTGACATTTATCAATCATACTATAAAGG !!!!!!!!!!$!!!$!!!!!$!!!!!!$!$!$$$!!$!!$!!!!!!!!!!!$!</td></tr>','<tr><td colspan="100%">!!!$!$!$$!!$$!!$!!!!!!!!!!!!!!!!!!!!!!!!!!$!!$!! 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({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 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=_.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 diff -r 8b301f6af8340f8cd01022035d5765cf0aba3ede -r 72f1dcdf1c542e6d4689305f5de2077c0bfb4035 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{}}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({}); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({tagName:"a",className:"icon-button",hrefVoidFn:["javascript",":void(0)"].join(""),fadeSpeed:0,initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){var a=this.model.attributes.icon_class+"_disabled";if(!this.model.attributes.visible){this.$el.fadeOut(this.fadeSpeed)}if(this.model.attributes.enabled){if(this.$el.hasClass(a)){this.$el.removeClass(a)}this.$el.addClass(this.model.attributes.icon_class)}else{this.$el.removeClass(this.model.attributes.icon_class);this.$el.addClass(a)}if(this.model.attributes.isMenuButton){this.$el.addClass("menu-button")}else{this.$el.removeClass("menu-button")}this.$el.data("tooltip",false);this.$el.attr("data-original-title",null);this.$el.removeClass("tooltip");if(this.model.attributes.title){this.$el.attr("title",this.model.attributes.title).addClass("tooltip");this.$el.tooltip(this.model.attributes.tooltip_config)}this.$el.attr("id",(this.model.attributes.id)?(this.model.attributes.id):(null));this.$el.attr("target",(this.model.attributes.target)?(this.model.attributes.target):(null));this.$el.attr("href",(this.model.attributes.href&&!this.model.attributes.on_click)?(this.model.attributes.href):(this.hrefVoidFn));if(this.model.attributes.visible){this.$el.fadeIn(this.fadeSpeed)}return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(c){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",c.attributes.title).addClass("icon-button menu-button").addClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_click);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var GalaxyLocalization=jQuery.extend({},{aliasName:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){try{return this.localizedStrings[b]}catch(a){return b}},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.aliasName]=function(a){return GalaxyLocalization.localize(a)}; \ No newline at end of file diff -r 8b301f6af8340f8cd01022035d5765cf0aba3ede -r 72f1dcdf1c542e6d4689305f5de2077c0bfb4035 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.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.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height;this.track_gap=5},render:function(){var b=this,c=this.dataset_arc_height;var a=d3.select(b.$el[0]).append("svg").attr("width",b.width).attr("height",b.height).append("g").attr("transform","translate("+b.width/2+","+b.height/2+")");this.model.get("tracks").each(function(f,l){var g=f.get("genome_wide_data"),k=b.radius_start+l*(c+b.track_gap),h=(g instanceof GenomeWideBigWigData?CircsterBigWigLayout:CircsterSummaryTreeLayout),n=new h({track:f,radius_start:k,radius_end:k+c,genome:b.genome,total_gap:b.total_gap}),d=n.chroms_layout(),i=n.genome_data_layout();var o=a.append("g").attr("id","inner-arc"),m=d3.svg.arc().innerRadius(k).outerRadius(k+c),e=o.selectAll("#inner-arc>path").data(d).enter().append("path").attr("d",m).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(q){return q.data.chrom});var p=f.get("prefs"),j=p.block_color;_.each(i,function(q){if(!q){return}var t=a.append("g"),s=d3.svg.arc().innerRadius(k),r=t.selectAll("path").data(q).enter().append("path").attr("d",s).style("stroke",j).style("fill",j)})})}});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 +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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Enhance replace_big_select_inputs to accept a list of elements instead of automatically grabbing all selects.
by Bitbucket 12 Sep '12

12 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8b301f6af834/ changeset: 8b301f6af834 user: dannon date: 2012-09-12 18:59:19 summary: Enhance replace_big_select_inputs to accept a list of elements instead of automatically grabbing all selects. affected #: 1 file diff -r 59e3badd56fd2805b9f89f9b5d2f7dcf6189e74c -r 8b301f6af8340f8cd01022035d5765cf0aba3ede static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -178,7 +178,7 @@ } // Replace select box with a text input box + autocomplete. -function replace_big_select_inputs(min_length, max_length) { +function replace_big_select_inputs(min_length, max_length, select_elts) { // To do replace, jQuery's autocomplete plugin must be loaded. if (!jQuery().autocomplete) { return; @@ -191,8 +191,10 @@ if (max_length === undefined) { max_length = 3000; } + + var select_elts = select_elts || $('select'); - $('select').each( function() { + select_elts.each( function() { var select_elt = $(this); // Make sure that options is within range. var num_options = select_elt.find('option').length; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Cleanup imports, fix reference to 'libraries' in example.
by Bitbucket 12 Sep '12

12 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/59e3badd56fd/ changeset: 59e3badd56fd user: dannon date: 2012-09-12 18:57:42 summary: Cleanup imports, fix reference to 'libraries' in example. affected #: 1 file diff -r 81529070d60df960ae226d7d31a422b6f8febb0c -r 59e3badd56fd2805b9f89f9b5d2f7dcf6189e74c lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -3,8 +3,7 @@ """ import logging from galaxy import web -from galaxy.web.base.controller import * -from galaxy.model.orm import * +from galaxy.web.base.controller import BaseAPIController, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesLibraryMixin, UsesLibraryMixinItems import pkg_resources pkg_resources.require( "Routes" ) @@ -73,7 +72,7 @@ @web.expose_api def create( self, trans, history_id, payload, **kwd ): """ - POST /api/libraries/{encoded_history_id}/contents + POST /api/histories/{encoded_history_id}/contents Creates a new history content item (file, aka HistoryDatasetAssociation). """ from_ld_id = payload.get( 'from_ld_id', None ) @@ -99,3 +98,4 @@ # TODO: implement other "upload" methods here. trans.response.status = 403 return "Not implemented." + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Whitespace cleanup, remove unused sa_session reference.
by Bitbucket 12 Sep '12

12 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/81529070d60d/ changeset: 81529070d60d user: dannon date: 2012-09-12 18:55:01 summary: Whitespace cleanup, remove unused sa_session reference. affected #: 1 file diff -r 93a04e500eb464b7dd7c0dba565b60661307e94b -r 81529070d60df960ae226d7d31a422b6f8febb0c lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -62,7 +62,7 @@ """ func.exposed = True return func - + def json( func ): @wraps(func) def decorator( self, trans, *args, **kwargs ): @@ -127,8 +127,8 @@ trans.set_user( provided_key.user ) if trans.request.body: def extract_payload_from_request(trans, func, kwargs): - content_type = trans.request.headers['content-type'] - if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'): + content_type = trans.request.headers['content-type'] + if content_type.startswith('application/x-www-form-urlencoded') or content_type.startswith('multipart/form-data'): # If the content type is a standard type such as multipart/form-data, the wsgi framework parses the request body # and loads all field values into kwargs. However, kwargs also contains formal method parameters etc. which # are not a part of the request body. This is a problem because it's not possible to differentiate between values @@ -136,7 +136,7 @@ # in the payload. Therefore, the decorated method's formal arguments are discovered through reflection and removed from # the payload dictionary. This helps to prevent duplicate argument conflicts in downstream methods. payload = kwargs.copy() - named_args, _, _, _ = inspect.getargspec(func) + named_args, _, _, _ = inspect.getargspec(func) for arg in named_args: payload.pop(arg, None) else: @@ -145,7 +145,7 @@ # such as multipart/form-data. Leaving it as is for backward compatibility, just in case. payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) ) return payload - try: + try: kwargs['payload'] = extract_payload_from_request(trans, func, kwargs) except ValueError: error_status = '400 Bad Request' @@ -210,7 +210,7 @@ def form( *args, **kwargs ): return FormBuilder( *args, **kwargs ) - + class WebApplication( base.WebApplication ): def __init__( self, galaxy_app, session_cookie='galaxysession' ): base.WebApplication.__init__( self ) @@ -322,7 +322,7 @@ except: event.user = None try: - event.session_id = self.galaxy_session.id + event.session_id = self.galaxy_session.id except: event.session_id = None self.sa_session.add( event ) @@ -339,23 +339,22 @@ return None def set_cookie( self, value, name='galaxysession', path='/', age=90, version='1' ): """Convenience method for setting a session cookie""" - # The galaxysession cookie value must be a high entropy 128 bit random number encrypted + # The galaxysession cookie value must be a high entropy 128 bit random number encrypted # using a server secret key. Any other value is invalid and could pose security issues. self.response.cookies[name] = value self.response.cookies[name]['path'] = path self.response.cookies[name]['max-age'] = 3600 * 24 * age # 90 days tstamp = time.localtime ( time.time() + 3600 * 24 * age ) - self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp ) + self.response.cookies[name]['expires'] = time.strftime( '%a, %d-%b-%Y %H:%M:%S GMT', tstamp ) self.response.cookies[name]['version'] = version def _ensure_valid_session( self, session_cookie, create=True): """ Ensure that a valid Galaxy session exists and is available as trans.session (part of initialization) - + Support for universe_session and universe_user cookies has been removed as of 31 Oct 2008. """ - sa_session = self.sa_session # Try to load an existing session secure_id = self.get_cookie( name=session_cookie ) galaxy_session = None @@ -369,7 +368,7 @@ # Decode the cookie value to get the session_key session_key = self.security.decode_guid( secure_id ) try: - # Make sure we have a valid UTF-8 string + # Make sure we have a valid UTF-8 string session_key = session_key.encode( 'utf8' ) except UnicodeDecodeError: # We'll end up creating a new galaxy_session @@ -384,7 +383,7 @@ if self.app.config.use_remote_user: assert "HTTP_REMOTE_USER" in self.environ, \ "use_remote_user is set but no HTTP_REMOTE_USER variable" - remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] + remote_user_email = self.environ[ 'HTTP_REMOTE_USER' ] if galaxy_session: # An existing session, make sure correct association exists if galaxy_session.user is None: @@ -429,13 +428,13 @@ # FIXME: If prev_session is a proper relation this would not # be needed. if prev_galaxy_session: - self.sa_session.add( prev_galaxy_session ) + self.sa_session.add( prev_galaxy_session ) self.sa_session.flush() # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() def _ensure_logged_in_user( self, environ, session_cookie ): - # The value of session_cookie can be one of + # The value of session_cookie can be one of # 'galaxysession' or 'galaxycommunitysession' # Currently this method does nothing unless session_cookie is 'galaxysession' if session_cookie == 'galaxysession' and self.galaxy_session.user is None: @@ -469,7 +468,7 @@ host = None if host in UCSC_SERVERS: return - external_display_path = url_for( controller='dataset', action='display_application' ) + external_display_path = url_for( controller='dataset', action='display_application' ) if self.request.path.startswith( external_display_path ): request_path_split = external_display_path.split( '/' ) try: @@ -484,13 +483,13 @@ Create a new GalaxySession for this request, possibly with a connection to a previous session (in `prev_galaxy_session`) and an existing user (in `user_for_new_session`). - + Caller is responsible for flushing the returned session. """ session_key = self.security.get_new_guid() galaxy_session = self.app.model.GalaxySession( session_key=session_key, - is_valid=True, + is_valid=True, remote_host = self.request.remote_host, remote_addr = self.request.remote_addr, referer = self.request.headers.get( 'Referer', None ) ) @@ -507,7 +506,7 @@ """ if not self.app.config.use_remote_user: return None - + user = self.sa_session.query( self.app.model.User ) \ .filter( self.app.model.User.table.c.email==remote_user_email ) \ .first() @@ -555,7 +554,7 @@ Login a new user (possibly newly created) - create a new session - associate new session with user - - if old session had a history and it was not associated with a user, associate it with the new session, + - if old session had a history and it was not associated with a user, associate it with the new session, otherwise associate the current session's history with the user - add the disk usage of the current session to the user's total disk usage """ @@ -637,7 +636,7 @@ return self.galaxy_session def get_history( self, create=False ): """ - Load the current history, creating a new one only if there is not + Load the current history, creating a new one only if there is not current history and we're told to create" """ history = self.galaxy_session.current_history @@ -709,7 +708,7 @@ return rval def set_message( self, message, type=None ): """ - Convenience method for setting the 'message' and 'message_type' + Convenience method for setting the 'message' and 'message_type' element of the template context. """ self.template_context['message'] = message @@ -724,11 +723,11 @@ def show_message( self, message, type='info', refresh_frames=[], cont=None, use_panels=False, active_view="" ): """ Convenience method for displaying a simple page with a single message. - + `type`: one of "error", "warning", "info", or "done"; determines the type of dialog box and icon displayed with the message - - `refresh_frames`: names of frames in the interface that should be + + `refresh_frames`: names of frames in the interface that should be refreshed when the message is displayed """ return self.fill_template( "message.mako", status=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view ) @@ -752,7 +751,7 @@ Convenience method for displaying a simple page with a single HTML form. """ - return self.fill_template( template, form=form, header=header, use_panels=( form.use_panels or use_panels ), + return self.fill_template( template, form=form, header=header, use_panels=( form.use_panels or use_panels ), active_view=active_view ) def fill_template(self, filename, **kwargs): """ @@ -764,19 +763,19 @@ if filename.endswith( ".mako" ): return self.fill_template_mako( filename, **kwargs ) else: - template = Template( file=os.path.join(self.app.config.template_path, filename), + template = Template( file=os.path.join(self.app.config.template_path, filename), searchList=[kwargs, self.template_context, dict(caller=self, t=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app)] ) return str( template ) def fill_template_mako( self, filename, **kwargs ): template = self.webapp.mako_template_lookup.get_template( filename ) - template.output_encoding = 'utf-8' + template.output_encoding = 'utf-8' data = dict( caller=self, t=self, trans=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app ) data.update( self.template_context ) data.update( kwargs ) return template.render( **data ) def stream_template_mako( self, filename, **kwargs ): template = self.webapp.mako_template_lookup.get_template( filename ) - template.output_encoding = 'utf-8' + template.output_encoding = 'utf-8' data = dict( caller=self, t=self, trans=self, h=helpers, util=util, request=self.request, response=self.response, app=self.app ) data.update( self.template_context ) data.update( kwargs ) @@ -808,31 +807,31 @@ dbnames = list() datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=self.history.id, extension="len" ) - + for dataset in datasets: dbnames.append( (dataset.dbkey, dataset.name) ) - + user = self.get_user() if user and 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): dbnames.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key) )) - + dbnames.extend( util.dbnames ) return dbnames @property def ucsc_builds( self ): return util.dlnames['ucsc'] - + @property def ensembl_builds( self ): return util.dlnames['ensembl'] - + @property def ncbi_builds( self ): return util.dlnames['ncbi'] - + def db_dataset_for( self, dbkey ): """ Returns the db_file dataset associated/needed by `dataset`, or `None`. @@ -855,7 +854,7 @@ if self.sa_session.query( self.app.model.RequestType ).filter_by( deleted=False ).count() > 0: return True return False - + class FormBuilder( object ): """ Simple class describing an HTML form @@ -875,7 +874,7 @@ def add_password( self, name, label, value=None, error=None, help=None ): return self.add_input( 'password', label, name, value, error, help ) def add_select( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): - self.inputs.append( SelectInput( name, label, value=value, options=options, error=error, help=help, use_label=use_label ) ) + self.inputs.append( SelectInput( name, label, value=value, options=options, error=error, help=help, use_label=use_label ) ) return self class FormInput( object ): @@ -893,7 +892,7 @@ class GalaxyWebAPITransaction( GalaxyWebTransaction ): """ - TODO: Unify this with WebUITransaction, since we allow session auth now. + TODO: Unify this with WebUITransaction, since we allow session auth now. Enable functionality of 'create' parameter in parent _ensure_valid_session """ def __init__( self, environ, app, webapp, session_cookie): @@ -915,7 +914,7 @@ # Decode the cookie value to get the session_key session_key = self.security.decode_guid( secure_id ) try: - # Make sure we have a valid UTF-8 string + # Make sure we have a valid UTF-8 string session_key = session_key.encode( 'utf8' ) except UnicodeDecodeError: # We'll end up creating a new galaxy_session @@ -991,7 +990,7 @@ dbnames.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key) )) dbnames.extend( util.dbnames ) return dbnames - + @property def ucsc_builds( self ): return util.dlnames['ucsc'] @@ -1029,7 +1028,7 @@ def __init__( self, name, label, value=None, options=[], error=None, help=None, use_label=True ): FormInput.__init__( self, "select", name, label, value=value, error=error, help=help, use_label=use_label ) self.options = options - + class FormData( object ): """ Class for passing data about a form to a template, very rudimentary, could @@ -1038,7 +1037,7 @@ def __init__( self ): self.values = Bunch() self.errors = Bunch() - + class Bunch( dict ): """ Bunch based on a dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Boto bumped to 2.5.2, async cloudlaunch update with downloadable keys and basic cluster picker.
