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commit/galaxy-central: Jeremy Goecks: Trackster: (a) default read track block colors to gray in order to show variants; (b) do not set default height of variant track.
by commits-noreply＠bitbucket.org 27 Mar '14

27 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6301e0c62a03/ Changeset: 6301e0c62a03 User: Jeremy Goecks Date: 2014-03-27 03:14:10 Summary: Trackster: (a) default read track block colors to gray in order to show variants; (b) do not set default height of variant track. Affected #: 2 files diff -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 -r 6301e0c62a03b508f2a6fd218dd71ef5d6163511 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4031,7 +4031,7 @@ { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true }, { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, - { key: 'height', type: 'int', default_value: 32, hidden: true } + { key: 'height', type: 'int', default_value: 0, hidden: true } ] ), config_onchange: function() { @@ -4169,8 +4169,8 @@ extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, { config_params: _.union( Drawable.prototype.config_params, [ - { key: 'block_color', label: 'Block and sense strand color', type: 'color' }, - { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' }, + { key: 'block_color', label: 'Block and sense strand color', type: 'color', 'default_value': '#DDDDDD' }, + { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', 'default_value': '#AAAAAA' }, { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true }, diff -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 -r 6301e0c62a03b508f2a6fd218dd71ef5d6163511 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -43,7 +43,7 @@ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { _.each(tracks, function(track) { - view.add_drawable( object_from_template(track, view, view) ); + view.add_drawable( object_from_template(track, view, view) ); }); }); } }, 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: Jeremy Goecks: Visualization JS: fix incorrect method call. Pack script.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8bb0825fe57b/ Changeset: 8bb0825fe57b User: Jeremy Goecks Date: 2014-03-26 22:53:07 Summary: Visualization JS: fix incorrect method call. Pack script. Affected #: 3 files diff -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,k,m,p){var f={toJSON:function(){var v=this,w={};t.each(v.constructor.to_json_keys,function(x){var y=v.get(x);if(x in v.constructor.to_json_mappers){y=v.constructor.to_json_mappers[x](y,v)}w[x]=y});return w}};var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var g=function(v){this.default_font=v!==undefined?v:"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")};t.extend(g.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(m.is_deferred(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(m.is_deferred(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!m.is_deferred(D)){var G=this.subset_entry(D,C);this.set(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new h({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new h({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return h.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=h.overlap_results.BEFORE}else{if(z<x){v=h.overlap_results.OVERLAP_START}else{v=h.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=h.overlap_results.AFTER}else{if(z<=x){v=h.overlap_results.CONTAINED_BY}else{v=h.overlap_results.OVERLAP_END}}}else{v=(z>=x?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===h.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new h(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(v){this.set("dataset",new k.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(w,v){if(t.size(w)===0){w={name:v.get("config").get("name").get("value"),color:v.get("config").get("color").get("value")}}return w},dataset:function(v){return{id:v.id,hda_ldda:v.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend(f).extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("drawables",new j(v.tracks));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs||{}));this.unset("tracks");this.get("drawables").each(function(w){w.unset("preloaded_data")})},add_tracks:function(v){this.get("drawables").add(v)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(w,v){return{obj_type:"View",prefs:{name:v.get("title"),content_visible:true},drawables:v.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:i,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,k,m,p){var f={toJSON:function(){var v=this,w={};t.each(v.constructor.to_json_keys,function(x){var y=v.get(x);if(x in v.constructor.to_json_mappers){y=v.constructor.to_json_mappers[x](y,v)}w[x]=y});return w}};var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var g=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};t.extend(g.