Grid framework refactoring to increase speed and ease of debugging: (1) create and use Backbone object for grid; (2) move grid javascript to its own file; (3) remove webapp parameter; (4) augment search box style so that search button does not wrap. Pack scripts.

2026-10-29 17:42:12 +08:00 · 2013-01-28 14:02:25 -05:00
parent 0ca2a0112f
commit 409ba63a4f
9 changed files with 587 additions and 526 deletions
@@ -1 +1 @@
-var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.updateHdas(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e)}})},updateHdas:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(f,c,d){var e="ERROR updating hdas from api history contents:";a.log(e,b,f,c,d);alert(e+b.join(","))},success:function(d,c,f){a.log(a+".updateHdas, success:",d,c,f);var e=[];_.each(d,function(h,i){var g=a.hdas.get(h.id);if(g){a.log("found existing model in list for id "+h.id+", updating...:");g.set(h)}else{a.log("NO existing model for id "+h.id+", creating...:");e.push(h)}});if(e.length){a.addHdas(e)}}})},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"});
+var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b){if(_.isArray(b)){this.hdas.reset(b);this.checkForUpdates()}else{if(_.isString(b)&&(b.match(/error/i))){alert(_l("Error loading bootstrapped history")+":\n"+b)}}}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e)}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{var g=_l("ERROR updating hdas from api history contents")+": ";a.log(g,b,h,c,d,errorJSON);alert(g+b.join(","))}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"});
@@ -1 +1 @@
-define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){var a=b.object_from_template;var f=g.Base.extend({initialize:function(j){this.baseURL=j},createButtonMenu:function(){var j=this,k=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){d.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":view.dbkey},function(l){c.each(l,function(m){view.add_drawable(a(m,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=j.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var l=[];$(".bookmark").each(function(){l.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var m=(view.overview_drawable?view.overview_drawable.name:null),n={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bookmarks:l};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(n)}}).success(function(o){hide_modal();view.vis_id=o.vis_id;view.has_changes=false;window.history.pushState({},"",o.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=j.baseURL+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=k;return k},add_bookmarks:function(){var j=this,k=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(l){show_modal("Select dataset for new bookmarks",l,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var m,n=$(this).val();if($(this).attr("name")==="id"){m={hda_id:n}}else{m={ldda_id:n}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:m,dataType:"json"}).then(function(o){for(i=0;i<o.data.length;i++){var p=o.data[i];j.add_bookmark(p[0],p[1])}})});hide_modal()}})}})},add_bookmark:function(n,l,j){var p=$("#bookmarks-container"),r=$("<div/>").addClass("bookmark").appendTo(p);var s=$("<div/>").addClass("position").appendTo(r),o=$("<a href=''/>").text(n).appendTo(s).click(function(){view.go_to(n);return false}),m=$("<div/>").text(l).appendTo(r);if(j){var q=$("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){r.slideUp("fast");r.remove();view.has_changes=true;return false}),k=$("<a href=''/>").addClass("icon-button delete").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return r},create_visualization:function(o,j,n,p,m){var l=this,k=new b.TracksterView(o);k.editor=true;$.when(k.load_chroms_deferred).then(function(A){if(j){var y=j.chrom,q=j.start,v=j.end,s=j.overview;if(y&&(q!==undefined)&&v){k.change_chrom(y,q,v)}}else{k.change_chrom(A[0].chrom)}if(n){var t,r,u;for(var w=0;w<n.length;w++){k.add_drawable(a(n[w],k,k))}}k.update_intro_div();var z;for(var w=0;w<k.drawables.length;w++){if(k.drawables[w].name===s){k.set_overview(k.drawables[w]);break}}if(p){var x;for(var w=0;w<p.length;w++){x=p[w];l.add_bookmark(x.position,x.annotation,m)}}k.has_changes=false});return k},init_keyboard_nav:function(j){$(document).keydown(function(k){if($(k.srcElement).is(":input")){return}switch(k.which){case 37:j.move_fraction(0.25);break;case 38:var l=Math.round(j.viewport_container.height()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()-20);break;case 39:j.move_fraction(-0.25);break;case 40:var l=Math.round(j.viewport_container.height()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:f}});
+define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){var a=b.object_from_template;var f=g.Base.extend({initialize:function(j){this.baseURL=j},createButtonMenu:function(){var j=this,k=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){d.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":view.dbkey},function(l){c.each(l,function(m){view.add_drawable(a(m,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=j.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var l=[];$(".bookmark").each(function(){l.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var m=(view.overview_drawable?view.overview_drawable.name:null),n={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bookmarks:l};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(n)}}).success(function(o){hide_modal();view.vis_id=o.vis_id;view.has_changes=false;window.history.pushState({},"",o.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=j.baseURL+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=k;return k},add_bookmarks:function(){var j=this,k=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(l){show_modal("Select dataset for new bookmarks",l,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var m,n=$(this).val();if($(this).attr("name")==="id"){m={hda_id:n}}else{m={ldda_id:n}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:m,dataType:"json"}).then(function(o){for(i=0;i<o.data.length;i++){var p=o.data[i];j.add_bookmark(p[0],p[1])}})});hide_modal()}})}})},add_bookmark:function(n,l,j){var p=$("#bookmarks-container"),r=$("<div/>").addClass("bookmark").appendTo(p);var s=$("<div/>").addClass("position").appendTo(r),o=$("<a href=''/>").text(n).appendTo(s).click(function(){view.go_to(n);return false}),m=$("<div/>").text(l).appendTo(r);if(j){var q=$("<div/>").addClass("delete-icon-container").prependTo(r).click(function(){r.slideUp("fast");r.remove();view.has_changes=true;return false}),k=$("<a href=''/>").addClass("icon-button delete").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return r},create_visualization:function(o,j,n,p,m){var l=this,k=new b.TracksterView(o);k.editor=true;$.when(k.load_chroms_deferred).then(function(A){if(j){var y=j.chrom,q=j.start,v=j.end,s=j.overview;if(y&&(q!==undefined)&&v){k.change_chrom(y,q,v)}else{k.change_chrom(A[0].chrom)}}else{k.change_chrom(A[0].chrom)}if(n){var t,r,u;for(var w=0;w<n.length;w++){k.add_drawable(a(n[w],k,k))}}k.update_intro_div();var z;for(var w=0;w<k.drawables.length;w++){if(k.drawables[w].name===s){k.set_overview(k.drawables[w]);break}}if(p){var x;for(var w=0;w<p.length;w++){x=p[w];l.add_bookmark(x.position,x.annotation,m)}}k.has_changes=false});return k},init_keyboard_nav:function(j){$(document).keydown(function(k){if($(k.srcElement).is(":input")){return}switch(k.which){case 37:j.move_fraction(0.25);break;case 38:var l=Math.round(j.viewport_container.height()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()-20);break;case 39:j.move_fraction(-0.25);break;case 40:var l=Math.round(j.viewport_container.height()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:f}});