by Bitbucket 12 Sep '12

12 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/93a04e500eb4/ changeset: 93a04e500eb4 user: dannon date: 2012-09-12 18:51:56 summary: Boto bumped to 2.5.2, async cloudlaunch update with downloadable keys and basic cluster picker. affected #: 3 files diff -r e2cb958b3f7596744bb08febc858fa25139fd1ac -r 93a04e500eb464b7dd7c0dba565b60661307e94b eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -33,7 +33,7 @@ [eggs:noplatform] amqplib = 0.6.1 Beaker = 1.4 -boto = 2.2.2 +boto = 2.5.2 decorator = 3.1.2 docutils = 0.7 drmaa = 0.4b3 diff -r e2cb958b3f7596744bb08febc858fa25139fd1ac -r 93a04e500eb464b7dd7c0dba565b60661307e94b lib/galaxy/web/controllers/cloudlaunch.py --- a/lib/galaxy/web/controllers/cloudlaunch.py +++ b/lib/galaxy/web/controllers/cloudlaunch.py @@ -8,38 +8,77 @@ import datetime import logging +import os +import tempfile import time +import boto +import pkg_resources from galaxy import eggs -import pkg_resources pkg_resources.require('boto') -import boto from galaxy import web from galaxy.web.base.controller import BaseUIController +from galaxy.util.json import to_json_string from boto.ec2.regioninfo import RegionInfo from boto.exception import EC2ResponseError +from boto.s3.connection import OrdinaryCallingFormat, S3Connection + log = logging.getLogger(__name__) +PKEY_PREFIX = 'gxy_pkey' +DEFAULT_KEYPAIR = 'deleteme_keypair' +DEFAULT_AMI = 'ami-da58aab3' + class CloudController(BaseUIController): + def __init__(self, app): BaseUIController.__init__(self, app) @web.expose def index(self, trans, share_string=None): - return trans.fill_template("cloud/index.mako", share_string=share_string) + return trans.fill_template("cloud/index.mako", default_keypair = DEFAULT_KEYPAIR, share_string=share_string) @web.expose - def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string): + def get_account_info(self, trans, key_id, secret, **kwargs): + """ + Get EC2 Account Info + """ + #Keypairs + account_info = {} + try: + ec2_conn = connect_ec2(key_id, secret) + kps = ec2_conn.get_all_key_pairs() + except EC2ResponseError, e: + log.error("Problem starting an instance: %s\n%s" % (e, e.body)) + account_info['keypairs'] = [akp.name for akp in kps] + #Existing Clusters + s3_conn = S3Connection(key_id, secret, calling_format=OrdinaryCallingFormat()) + buckets = s3_conn.get_all_buckets() + clusters = [] + for bucket in buckets: + pd = bucket.get_key('persistent_data.yaml') + if pd: + # This is a cloudman bucket. + # We need to get persistent data, and the cluster name. + for key in bucket.list(): + if key.name.endswith('.clusterName'): + clusters.append({'name':key.name.split('.clusterName')[0], 'persistent_data': pd.get_contents_as_string()}) + account_info['clusters'] = clusters + return to_json_string(account_info) + + @web.expose + def launch_instance(self, trans, cluster_name, password, key_id, secret, instance_type, share_string, keypair, **kwargs): ec2_error = None try: # Create security group & key pair used when starting an instance ec2_conn = connect_ec2(key_id, secret) sg_name = create_cm_security_group(ec2_conn) - kp_name, kp_material = create_key_pair(ec2_conn) + kp_name, kp_material = create_key_pair(ec2_conn, key_name=keypair) except EC2ResponseError, err: ec2_error = err.error_message if ec2_error: - return trans.fill_template("cloud/run.mako", error = ec2_error) + #return trans.fill_template("cloud/run.mako", error = ec2_error) + return {'errors':[ec2_error]} else: user_provided_data={'cluster_name':cluster_name, 'access_key':key_id, @@ -62,13 +101,41 @@ instance.update() ct +=1 time.sleep(1) - return trans.fill_template("cloud/run.mako", - instance = rs.instances[0], - kp_name = kp_name, - kp_material = kp_material) + if kp_material: + #We have created a keypair. Save to tempfile for one time retrieval. + (fd, fname) = tempfile.mkstemp(prefix=PKEY_PREFIX, dir=trans.app.config.new_file_path) + f = os.fdopen(fd, 'wt') + f.write(kp_material) + f.close() + kp_material_tag = fname[fname.rfind(PKEY_PREFIX) + len(PKEY_PREFIX):] + else: + kp_material_tag = None + return to_json_string({ + 'cluster_name': cluster_name, + 'instance_id': rs.instances[0].id, + 'image_id': rs.instances[0].image_id, + 'public_dns_name': rs.instances[0].public_dns_name, + 'kp_name': kp_name, + 'kp_material_tag':kp_material_tag + }) else: - return trans.fill_template("cloud/run.mako", - error = "Instance failure, but no specific error was detected. Please check your AWS Console.") + return {'errors':["Instance failure, but no specific error was detected. Please check your AWS Console."]} + + @web.expose + def get_pkey(self, trans, kp_material_tag=None): + if kp_material_tag: + expected_path = os.path.join(trans.app.config.new_file_path, PKEY_PREFIX + kp_material_tag) + if os.path.exists(expected_path): + f = open(expected_path) + kp_material = f.read() + f.close() + trans.response.headers['Content-Length'] = int( os.stat( expected_path ).st_size ) + trans.response.set_content_type( "application/octet-stream" ) #force octet-stream so Safari doesn't append mime extensions to filename + trans.response.headers["Content-Disposition"] = 'attachment; filename="%s.pem"' % DEFAULT_KEYPAIR + os.remove(expected_path) + return kp_material + trans.response.status = 400 + return "Invalid identifier" # ## Cloud interaction methods def connect_ec2(a_key, s_key): @@ -150,7 +217,7 @@ return True return False -def create_key_pair(ec2_conn, key_name='cloudman_key_pair'): +def create_key_pair(ec2_conn, key_name=DEFAULT_KEYPAIR): """ Create a key pair with the provided name. Return the name of the key or None if there was an error creating the key. """ @@ -169,8 +236,8 @@ return None, None return kp.name, kp.material -def run_instance(ec2_conn, user_provided_data, image_id='ami-da58aab3', - kernel_id=None, ramdisk_id=None, key_name='cloudman_key_pair', +def run_instance(ec2_conn, user_provided_data, image_id=DEFAULT_AMI, + kernel_id=None, ramdisk_id=None, key_name=DEFAULT_KEYPAIR, security_groups=['CloudMan']): """ Start an instance. If instance start was OK, return the ResultSet object else return None. diff -r e2cb958b3f7596744bb08febc858fa25139fd1ac -r 93a04e500eb464b7dd7c0dba565b60661307e94b templates/cloud/index.mako --- a/templates/cloud/index.mako +++ b/templates/cloud/index.mako @@ -27,6 +27,9 @@ #ec_button_container{ float:right; } + #hidden_options{ + display:none; + } div.toolForm{ margin-top: 10px; margin-bottom: 10px; @@ -45,57 +48,215 @@ .workflow-annotation { margin-bottom: 1em; } + #loading_indicator{ + position:fixed; + top:40px; + } </style></%def> +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + var ACCOUNT_URL = "${h.url_for( controller='/cloudlaunch', action='get_account_info')}"; + var PKEY_DL_URL = "${h.url_for( controller='/cloudlaunch', action='get_pkey')}"; + $(document).ready(function(){ + $('#id_existing_instance').change(function(){ + var ei_name = $(this).val(); + if (ei_name === "New Cluster"){ + //For new instances, need to see the cluster name field. + $('#id_cluster_name').val("New Cluster") + $('#cluster_name_wrapper').show('fast'); + }else{ + //Hide the Cluster Name field, but set the value + $('#id_cluster_name').val($(this).val()); + $('#cluster_name_wrapper').hide('fast'); + } + }); + //When id_secret and id_key are complete, submit to get_account_info + $("#id_secret, #id_key_id").bind("change paste keyup", function(){ + secret_el = $("#id_secret"); + key_el = $("#id_key_id"); + if (secret_el.val().length === 40 && key_el.val().length === 20){ + //Submit these to get_account_info, unhide fields, and update as appropriate + $.getJSON(ACCOUNT_URL, + {key_id: key_el.val(),secret:secret_el.val()}, + function(result){ + var kplist = $("#id_keypair"); + var clusterlist = $("#id_existing_instance"); + kplist.find('option').remove(); + clusterlist.find('option').remove(); + //Update fields with appropriate elements + if (_.size(result.clusters) > 0){ + clusterlist.append($('<option/>').val('New Cluster').text('New Cluster')); + _.each(result.clusters, function(cluster, index){ + clusterlist.append($('<option/>').val(cluster.name).text(cluster.name)); + }); + $('#existing_instance_wrapper').show(); + } + if (!_.include(result.keypairs, '${default_keypair}')){ + kplist.append($('<option/>').val('${default_keypair}').text('Create New - ${default_keypair}')); + } + _.each(result.keypairs, function(keypair, index){ + kplist.append($('<option/>').val(keypair).text(keypair)); + }); + $('#hidden_options').show('fast'); + }); + } + }); + $('#loading_indicator').ajaxStart(function(){ + $(this).show('fast'); + }).ajaxStop(function(){ + $(this).hide('fast'); + }); + $('form').ajaxForm({ + type: 'POST', + dataType: 'json', + beforeSubmit: function(data){ + //Hide the form, show pending box with spinner. + $('#launchFormContainer').hide('fast'); + $('#responsePanel').show('fast'); + }, + success: function(data){ + //Success Message, link to key download if required, link to server itself. + $('#launchPending').hide('fast'); + //Check for success/error. + if (data.error){ + //Apologize profusely. + $("launchPending").hide(); + $("#launchError").show(); + }else{ + //Set appropriate fields (dns, key, ami) and then display. + if(data.kp_material_tag){ + var kp_download_link = $('<a/>').attr('href', PKEY_DL_URL + '?kp_material_tag=' + data.kp_material_tag) + .attr('target','_blank') + .text("Download your key now"); + $('#keypairInfo').append(kp_download_link); + $('#keypairInfo').show(); + } + $('.kp_name').text(data.kp_name); + $('#instance_id').text(data.instance_id); + $('#image_id').text(data.image_id); + $('#instance_link').html($('<a/>') + .attr('href', 'http://' + data.public_dns_name + '/cloud') + .attr('target','_blank') + .text(data.public_dns_name + '/cloud')); + $('#instance_dns').text(data.public_dns_name); + $('#launchSuccess').show('fast'); + } + } + }); + }); + </script> +</%def><%def name="center_panel()"><div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> + <div id="loading_indicator"></div><h2>Launch a Galaxy Cloud Instance</h2> - <div class="toolForm"> - <form action="${h.url_for( controller='cloudlaunch', action='launch_instance' )}" method="post"> - <div class="form-row"> - <label for="id_cluster_name">Cluster Name</label> - <input type="text" size="40" name="cluster_name" id="id_cluster_name"/><br/> - </div> - <div class="form-row"> - <label for="id_password">Password</label> - <input type="password" size="40" name="password" id="id_password"/><br/> - </div> + <div id="launchFormContainer" class="toolForm"> + <form id="cloudlaunch_form" action="${h.url_for( controller='/cloudlaunch', action='launch_instance')}" method="post"> + + <p>To launch a Galaxy Cloud Cluster, enter your AWS Secret Key ID, and Secret Key. Galaxy will use these to present appropriate +options for launching your cluster.</p> + <div class="form-row"><label for="id_key_id">Key ID</label> - <input type="text" size="40" name="key_id" id="id_key_id"/><br/> + <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value=""/><br/> + <div class="toolParamHelp"> + This is the text string that uniquely identifies your account, found in the <a +href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS +Console</a>. + </div></div> + <div class="form-row"><label for="id_secret">Secret Key</label> - <input type="password" size="120" name="secret" id="id_secret"/><br/> + <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value=""/><br/> + <div class="toolParamHelp"> + This is your AWS Secret Key, also found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security +Credentials section of the AWS Console</a>. </div></div> - %if share_string: - <input type='hidden' name='share_string' value='${share_string}'/> - %else: - <div class="form-row"> - <label for="id_share_string">Instance Share String (optional)</label> - <input type="text" size="120" name="share_string" id="id_share_string"/><br/> + + <div id="hidden_options"> + <div id='existing_instance_wrapper' style="display:none;" class="form-row"> + <label for="id_existing_instance">Instances in your account</label> + <select name="existing_instance" id="id_existing_instance"> + </select> + </div> + <div id='cluster_name_wrapper' class="form-row"> + <label for="id_cluster_name">Cluster Name</label> + <input type="text" size="40" class="text-and-autocomplete-select" name="cluster_name" id="id_cluster_name"/><br/> + <div class="toolParamHelp"> + This is the name for your cluster. You'll use this when you want to restart. + </div> + </div> + + <div class="form-row"> + <label for="id_password">Cluster Password</label> + <input type="password" size="40" name="password" id="id_password"/><br/> + </div> + + <div class="form-row"> + <label for="id_keypair">Key Pair</label> + <select name="keypair" id="id_keypair"> + <option name="Create" value="cloudman_keypair">cloudman_keypair</option> + </select> + </div> + + %if share_string: + <input type='hidden' name='share_string' value='${share_string}'/> + %else: + <div class="form-row"> + <label for="id_share_string">Instance Share String (optional)</label> + <input type="text" size="120" name="share_string" id="id_share_string"/><br/> + </div> + %endif + <div class="form-row"> + <label for="id_instance_type">Instance Type</label> + <select name="instance_type" id="id_instance_type"> + <option value="m1.large">Large</option> + <option value="m1.xlarge">Extra Large</option> + <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option> + </select> + </div> + <div class="form-row"> + <p>Requesting the instance may take a moment, please be patient. Do not refresh your browser or navigate away from the page</p> + <input type="submit" value="Submit" id="id_submit"/> + </div></div> - %endif - <div class="form-row"> - <label for="id_instance_type">Instance Type</label> - <select name="instance_type" id="id_instance_type"> - <option value="m1.large">Large</option> - <option value="t1.micro">Micro</option> - <option value="m1.xlarge">Extra Large</option> - <option value="m2.4xlarge">High-Memory Quadruple Extra Large</option> - </select> - </div> - <div class="form-row"> - <p>Requesting the instance may take a moment, please be patient. Do not refresh your browser or navigate away from the page</p> - <input type="submit" value="Submit" id="id_submit"/> - </div> + <div class="form-row"> + <div id="loading_indicator" style="position:relative;left:10px;right:0px"></div> + </div></form></div> + <div id="responsePanel" class="toolForm" style="display:none;"> + <div id="launchPending">Launch Pending, please be patient.</div> + <div id="launchError" style="display:none;">ERROR</div> + <div id="launchSuccess" style="display:none;"> + <div id="keypairInfo" style="display:none;margin-bottom:20px;"> + <h3>Very Important Key Pair Information</h3> + <p>A new key pair named <strong><span class="kp_name">kp_name</span></strong> has been created in your AWS + account and will be used to access this instance via ssh. It is + <strong>very important</strong> that you save the following private key + as it is not saved on this Galaxy instance and will be permanently lost if not saved. Additionally, this link will + only allow a single download, after which the key is removed from the Galaxy server permanently.<br/> + </div> + <div> + <h3>Access Information</h3> + <ul> + <li>Your instance '<span id="instance_id">undefined</span>' has been successfully launched using the + '<span id="image_id">undefined</span>' AMI.</li> + <li>While it may take a few moments to boot, you will be able to access the cloud control + panel at <span id="instance_link">undefined.</span>.</li> + <li>SSH access is also available using your private key. From the terminal, you would execute something like:</br>    `ssh -i <span class="kp_name">undefined</span>.pem ubuntu@<span +id="instance_dns">undefined</span>`</li> + </ul> + </div> + </div></div></div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 12 Sep '12

12 Sep '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ce64f5d64ff4/ changeset: ce64f5d64ff4 user: carlfeberhard date: 2012-09-12 17:03:17 summary: Client side templates for history panel; IconButtonView in ui.js; copied BaseModel/View into base-mvc.js; stubs for annotations, tags MVC; cleaned up controllers/root.py affected #: 18 files diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -120,9 +120,9 @@ show_hidden = util.string_as_bool( show_hidden ) datasets = self.get_history_datasets( trans, history, show_deleted, show_hidden, show_purged ) + history_panel_template = "root/history.mako" # history panel -> backbone - history_panel_template = "root/history.mako" - #history_panel_template = "root/alternate_history.mako" + ##history_panel_template = "root/alternate_history.mako" return trans.stream_template_mako( history_panel_template, history = history, annotation = self.get_item_annotation_str( trans.sa_session, trans.user, history ), @@ -512,85 +512,3 @@ @web.expose def generate_error( self, trans ): raise Exception( "Fake error!" ) - - - -""" -import galaxy.web.framework.helpers as web_helpers -from functools import wraps -def debug_mako_template( template_fn ): - # Wrap a function that produces a mako template for better debugging - - # http://stackoverflow.com/questions/390409/how-do-you-debug-mako-templates - @wraps( template_fn ) - def wrapper( *args, **kwargs ): - try: - log.debug( 'rendering template' ) - return template_fn( *args, **kwargs ) - log.debug( 'done rendering template' ) - except Exception, ex: - log.error( "Mako Exception: " + str( ex ), exc_info=True ) - return exceptions.html_error_template().render() - return wrapper - -def prep_dataset( hda, trans ): - states = trans.app.model.Dataset.states - print states - STATES_INTERPRETED_AS_QUEUED = [ 'no state', '', None ] - ## dataset is actually a HistoryDatasetAssociation - #ported mostly from history_common - #post: return dictionary form - #??: move out of templates? - #??: gather data from model? - - - #TODO: clean up magic strings - - hda_dict = hda.get_api_value() - #TODO: use hda_dict.update to add these (instead of localvars) - def add_to_hda( **kwargs ): - hda_dict.update( kwargs ) - - # trans - encoded_hda_id = trans.security.encode_id( hda.id ) - add_to_hda( id=encoded_hda_id ) - - add_to_hda( state=hda.state ) - if hda.state in STATES_INTERPRETED_AS_QUEUED: - #TODO: magic string - add_to_hda( state='queued' ) - - # trans - current_user_roles = trans.get_current_user_roles() - add_to_hda( can_edit=( not ( hda.deleted or hda.purged ) ) ) - - # considered accessible if user can access or user isn't admin - # trans - accessible = trans.app.security_agent.can_access_dataset( current_user_roles, hda.dataset ) - accessible = trans.user_is_admin() or accessible - add_to_hda( accessible=accessible ) - - #TODO: move urls into js galaxy_paths (decorate) - deleted = hda.deleted - purged = hda.purged - dataset_purged = hda.dataset.purged - if not ( dataset_purged or purged ) and for_editing: - undelete_url = web_helpers.url_for( controller='dataset', action='undelete', dataset_id=encoded_hda_id ) - # trans - if trans.app.config.allow_user_dataset_purge: - purge_url = web_helpers.url_for( controller='dataset', action='purge', dataset_id=encoded_hda_id ) - - if not hda.visible: - unhide_url = web_helpers.url_for( controller='dataset', action='unhide', dataset_id=encoded_hda_id ) - - - print 'dataset:', dataset - - undelete_url = web_helpers.url_for( controller='dataset', action='undelete', dataset_id=encoded_hda_id ) - purge_url = web_helpers.url_for( controller='dataset', action='purge', dataset_id=encoded_hda_id ) - unhide_url = web_helpers.url_for( controller='dataset', action='unhide', dataset_id=encoded_hda_id ) - print 'urls:', '\n'.join( undelete_url, purge_url, unhide_url ) - - return hda_dict - -""" \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/libs/handlebars.full.js --- /dev/null +++ b/static/scripts/libs/handlebars.full.js @@ -0,0 +1,1550 @@ +// lib/handlebars/base.js +var Handlebars = {}; + +Handlebars.VERSION = "1.0.beta.6"; + +Handlebars.helpers = {}; +Handlebars.partials = {}; + +Handlebars.registerHelper = function(name, fn, inverse) { + if(inverse) { fn.not = inverse; } + this.helpers[name] = fn; +}; + +Handlebars.registerPartial = function(name, str) { + this.partials[name] = str; +}; + +Handlebars.registerHelper('helperMissing', function(arg) { + if(arguments.length === 2) { + return undefined; + } else { + throw new Error("Could not find property '" + arg + "'"); + } +}); + +var toString = Object.prototype.toString, functionType = "[object Function]"; + +Handlebars.registerHelper('blockHelperMissing', function(context, options) { + var inverse = options.inverse || function() {}, fn = options.fn; + + + var ret = ""; + var type = toString.call(context); + + if(type === functionType) { context = context.call(this); } + + if(context === true) { + return fn(this); + } else if(context === false || context == null) { + return inverse(this); + } else if(type === "[object Array]") { + if(context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; + } else { + return fn(context); + } +}); + +Handlebars.registerHelper('each', function(context, options) { + var fn = options.fn, inverse = options.inverse; + var ret = ""; + + if(context && context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; +}); + +Handlebars.registerHelper('if', function(context, options) { + var type = toString.call(context); + if(type === functionType) { context = context.call(this); } + + if(!context || Handlebars.Utils.isEmpty(context)) { + return options.inverse(this); + } else { + return options.fn(this); + } +}); + +Handlebars.registerHelper('unless', function(context, options) { + var fn = options.fn, inverse = options.inverse; + options.fn = inverse; + options.inverse = fn; + + return Handlebars.helpers['if'].call(this, context, options); +}); + +Handlebars.registerHelper('with', function(context, options) { + return options.fn(context); +}); + +Handlebars.registerHelper('log', function(context) { + Handlebars.log(context); +}); +; +// lib/handlebars/compiler/parser.js +/* Jison generated parser */ +var handlebars = (function(){ + +var parser = {trace: function trace() { }, +yy: {}, +symbols_: {"error":2,"root":3,"program":4,"EOF":5,"statements":6,"simpleInverse":7,"statement":8,"openInverse":9,"closeBlock":10,"openBlock":11,"mustache":12,"partial":13,"CONTENT":14,"COMMENT":15,"OPEN_BLOCK":16,"inMustache":17,"CLOSE":18,"OPEN_INVERSE":19,"OPEN_ENDBLOCK":20,"path":21,"OPEN":22,"OPEN_UNESCAPED":23,"OPEN_PARTIAL":24,"params":25,"hash":26,"param":27,"STRING":28,"INTEGER":29,"BOOLEAN":30,"hashSegments":31,"hashSegment":32,"ID":33,"EQUALS":34,"pathSegments":35,"SEP":36,"$accept":0,"$end":1}, +terminals_: {2:"error",5:"EOF",14:"CONTENT",15:"COMMENT",16:"OPEN_BLOCK",18:"CLOSE",19:"OPEN_INVERSE",20:"OPEN_ENDBLOCK",22:"OPEN",23:"OPEN_UNESCAPED",24:"OPEN_PARTIAL",28:"STRING",29:"INTEGER",30:"BOOLEAN",33:"ID",34:"EQUALS",36:"SEP"}, +productions_: [0,[3,2],[4,3],[4,1],[4,0],[6,1],[6,2],[8,3],[8,3],[8,1],[8,1],[8,1],[8,1],[11,3],[9,3],[10,3],[12,3],[12,3],[13,3],[13,4],[7,2],[17,3],[17,2],[17,2],[17,1],[25,2],[25,1],[27,1],[27,1],[27,1],[27,1],[26,1],[31,2],[31,1],[32,3],[32,3],[32,3],[32,3],[21,1],[35,3],[35,1]], +performAction: function anonymous(yytext,yyleng,yylineno,yy,yystate,$$,_$) { + +var $0 = $$.length - 1; +switch (yystate) { +case 1: return $$[$0-1] +break; +case 2: this.$ = new yy.ProgramNode($$[$0-2], $$[$0]) +break; +case 3: this.$ = new yy.ProgramNode($$[$0]) +break; +case 4: this.$ = new yy.ProgramNode([]) +break; +case 5: this.$ = [$$[$0]] +break; +case 6: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] +break; +case 7: this.$ = new yy.InverseNode($$[$0-2], $$[$0-1], $$[$0]) +break; +case 8: this.$ = new yy.BlockNode($$[$0-2], $$[$0-1], $$[$0]) +break; +case 9: this.$ = $$[$0] +break; +case 10: this.$ = $$[$0] +break; +case 11: this.$ = new yy.ContentNode($$[$0]) +break; +case 12: this.$ = new yy.CommentNode($$[$0]) +break; +case 13: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 14: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 15: this.$ = $$[$0-1] +break; +case 16: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 17: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], true) +break; +case 18: this.$ = new yy.PartialNode($$[$0-1]) +break; +case 19: this.$ = new yy.PartialNode($$[$0-2], $$[$0-1]) +break; +case 20: +break; +case 21: this.$ = [[$$[$0-2]].concat($$[$0-1]), $$[$0]] +break; +case 22: this.$ = [[$$[$0-1]].concat($$[$0]), null] +break; +case 23: this.$ = [[$$[$0-1]], $$[$0]] +break; +case 24: this.$ = [[$$[$0]], null] +break; +case 25: $$[$0-1].push($$[$0]); this.$ = $$[$0-1]; +break; +case 26: this.$ = [$$[$0]] +break; +case 27: this.$ = $$[$0] +break; +case 28: this.$ = new yy.StringNode($$[$0]) +break; +case 29: this.$ = new yy.IntegerNode($$[$0]) +break; +case 30: this.$ = new yy.BooleanNode($$[$0]) +break; +case 31: this.$ = new yy.HashNode($$[$0]) +break; +case 32: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] +break; +case 33: this.$ = [$$[$0]] +break; +case 34: this.$ = [$$[$0-2], $$[$0]] +break; +case 35: this.$ = [$$[$0-2], new yy.StringNode($$[$0])] +break; +case 36: this.$ = [$$[$0-2], new yy.IntegerNode($$[$0])] +break; +case 37: this.$ = [$$[$0-2], new yy.BooleanNode($$[$0])] +break; +case 38: this.$ = new yy.IdNode($$[$0]) +break; +case 39: $$[$0-2].push($$[$0]); this.$ = $$[$0-2]; +break; +case 40: this.$ = [$$[$0]] +break; +} +}, +table: [{3:1,4:2,5:[2,4],6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{1:[3]},{5:[1,16]},{5:[2,3],7:17,8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,19],20:[2,3],22:[1,13],23:[1,14],24:[1,15]},{5:[2,5],14:[2,5],15:[2,5],16:[2,5],19:[2,5],20:[2,5],22:[2,5],23:[2,5],24:[2,5]},{4:20,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{4:21,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{5:[2,9],14:[2,9],15:[2,9],16:[2,9],19:[2,9],20:[2,9],22:[2,9],23:[2,9],24:[2,9]},{5:[2,10],14:[2,10],15:[2,10],16:[2,10],19:[2,10],20:[2,10],22:[2,10],23:[2,10],24:[2,10]},{5:[2,11],14:[2,11],15:[2,11],16:[2,11],19:[2,11],20:[2,11],22:[2,11],23:[2,11],24:[2,11]},{5:[2,12],14:[2,12],15:[2,12],16:[2,12],19:[2,12],20:[2,12],22:[2,12],23:[2,12],24:[2,12]},{17:22,21:23,33:[1,25],35:24},{17:26,21:23,33:[1,25],35:24},{17:27,21:23,33:[1,25],35:24},{17:28,21:23,33:[1,25],35:24},{21:29,33:[1,25],35:24},{1:[2,1]},{6:30,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{5:[2,6],14:[2,6],15:[2,6],16:[2,6],19:[2,6],20:[2,6],22:[2,6],23:[2,6],24:[2,6]},{17:22,18:[1,31],21:23,33:[1,25],35:24},{10:32,20:[1,33]},{10:34,20:[1,33]},{18:[1,35]},{18:[2,24],21:40,25:36,26:37,27:38,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,38],28:[2,38],29:[2,38],30:[2,38],33:[2,38],36:[1,46]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],36:[2,40]},{18:[1,47]},{18:[1,48]},{18:[1,49]},{18:[1,50],21:51,33:[1,25],35:24},{5:[2,2],8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,2],22:[1,13],23:[1,14],24:[1,15]},{14:[2,20],15:[2,20],16:[2,20],19:[2,20],22:[2,20],23:[2,20],24:[2,20]},{5:[2,7],14:[2,7],15:[2,7],16:[2,7],19:[2,7],20:[2,7],22:[2,7],23:[2,7],24:[2,7]},{21:52,33:[1,25],35:24},{5:[2,8],14:[2,8],15:[2,8],16:[2,8],19:[2,8],20:[2,8],22:[2,8],23:[2,8],24:[2,8]},{14:[2,14],15:[2,14],16:[2,14],19:[2,14],20:[2,14],22:[2,14],23:[2,14],24:[2,14]},{18:[2,22],21:40,26:53,27:54,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,23]},{18:[2,26],28:[2,26],29:[2,26],30:[2,26],33:[2,26]},{18:[2,31],32:55,33:[1,56]},{18:[2,27],28:[2,27],29:[2,27],30:[2,27],33:[2,27]},{18:[2,28],28:[2,28],29:[2,28],30:[2,28],33:[2,28]},{18:[2,29],28:[2,29],29:[2,29],30:[2,29],33:[2,29]},{18:[2,30],28:[2,30],29:[2,30],30:[2,30],33:[2,30]},{18:[2,33],33:[2,33]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],34:[1,57],36:[2,40]},{33:[1,58]},{14:[2,13],15:[2,13],16:[2,13],19:[2,13],20:[2,13],22:[2,13],23:[2,13],24:[2,13]},{5:[2,16],14:[2,16],15:[2,16],16:[2,16],19:[2,16],20:[2,16],22:[2,16],23:[2,16],24:[2,16]},{5:[2,17],14:[2,17],15:[2,17],16:[2,17],19:[2,17],20:[2,17],22:[2,17],23:[2,17],24:[2,17]},{5:[2,18],14:[2,18],15:[2,18],16:[2,18],19:[2,18],20:[2,18],22:[2,18],23:[2,18],24:[2,18]},{18:[1,59]},{18:[1,60]},{18:[2,21]},{18:[2,25],28:[2,25],29:[2,25],30:[2,25],33:[2,25]},{18:[2,32],33:[2,32]},{34:[1,57]},{21:61,28:[1,62],29:[1,63],30:[1,64],33:[1,25],35:24},{18:[2,39],28:[2,39],29:[2,39],30:[2,39],33:[2,39],36:[2,39]},{5:[2,19],14:[2,19],15:[2,19],16:[2,19],19:[2,19],20:[2,19],22:[2,19],23:[2,19],24:[2,19]},{5:[2,15],14:[2,15],15:[2,15],16:[2,15],19:[2,15],20:[2,15],22:[2,15],23:[2,15],24:[2,15]},{18:[2,34],33:[2,34]},{18:[2,35],33:[2,35]},{18:[2,36],33:[2,36]},{18:[2,37],33:[2,37]}], +defaultActions: {16:[2,1],37:[2,23],53:[2,21]}, +parseError: function parseError(str, hash) { + throw new Error(str); +}, +parse: function parse(input) { + var self = this, stack = [0], vstack = [null], lstack = [], table = this.table, yytext = "", yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1; + this.lexer.setInput(input); + this.lexer.yy = this.yy; + this.yy.lexer = this.lexer; + if (typeof this.lexer.yylloc == "undefined") + this.lexer.yylloc = {}; + var yyloc = this.lexer.yylloc; + lstack.push(yyloc); + if (typeof this.yy.parseError === "function") + this.parseError = this.yy.parseError; + function popStack(n) { + stack.length = stack.length - 2 * n; + vstack.length = vstack.length - n; + lstack.length = lstack.length - n; + } + function lex() { + var token; + token = self.lexer.lex() || 1; + if (typeof token !== "number") { + token = self.symbols_[token] || token; + } + return token; + } + var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected; + while (true) { + state = stack[stack.length - 1]; + if (this.defaultActions[state]) { + action = this.defaultActions[state]; + } else { + if (symbol == null) + symbol = lex(); + action = table[state] && table[state][symbol]; + } + if (typeof action === "undefined" || !action.length || !action[0]) { + if (!recovering) { + expected = []; + for (p in table[state]) + if (this.terminals_[p] && p > 2) { + expected.push("'" + this.terminals_[p] + "'"); + } + var errStr = ""; + if (this.lexer.showPosition) { + errStr = "Parse error on line " + (yylineno + 1) + ":\n" + this.lexer.showPosition() + "\nExpecting " + expected.join(", ") + ", got '" + this.terminals_[symbol] + "'"; + } else { + errStr = "Parse error on line " + (yylineno + 1) + ": Unexpected " + (symbol == 1?"end of input":"'" + (this.terminals_[symbol] || symbol) + "'"); + } + this.parseError(errStr, {text: this.lexer.match, token: this.terminals_[symbol] || symbol, line: this.lexer.yylineno, loc: yyloc, expected: expected}); + } + } + if (action[0] instanceof Array && action.length > 1) { + throw new Error("Parse Error: multiple actions possible at state: " + state + ", token: " + symbol); + } + switch (action[0]) { + case 1: + stack.push(symbol); + vstack.push(this.lexer.yytext); + lstack.push(this.lexer.yylloc); + stack.push(action[1]); + symbol = null; + if (!preErrorSymbol) { + yyleng = this.lexer.yyleng; + yytext = this.lexer.yytext; + yylineno = this.lexer.yylineno; + yyloc = this.lexer.yylloc; + if (recovering > 0) + recovering--; + } else { + symbol = preErrorSymbol; + preErrorSymbol = null; + } + break; + case 2: + len = this.productions_[action[1]][1]; + yyval.$ = vstack[vstack.length - len]; + yyval._$ = {first_line: lstack[lstack.length - (len || 1)].first_line, last_line: lstack[lstack.length - 1].last_line, first_column: lstack[lstack.length - (len || 1)].first_column, last_column: lstack[lstack.length - 1].last_column}; + r = this.performAction.call(yyval, yytext, yyleng, yylineno, this.yy, action[1], vstack, lstack); + if (typeof r !== "undefined") { + return r; + } + if (len) { + stack = stack.slice(0, -1 * len * 2); + vstack = vstack.slice(0, -1 * len); + lstack = lstack.slice(0, -1 * len); + } + stack.push(this.productions_[action[1]][0]); + vstack.push(yyval.$); + lstack.push(yyval._$); + newState = table[stack[stack.length - 2]][stack[stack.length - 1]]; + stack.push(newState); + break; + case 3: + return true; + } + } + return true; +} +};/* Jison generated lexer */ +var lexer = (function(){ + +var lexer = ({EOF:1, +parseError:function parseError(str, hash) { + if (this.yy.parseError) { + this.yy.parseError(str, hash); + } else { + throw new Error(str); + } + }, +setInput:function (input) { + this._input = input; + 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 ch = this._input[0]; + this.yytext+=ch; + this.yyleng++; + this.match+=ch; + this.matched+=ch; + var lines = ch.match(/\n/); + if (lines) this.yylineno++; + this._input = this._input.slice(1); + return ch; + }, +unput:function (ch) { + this._input = ch + this._input; + return this; + }, +more:function () { + this._more = true; + return this; + }, +pastInput:function () { + var past = this.matched.substr(0, this.matched.length - this.match.length); + return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\n/g, ""); + }, +upcomingInput:function () { + var next = this.match; + if (next.length < 20) { + next += this._input.substr(0, 20-next.length); + } + return (next.substr(0,20)+(next.length > 20 ? '...':'')).replace(/\n/g, ""); + }, +showPosition:function () { + var pre = this.pastInput(); + var c = new Array(pre.length + 1).join("-"); + return pre + this.upcomingInput() + "\n" + c+"^"; + }, +next:function () { + if (this.done) { + return this.EOF; + } + if (!this._input) this.done = true; + + var token, + match, + col, + lines; + if (!this._more) { + this.yytext = ''; + this.match = ''; + } + var rules = this._currentRules(); + for (var i=0;i < rules.length; i++) { + match = this._input.match(this.rules[rules[i]]); + if (match) { + lines = match[0].match(/\n.*/g); + if (lines) this.yylineno += lines.length; + this.yylloc = {first_line: this.yylloc.last_line, + last_line: this.yylineno+1, + first_column: this.yylloc.last_column, + last_column: lines ? lines[lines.length-1].length-1 : this.yylloc.last_column + match[0].length} + this.yytext += match[0]; + this.match += match[0]; + this.matches = match; + this.yyleng = this.yytext.length; + this._more = false; + this._input = this._input.slice(match[0].length); + this.matched += match[0]; + token = this.performAction.call(this, this.yy, this, rules[i],this.conditionStack[this.conditionStack.length-1]); + if (token) return token; + 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 lex() { + var r = this.next(); + if (typeof r !== 'undefined') { + return r; + } else { + return this.lex(); + } + }, +begin:function begin(condition) { + this.conditionStack.push(condition); + }, +popState:function popState() { + return this.conditionStack.pop(); + }, +_currentRules:function _currentRules() { + return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules; + }, +topState:function () { + return this.conditionStack[this.conditionStack.length-2]; + }, +pushState:function begin(condition) { + this.begin(condition); + }}); +lexer.performAction = function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) { + +var YYSTATE=YY_START +switch($avoiding_name_collisions) { +case 0: + if(yy_.yytext.slice(-1) !== "\\") this.begin("mu"); + if(yy_.yytext.slice(-1) === "\\") yy_.yytext = yy_.yytext.substr(0,yy_.yyleng-1), this.begin("emu"); + if(yy_.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: yy_.yytext = yy_.yytext.substr(3,yy_.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: /*ignore whitespace*/ +break; +case 17: this.popState(); return 18; +break; +case 18: this.popState(); return 18; +break; +case 19: yy_.yytext = yy_.yytext.substr(1,yy_.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: yy_.yytext = yy_.yytext.substr(1, yy_.yyleng-2); return 33; +break; +case 25: return 'INVALID'; +break; +case 26: return 5; +break; +} +}; +lexer.rules = [/^[^\x00]*?(?=(\{\{))/,/^[^\x00]+/,/^[^\x00]{2,}?(?=(\{\{))/,/^\{\{>/,/^\{\{#/,/^\{\{\//,/^\{\{\^/,/^\{\{\s*else\b/,/^\{\{\{/,/^\{\{&/,/^\{\{![\s\S]*?\}\}/,/^\{\{/,/^=/,/^\.(?=[} ])/,/^\.\./,/^[\/.]/,/^\s+/,/^\}\}\}/,/^\}\}/,/^"(\\["]|[^"])*"/,/^true(?=[}\s])/,/^false(?=[}\s])/,/^[0-9]+(?=[}\s])/,/^[a-zA-Z0-9_$-]+(?=[=}\s\/.])/,/^\[[^\]]*\]/,/^./,/^$/]; +lexer.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 lexer;})() +parser.lexer = lexer; +return parser; +})(); +if (typeof require !== 'undefined' && typeof exports !== 'undefined') { +exports.parser = handlebars; +exports.parse = function () { return handlebars.parse.apply(handlebars, arguments); } +exports.main = function commonjsMain(args) { + if (!args[1]) + throw new Error('Usage: '+args[0]+' FILE'); + if (typeof process !== 'undefined') { + var source = require('fs').readFileSync(require('path').join(process.cwd(), args[1]), "utf8"); + } else { + var cwd = require("file").path(require("file").cwd()); + var source = cwd.join(args[1]).read({charset: "utf-8"}); + } + return exports.parser.parse(source); +} +if (typeof module !== 'undefined' && require.main === module) { + exports.main(typeof process !