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(m.is_deferred(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(m.is_deferred(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!m.is_deferred(D)){var G=this.subset_entry(D,C);this.set_data(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new h({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new h({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return h.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=h.overlap_results.BEFORE}else{if(z<x){v=h.overlap_results.OVERLAP_START}else{v=h.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=h.overlap_results.AFTER}else{if(z<=x){v=h.overlap_results.CONTAINED_BY}else{v=h.overlap_results.OVERLAP_END}}}else{v=(z>=x?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===h.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new h(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(v){this.set("dataset",new k.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(w,v){if(t.size(w)===0){w={name:v.get("config").get("name").get("value"),color:v.get("config").get("color").get("value")}}return w},dataset:function(v){return{id:v.id,hda_ldda:v.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend(f).extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("drawables",new j(v.tracks));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs||{}));this.unset("tracks");this.get("drawables").each(function(w){w.unset("preloaded_data")})},add_tracks:function(v){this.get("drawables").add(v)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(w,v){return{obj_type:"View",prefs:{name:v.get("title"),content_visible:true},drawables:v.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:i,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file diff -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -120,7 +120,7 @@ this.view_start = view_start; this.view_end = view_end; // Drawing prefs - this.prefs = extend( {}, this.default_prefs, prefs ); + this.prefs = extend({}, this.default_prefs, prefs); this.mode = mode; }; diff -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -403,7 +403,7 @@ // If there's data, subset it. if ( !util_mod.is_deferred(entry) ) { var subset_entry = this.subset_entry(entry, region); - this.set(region, subset_entry); + this.set_data(region, subset_entry); entry = subset_entry; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: Jeremy Goecks: Pack scripts.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/231a61e88777/ Changeset: 231a61e88777 User: Jeremy Goecks Date: 2014-03-26 22:39:58 Summary: Pack scripts. Affected #: 5 files diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(!this.get("value")){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("value")===undefined){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode);var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){if("MDN=X".indexOf(cig_op)!==-1){base_offset+=cig_len}continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start,1);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an||ab===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(ag){aa.each(ag,function(ah){ab.add_drawable(n(ah,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}ag.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ab.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ab.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ah)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ab.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ab.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ab.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ab.container.offset().left,aj=(ab.high-ab.low),ai=ab.viewport_container.width();ab.update_location(Math.round(ah/ai*aj)+ab.low,Math.round(ag/ai*aj)+ab.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ab.high-ab.low),ai=ab.viewport_container.width(),ak=ab.low;ab.low=Math.round(ah/ai*aj)+ak;ab.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ab.request_redraw()});var ae=$("<div/>").addClass("mouse-pos").appendTo(ad);ad.hover(function(){ae.show();ad.mousemove(function(ag){ae.css({left:ag.pageX-1})})},function(){ad.off("mousemove");ae.hide()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_param_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){L.prototype.before_draw.call(this);var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){L.prototype.postdraw_actions.call(this,ah,ab,ak,ag);var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=(ac.reference_track?J.RefBasedReadPainter:J.ReadPainter);this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an||ab===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=R.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],{name:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=P.Tool.extend({defaults:{track:null},initialize:function(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.config.get_value("height");this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("name") %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof V){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);if(!this.config.get_value("content_visible")){this.tiles_div.hide()}this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};o(L.