== 'undefined' ? process.argv.slice(1) : require("system").args); +} +}; +; +// lib/handlebars/compiler/base.js +Handlebars.Parser = handlebars; + +Handlebars.parse = function(string) { + Handlebars.Parser.yy = Handlebars.AST; + return Handlebars.Parser.parse(string); +}; + +Handlebars.print = function(ast) { + return new Handlebars.PrintVisitor().accept(ast); +}; + +Handlebars.logger = { + DEBUG: 0, INFO: 1, WARN: 2, ERROR: 3, level: 3, + + // override in the host environment + log: function(level, str) {} +}; + +Handlebars.log = function(level, str) { Handlebars.logger.log(level, str); }; +; +// lib/handlebars/compiler/ast.js +(function() { + + Handlebars.AST = {}; + + Handlebars.AST.ProgramNode = function(statements, inverse) { + this.type = "program"; + this.statements = statements; + if(inverse) { this.inverse = new Handlebars.AST.ProgramNode(inverse); } + }; + + Handlebars.AST.MustacheNode = function(params, hash, unescaped) { + this.type = "mustache"; + this.id = params[0]; + this.params = params.slice(1); + this.hash = hash; + this.escaped = !unescaped; + }; + + Handlebars.AST.PartialNode = function(id, context) { + this.type = "partial"; + + // TODO: disallow complex IDs + + this.id = id; + this.context = context; + }; + + var verifyMatch = function(open, close) { + if(open.original !== close.original) { + throw new Handlebars.Exception(open.original + " doesn't match " + close.original); + } + }; + + Handlebars.AST.BlockNode = function(mustache, program, close) { + verifyMatch(mustache.id, close); + this.type = "block"; + this.mustache = mustache; + this.program = program; + }; + + Handlebars.AST.InverseNode = function(mustache, program, close) { + verifyMatch(mustache.id, close); + this.type = "inverse"; + this.mustache = mustache; + this.program = program; + }; + + Handlebars.AST.ContentNode = function(string) { + this.type = "content"; + this.string = string; + }; + + Handlebars.AST.HashNode = function(pairs) { + this.type = "hash"; + this.pairs = pairs; + }; + + Handlebars.AST.IdNode = function(parts) { + this.type = "ID"; + this.original = parts.join("."); + + var dig = [], depth = 0; + + for(var i=0,l=parts.length; i<l; i++) { + var part = parts[i]; + + if(part === "..") { depth++; } + else if(part === "." || part === "this") { this.isScoped = true; } + else { dig.push(part); } + } + + this.parts = dig; + this.string = dig.join('.'); + this.depth = depth; + this.isSimple = (dig.length === 1) && (depth === 0); + }; + + Handlebars.AST.StringNode = function(string) { + this.type = "STRING"; + this.string = string; + }; + + Handlebars.AST.IntegerNode = function(integer) { + this.type = "INTEGER"; + this.integer = integer; + }; + + Handlebars.AST.BooleanNode = function(bool) { + this.type = "BOOLEAN"; + this.bool = bool; + }; + + Handlebars.AST.CommentNode = function(comment) { + this.type = "comment"; + this.comment = comment; + }; + +})();; +// lib/handlebars/utils.js +Handlebars.Exception = function(message) { + var tmp = Error.prototype.constructor.apply(this, arguments); + + for (var p in tmp) { + if (tmp.hasOwnProperty(p)) { this[p] = tmp[p]; } + } + + this.message = tmp.message; +}; +Handlebars.Exception.prototype = new Error; + +// Build out our basic SafeString type +Handlebars.SafeString = function(string) { + this.string = string; +}; +Handlebars.SafeString.prototype.toString = function() { + return this.string.toString(); +}; + +(function() { + var escape = { + "<": "<", + ">": ">", + '"': """, + "'": "'", + "`": "`" + }; + + var badChars = /&(?!\w+;)|[<>"'`]/g; + var possible = /[&<>"'`]/; + + var escapeChar = function(chr) { + return escape[chr] || "&"; + }; + + Handlebars.Utils = { + escapeExpression: function(string) { + // don't escape SafeStrings, since they're already safe + if (string instanceof Handlebars.SafeString) { + return string.toString(); + } else if (string == null || string === false) { + return ""; + } + + if(!possible.test(string)) { return string; } + return string.replace(badChars, escapeChar); + }, + + isEmpty: function(value) { + if (typeof value === "undefined") { + return true; + } else if (value === null) { + return true; + } else if (value === false) { + return true; + } else if(Object.prototype.toString.call(value) === "[object Array]" && value.length === 0) { + return true; + } else { + return false; + } + } + }; +})();; +// lib/handlebars/compiler/compiler.js +Handlebars.Compiler = function() {}; +Handlebars.JavaScriptCompiler = function() {}; + +(function(Compiler, JavaScriptCompiler) { + Compiler.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 + }; + + Compiler.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 + }; + + Compiler.DISASSEMBLE_MAP = {}; + + for(var prop in Compiler.OPCODE_MAP) { + var value = Compiler.OPCODE_MAP[prop]; + Compiler.DISASSEMBLE_MAP[value] = prop; + } + + Compiler.multiParamSize = function(code) { + return Compiler.MULTI_PARAM_OPCODES[Compiler.DISASSEMBLE_MAP[code]]; + }; + + Compiler.prototype = { + compiler: Compiler, + + disassemble: function() { + var opcodes = this.opcodes, opcode, nextCode; + var out = [], str, name, value; + + for(var i=0, l=opcodes.length; i<l; i++) { + opcode = opcodes[i]; + + if(opcode === 'DECLARE') { + name = opcodes[++i]; + value = opcodes[++i]; + out.push("DECLARE " + name + " = " + value); + } else { + str = Compiler.DISASSEMBLE_MAP[opcode]; + + var extraParams = Compiler.multiParamSize(opcode); + var codes = []; + + for(var j=0; j<extraParams; j++) { + nextCode = opcodes[++i]; + + if(typeof nextCode === "string") { + nextCode = "\"" + nextCode.replace("\n", "\\n") + "\""; + } + + codes.push(nextCode); + } + + str = str + " " + codes.join(" "); + + out.push(str); + } + } + + return out.join("\n"); + }, + + guid: 0, + + compile: function(program, options) { + this.children = []; + this.depths = {list: []}; + this.options = options; + + // These changes will propagate to the other compiler components + var knownHelpers = this.options.knownHelpers; + this.options.knownHelpers = { + 'helperMissing': true, + 'blockHelperMissing': true, + 'each': true, + 'if': true, + 'unless': true, + 'with': true, + 'log': true + }; + if (knownHelpers) { + for (var name in knownHelpers) { + this.options.knownHelpers[name] = knownHelpers[name]; + } + } + + return this.program(program); + }, + + accept: function(node) { + return this[node.type](node); + }, + + program: function(program) { + var statements = program.statements, statement; + this.opcodes = []; + + for(var i=0, l=statements.length; i<l; i++) { + statement = statements[i]; + this[statement.type](statement); + } + this.isSimple = l === 1; + + this.depths.list = this.depths.list.sort(function(a, b) { + return a - b; + }); + + return this; + }, + + compileProgram: function(program) { + var result = new this.compiler().compile(program, this.options); + var guid = this.guid++; + + this.usePartial = this.usePartial || result.usePartial; + + this.children[guid] = result; + + for(var i=0, l=result.depths.list.length; i<l; i++) { + depth = result.depths.list[i]; + + if(depth < 2) { continue; } + else { this.addDepth(depth - 1); } + } + + return guid; + }, + + block: function(block) { + var mustache = block.mustache; + var depth, child, inverse, inverseGuid; + + var params = this.setupStackForMustache(mustache); + + var programGuid = this.compileProgram(block.program); + + if(block.program.inverse) { + inverseGuid = this.compileProgram(block.program.inverse); + this.declare('inverse', inverseGuid); + } + + this.opcode('invokeProgram', programGuid, params.length, !!mustache.hash); + this.declare('inverse', null); + this.opcode('append'); + }, + + inverse: function(block) { + var params = this.setupStackForMustache(block.mustache); + + var programGuid = this.compileProgram(block.program); + + this.declare('inverse', programGuid); + + this.opcode('invokeProgram', null, params.length, !!block.mustache.hash); + this.declare('inverse', null); + this.opcode('append'); + }, + + hash: function(hash) { + var pairs = hash.pairs, pair, val; + + this.opcode('push', '{}'); + + for(var i=0, l=pairs.length; i<l; i++) { + pair = pairs[i]; + val = pair[1]; + + this.accept(val); + this.opcode('assignToHash', pair[0]); + } + }, + + partial: function(partial) { + var id = partial.id; + this.usePartial = true; + + if(partial.context) { + this.ID(partial.context); + } else { + this.opcode('push', 'depth0'); + } + + this.opcode('invokePartial', id.original); + this.opcode('append'); + }, + + content: function(content) { + this.opcode('appendContent', content.string); + }, + + mustache: function(mustache) { + var params = this.setupStackForMustache(mustache); + + this.opcode('invokeMustache', params.length, mustache.id.original, !!mustache.hash); + + if(mustache.escaped && !this.options.noEscape) { + this.opcode('appendEscaped'); + } else { + this.opcode('append'); + } + }, + + ID: function(id) { + this.addDepth(id.depth); + + this.opcode('getContext', id.depth); + + this.opcode('lookupWithHelpers', id.parts[0] || null, id.isScoped || false); + + for(var i=1, l=id.parts.length; i<l; i++) { + this.opcode('lookup', id.parts[i]); + } + }, + + STRING: function(string) { + this.opcode('pushString', string.string); + }, + + INTEGER: function(integer) { + this.opcode('push', integer.integer); + }, + + BOOLEAN: function(bool) { + this.opcode('push', bool.bool); + }, + + comment: function() {}, + + // HELPERS + pushParams: function(params) { + var i = params.length, param; + + while(i--) { + param = params[i]; + + if(this.options.stringParams) { + if(param.depth) { + this.addDepth(param.depth); + } + + this.opcode('getContext', param.depth || 0); + this.opcode('pushStringParam', param.string); + } else { + this[param.type](param); + } + } + }, + + opcode: function(name, val1, val2, val3) { + this.opcodes.push(Compiler.OPCODE_MAP[name]); + if(val1 !== undefined) { this.opcodes.push(val1); } + if(val2 !== undefined) { this.opcodes.push(val2); } + if(val3 !== undefined) { this.opcodes.push(val3); } + }, + + declare: function(name, value) { + this.opcodes.push('DECLARE'); + this.opcodes.push(name); + this.opcodes.push(value); + }, + + addDepth: function(depth) { + if(depth === 0) { return; } + + if(!this.depths[depth]) { + this.depths[depth] = true; + this.depths.list.push(depth); + } + }, + + setupStackForMustache: function(mustache) { + var params = mustache.params; + + this.pushParams(params); + + if(mustache.hash) { + this.hash(mustache.hash); + } + + this.ID(mustache.id); + + return params; + } + }; + + JavaScriptCompiler.prototype = { + // PUBLIC API: You can override these methods in a subclass to provide + // alternative compiled forms for name lookup and buffering semantics + nameLookup: function(parent, name, type) { + if (/^[0-9]+$/.test(name)) { + return parent + "[" + name + "]"; + } else if (JavaScriptCompiler.isValidJavaScriptVariableName(name)) { + return parent + "." + name; + } + else { + return parent + "['" + name + "']"; + } + }, + + appendToBuffer: function(string) { + if (this.environment.isSimple) { + return "return " + string + ";"; + } else { + return "buffer += " + string + ";"; + } + }, + + initializeBuffer: function() { + return this.quotedString(""); + }, + + namespace: "Handlebars", + // END PUBLIC API + + compile: function(environment, options, context, asObject) { + this.environment = environment; + this.options = options || {}; + + this.name = this.environment.name; + this.isChild = !!context; + this.context = context || { + programs: [], + aliases: { self: 'this' }, + registers: {list: []} + }; + + this.preamble(); + + this.stackSlot = 0; + this.stackVars = []; + + this.compileChildren(environment, options); + + var opcodes = environment.opcodes, opcode; + + this.i = 0; + + for(l=opcodes.length; this.i<l; this.i++) { + opcode = this.nextOpcode(0); + + if(opcode[0] === 'DECLARE') { + this.i = this.i + 2; + this[opcode[1]] = opcode[2]; + } else { + this.i = this.i + opcode[1].length; + this[opcode[0]].apply(this, opcode[1]); + } + } + + return this.createFunctionContext(asObject); + }, + + nextOpcode: function(n) { + var opcodes = this.environment.opcodes, opcode = opcodes[this.i + n], name, val; + var extraParams, codes; + + if(opcode === 'DECLARE') { + name = opcodes[this.i + 1]; + val = opcodes[this.i + 2]; + return ['DECLARE', name, val]; + } else { + name = Compiler.DISASSEMBLE_MAP[opcode]; + + extraParams = Compiler.multiParamSize(opcode); + codes = []; + + for(var j=0; j<extraParams; j++) { + codes.push(opcodes[this.i + j + 1 + n]); + } + + return [name, codes]; + } + }, + + eat: function(opcode) { + this.i = this.i + opcode.length; + }, + + preamble: function() { + var out = []; + + // this register will disambiguate helper lookup from finding a function in + // a context. This is necessary for mustache compatibility, which requires + // that context functions in blocks are evaluated by blockHelperMissing, and + // then proceed as if the resulting value was provided to blockHelperMissing. + this.useRegister('foundHelper'); + + if (!this.isChild) { + var namespace = this.namespace; + var copies = "helpers = helpers || " + namespace + ".helpers;"; + if(this.environment.usePartial) { copies = copies + " partials = partials || " + namespace + ".partials;"; } + out.push(copies); + } else { + out.push(''); + } + + if (!this.environment.isSimple) { + out.push(", buffer = " + this.initializeBuffer()); + } else { + out.push(""); + } + + // track the last context pushed into place to allow skipping the + // getContext opcode when it would be a noop + this.lastContext = 0; + this.source = out; + }, + + createFunctionContext: function(asObject) { + var locals = this.stackVars; + if (!this.isChild) { + locals = locals.concat(this.context.registers.list); + } + + if(locals.length > 0) { + this.source[1] = this.source[1] + ", " + locals.join(", "); + } + + // Generate minimizer alias mappings + if (!this.isChild) { + var aliases = [] + for (var alias in this.context.aliases) { + this.source[1] = this.source[1] + ', ' + alias + '=' + this.context.aliases[alias]; + } + } + + if (this.source[1]) { + this.source[1] = "var " + this.source[1].substring(2) + ";"; + } + + // Merge children + if (!this.isChild) { + this.source[1] += '\n' + this.context.programs.join('\n') + '\n'; + } + + if (!this.environment.isSimple) { + this.source.push("return buffer;"); + } + + var params = this.isChild ? ["depth0", "data"] : ["Handlebars", "depth0", "helpers", "partials", "data"]; + + for(var i=0, l=this.environment.depths.list.length; i<l; i++) { + params.push("depth" + this.environment.depths.list[i]); + } + + if (asObject) { + params.push(this.source.join("\n ")); + + return Function.apply(this, params); + } else { + var functionSource = 'function ' + (this.name || '') + '(' + params.join(',') + ') {\n ' + this.source.join("\n ") + '}'; + Handlebars.log(Handlebars.logger.DEBUG, functionSource + "\n\n"); + return functionSource; + } + }, + + appendContent: function(content) { + this.source.push(this.appendToBuffer(this.quotedString(content))); + }, + + append: function() { + var local = this.popStack(); + this.source.push("if(" + local + " || " + local + " === 0) { " + this.appendToBuffer(local) + " }"); + if (this.environment.isSimple) { + this.source.push("else { " + this.appendToBuffer("''") + " }"); + } + }, + + appendEscaped: function() { + var opcode = this.nextOpcode(1), extra = ""; + this.context.aliases.escapeExpression = 'this.escapeExpression'; + + if(opcode[0] === 'appendContent') { + extra = " + " + this.quotedString(opcode[1][0]); + this.eat(opcode); + } + + this.source.push(this.appendToBuffer("escapeExpression(" + this.popStack() + ")" + extra)); + }, + + getContext: function(depth) { + if(this.lastContext !== depth) { + this.lastContext = depth; + } + }, + + lookupWithHelpers: function(name, isScoped) { + if(name) { + var topStack = this.nextStack(); + + this.usingKnownHelper = false; + + var toPush; + if (!isScoped && this.options.knownHelpers[name]) { + toPush = topStack + " = " + this.nameLookup('helpers', name, 'helper'); + this.usingKnownHelper = true; + } else if (isScoped || this.options.knownHelpersOnly) { + toPush = topStack + " = " + this.nameLookup('depth' + this.lastContext, name, 'context'); + } else { + this.register('foundHelper', this.nameLookup('helpers', name, 'helper')); + toPush = topStack + " = foundHelper || " + this.nameLookup('depth' + this.lastContext, name, 'context'); + } + + toPush += ';'; + this.source.push(toPush); + } else { + this.pushStack('depth' + this.lastContext); + } + }, + + lookup: function(name) { + var topStack = this.topStack(); + this.source.push(topStack + " = (" + topStack + " === null || " + topStack + " === undefined || " + topStack + " === false ? " + + topStack + " : " + this.nameLookup(topStack, name, 'context') + ");"); + }, + + pushStringParam: function(string) { + this.pushStack('depth' + this.lastContext); + this.pushString(string); + }, + + pushString: function(string) { + this.pushStack(this.quotedString(string)); + }, + + push: function(name) { + this.pushStack(name); + }, + + invokeMustache: function(paramSize, original, hasHash) { + this.populateParams(paramSize, this.quotedString(original), "{}", null, hasHash, function(nextStack, helperMissingString, id) { + if (!this.usingKnownHelper) { + this.context.aliases.helperMissing = 'helpers.helperMissing'; + this.context.aliases.undef = 'void 0'; + this.source.push("else if(" + id + "=== undef) { " + nextStack + " = helperMissing.call(" + helperMissingString + "); }"); + if (nextStack !== id) { + this.source.push("else { " + nextStack + " = " + id + "; }"); + } + } + }); + }, + + invokeProgram: function(guid, paramSize, hasHash) { + var inverse = this.programExpression(this.inverse); + var mainProgram = this.programExpression(guid); + + this.populateParams(paramSize, null, mainProgram, inverse, hasHash, function(nextStack, helperMissingString, id) { + if (!this.usingKnownHelper) { + this.context.aliases.blockHelperMissing = 'helpers.blockHelperMissing'; + this.source.push("else { " + nextStack + " = blockHelperMissing.call(" + helperMissingString + "); }"); + } + }); + }, + + populateParams: function(paramSize, helperId, program, inverse, hasHash, fn) { + var needsRegister = hasHash || this.options.stringParams || inverse || this.options.data; + var id = this.popStack(), nextStack; + var params = [], param, stringParam, stringOptions; + + if (needsRegister) { + this.register('tmp1', program); + stringOptions = 'tmp1'; + } else { + stringOptions = '{ hash: {} }'; + } + + if (needsRegister) { + var hash = (hasHash ? this.popStack() : '{}'); + this.source.push('tmp1.hash = ' + hash + ';'); + } + + if(this.options.stringParams) { + this.source.push('tmp1.contexts = [];'); + } + + for(var i=0; i<paramSize; i++) { + param = this.popStack(); + params.push(param); + + if(this.options.stringParams) { + this.source.push('tmp1.contexts.push(' + this.popStack() + ');'); + } + } + + if(inverse) { + this.source.push('tmp1.fn = tmp1;'); + this.source.push('tmp1.inverse = ' + inverse + ';'); + } + + if(this.options.data) { + this.source.push('tmp1.data = data;'); + } + + params.push(stringOptions); + + this.populateCall(params, id, helperId || id, fn, program !