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.config.to_key_value_dict(),mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_param_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){L.prototype.before_draw.call(this);var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){L.prototype.postdraw_actions.call(this,ah,ab,ak,ag);var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.canvas_manager.char_width_px;this.container_div.addClass("reference-track");this.data_url=galaxy_config.root+"api/genomes/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,L.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Color",type:"color"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:30,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},before_draw:function(){},draw_tile:function(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.union(p.prototype.config_params,[{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);this.container_div.addClass("feature-track");this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.set_painter_from_config();this.request_draw({clear_tile_cache:true})},set_painter_from_config:function(){if(this.config.get_value("connector_style")==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.union(p.prototype.config_params,[{key:"color",label:"Histogram color",type:"color"},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},draw_tile:function(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})}});var d={CompositeTrack:e,DrawableGroup:N,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:S,VariantTrack:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/viz/trackster/util.js --- a/static/scripts/packed/viz/trackster/util.js +++ b/static/scripts/packed/viz/trackster/util.js @@ -1,1 +1,1 @@ -define(function(){var b=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(c){return true}},go:function(){var f=$.Deferred(),e=this,h=e.get("ajax_settings"),g=e.get("success_fn"),d=e.get("interval"),c=function(){$.ajax(h).success(function(i){if(g(i)){f.resolve(i)}else{setTimeout(c,d)}})};c();return f}});var a=function(c){if(!c){c="#ffffff"}if(typeof(c)==="string"){c=[c]}for(var l=0;l<c.length;l++){c[l]=parseInt(c[l].slice(1),16)}var p=function(v,u,i){return((v*299)+(u*587)+(i*114))/1000};var g=function(x,w,y,u,i,v){return(Math.max(x,u)-Math.min(x,u))+(Math.max(w,i)-Math.min(w,i))+(Math.max(y,v)-Math.min(y,v))};var j,q,h,m,s,k,t,e,f,d,r,o=false,n=0;do{j=Math.round(Math.random()*16777215);q=(j&16711680)>>16;h=(j&65280)>>8;m=j&255;f=p(q,h,m);o=true;for(l=0;l<c.length;l++){s=c[l];k=(s&16711680)>>16;t=(s&65280)>>8;e=s&255;d=p(k,t,e);r=g(q,h,m,k,t,e);if((Math.abs(f-d)<40)||(r<200)){o=false;break}}n++}while(!o&&n<=10);return"#"+(16777216+j).toString(16).substr(1,6)};return{ServerStateDeferred:b,get_random_color:a}}); \ No newline at end of file +define(function(){var b=function(e){return("promise" in e)};var c=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(d){return true}},go:function(){var g=$.Deferred(),f=this,i=f.get("ajax_settings"),h=f.get("success_fn"),e=f.get("interval"),d=function(){$.ajax(i).success(function(j){if(h(j)){g.resolve(j)}else{setTimeout(d,e)}})};d();return g}});var a=function(d){if(!d){d="#ffffff"}if(typeof(d)==="string"){d=[d]}for(var m=0;m<d.length;m++){d[m]=parseInt(d[m].slice(1),16)}var q=function(w,v,i){return((w*299)+(v*587)+(i*114))/1000};var h=function(y,x,z,v,i,w){return(Math.max(y,v)-Math.min(y,v))+(Math.max(x,i)-Math.min(x,i))+(Math.max(z,w)-Math.min(z,w))};var k,r,j,n,t,l,u,f,g,e,s,p=false,o=0;do{k=Math.round(Math.random()*16777215);r=(k&16711680)>>16;j=(k&65280)>>8;n=k&255;g=q(r,j,n);p=true;for(m=0;m<d.length;m++){t=d[m];l=(t&16711680)>>16;u=(t&65280)>>8;f=t&255;e=q(l,u,f);s=h(r,j,n,l,u,f);if((Math.abs(g-e)<40)||(s<200)){p=false;break}}o++}while(!p&&o<=10);return"#"+(16777216+k).toString(16).substr(1,6)};return{is_deferred:b,ServerStateDeferred:c,get_random_color:a}}); \ No newline at end of file diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(u,k,n,q){var f={toJSON:function(){var w=this,x={};u.each(w.constructor.to_json_keys,function(y){var z=w.get(y);if(y in w.constructor.to_json_mappers){z=w.constructor.to_json_mappers[y](z,w)}x[y]=z});return x}};var a=function(w,z,y,x){$.ajax({url:w,data:y,error:function(){alert("Grid failed")},success:function(A){Galaxy.modal.show({title:"Select datasets for new tracks",body:A,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var B=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var C={data_type:"track_config",hda_ldda:"hda"},D=$(this).val();if($(this).attr("name")!=="id"){C.hda_ldda="ldda"}B[B.length]=$.ajax({url:z+"/"+D,data:C,dataType:"json"})});$.when.apply($,B).then(function(){var C=(arguments[0] instanceof Array?$.map(arguments,function(D){return D[0]}):[arguments[0]]);x(C)});Galaxy.modal.hide()}}})}})};var l=function(w){return("promise" in w)};var g=function(w){this.default_font=w!==undefined?w:"9px Monaco, Lucida Console, 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s=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(w){this.clear()},get_elt:function(y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,x=y.toString(),w=u.indexOf(A,function(B){return B.toString()===x});if(w!==-1){if(z[x].stale){A.splice(w,1);delete z[x]}else{this.move_key_to_end(y,w)}}return z[x]},set_elt:function(y,A){var B=this.attributes.obj_cache,C=this.attributes.key_ary,x=y.toString(),z=this.attributes.num_elements;if(!B[x]){if(C.length>=z){var w=C.shift();delete B[w.toString()]}C.push(y)}B[x]=A;return A},move_key_to_end:function(x,w){this.attributes.key_ary.splice(w,1);this.attributes.key_ary.push(x)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=s.extend({defaults:u.extend({},s.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(w,x){return true},can_subset:function(w){return false}}),initialize:function(w){s.prototype.initialize.call(this);var x=this.get("init_data");if(x){this.add_data(x)}},add_data:function(w){if(this.get("num_elements")<w.length){this.set("num_elements",w.length)}var x=this;u.each(w,function(y){x.set_data(y.region,y)})},data_is_ready:function(){var z=this.get("dataset"),y=$.Deferred(),w=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),x=new n.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:z.get("hda_ldda"),data_type:w},dataType:"json"},interval:5000,success_fn:function(A){return A!=="pending"}});$.when(x.go()).then(function(A){y.resolve(A==="ok"||A==="data")});return y},search_features:function(w){var x=this.get("dataset"),y={query:w,hda_ldda:x.get("hda_ldda"),data_type:"features"};return $.getJSON(x.url(),y)},load_data:function(E,D,x,C){var A=this.get("dataset"),z={data_type:this.get("data_type"),chrom:E.get("chrom"),low:E.get("start"),high:E.get("end"),mode:D,resolution:x,hda_ldda:A.get("hda_ldda")};$.extend(z,C);var G=this.get("filters_manager");if(G){var H=[];var w=G.filters;for(var B=0;B<w.length;B++){H.push(w[B].name)}z.filter_cols=JSON.stringify(H)}var y=this,F=$.getJSON(A.url(),z,function(I){I.region=E;y.set_data(E,I)});this.set_data(E,F);return F},get_data:function(D,C,y,A){var E=this.get_elt(D);if(E&&(l(E)||this.get("data_mode_compatible")(E,C))){return E}var F=this.get("key_ary"),w=this.get("obj_cache"),x,B;for(var z=0;z<F.length;z++){x=F[z];if(x.contains(D)){B=true;E=w[x.toString()];if(l(E)||(this.get("data_mode_compatible")(E,C)&&this.get("can_subset")(E))){this.move_key_to_end(x,z);if(!l(E)){var H=this.subset_entry(E,D);this.set(D,H);E=H}return E}}}if(!B&&D.length()<this.attributes.min_region_size){D=D.copy();var G=this.most_recently_added();if(!G||(D.get("start")>G.get("start"))){D.set("end",D.get("start")+this.attributes.min_region_size)}else{D.set("start",D.get("end")-this.attributes.min_region_size)}D.set("genome",this.attributes.genome);D.trim()}return this.load_data(D,C,y,A)},set_data:function(x,w){this.set_elt(x,w)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(E,D,z,C,A){var G=this._mark_stale(E);if(!(G&&this.get("data_mode_compatible")(G,D))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var y=E.get("start");if(A===this.DEEP_DATA_REQ){$.extend(C,{start_val:G.data.length+1})}else{if(A===this.BROAD_DATA_REQ){y=(G.max_high?G.max_high:G.data[G.data.length-1][2])+1}}var F=E.copy().set("start",y);var x=this,B=this.load_data(F,D,z,C),w=$.Deferred();this.set_data(E,w);$.when(B).then(function(H){if(H.data){H.data=G.data.concat(H.data);if(H.max_low){H.max_low=G.max_low}if(H.message){H.message=H.message.replace(/[0-9]+/,H.data.length)}}x.set_data(E,H);w.resolve(H)});return w},can_get_more_detailed_data:function(x){var w=this.get_elt(x);return(w.dataset_type==="bigwig"&&w.data.length<8000)},get_more_detailed_data:function(z,B,x,A,y){var w=this._mark_stale(z);if(!w){console.log("ERROR getting more detailed data: no current data");return}if(!y){y={}}if(w.dataset_type==="bigwig"){y.num_samples=1000*A}return this.load_data(z,B,x,y)},_mark_stale:function(x){var w=this.get_elt(x);if(!w){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),x.toString())}w.stale=true;return w},get_genome_wide_data:function(w){var y=this,A=true,z=u.map(w.get("chroms_info").chrom_info,function(C){var B=y.get_elt(new h({chrom:C.chrom,start:0,end:C.len}));if(!B){A=false}return B});if(A){return z}var x=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(B){y.add_data(B.data);x.resolve(B.data)});return x},subset_entry:function(y,z){var w={bigwig:function(A,B){return u.filter(A,function(C){return C[0]>=B.get("start")&&C[0]<=B.get("end")})},refseq:function(B,C){var D=C.get("start")-y.region.get("start"),A=y.data.length-(y.region.get("end")-C.get("end"));return y.data.slice(D,A)}};var x=y.data;if(!y.region.same(z)&&y.dataset_type in w){x=w[y.dataset_type](y.data,z)}return{region:z,data:x,dataset_type:y.dataset_type}}});var r=d.extend({initialize:function(w){var x=new Backbone.Model();x.urlRoot=w.data_url;this.set("dataset",x)},load_data:function(y,z,w,x){return(y.length()<=100000?d.prototype.load_data.call(this,y,z,w,x):{data:null,region:y})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(w){this.id=w.