== '{}'); + }, + + populateCall: function(params, id, helperId, fn, program) { + var paramString = ["depth0"].concat(params).join(", "); + var helperMissingString = ["depth0"].concat(helperId).concat(params).join(", "); + + var nextStack = this.nextStack(); + + if (this.usingKnownHelper) { + this.source.push(nextStack + " = " + id + ".call(" + paramString + ");"); + } else { + this.context.aliases.functionType = '"function"'; + var condition = program ? "foundHelper && " : "" + this.source.push("if(" + condition + "typeof " + id + " === functionType) { " + nextStack + " = " + id + ".call(" + paramString + "); }"); + } + fn.call(this, nextStack, helperMissingString, id); + this.usingKnownHelper = false; + }, + + invokePartial: function(context) { + params = [this.nameLookup('partials', context, 'partial'), "'" + context + "'", this.popStack(), "helpers", "partials"]; + + if (this.options.data) { + params.push("data"); + } + + this.pushStack("self.invokePartial(" + params.join(", ") + ");"); + }, + + assignToHash: function(key) { + var value = this.popStack(); + var hash = this.topStack(); + + this.source.push(hash + "['" + key + "'] = " + value + ";"); + }, + + // HELPERS + + compiler: JavaScriptCompiler, + + compileChildren: function(environment, options) { + var children = environment.children, child, compiler; + + for(var i=0, l=children.length; i<l; i++) { + child = children[i]; + compiler = new this.compiler(); + + this.context.programs.push(''); // Placeholder to prevent name conflicts for nested children + var index = this.context.programs.length; + child.index = index; + child.name = 'program' + index; + this.context.programs[index] = compiler.compile(child, options, this.context); + } + }, + + programExpression: function(guid) { + if(guid == null) { return "self.noop"; } + + var child = this.environment.children[guid], + depths = child.depths.list; + var programParams = [child.index, child.name, "data"]; + + for(var i=0, l = depths.length; i<l; i++) { + depth = depths[i]; + + if(depth === 1) { programParams.push("depth0"); } + else { programParams.push("depth" + (depth - 1)); } + } + + if(depths.length === 0) { + return "self.program(" + programParams.join(", ") + ")"; + } else { + programParams.shift(); + return "self.programWithDepth(" + programParams.join(", ") + ")"; + } + }, + + register: function(name, val) { + this.useRegister(name); + this.source.push(name + " = " + val + ";"); + }, + + useRegister: function(name) { + if(!this.context.registers[name]) { + this.context.registers[name] = true; + this.context.registers.list.push(name); + } + }, + + pushStack: function(item) { + this.source.push(this.nextStack() + " = " + item + ";"); + return "stack" + this.stackSlot; + }, + + nextStack: function() { + this.stackSlot++; + if(this.stackSlot > this.stackVars.length) { this.stackVars.push("stack" + this.stackSlot); } + return "stack" + this.stackSlot; + }, + + popStack: function() { + return "stack" + this.stackSlot--; + }, + + topStack: function() { + return "stack" + this.stackSlot; + }, + + quotedString: function(str) { + return '"' + str + .replace(/\\/g, '\\\\') + .replace(/"/g, '\\"') + .replace(/\n/g, '\\n') + .replace(/\r/g, '\\r') + '"'; + } + }; + + var reservedWords = ( + "break else new var" + + " case finally return void" + + " catch for switch while" + + " continue function this with" + + " default if throw" + + " delete in try" + + " do instanceof typeof" + + " abstract enum int short" + + " boolean export interface static" + + " byte extends long super" + + " char final native synchronized" + + " class float package throws" + + " const goto private transient" + + " debugger implements protected volatile" + + " double import public let yield" + ).split(" "); + + var compilerWords = JavaScriptCompiler.RESERVED_WORDS = {}; + + for(var i=0, l=reservedWords.length; i<l; i++) { + compilerWords[reservedWords[i]] = true; + } + + JavaScriptCompiler.isValidJavaScriptVariableName = function(name) { + if(!JavaScriptCompiler.RESERVED_WORDS[name] && /^[a-zA-Z_$][0-9a-zA-Z_$]+$/.test(name)) { + return true; + } + return false; + } + +})(Handlebars.Compiler, Handlebars.JavaScriptCompiler); + +Handlebars.precompile = function(string, options) { + options = options || {}; + + var ast = Handlebars.parse(string); + var environment = new Handlebars.Compiler().compile(ast, options); + return new Handlebars.JavaScriptCompiler().compile(environment, options); +}; + +Handlebars.compile = function(string, options) { + options = options || {}; + + var compiled; + function compile() { + var ast = Handlebars.parse(string); + var environment = new Handlebars.Compiler().compile(ast, options); + var templateSpec = new Handlebars.JavaScriptCompiler().compile(environment, options, undefined, true); + return Handlebars.template(templateSpec); + } + + // Template is only compiled on first use and cached after that point. + return function(context, options) { + if (!compiled) { + compiled = compile(); + } + return compiled.call(this, context, options); + }; +}; +; +// lib/handlebars/runtime.js +Handlebars.VM = { + template: function(templateSpec) { + // Just add water + var container = { + escapeExpression: Handlebars.Utils.escapeExpression, + invokePartial: Handlebars.VM.invokePartial, + programs: [], + program: function(i, fn, data) { + var programWrapper = this.programs[i]; + if(data) { + return Handlebars.VM.program(fn, data); + } else if(programWrapper) { + return programWrapper; + } else { + programWrapper = this.programs[i] = Handlebars.VM.program(fn); + return programWrapper; + } + }, + programWithDepth: Handlebars.VM.programWithDepth, + noop: Handlebars.VM.noop + }; + + return function(context, options) { + options = options || {}; + return templateSpec.call(container, Handlebars, context, options.helpers, options.partials, options.data); + }; + }, + + programWithDepth: function(fn, data, $depth) { + var args = Array.prototype.slice.call(arguments, 2); + + return function(context, options) { + options = options || {}; + + return fn.apply(this, [context, options.data || data].concat(args)); + }; + }, + program: function(fn, data) { + return function(context, options) { + options = options || {}; + + return fn(context, options.data || data); + }; + }, + noop: function() { return ""; }, + invokePartial: function(partial, name, context, helpers, partials, data) { + options = { helpers: helpers, partials: partials, data: data }; + + if(partial === undefined) { + throw new Handlebars.Exception("The partial " + name + " could not be found"); + } else if(partial instanceof Function) { + return partial(context, options); + } else if (!Handlebars.compile) { + throw new Handlebars.Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); + } else { + partials[name] = Handlebars.compile(partial); + return partials[name](context, options); + } + } +}; + +Handlebars.template = Handlebars.VM.template; +; diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/annotations.js --- /dev/null +++ b/static/scripts/mvc/annotations.js @@ -0,0 +1,35 @@ +/*============================================================================== +Backbone MV for Annotations + + +TODO: + +==============================================================================*/ +/** Single Tag model + */ +var Annotation = BaseModel.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'Annotation()'; + } +}); + +//------------------------------------------------------------------------------ +/** Single Tag view + */ +var AnnotationView = BaseView.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'AnnotationView()'; + } +}); + +//============================================================================== +/** YAGNI? A collection of Annotations, mainView? + */ diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/base-mvc.js --- /dev/null +++ b/static/scripts/mvc/base-mvc.js @@ -0,0 +1,271 @@ +/** + * Simple base model for any visible element. Includes useful attributes and ability + * to set and track visibility. + */ +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; + } +}); + + +/** + * Base view that handles visibility based on model's hidden attribute. + */ +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.$el.show(); + } + } +}); + +//============================================================================== +/** + * Adds logging capabilities to your Models/Views + * can be used with plain browser console (or something more complex like an AJAX logger) + * + * add to your models/views at the definition using chaining: + * var MyModel = BaseModel.extend( LoggableMixin ).extend({ // ... }); + * + * or - more explicitly AFTER the definition: + * var MyModel = BaseModel.extend({ + * logger : console + * // ... + * this.log( '$#%& it! - broken already...' ); + * }) + * _.extend( MyModel.prototype, LoggableMixin ) + * + * NOTE: currently only uses the console.debug log function (as opposed to debug, error, warn, etc.) + */ +var LoggableMixin = { + // replace null with console (if available) to see all logs + logger : null, + + log : function(){ + return ( this.logger )?( this.logger.log.apply( this, arguments ) ) + :( undefined ); + } +}; + + +//============================================================================== +/** + * Base class for template loaders: + * The main interface is loader.getTemplates( templatesToLoad ) + * where templatesToLoad is in the form: + * { + * remoteTemplateFilename1: { + * templateFunctionName1 : templateID1, + * templateFunctionName2 : templateID2, + * ... + * }, + * remoteTemplateFilename2: { + * templateFunctionName3 : templateID3, + * templateFunctionName4 : templateID4, + * ... + * } + * } + * getTemplates will return a map of the templates in the form: + * { + * templateFunctionName1 : compiledTemplateFn1(), + * templateFunctionName2 : compiledTemplateFn2(), + * templateFunctionName3 : compiledTemplateFn3(), + * ... + * } + * + * Generally meant to be called for Backbone views, etc like this: + * BackboneView.templates = CompiledTemplateLoader( templatesToLoad ); + */ +var TemplateLoader = _.extend( {}, LoggableMixin, { + //TODO: incorporate caching of template functions (for use across objects) + //TODO: only require and use 2 level (or some variation) map templatesToLoad for the remote loader + + // comment next line out to suppress logging + //logger : console, + + //cachedTemplates : {}, + + getTemplateLoadFn : function(){ + throw( "There is no templateLoadFn. Make sure you're using a subclass of TemplateLoader" ); + }, + + // loop through templatesToLoad assuming it is a map in the form mentioned above + getTemplates : function( templatesToLoad, forceReload ){ + forceReload = forceReload || false; + this.log( this, 'getTemplates:', templatesToLoad, ', forceReload:', forceReload ); + + //!TODO: cache templates here + var templates = {}, + loader = this, + templateLoadFn = this.getTemplateLoadFn(); + + if( !templatesToLoad ){ return templates; } + jQuery.each( templatesToLoad, function( templateFile, templateData ){ + + //TODO: handle flatter map versions of templatesToLoad ({ name : id }) + jQuery.each( templateData, function( templateName, templateID ){ + loader.log( loader + ', templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID ); + templates[ templateName ] = templateLoadFn.call( loader, templateFile, templateName, templateID ); + }); + }); + return templates; + } +}); + + +//.............................................................................. +/** find the compiled template in Handlebars.templates by templateName + * and return the entire, requested templates map + */ +var CompiledTemplateLoader = _.extend( {}, TemplateLoader, { + getTemplateLoadFn : function(){ return this.loadCompiledHandlebarsTemplate; }, + + // override if new compiler + loadCompiledHandlebarsTemplate : function( templateFile, templateName, templateID ){ + //pre: compiled templates should have been loaded with the mako helper h.templates + // (although these could be dynamically loaded as well?) + this.log( 'getInDomTemplates, templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID ); + + if( !Handlebars.templates || !Handlebars.templates[ templateID ] ){ + throw( 'Template not found: Handlebars.' + templateID + + '. Check your h.templates() call in the mako file that rendered this page' ); + } + this.log( 'found template function:', templateID ); + // really this is just a lookup + return Handlebars.templates[ templateID ]; + } + + //TEST: Handlebars.full NOT runtime + //TEST: no Handlebars + //TEST: bad id + //TEST: Handlebars.runtime, good id +}); + +//.............................................................................. +/** find the NON-compiled template templateID in the DOM, compile it (using Handlebars), + * and return the entire, requested templates map + * (Note: for use with Mako.include and multiple templates) + */ +var InDomTemplateLoader = _.extend( {}, TemplateLoader, { + + // override or change if a new compiler (Underscore, etc.) is being used + compileTemplate : function( templateText ){ + // we'll need the compiler + if( !Handlebars || !Handlebars.compile ){ + throw( 'No Handlebars.compile found. You may only have Handlebars.runtime loaded.' + + 'Include handlebars.full for this to work' ); + } + // copy fn ref to this view under the templateName + this.log( 'compiling template:', templateText ); + return Handlebars.compile( templateText ); + }, + + findTemplateInDom : function( templateFile, templateName, templateID ){ + // assume the last is best + return $( 'script#' + templateID ).last(); + }, + + getTemplateLoadFn : function(){ return this.loadInDomTemplate; }, + + loadInDomTemplate : function( templateFile, templateName, templateID ){ + this.log( 'getInDomTemplate, templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID ); + + // find it in the dom by the id and compile + var template = this.findTemplateInDom( templateFile, templateName, templateID ); + if( !template || !template.length ){ + throw( 'Template not found within the DOM: ' + templateID + + '. Check that this template has been included in the page' ); + } + this.log( 'found template in dom:', template.html() ); + return this.compileTemplate( template.html() ); + } + + //TEST: no compiler + //TEST: good url, good id, in DOM + //TEST: good url, good id, NOT in DOM +}); + +//.............................................................................. +/** HTTP GET the NON-compiled templates, append into the DOM, compile them, + * and return the entire, requested templates map + * (for use with dynamically loaded views) + */ +var RemoteTemplateLoader = _.extend( {}, InDomTemplateLoader, { + templateBaseURL : 'static/scripts/templates/', + + getTemplateLoadFn : function(){ return this.loadViaHttpGet; }, + + loadViaHttpGet : function( templateFile, templateName, templateID ){ + var templateBaseURL = 'static/scripts/templates/'; + this.log( 'loadViaHttpGet, templateFile:', templateFile, + 'templateName:', templateName, ', templateID:', templateID, + 'templateBaseURL:', this.templateBaseURL ); + + //??: possibly not the best pattern here... + // try in-dom first (prevent loading the same templateFile for each of its templates) + var template = null; + try { + template = this.loadInDomTemplate( templateFile, templateName, templateID ); + + // if that didn't work, load the templateFile via GET,... + } catch( exception ){ + this.log( 'getInDomTemplate exception:' + exception ); + // handle no compiler exception + if( !Handlebars.compile ){ throw( exception ); } + //TEST: + + this.log( "Couldn't locate template in DOM: " + templateID ); + var loader = this; + var url = templateBaseURL + templateFile; + //??: async : false may cause problems in the long run + jQuery.ajax( url, { + method : 'GET', + async : false, + success : function( data ){ + loader.log( templateFile + ' loaded via GET. Attempting compile...' ); + //...move the templateFile into the DOM and try that again + $( 'body' ).append( data ); + template = loader.loadInDomTemplate( templateFile, templateName, templateID ); + }, + error : function( data, status, xhr ){ + throw( 'Failed to fetch ' + url + ':' + status ); + } + }); + } + if( !template ){ + throw( "Couldn't load or fetch template: " + templateID ); + } + return template; + } + + //TEST: no compiler + //TEST: good url, good id, already local + //TEST: good url, good id, remote load + //TEST: good url, bad template id + //TEST: bad url, error from ajax +}); diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -1,3 +1,4 @@ +if( console ){ console.debug( 'history mvc loaded' ); } /* Backbone.js implementation of history panel @@ -13,6 +14,8 @@ convert function comments to /** style complete comments + don't draw body until it's first unhide event + as always: where does the model end and the view begin? HistoryPanel HistoryCollection: (collection of History: 'Saved Histories') @@ -30,23 +33,12 @@ poly HistoryItemView on: can/cant_edit */ -_ = _; //============================================================================== -var Loggable = { - // replace null with console (if available) to see all logs - logger : null, - - log : function(){ - return ( this.logger )?( this.logger.debug.apply( this, arguments ) ) - :( undefined ); - } -}; -var LoggingModel = BaseModel.extend( Loggable ); -var LoggingView = BaseView.extend( Loggable ); //============================================================================== //TODO: move to Galaxy obj./namespace, decorate for current page (as GalaxyPaths) +/* var Localizable = { localizedStrings : {}, setLocalizedString : function( str, localizedString ){ @@ -58,6 +50,7 @@ } }; var LocalizableView = LoggingView.extend( Localizable ); +*/ //TODO: wire up to views //============================================================================== @@ -93,7 +86,8 @@ } //============================================================================== -var HistoryItem = LoggingModel.extend({ +//TODO: use initialize (or validate) to check purged AND deleted -> purged XOR deleted +var HistoryItem = BaseModel.extend( LoggableMixin ).extend({ // a single HDA model // uncomment this out see log messages @@ -141,7 +135,11 @@ }, toString : function(){ - return 'HistoryItem(' + ( this.get( 'name' ) || this.get( 'id' ) || '' ) + ')'; + var nameAndId = this.get( 'id' ) || ''; + if( this.get( 'name' ) ){ + nameAndId += ':"' + this.get( 'name' ) + '"'; + } + return 'HistoryItem(' + nameAndId + ')'; } }); @@ -161,20 +159,19 @@ //============================================================================== -var HistoryItemView = LoggingView.extend({ +var HistoryItemView = BaseView.extend( LoggableMixin ).extend({ // view for HistoryItem model above // uncomment this out see log messages - logger : console, + //logger : console, tagName : "div", className : "historyItemContainer", - // ................................................................................ SET UP initialize : function(){ this.log( this + '.initialize:', this, this.model ); - return this; + }, // ................................................................................ RENDER MAIN @@ -190,12 +187,8 @@ .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) .addClass( 'historyItem-' + state ); - itemWrapper.append( this._render_purgedWarning() ); - itemWrapper.append( this._render_deletionWarning() ); - itemWrapper.append( this._render_visibleWarning() ); - + itemWrapper.append( this._render_warnings() ); itemWrapper.append( this._render_titleBar() ); - this.body = $( this._render_body() ); itemWrapper.append( this.body ); @@ -215,52 +208,9 @@ }, // ................................................................................ RENDER WARNINGS - //TODO: refactor into generalized warning widget/view - //TODO: refactor the three following - too much common ground - _render_purgedWarning : function(){ - // Render warnings for purged - //this.log( this + '_render_purgedWarning' ); - var warning = null; - if( this.model.get( 'purged' ) ){ - warning = $( HistoryItemView.STRINGS.purgedMsg ); - } - //this.log( 'warning:', warning ); - return warning; - }, - - _render_deletionWarning : function(){ - //this.log( this + '_render_deletionWarning' ); - // Render warnings for deleted items (and links: undelete and purge) - //pre: this.model.purge_url will be undefined if trans.app.config.allow_user_dataset_purge=False - var warningElem = null; - if( this.model.get( 'deleted' ) ){ - var warning = ''; - - if( this.model.get( 'undelete_url' ) ){ - warning += HistoryItemView.TEMPLATES.undeleteLink( this.model.attributes ); - } - if( this.model.get( 'purge_url' ) ){ - warning += HistoryItemView.TEMPLATES.purgeLink( this.model.attributes ); - } - // wrap it in the standard warning msg - warningElem = $( HistoryItemView.TEMPLATES.warningMsg({ warning: warning }) ); - } - //this.log( 'warning:', warning ); - return warningElem; - }, - - _render_visibleWarning : function(){ - //this.log( this + '_render_visibleWarning' ); - // Render warnings for hidden items (and link: unhide) - var warningElem = null; - if( !this.model.get( 'visible' ) && this.model.get( 'unhide_url' ) ){ - var warning = HistoryItemView.TEMPLATES.hiddenMsg( this.model.attributes ); - - // wrap it in the standard warning msg - warningElem = $( HistoryItemView.TEMPLATES.warningMsg({ warning: warning }) ); - } - //this.log( 'warning:', warning ); - return warningElem; + _render_warnings : function(){ + // jQ errs on building dom with whitespace - if there are no messages, trim -> '' + return $( jQuery.trim( HistoryItemView.templates.messages( this.model.toJSON() ) ) ); }, // ................................................................................ RENDER TITLEBAR @@ -292,23 +242,21 @@ //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(){ - // render the display icon-button - // show a disabled display if the data's been purged - if( this.model.get( 'purged' ) ){ - return $( '<span class="icon-button display_disabled tooltip" ' + - 'title="Cannot display datasets removed from disk"></span>' ); - } - var id = this.model.get( 'id' ), - displayBtnData = { - //TODO: localized title - title : 'Display data in browser', - //TODO: need generated url here - href : '/datasets/' + id + '/display/?preview=True', - target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( '' ), - classes : [ 'icon-button', 'tooltip', 'display' ], - dataset_id : id - }; - return $( linkHTMLTemplate( displayBtnData ) ); + displayBtnData = ( this.model.get( 'purged' ) )?({ + // show a disabled display if the data's been purged + title : 'Cannot display datasets removed from disk', + icon_class : 'display', + enabled : false, + }):({ + // if not, render the display icon-button with href + title : 'Display data in browser', + //TODO: need generated url here + href : this.model.get( 'display_url' ), + target : ( this.model.get( 'for_editing' ) )?( 'galaxy_main' ):( null ), + icon_class : 'display', + }); + this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); + return this.displayButton.render().$el; }, _render_editButton : function(){ @@ -317,44 +265,42 @@ purged = this.model.get( 'purged' ), deleted = this.model.get( 'deleted' ); + 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 ){ - if( !purged ){ - return $( '<span class="icon-button edit_disabled tooltip" ' + - 'title="Undelete dataset to edit attributes"></span>' ); - } else { - return $( '<span class="icon-button edit_disabled tooltip" ' + - 'title="Cannot edit attributes of datasets removed from disk"></span>' ); - } + editBtnData = { + enabled : false, + icon_class : 'edit' + }; + editBtnData.title = ( !purged )?( 'Undelete dataset to edit attributes' ): + ( 'Cannot edit attributes of datasets removed from disk' ); } - return $( linkHTMLTemplate({ - title : 'Edit attributes', - //TODO: need generated url here - href : '/datasets/' + id + '/edit', - target : 'galaxy_main', - classes : [ 'icon-button', 'tooltip', 'edit' ] - }) ); + this.editButton = new IconButtonView({ model : new IconButton( editBtnData ) }); + return this.editButton.render().$el; }, _render_deleteButton : function(){ - // render the delete icon-button - var id = this.model.get( 'id' ), - purged = this.model.get( 'purged' ), - deleted = this.model.get( 'deleted' ); - - //??: WHAAAA? can_edit == deleted?? - // yes! : (history_common.mako) can_edit=( not ( data.deleted or data.purged ) ) - if( purged || deleted ){ - return $( '<span title="Dataset is already deleted" ' + - 'class="icon-button delete_disabled tooltip"></span>' ); - } - return $( linkHTMLTemplate({ + if( !this.model.get( 'for_editing' ) ){ return null; } + + var deleteBtnData = ( this.model.get( 'delete_url' ) )?({ title : 'Delete', - //TODO: need generated url here - href : '/datasets/' + id + '/delete?show_deleted_on_refresh=False', + href : this.model.get( 'delete_url' ), target : 'galaxy_main', - id : 'historyItemDeleter-' + id, - classes : [ 'icon-button', 'tooltip', 'delete' ] - })); + id : 'historyItemDeleter-' + this.model.get( 'id' ), + icon_class : 'delete' + }):({ + title : 'Dataset is already deleted', + icon_class : 'delete', + enabled : false + }); + this.deleteButton = new IconButtonView({ model : new IconButton( deleteBtnData ) }); + return this.deleteButton.render().$el; }, _render_titleLink : function(){ @@ -441,7 +387,7 @@ }); warningMsgText += 'You may be able to ' + editLink + '.'; } - parent.append( $( HistoryItemView.TEMPLATES.warningMsg({ warning: warningMsgText }) ) ); + parent.append( $( HistoryItemView.templates.warningMsg({ warning: warningMsgText }) ) ); //...render the remaining body as STATES.OK (only diff between these states is the box above) this._render_body_ok( parent ); @@ -497,7 +443,8 @@ // if trans.user if( this.model.get( 'retag_url' ) && this.model.get( 'annotate_url' ) ){ - // tags, annotation buttons and display areas + // tag, annotate buttons + //TODO: move to tag, Annot MV var tagsAnnotationsBtns = $( '<div style="float: right;"></div>' ); tagsAnnotationsBtns.append( $( linkHTMLTemplate({ title : 'Edit dataset tags', @@ -514,17 +461,20 @@ actionBtnDiv.append( tagsAnnotationsBtns ); actionBtnDiv.append( '<div style="clear: both"></div>' ); - var tagArea = $( '<div class="tag-area" style="display: none">' ); - tagArea.append( '<strong>Tags:</strong>' ); - tagArea.append( '<div class="tag-elt"></div>' ); - actionBtnDiv.append( tagArea ); + // tag/annot display areas + this.tagArea = $( '<div class="tag-area" style="display: none">' ); + this.tagArea.append( '<strong>Tags:</strong>' ); + this.tagElt = $( '<div class="tag-elt"></div>' ); + actionBtnDiv.append( this.tagArea.append( this.tagElt ) ); var annotationArea = $( ( '<div id="${dataset_id}-annotation-area"' + ' class="annotation-area" style="display: none">' ) ); + this.annotationArea = annotationArea; annotationArea.append( '<strong>Annotation:</strong>' ); - annotationArea.append( ( '<div id="${dataset_id}-annotation-elt" ' + 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>' ) ); + + 'title="Edit dataset annotation"></div>' ); + annotationArea.append( this.annotationElem ); actionBtnDiv.append( annotationArea ); } } @@ -564,10 +514,10 @@ }, _render_body : function(){ - this.log( this + '_render_body' ); + //this.log( this + '_render_body' ); var state = this.model.get( 'state' ), for_editing = this.model.get( 'for_editing' ); - this.log( 'state:', state, 'for_editing', for_editing ); + //this.log( 'state:', state, 'for_editing', for_editing ); //TODO: incorrect id (encoded - use hid?) var body = $( '<div/>' ) @@ -708,10 +658,86 @@ // ................................................................................ EVENTS events : { - 'click .historyItemTitle' : 'toggleBodyVisibility' + 'click .historyItemTitle' : 'toggleBodyVisibility', + 'click a.icon-button.tags' : 'loadAndDisplayTags', + 'click a.icon-button.annotate' : 'loadAndDisplayAnnotation' }, // ................................................................................ STATE CHANGES / MANIPULATION + loadAndDisplayTags : function( event ){ + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this, '.loadAndDisplayTags', event ); + var tagArea = this.tagArea; + var tagElt = this.tagElt; + + // Show or hide tag area; if showing tag area and it's empty, fill it. + if( tagArea.is( ":hidden" ) ){ + if( !tagElt.html() ){ + // Need to fill tag element. + $.ajax({ + url: this.model.get( 'ajax_get_tag_url' ), + error: function() { alert( "Tagging failed" ) }, + success: function(tag_elt_html) { + console.debug( 'tag_elt_html:', tag_elt_html ); + tagElt.html(tag_elt_html); + tagElt.find(".tooltip").tooltip(); + tagArea.slideDown("fast"); + } + }); + } else { + // Tag element is filled; show. + tagArea.slideDown("fast"); + } + + } else { + // Hide. + tagArea.slideUp("fast"); + } + return false; + }, + + loadAndDisplayAnnotation : function( event ){ + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this, '.loadAndDisplayAnnotation', event ); + var annotationArea = this.annotationArea, + annotationElem = this.annotationElem, + setAnnotationUrl = this.model.get( 'ajax_set_annotation_url' ); + + // Show or hide annotation area; if showing annotation area and it's empty, fill it. + this.log( 'annotationArea hidden:', annotationArea.is( ":hidden" ) ); + this.log( 'annotationElem html:', annotationElem.html() ); + if ( annotationArea.is( ":hidden" ) ){ + if( !annotationElem.html() ){ + // Need to fill annotation element. + $.ajax({ + url: this.model.get( 'ajax_get_annotation_url' ), + error: function(){ alert( "Annotations failed" ) }, + success: function( htmlFromAjax ){ + if( htmlFromAjax === "" ){ + htmlFromAjax = "<em>Describe or add notes to dataset</em>"; + } + annotationElem.html( htmlFromAjax ); + annotationArea.find(".tooltip").tooltip(); + + async_save_text( + annotationElem.attr("id"), annotationElem.attr("id"), + setAnnotationUrl, + "new_annotation", 18, true, 4 + ); + annotationArea.slideDown("fast"); + } + }); + } else { + annotationArea.slideDown("fast"); + } + + } else { + // Hide. + annotationArea.slideUp("fast"); + } + return false; + }, + toggleBodyVisibility : function(){ this.log( this + '.toggleBodyVisibility' ); this.$el.find( '.historyItemBody' ).toggle(); @@ -723,30 +749,8 @@ return 'HistoryItemView(' + modelString + ')'; } }); - -//------------------------------------------------------------------------------ HistoryItemView.TEMPLATES = {}; -//TODO: move next one out - doesn't belong -HistoryItemView.TEMPLATES.warningMsg = - _.template( '<div class=warningmessagesmall><strong><%= warning %></strong></div>' ); - - -//??TODO: move into functions? -HistoryItemView.TEMPLATES.undeleteLink = _.template( - 'This dataset has been deleted. ' + - 'Click <a href="<%= undelete_url %>" class="historyItemUndelete" id="historyItemUndeleter-{{ id }}" ' + - ' target="galaxy_history">here</a> to undelete it.' ); - -HistoryItemView.TEMPLATES.purgeLink = _.template( - ' or <a href="<%= purge_url %>" class="historyItemPurge" id="historyItemPurger-{{ id }}"' + - ' target="galaxy_history">here</a> to immediately remove it from disk.' ); - -HistoryItemView.TEMPLATES.hiddenMsg = _.template( - 'This dataset has been hidden. ' + - 'Click <a href="<%= unhide_url %>" class="historyItemUnhide" id="historyItemUnhider-{{ id }}" ' + - ' target="galaxy_history">here</a> to unhide it.' ); - //TODO: contains localized strings HistoryItemView.TEMPLATES.hdaSummary = _.template([ '<%= misc_blurb %><br />', @@ -754,13 +758,18 @@ 'database: <%= dbkeyHTML %>' ].join( '' )); - -//------------------------------------------------------------------------------ -HistoryItemView.STRINGS = {}; -HistoryItemView.STRINGS.purgedMsg = HistoryItemView.TEMPLATES.warningMsg( - { warning: 'This dataset has been deleted and removed from disk.' }); - +//============================================================================== +//HistoryItemView.templates = InDomTemplateLoader.getTemplates({ +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({ @@ -773,10 +782,10 @@ //============================================================================== -var History = LoggingModel.extend({ +var History = BaseModel.extend( LoggableMixin ).extend({ // uncomment this out see log messages - logger : console, + //logger : console, // values from api (may need more) defaults : { @@ -867,11 +876,11 @@ }); //------------------------------------------------------------------------------ -var HistoryView = LoggingView.extend({ +var HistoryView = BaseView.extend( LoggableMixin ).extend({ // view for the HistoryCollection (as per current right hand panel) // uncomment this out see log messages - logger : console, + //logger : console, // direct attachment to existing element el : 'body.historyPage', @@ -908,8 +917,7 @@ //============================================================================== -//USE_MOCK_DATA = true; -if( window.USE_MOCK_DATA ){ +function createMockHistoryData(){ mockHistory = {}; mockHistory.data = { @@ -986,6 +994,7 @@ notvisible : _.extend( _.clone( mockHistory.data.template ), { visible : false }), + hasDisplayApps : _.extend( _.clone( mockHistory.data.template ), { display_apps : { @@ -1041,7 +1050,8 @@ failed_metadata : _.extend( _.clone( mockHistory.data.template ), { state : HistoryItem.STATES.FAILED_METADATA }) - +/* +*/ }); $( document ).ready( function(){ diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/tags.js --- /dev/null +++ b/static/scripts/mvc/tags.js @@ -0,0 +1,66 @@ +/*============================================================================== +Backbone MV for Tags + + +TODO: +move rendering from tagging_common.py +move functionality from controllers/tag.py +?? - polymorph on class or simply class as attr? + +==============================================================================*/ +/** Single Tag model + */ +var Tag = BaseModel.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + defaults : { + id : null, + itemClass : null + }, + + toString : function(){ + return 'Tag()'; + } +}); + +//------------------------------------------------------------------------------ +/** Single Tag view + */ +var TagView = BaseView.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'TagView()'; + } +}); + +//============================================================================== +/** A collection of Tags + */ +var TagCollection = Backbone.Collection.extend( LoggableMixin ).extend({ + model : Tag, + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'TagCollection()'; + } +}); + +//------------------------------------------------------------------------------ +/** View for a TagCollection (and it's controls) - as per an hda's tag controls on the history panel + */ +var TagList = BaseView.extend( LoggableMixin ).extend({ + + // uncomment this out see log messages + logger : console, + + toString : function(){ + return 'TagList()'; + } +}); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -1,41 +1,12 @@ /** * -- Functions for creating large UI elements. -- */ - -/** - * Returns an IconButtonMenuView for the provided configuration. - * Configuration is a list of dictionaries where each dictionary - * defines an icon button. Each dictionary must have the following - * elements: icon_class, title, and on_click. - */ -var create_icon_buttons_menu = function(config, global_config) { - if (!global_config) { global_config = {}; } - - // Create and initialize menu. - var buttons = new IconButtonCollection( - _.map(config, function(button_config) { - return new IconButton(_.extend(button_config, global_config)); - }) - ); - - return new IconButtonMenuView( {collection: buttons} ); -}; - +// ============================================================================= /** * -- Utility models and views for Galaxy objects. -- */ /** - * Necessary Galaxy paths. - */ -var GalaxyPaths = Backbone.Model.extend({ - defaults: { - root_path: "", - image_path: "" - } -}); - -/** * Clickable button represented as an icon. */ var IconButton = Backbone.Model.extend({ @@ -43,14 +14,107 @@ title: "", icon_class: "", on_click: null, - tooltip_config: {} + tooltip_config: {}, + + isMenuButton : true, + id : null, + href : null, + target : null, + enabled : true, + visible : true + } + + //validate : function( attributes ){ + //TODO: validate href or on_click + //TODO: validate icon_class + //} +}); + + +/** + * + */ +var IconButtonView = Backbone.View.extend({ + tagName : 'a', + className : 'icon-button', + + // jsHint.shut( up ) + hrefVoidFn : [ 'javascript', ':void(0)' ].join( '' ), + fadeSpeed : 0, + + initialize : function(){ + // better rendering this way (for me anyway) + this.model.attributes.tooltip_config = { placement : 'bottom' }; + this.model.bind( 'change', this.render, this ); + }, + + render : function(){ + //NOTE: this is meant to be rerendered on a model change + // - since most of the rendering is attributes, it gets complicated + //TODO: template would be faster, more concise - more PITA + var disabled_class = this.model.attributes.icon_class + '_disabled'; + + if( !this.model.attributes.visible ){ + //TODO: fancy - but may not work as you expect + this.$el.fadeOut( this.fadeSpeed ); + } + + if( this.model.attributes.enabled ){ + if( this.$el.hasClass( disabled_class ) ){ + this.$el.removeClass( disabled_class ); + } + this.$el.addClass( this.model.attributes.icon_class ); + } else { + this.$el.removeClass( this.model.attributes.icon_class ); + this.$el.addClass( disabled_class ); + } + + if( this.model.attributes.isMenuButton ){ + this.$el.addClass( 'menu-button' ); + } else { + this.$el.removeClass( 'menu-button' ); + } + + this.$el.data( 'tooltip', false ); + this.$el.attr( 'data-original-title', null ); + this.$el.removeClass( 'tooltip' ); + if( this.model.attributes.title ){ + this.$el.attr( 'title', this.model.attributes.title ).addClass( 'tooltip' ); + this.$el.tooltip( this.model.attributes.tooltip_config ); + } + + this.$el.attr( 'id', ( this.model.attributes.id )?( this.model.attributes.id ):( null ) ); + this.$el.attr( 'target', ( this.model.attributes.target )?( this.model.attributes.target ):( null ) ); + this.$el.attr( 'href', ( this.model.attributes.href && !this.model.attributes.on_click )? + ( this.model.attributes.href ):( this.hrefVoidFn ) ); + + if( this.model.attributes.visible ){ + this.$el.fadeIn( this.fadeSpeed ); + } + return this; + }, + + events : { + 'click' : 'click' + }, + + click : function( event ){ + // if on_click pass to that function + if( this.model.attributes.on_click ){ + this.model.attributes.on_click( event ); + return false; + } + // otherwise, bubble up (to href or whatever) + return true; } }); + var IconButtonCollection = Backbone.Collection.extend({ model: IconButton }); +//------------------------------------------------------------------------------ /** * Menu with multiple icon buttons. Views are not needed nor used for individual buttons. */ @@ -82,6 +146,27 @@ }); /** + * Returns an IconButtonMenuView for the provided configuration. + * Configuration is a list of dictionaries where each dictionary + * defines an icon button. Each dictionary must have the following + * elements: icon_class, title, and on_click. + */ +var create_icon_buttons_menu = function(config, global_config) { + if (!global_config) { global_config = {}; } + + // Create and initialize menu. + var buttons = new IconButtonCollection( + _.map(config, function(button_config) { + return new IconButton(_.extend(button_config, global_config)); + }) + ); + + return new IconButtonMenuView( {collection: buttons} ); +}; + + +// ============================================================================= +/** * */ var Grid = Backbone.Collection.extend({ @@ -95,4 +180,101 @@ }); +// ============================================================================= +/** + * Necessary Galaxy paths. + */ +var GalaxyPaths = Backbone.Model.extend({ + defaults: { + root_path: "", + image_path: "" + } +}); +// ============================================================================= +/** Global string localization object (and global short form alias) + * set with either: + * GalaxyLocalization.setLocalizedString( original, localized ) + * GalaxyLocalization.setLocalizedString({ original1 : localized1, original2 : localized2 }) + * get with either: + * _l( original ) + */ +//TODO: move to Galaxy.Localization +var GalaxyLocalization = jQuery.extend({}, { + aliasName : '_l', + localizedStrings : {}, + + setLocalizedString : function( str_or_obj, localizedString ){ + // pass in either two strings (english, translated) or an obj (map) of english : translated attributes + //console.debug( this + '.setLocalizedString:', str_or_obj, localizedString ); + var self = this; + + // DRY non-duplicate assignment function + var setStringIfNotDuplicate = function( original, localized ){ + // do not set if identical - strcmp expensive but should only happen once per page per word + if( original !== localized ){ + self.localizedStrings[ original ] = localized; + } + }; + + if( jQuery.type( str_or_obj ) === "string" ){ + setStringIfNotDuplicate( str_or_obj, localizedString ); + + } else if( jQuery.type( str_or_obj ) === "object" ){ + jQuery.each( str_or_obj, function( key, val ){ + //console.debug( 'key=>val', key, '=>', val ); + // could recurse here but no reason + setStringIfNotDuplicate( key, val ); + }); + + } else { + throw( 'Localization.setLocalizedString needs either a string or object as the first argument,' + + ' given: ' + str_or_obj ); + } + }, + + localize : function( strToLocalize ){ + //console.debug( this + '.localize:', strToLocalize ); + // return the localized version if it's there, the strToLocalize if not + // try/catch cheaper than if in + try { + //var localized = this.localizedStrings[ strToLocalize ]; + //return localized; + return this.localizedStrings[ strToLocalize ]; + } catch( err ){ + //TODO??: potentially problematic catch all + //console.error( err ); + return strToLocalize; + } + }, + + toString : function(){ return 'GalaxyLocalization'; } +}); + +// global localization alias +window[ GalaxyLocalization.aliasName ] = function( str ){ return GalaxyLocalization.localize( str ); }; + +//TEST: setLocalizedString( string, string ), _l( string ) +//TEST: setLocalizedString( hash ), _l( string ) +//TEST: setLocalizedString( string === string ), _l( string ) +//TEST: _l( non assigned string ) + + +// ============================================================================= +/** UI icon-button (Backbone.View only - no model) + * + */ + + + + + + + + + + + + + + diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/common-templates.html --- /dev/null +++ b/static/scripts/templates/common-templates.html @@ -0,0 +1,3 @@ +<script type="text/template" class="template-common" id="template-warningmessagesmall"> + <div class=warningmessagesmall><strong>{{{warning}}}</strong></div> +</script> diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compile_templates.py --- a/static/scripts/templates/compile_templates.py +++ b/static/scripts/templates/compile_templates.py @@ -3,24 +3,274 @@ # Script requires handlebars compiler be installed; use node package manager # to install handlebars. +"""%prog [options] [ specific .handlebars or .html template file to compile ] + Compiles handlebars templates into javascript for better load times and performance. + + Handlebars compilation errors will print to stderr. + NOTE!: you will need node.js, npm, and handlebars (installed from npm) in order to compile templates + See http://handlebarsjs.com/precompilation.html for more info. + + Should be called from the $GLX_ROOT/static/scripts/templates directory. + Compiled templates will be written to the compiled/ directory. + + If the --multi-ext option is passed a file extension string, the script will: + * search for *.<extension> in the current directory, + * extract each '<script type="text/template"> from the file and write them into a new handlebars file + named using the id of the script tag (eg. id="undeleteMsg" -> undeleteMsg.handlebars) + * these new handlebars scripts will be compiled along with any other handlebars templates in the dir + + additionally for each of those files, the script will: + * extract each '<script type="text/javascript"> from the file and write them ALL into a single js file + named using the prefix 'helpers-' and the basename of the enclosing file + (eg. common-templates.html -> helpers-common-templates.js ) + * these new handlebars scripts will be compiled along with any other handlebars templates in the dir + These files can be included as if they were templates (eg. h.templates( 'helpers-common-templates' ) ) + + This hopefully will allow both multiple templates and their associated Handlebars helper functions to be + included in one file. + + Currently, this works (best?) if: + * the multiple templates are within one html file + * each template is enclosed in a <script> tag with type="text/template" and some id attribute + * each helper fn is enclosed in a <script> tag with type="text/javascript" and some id attribute + e.g. <script type="text/template" id="history-deletedMsg" class="template">Deleted {{ msg }}</script> + +""" +# ------------------------------------------------------------------------------ + +TODO = """ +""" + import sys from glob import glob from subprocess import call from shutil import copyfile from os import path +from optparse import OptionParser +from HTMLParser import HTMLParser -cmd = "handlebars %s -f compiled/%s.js" +import logging +log = logging.getLogger( __name__ ) -# If specific scripts specified on command line, just pack them, otherwise pack -# all. +COMPILED_DIR = 'compiled' +COMPILED_EXT = '.js' +COMPILE_CMD_STR = "handlebars %s -f %s" +COMPILE_MINIMIZE_SWITCH = ' -m' -if len( sys.argv ) > 1: - to_pack = sys.argv[1:] -else: - to_pack = glob( "*.handlebars" ) +# both of these are off by default for backward compat +DEFAULT_MINIMIZATION = False +DEFAULT_MULTI_EXT = None #'.html' + +# ------------------------------------------------------------------------------ +class HTMLMultiTemplateParser( HTMLParser ): + """Parses multiple templates from an HTML file, saving them to a map of: + { id : template_text, ... } + + Templates must: + * be within the TEMPLATE_TAG + * TEMPLATE_TAG must have a type attribute + * that attr must == TEMPLATE_TYPE + * TEMPLATE_TAG cannot be nested within one another + * TEMPLATE_TAG must have an id attribute + """ + TEMPLATE_TAG = 'script' + TEMPLATE_TYPES = [ 'text/template' ] -for fname in to_pack: - fname_base = path.splitext( path.split( fname )[1] )[0] - print "%s --> compiled/%s.js" % ( fname, fname_base ) - out = call( cmd % ( fname, fname_base ), shell=True ) + HELPER_TAG = 'script' + HELPER_TYPES = [ 'text/javascript' ] + + def __init__( self ): + HTMLParser.__init__( self ) + self.templates = {} + self.curr_template_id = None + self.template_data = '' + + self.helpers = {} + self.curr_helper_id = None + self.helper_data = '' + + def is_template_tag( self, tag, attr_dict ): + # both tag and type attr must match + return ( ( tag == self.TEMPLATE_TAG ) + and ( 'type' in attr_dict ) + and ( attr_dict[ 'type' ] in self.TEMPLATE_TYPES ) ) + + def is_helper_tag( self, tag, attr_dict ): + # both tag and type attr must match + return ( ( tag == self.HELPER_TAG ) + and ( 'type' in attr_dict ) + and ( attr_dict[ 'type' ] in self.HELPER_TYPES ) ) + + def handle_starttag( self, tag, attrs ): + attr_dict = dict( attrs ) + if self.is_template_tag( tag, attr_dict ): + log.debug( "\t template tag: %s, %s", tag, str( attr_dict ) ); + + # as far as I know these tags can't/shouldn't nest/overlap + #pre: not already inside a template/helper tag + assert self.curr_template_id == None, "Found nested template tag: %s" % ( self.curr_template_id ) + assert self.curr_helper_id == None, "Found template tag inside helper: %s" % ( self.curr_helper_id ) + #pre: must have an id + assert 'id' in attr_dict, "No id attribute in template: " + str( attr_dict ) + + self.curr_template_id = attr_dict[ 'id' ] + + elif self.is_helper_tag( tag, attr_dict ): + log.debug( "\t helper tag: %s, %s", tag, str( attr_dict ) ); + + #pre: not already inside a template/helper tag + assert self.curr_helper_id == None, "Found nested helper tag: %s" % ( self.curr_helper_id ) + assert self.curr_template_id == None, "Found helper tag inside template: %s" % ( self.curr_template_id ) + #pre: must have an id + assert 'id' in attr_dict, "No id attribute in helper: " + str( attr_dict ) + + self.curr_helper_id = attr_dict[ 'id' ] + + def handle_endtag( self, tag ): + if( ( tag == self.TEMPLATE_TAG ) + and ( self.curr_template_id ) ): + log.debug( "\t ending template tag :", tag, self.curr_template_id ); + + # store the template data by the id + if self.template_data: + self.templates[ self.curr_template_id ] = self.template_data + + #! reset for next template + self.curr_template_id = None + self.template_data = '' + + elif( ( tag == self.HELPER_TAG ) + and ( self.curr_helper_id ) ): + log.debug( "\t ending helper tag :", tag, self.curr_template_id ); + + # store the template data by the id + if self.helper_data: + self.helpers[ self.curr_helper_id ] = self.helper_data + + #! reset for next template + self.curr_helper_id = None + self.helper_data = '' + + def handle_data(self, data): + data = data.strip() + if data: + if self.curr_template_id: + log.debug( "\t template text :", data ); + self.template_data += data + + elif self.curr_helper_id: + log.debug( "\t helper js fn :", data ); + self.helper_data += data + + +# ------------------------------------------------------------------------------ +def break_multi_template( multi_template_filename ): + """parse the multi template, writing each template into a new handlebars tmpl and returning their names""" + template_filenames = [] + parser = HTMLMultiTemplateParser() + + # parse the multi template + print "\nBreaking multi-template file %s into individual templates and helpers:" % ( multi_template_filename ) + with open( multi_template_filename, 'r' ) as multi_template_file: + # wish I could use a gen here + parser.feed( multi_template_file.read() ) + + # after breaking, write each indiv. template and save the names + for template_id, template_text in parser.templates.items(): + handlebar_template_filename = template_id + '.handlebars' + with open( handlebar_template_filename, 'w' ) as handlebar_template_file: + handlebar_template_file.write( template_text ) + + template_filenames.append( handlebar_template_filename ) + + # write all helpers to a 'helper-' prefixed js file in the compilation dir + if parser.helpers: + helper_filename = 'helpers-' + path.splitext( multi_template_filename )[0] + '.js' + helper_filename = path.join( COMPILED_DIR, helper_filename ) + with open( helper_filename, 'w' ) as helper_file: + for helper_fn_name, helper_fn in parser.helpers.items(): + print '(helper)', helper_fn_name + helper_file.write( helper_fn + '\n' ) + + print '\n'.join( template_filenames ) + return template_filenames + + +# ------------------------------------------------------------------------------ +def compile_template( template_filename, minimize=False ): + """compile the given template file (optionally minimizing the js) using subprocess. + + Use the basename of the template file for the outputed js. + """ + template_basename = path.splitext( path.split( template_filename )[1] )[0] + compiled_filename = path.join( COMPILED_DIR, template_basename + COMPILED_EXT ) + + command_string = COMPILE_CMD_STR % ( template_filename, compiled_filename ) + if minimize: + command_string += COMPILE_MINIMIZE_SWITCH + print command_string + return call( command_string, shell=True ) + + +# ------------------------------------------------------------------------------ +def main( options, args ): + """Break multi template files into single templates, compile all single templates. + + If args, compile that as a list of specific handlebars and/or multi template files. + """ + print "(Call this script with the '-h' option for more help)" + + handlebars_templates = [] + # If specific scripts specified on command line, just compile them, + if len( args ) >= 1: + handlebars_templates = filter( lambda( x ): x.endswith( '.handlebars' ), args ) + + # otherwise compile all in the current dir + else: + handlebars_templates = glob( '*.handlebars' ) + + # if desired, break up any passed-in or found multi template files + # adding the names of the new single templates to those needing compilation + if options.multi_ext: + multi_templates = [] + if len( args ) >= 1: + multi_templates = filter( lambda( x ): x.endswith( options.multi_ext ), args ) + else: + multi_templates = glob( '*' + options.multi_ext ) + + for multi_template_filename in multi_templates: + handlebars_templates.extend( break_multi_template( multi_template_filename ) ) + + # unique filenames only (Q&D) + handlebars_templates = list( set( handlebars_templates ) ) + + # compile the templates + print "\nCompiling templates:" + filenames_w_possible_errors = [] + for handlebars_template in handlebars_templates: + shell_ret = compile_template( handlebars_template, options.minimize ) + if shell_ret: + filenames_w_possible_errors.append( handlebars_template ) + + # report any possible errors + if filenames_w_possible_errors: + print "\nThere may have been errors on the following files:" + print ',\n'.join( filenames_w_possible_errors ) + print "\nCall this script with the '-h' for more help" + + +# ------------------------------------------------------------------------------ +if __name__ == '__main__': + optparser = OptionParser( usage=__doc__ ) + optparser.add_option( '-m', '--minimize', dest='minimize', action='store_true', default=DEFAULT_MINIMIZATION, + help=( 'minimize compiled template scripts via handlebars ' + + '(defaults to %s)' % DEFAULT_MINIMIZATION ) ) + optparser.add_option( '--multi-ext', dest='multi_ext', metavar="FILE_EXTENSION", default=DEFAULT_MULTI_EXT, + help=( 'indicates that files ending with the given string contain multiple ' + + 'templates and the script should break those into individual ' + + 'handlebars templates (defaults to "%s")' ) % DEFAULT_MULTI_EXT ) + + ( options, args ) = optparser.parse_args() + sys.exit( main( options, args ) ) + \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compiled/template-history-hdaSummary.js --- /dev/null +++ b/static/scripts/templates/compiled/template-history-hdaSummary.js @@ -0,0 +1,25 @@ +(function() { + 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; + + + foundHelper = helpers.misc_blurb; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "<br />\nformat: <span class=\""; + 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) + "\">"; + 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); + return buffer;}); +})(); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compiled/template-history-warning-messages.js --- /dev/null +++ b/static/scripts/templates/compiled/template-history-warning-messages.js @@ -0,0 +1,87 @@ +(function() { + 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; + +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;} +function program2(depth0,data) { + + var buffer = "", stack1, foundHelper; + 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; } + buffer += escapeExpression(stack1) + "\" class=\"historyItemUndelete\" id=\"historyItemUndeleter-"; + 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 "; + stack1 = depth0.purge_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 or\n <a href=\""; + foundHelper = helpers.purge_url; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.purge_url; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" class=\"historyItemPurge\" id=\"historyItemPurger-"; + 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 immediately remove it from disk\n "; + return buffer;} + +function program5(depth0,data) { + + + return "\n<div class=warningmessagesmall><strong>\nThis dataset has been deleted and removed from disk.