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(w){var x=u.find(this.get_chroms_info(),function(y){return y.chrom===w});return new h({chrom:x.chrom,end:x.len})},get_chrom_len:function(w){return u.find(this.get_chroms_info(),function(x){return x.chrom===w}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(w){return this.attributes.chrom===w.get("chrom")&&this.attributes.start===w.get("start")&&this.attributes.end===w.get("end")},initialize:function(x){if(x.from_str){var z=x.from_str.split(":"),y=z[0],w=z[1].split("-");this.set({chrom:y,start:parseInt(w[0],10),end:parseInt(w[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(D){var x=this.get("chrom"),C=D.get("chrom"),B=this.get("start"),z=D.get("start"),A=this.get("end"),y=D.get("end"),w;if(x&&C&&x!==C){return h.overlap_results.DIF_CHROMS}if(B<z){if(A<z){w=h.overlap_results.BEFORE}else{if(A<y){w=h.overlap_results.OVERLAP_START}else{w=h.overlap_results.CONTAINS}}}else{if(B>z){if(B>y){w=h.overlap_results.AFTER}else{if(A<=y){w=h.overlap_results.CONTAINED_BY}else{w=h.overlap_results.OVERLAP_END}}}else{w=(A>=y?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return w},trim:function(w){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var x=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>x){this.attributes.end=x-1}}return this},contains:function(w){return this.compute_overlap(w)===h.overlap_results.CONTAINS},overlaps:function(w){return u.intersection([this.compute_overlap(w)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var o=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(w){this.set("region",new h(w.region))}});var t=Backbone.Collection.extend({model:e});var v=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(w){this.set("dataset",new k.Dataset(w.dataset));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var x=this.get("preloaded_data");if(x){x=x.data}else{x=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:x}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(x,w){if(u.size(x)===0){x={name:w.get("config").get("name").get("value"),color:w.get("config").get("color").get("value")}}return x},dataset:function(w){return{id:w.id,hda_ldda:w.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:v});var p=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var m=p.extend(f).extend({defaults:u.extend({},p.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(w){this.set("drawables",new j(w.tracks));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs||{}));this.unset("tracks");this.get("drawables").each(function(x){x.unset("preloaded_data")})},add_tracks:function(w){this.get("drawables").add(w)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(x,w){return{obj_type:"View",prefs:{name:w.get("title"),content_visible:true},drawables:w.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(x){this.view=x.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var w=this;w.view.on("navigate",function(y){w.navigate(y)})},change_location:function(w){this.view.go_to(w)}});return{BackboneTrack:v,BrowserBookmark:e,BrowserBookmarkCollection:t,Cache:s,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:o,GenomeVisualization:m,GenomeReferenceDataManager:r,TrackBrowserRouter:i,TrackConfig:b,Visualization:p,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,k,m,p){var f={toJSON:function(){var v=this,w={};t.each(v.constructor.to_json_keys,function(x){var y=v.get(x);if(x in v.constructor.to_json_mappers){y=v.constructor.to_json_mappers[x](y,v)}w[x]=y});return w}};var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var g=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, 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r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(m.is_deferred(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(m.is_deferred(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!m.is_deferred(D)){var G=this.subset_entry(D,C);this.set(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new h({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new h({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return h.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=h.overlap_results.BEFORE}else{if(z<x){v=h.overlap_results.OVERLAP_START}else{v=h.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=h.overlap_results.AFTER}else{if(z<=x){v=h.overlap_results.CONTAINED_BY}else{v=h.overlap_results.OVERLAP_END}}}else{v=(z>=x?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===h.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new h(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(v){this.set("dataset",new k.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(w,v){if(t.size(w)===0){w={name:v.get("config").get("name").get("value"),color:v.get("config").get("color").get("value")}}return w},dataset:function(v){return{id:v.id,hda_ldda:v.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend(f).extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("drawables",new j(v.tracks));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs||{}));this.unset("tracks");this.get("drawables").each(function(w){w.unset("preloaded_data")})},add_tracks:function(v){this.get("drawables").add(v)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(w,v){return{obj_type:"View",prefs:{name:v.get("title"),content_visible:true},drawables:v.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:i,TrackConfig:b,Visualization:o,select_datasets:a}}); \ 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: 6 new changesets
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9e7f9282deba/ Changeset: 9e7f9282deba User: Jeremy Goecks Date: 2014-03-26 18:42:54 Summary: Trackster: consolidate read painters. Affected #: 2 files diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 9e7f9282deba9d383e708e210acea5dea8eb7673 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -736,297 +736,6 @@ }; }, - // FIXME: extract common functionality from draw_read functions for ReadPainters. - - /** - * Draw a single read. - */ - draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) { - ctx.textAlign = "center"; - var tile_region = [tile_low, tile_high], - base_offset = 0, - seq_offset = 0, - gap = Math.round(w_scale/2), - char_width_px = ctx.canvas.manager.char_width_px, - block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color), - pack_mode = (mode === 'Pack'), - paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale, mode); - - // Keep list of items that need to be drawn on top of initial drawing layer. - var draw_last = []; - - // If no cigar string, then assume all matches. - if (!cigar) { - cigar = [ [0, read_seq.length] ]; - } - - // Draw read by processing cigar. - for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) { - var cig = cigar[cig_id], - cig_op = "MIDNSHP=X"[ cig[0] ], - cig_len = cig[1]; - - var seq_start = feature_start + base_offset, - // -0.5 to offset sequence between bases. - s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), - s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) ); - - if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) { - // Increment base offset only for certain operations. - if ("MDN=X".indexOf(cig_op) !== -1) { - base_offset += cig_len; - } - continue; - } - - // Make sure that read is drawn even if it too small to be rendered officially; in this case, - // read is drawn at 1px. - // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting - // and drawing. - if (s_start === s_end) { - s_end += 1; - } - - switch (cig_op) { - case "H": // Hard clipping. - // Sequence not present, so do not increment seq_offset. - break; - case "S": // Soft clipping. - seq_offset += cig_len; - break; - case "M": // Loose match with reference; can be match or mismatch. - case "=": // Strict match with reference. - case "X": // Strict mismatch with reference. - // Draw read base as rectangle. - ctx.fillStyle = block_color; - ctx.fillRect(s_start, - y_start + (pack_mode ? 1 : 4 ), - s_end - s_start, - (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); - - // Draw sequence and/or variants. - var seq = read_seq.slice(seq_offset, seq_offset + cig_len), - ref_char, - read_char; - for (var c = 0, str_len = seq.length; c < str_len; c++) { - // Draw base if it's on tile: - if (seq_start + c >= tile_low && seq_start + c <= tile_high) { - // Get reference and read character. - ref_char = (this.ref_seq ? this.ref_seq[seq_start - tile_low + c] : null); - read_char = seq[c]; - - // Draw base depending on (a) available reference data and (b) config options. - if ( - // If there's reference data and (a) showing all (i.e. not showing - // differences) or (b) if there is a variant. - (ref_char && - (!this.prefs.show_differences || - (read_char.toLowerCase !== 'n' && (ref_char.toLowerCase() !== read_char.toLowerCase()))) - ) || - // If there's no reference data and showing all. - (!ref_char && !this.prefs.show_differences) - ) { - - // Draw base. - var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillStyle = this.base_color_fn(seq[c]); - if (pack_mode && w_scale > char_width_px) { - ctx.fillText(seq[c], c_start, y_start + 9); - } - // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in. - else if (w_scale > 0.05) { - ctx.fillRect(c_start - gap, - y_start + (pack_mode ? 