\n</strong></div>\n";} + +function program7(depth0,data) { + + var buffer = "", stack1; + buffer += "\n<div class=warningmessagesmall><strong>\nThis 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)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</strong></div>\n"; + return buffer;} +function program8(depth0,data) { + + var buffer = "", stack1, foundHelper; + 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; } + buffer += escapeExpression(stack1) + "\" class=\"historyItemUnhide\" id=\"historyItemUnhider-"; + 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 "; + return buffer;} + + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + 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)}); + 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)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + return buffer;}); +})(); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/compiled/template-warningmessagesmall.js --- /dev/null +++ b/static/scripts/templates/compiled/template-warningmessagesmall.js @@ -0,0 +1,15 @@ +(function() { + 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"; + + + buffer += "<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>"; + return buffer;}); +})(); \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/history-templates.html --- /dev/null +++ b/static/scripts/templates/history-templates.html @@ -0,0 +1,38 @@ +<script type="text/template" class="template-history" id="template-history-warning-messages"> +{{#if deleted}} +<div class=warningmessagesmall><strong> +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 + {{#if purge_url}} + 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}} + +{{#if purged}} +<div class=warningmessagesmall><strong> +This dataset has been deleted and removed from disk. +</strong></div> +{{/if}} + +{{#unless visible}} +<div class=warningmessagesmall><strong> +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 + {{/if}} +</strong></div> +{{/unless}} +</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 }} +</script> diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/template-history-hdaSummary.handlebars --- /dev/null +++ b/static/scripts/templates/template-history-hdaSummary.handlebars @@ -0,0 +1,3 @@ +{{ misc_blurb }}<br /> +format: <span class="{{ data_type }}">{{ data_type }}</span>, ', +database: {{ dbkeyHTML }} \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/template-history-warning-messages.handlebars --- /dev/null +++ b/static/scripts/templates/template-history-warning-messages.handlebars @@ -0,0 +1,30 @@ +{{#if deleted}} +<div class=warningmessagesmall><strong> +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 + {{#if purge_url}} + 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}} + +{{#if purged}} +<div class=warningmessagesmall><strong> +This dataset has been deleted and removed from disk. +</strong></div> +{{/if}} + +{{#unless visible}} +<div class=warningmessagesmall><strong> +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 + {{/if}} +</strong></div> +{{/unless}} \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 static/scripts/templates/template-warningmessagesmall.handlebars --- /dev/null +++ b/static/scripts/templates/template-warningmessagesmall.handlebars @@ -0,0 +1,1 @@ +<div class=warningmessagesmall><strong>{{{warning}}}</strong></div> \ No newline at end of file diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -26,7 +26,18 @@ ##  - ${h.js( "libs/jquery/jquery", "libs/bootstrap", "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", "mvc/ui" )} + + ${h.js( + "libs/jquery/jquery", + "libs/bootstrap", + "galaxy.base", + "libs/underscore", + "libs/backbone/backbone", + "libs/backbone/backbone-relational", + "libs/handlebars.runtime", + "mvc/ui" + )} + <script type="text/javascript"> // Set up needed paths. var galaxy_paths = new GalaxyPaths({ diff -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -54,7 +54,7 @@ <%def name="get_urls_for_hda( hda, encoded_data_id, for_editing )"><% from galaxy.datatypes.metadata import FileParameter - + data_dict = {} def add_to_data( **kwargs ): data_dict.update( kwargs ) @@ -79,7 +79,10 @@ #TODO??: better way to do urls (move into js galaxy_paths (decorate) - _not_ dataset specific) deleted = hda.deleted - purged = hda.purged or hda.dataset.purged + purged = hda.purged + + #purged = purged or hda.dataset.purged //?? + # all of these urls are 'datasets/data_id/<action> if not ( dataset_purged or purged ) and for_editing: add_to_data( undelete_url=h.url_for( controller='dataset', action='undelete', dataset_id=encoded_data_id ) ) @@ -106,7 +109,21 @@ display_url = h.url_for( controller='dataset', action='display', dataset_id=encoded_data_id, preview=True, filename='' ) add_to_data( display_url=display_url ) - if app.config.get_bool( 'enable_tracks', False ) and hda.ext in app.datatypes_registry.get_available_tracks(): + # edit attr button + if for_editing: + if not( hda.deleted or hda.purged ): + edit_url = h.url_for( controller='dataset', action='edit', dataset_id=encoded_data_id ) + 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 ) ) + ##TODO: loose end + ##show_deleted_on_refresh=show_deleted_on_refresh ) ) + #show_deleted_on_refresh=False ) ) + + #print app + if hda.ext in app.datatypes_registry.get_available_tracks(): # do these need _localized_ dbkeys? trackster_urls = {} if hda.dbkey != '?': @@ -117,11 +134,21 @@ trackster_urls[ 'hda-url' ] = data_url trackster_urls[ 'action-url' ] = h.url_for( controller='tracks', action='browser', dataset_id=encoded_data_id ) trackster_urls[ 'new-url' ] = h.url_for( controller='tracks', action='index', dataset_id=encoded_data_id, default_dbkey=hda.dbkey ) - add_to_data( trackster_url=trackster_url ) + add_to_data( trackster_url=trackster_urls ) if trans.user: - add_to_data( retag_url=( h.url_for( controller='tag', action='retag', item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) + add_to_data( ajax_get_tag_url=( h.url_for( + controller='tag', action='get_tagging_elt_async', + item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) + add_to_data( retag_url=( h.url_for( + controller='tag', action='retag', + item_class=hda.__class__.__name__, item_id=encoded_data_id ) ) ) + add_to_data( annotate_url=( h.url_for( controller='dataset', action='annotate', id=encoded_data_id ) ) ) + add_to_data( ajax_get_annotation_url=( h.url_for( + controller='dataset', action='get_annotation_async', id=encoded_data_id ) ) ) + add_to_data( ajax_set_annotation_url=( h.url_for( + controller='/dataset', action='annotate_async', id=encoded_data_id ) ) ) display_type_display_links = {} #TODO: this doesn't seem to get called with the hda I'm using. What would call this? How can I spoof it? @@ -182,8 +209,8 @@ data_dict.update( kwargs ) # trans + add_to_data( non_encoded_id=data.id ) encoded_data_id = trans.security.encode_id( data.id ) - #print data.name, encoded_data_id add_to_data( id=encoded_data_id ) # localize dbkey @@ -205,8 +232,8 @@ add_to_data( accessible=accessible ) url_dict = get_urls_for_hda( data, encoded_data_id, for_editing ) + data_dict.update( url_dict ) #print 'url_dict:', pformat( url_dict, indent=2 ) - data_dict.update( url_dict ) #print 'data_dict:', pformat( data_dict, indent=2 ), "\n" #print data_dict @@ -227,7 +254,7 @@ user_is_admin = trans.user_is_admin() user_roles = trans.get_current_user_roles() prepped_hdas = [ - prep_hda( hda, true ) for hda in datasets ] + prep_hda( hda, True ) for hda in datasets ] context_dict = { 'history' : { @@ -257,74 +284,66 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.templates( "tool_link", "panel_section", "tool_search" )} - ${h.js( "galaxy.base", "json2", "autocomplete_tagging", "bootstrap", "mvc/tools", "mvc/history" )} + + ${h.js( + "libs/json2", "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", + ##"libs/handlebars.full", + "galaxy.autocom_tagging", + "mvc/base-mvc", "mvc/ui" + )} + + ${h.templates( + "helpers-common-templates", + "template-warningmessagesmall", + + "template-history-warning-messages", + "template-history-hdaSummary" + )} + + ## if using in-dom templates they need to go here (before the Backbone classes are defined) + ##NOTE: it's impossible(?) to include _ templates in this way bc they use identical delims as mako + ## (without altering Underscore.templateSettings) + ##<%include file="../../static/scripts/templates/common-templates.html" /> + ##<%include file="../../static/scripts/templates/history-templates.html" /> + + ${h.js( + "mvc/history" + ##"mvc/tags", "mvc/annotations" + )} <script type="text/javascript"> - ##//var localization = local( ${ create_localization_json( get_page_localized_strings() ) } ); + GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); + // add needed controller urls to GalaxyPaths + galaxy_paths.set( 'dataset_path', "${h.url_for( controller='dataset' )}" ) + // Init. on document load. var pageData = ${context_to_js()}; - // add needed controller urls to GalaxyPaths - galaxy_paths.set( 'dataset_path', "${h.url_for( controller='dataset' )}" ) + //USE_MOCK_DATA = true; $(function(){ if( console && console.debug ){ console.debug( 'using backbone.js in history panel' ); } - if( window.USE_MOCK_DATA ){ return; } + if( window.USE_MOCK_DATA ){ + if( console && console.debug ){ console.debug( '\t using mock data' ); } + createMockHistoryData(); + return; + } glx_history = new History( pageData.history ).loadDatasetsAsHistoryItems( pageData.hdas ); glx_history_view = new HistoryView({ model: glx_history }); glx_history_view.render(); - //hi = glx_history.items.at( 0 ); - //hi_view = new HistoryItemView({ model: hi }); - //$( 'body' ).append( hi_view.render() ); + hi = glx_history.items.at( 0 ); + hi_view = new HistoryItemView({ model: hi }); + $( 'body' ).append( hi_view.render() ); }); </script> - - <script type='text/javascript'> -function tag_handling(parent_elt) { - $(parent_elt).find("a.icon-button.tags").each( function() { - // Use links parameters but custom URL as ajax URL. - $(this).click( function() { - // Get tag area, tag element. - var history_item = $(this).parents(".historyItem"); - var tag_area = history_item.find(".tag-area"); - var tag_elt = history_item.find(".tag-elt"); - - // Show or hide tag area; if showing tag area and it's empty, fill it. - if ( tag_area.is( ":hidden" ) ) { - if (!tag_elt.html()) { - // Need to fill tag element. - var href_parms = $(this).attr("href").split("?")[1]; - var ajax_url = "${h.url_for( controller='tag', action='get_tagging_elt_async' )}?" + href_parms; - $.ajax({ - url: ajax_url, - error: function() { alert( "Tagging failed" ) }, - success: function(tag_elt_html) { - tag_elt.html(tag_elt_html); - tag_elt.find(".tooltip").tooltip(); - tag_area.slideDown("fast"); - } - }); - } else { - // Tag element is filled; show. - tag_area.slideDown("fast"); - } - } else { - // Hide. - tag_area.slideUp("fast"); - } - return false; - }); - }); -}; - </script></%def><%def name="stylesheets()"> ${parent.stylesheets()} - <style> + ${h.css("base", "history", "autocomplete_tagging" )} + <style>" .historyItemBody { display: none; } https://bitbucket.org/galaxy/galaxy-central/changeset/e2cb958b3f75/ changeset: e2cb958b3f75 user: carlfeberhard date: 2012-09-12 17:09:09 summary: clean debug statements from history.js affected #: 1 file diff -r ce64f5d64ff4a55d85bd0e9ba2c3ec712357c115 -r e2cb958b3f7596744bb08febc858fa25139fd1ac static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -1,4 +1,3 @@ -if( console ){ console.debug( 'history mvc loaded' ); } /* Backbone.js implementation of history panel @@ -678,7 +677,7 @@ url: this.model.get( 'ajax_get_tag_url' ), error: function() { alert( "Tagging failed" ) }, success: function(tag_elt_html) { - console.debug( 'tag_elt_html:', tag_elt_html ); + this.log( 'tag_elt_html:', tag_elt_html ); tagElt.html(tag_elt_html); tagElt.find(".tooltip").tooltip(); tagArea.slideDown("fast"); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Allow for overriding app.config.track_jobs_in_database.
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/244b4cb100d1/ changeset: 244b4cb100d1 user: natefoo date: 2012-09-11 20:58:13 summary: Allow for overriding app.config.track_jobs_in_database. affected #: 2 files diff -r 9a8614de4141be276ab4a416ef7b0def8c5703d2 -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -105,6 +105,7 @@ self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) self.smtp_password = kwargs.get( 'smtp_password', None ) + self.track_jobs_in_database = kwargs.get( 'track_jobs_in_database', None ) self.start_job_runners = kwargs.get( 'start_job_runners', None ) self.expose_dataset_path = string_as_bool( kwargs.get( 'expose_dataset_path', 'False' ) ) # External Service types used in sample tracking @@ -210,9 +211,12 @@ self.job_handlers = [ x.strip() for x in kwargs.get('job_handlers', self.server_name).split(',') ] self.default_job_handlers = [ x.strip() for x in kwargs.get('default_job_handlers', ','.join( self.job_handlers ) ).split(',') ] # Use database for IPC unless this is a standalone server (or multiple servers doing self dispatching in memory) - self.track_jobs_in_database = True - if ( len( self.job_handlers ) == 1 ) and ( self.job_handlers[0] == self.server_name ) and ( self.job_manager == self.server_name ): - self.track_jobs_in_database = False + if self.track_jobs_in_database is None or self.track_jobs_in_database == "None": + self.track_jobs_in_database = True + if ( len( self.job_handlers ) == 1 ) and ( self.job_handlers[0] == self.server_name ) and ( self.job_manager == self.server_name ): + self.track_jobs_in_database = False + else: + self.track_jobs_in_database = string_as_bool( self.track_jobs_in_database ) # Store per-tool runner configs self.tool_handlers = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_handlers', 'name' ) self.tool_runners = self.__read_tool_job_config( global_conf_parser, 'galaxy:tool_runners', 'url' ) diff -r 9a8614de4141be276ab4a416ef7b0def8c5703d2 -r 244b4cb100d19ed7d005fabcf2390204b3630aa5 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -586,6 +586,15 @@ # used for jobs without explicit handlers. #default_job_handlers = main +# In multiprocess configurations, notification between processes about new jobs +# is done via the database. In single process configurations, this is done in +# memory, which is a bit quicker. Galaxy tries to automatically determine +# which method it should used based on your manager/handler configuration +# above, but can't reliably determine if you have multiple processes for web +# servers but only a single process as a manager/handler. In that scenario, +# you can override the tracking method by setting the following to True: +#track_jobs_in_database = None + # This enables splitting of jobs into tasks, if specified by the particular tool config. # This is a new feature and not recommended for production servers yet. #use_tasked_jobs = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: removed console.debug statement from history.mako
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9a8614de4141/ changeset: 9a8614de4141 user: carlfeberhard date: 2012-09-11 19:52:55 summary: removed console.debug statement from history.mako affected #: 1 file diff -r 7b1b6e81b1756234001eb1c3a32d7a9b98da92c3 -r 9a8614de4141be276ab4a416ef7b0def8c5703d2 templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -233,7 +233,6 @@ //TODO: hack (github has an issue on this - see how it's resolved) // fix for two line bootstrap tooltips when placement: above $( this ).find( '.tooltip' ).each( function(){ - console.debug( 'tooltip:', this ); var $this = $( this ); // documented method - that doesn't seem to work Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Do not report the disk usage of purged HDAs in history disk usage.
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7b1b6e81b175/ changeset: 7b1b6e81b175 user: natefoo date: 2012-09-11 19:33:20 summary: Do not report the disk usage of purged HDAs in history disk usage. affected #: 1 file diff -r 2b4111248390ae6340f4bec54d0cff29f48665fb -r 7b1b6e81b1756234001eb1c3a32d7a9b98da92c3 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -685,6 +685,7 @@ db_session = object_session( self ) rval = db_session.query( func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset ) .filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + .filter( HistoryDatasetAssociation.purged != True ) .filter( Dataset.purged != True ) .distinct().subquery().c.total_size ) ).first()[0] if rval is None: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Distributed object store fixes for pgcleanup.py.
by Bitbucket 11 Sep '12

11 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2b4111248390/ changeset: 2b4111248390 user: natefoo date: 2012-09-11 18:22:03 summary: Distributed object store fixes for pgcleanup.py. affected #: 1 file diff -r 63cd6402badaf98f26080e71b1f0ed49db30e3ab -r 2b4111248390ae6340f4bec54d0cff29f48665fb scripts/cleanup_datasets/pgcleanup.py --- a/scripts/cleanup_datasets/pgcleanup.py +++ b/scripts/cleanup_datasets/pgcleanup.py @@ -31,6 +31,12 @@ log = logging.getLogger() +class MetadataFile(Bunch): + pass + +class Dataset(Bunch): + pass + class Cleanup(object): def __init__(self): self.options = None @@ -199,12 +205,13 @@ log.info("All changes committed") def _remove_metadata_file(self, id, object_store_id, action_name): - metadata_file = Bunch(id=id, object_store_id=object_store_id) + metadata_file = MetadataFile(id=id, object_store_id=object_store_id) try: filename = self.object_store.get_filename(metadata_file, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % id) self._log('Removing from disk: %s' % filename, action_name) - except ObjectNotFound: + except (ObjectNotFound, AttributeError), e: + log.error('Unable to get MetadataFile %s filename: %s' % (id, e)) return if not self.options.dry_run: @@ -656,8 +663,6 @@ """ log.info('Marking purged all Datasets marked deleted that are older than the specified number of days.') - # TODO: force retry option - event_id = self._create_event(inspect.stack()[0][3]) sql = """ @@ -700,15 +705,16 @@ self._log('Marked Dataset purged: %s in Object Store: %s' % (tup[0], tup[1])) # always try to remove the "object store path" - if it's at an external_filename, that file will be untouched anyway (which is what we want) - dataset = Bunch(id=tup[0], object_store_id=tup[1]) + dataset = Dataset(id=tup[0], object_store_id=tup[1]) try: filename = self.object_store.get_filename(dataset) - except ObjectNotFound, AttributeError: + except (ObjectNotFound, AttributeError), e: + log.error('Unable to get Dataset %s filename: %s' % (tup[0], e)) continue try: extra_files_dir = self.object_store.get_filename(dataset, dir_only=True, extra_dir="dataset_%d_files" % tup[0]) - except ObjectNotFound, AttributeError: + except (ObjectNotFound, AttributeError): extra_files_dir = None # don't check for existence of the dataset, it should exist Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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