1 : 4), - Math.max( 1, Math.round(w_scale) ), - (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT)); - } - } - - } - } - - seq_offset += cig_len; - base_offset += cig_len; - break; - case "N": // Skipped bases. - ctx.fillStyle = CONNECTOR_COLOR; - ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1); - //ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5); - base_offset += cig_len; - break; - case "D": // Deletion. - paint_utils.draw_deletion(s_start, y_start, 1); - base_offset += cig_len; - break; - case "P": // TODO: No good way to draw insertions/padding right now, so ignore - // Sequences not present, so do not increment seq_offset. - break; - case "I": // Insertion. - // Check to see if sequence should be drawn at all by looking at the overlap between - // the sequence region and the tile region. - var insert_x_coord = s_start - gap; - - if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { - var seq = read_seq.slice(seq_offset, seq_offset + cig_len); - // Insertion point is between the sequence start and the previous base: (-gap) moves - // back from sequence start to insertion point. - if (this.prefs.show_insertions) { - // - // Show inserted sequence above, centered on insertion point. - // - - // Draw sequence. - // X center is offset + start - <half_sequence_length> - var x_center = s_start - (s_end - s_start)/2; - if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { - // Draw sequence container. - ctx.fillStyle = "yellow"; - ctx.fillRect(x_center - gap, y_start - 9, s_end - s_start, 9); - draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_start + 4, 5]}; - ctx.fillStyle = CONNECTOR_COLOR; - // Based on overlap b/t sequence and tile, get sequence to be drawn. - switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) { - case(OVERLAP_START): - seq = seq.slice(tile_low-seq_start); - break; - case(OVERLAP_END): - seq = seq.slice(0, seq_start-tile_high); - break; - case(CONTAINED_BY): - // All of sequence drawn. - break; - case(CONTAINS): - seq = seq.slice(tile_low-seq_start, seq_start-tile_high); - break; - } - // Draw sequence. - for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_start); - } - } - else { - // Draw block. - ctx.fillStyle = "yellow"; - // TODO: This is a pretty hack-ish way to fill rectangle based on mode. - ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5), - s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT)); - } - } - else { - if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { - // Show insertions with a single number at the insertion point. - draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_start + 9] } ); - } - else { - // TODO: probably can merge this case with code above. - } - } - } - seq_offset += cig_len; - // No change to base offset because insertions are drawn above sequence/read. - break; - } - } - - // - // Draw last items. - // - ctx.fillStyle = "yellow"; - var item, type, data; - for (var i = 0; i < draw_last.length; i++) { - item = draw_last[i]; - type = item.type; - data = item.data; - if (type === "text") { - ctx.save(); - ctx.font = "bold " + ctx.font; - ctx.fillText(data[0], data[1], data[2]); - ctx.restore(); - } - else if (type === "triangle") { - drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]); - } - } - }, - - /** - * Draw a complete read pair - */ - draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) { - // All features need a start, end, and vertical center. - var feature_uid = feature[0], - feature_start = feature[1], - feature_end = feature[2], - feature_name = feature[3], - // -0.5 to put element between bases. - f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ), - f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ), - y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, - label_color = this.prefs.label_color; - - // Draw read. - if (feature[5] instanceof Array) { - // Read is paired. - var connector = true; - - // Draw left/forward read. - if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { - this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]); - } - else { - connector = false; - } - - // Draw right/reverse read. - if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) { - this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]); - } - else { - connector = false; - } - - // Draw connector if both reads were drawn. - // TODO: currently, there is no way to connect reads drawn on different tiles; to connect reads on different tiles, data manager - // code is needed to join mate pairs from different regions. Alternatively, requesting multiple regions of data at once would - // make it possible to put together more easily. - // -0.5 to position connector correctly between reads. - var b1_end = Math.ceil( Math.min(width, Math.max(-0.5 * w_scale, (feature[4][1] - tile_low - 0.5) * w_scale)) ), - b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) ); - if (connector && b2_start > b1_end) { - ctx.fillStyle = CONNECTOR_COLOR; - dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5); - } - } else { - // Read is single. - this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]); - } - if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") { - // Draw label. - ctx.fillStyle = this.prefs.label_color; - if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { - ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8); - } else { - ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8); - } - } - - // FIXME: provide actual coordinates for drawn read. - return [0,0]; - } -}); - -/** - * Painter for reads encoded using reference-based compression. - */ -var RefBasedReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq, base_color_fn) { - ReadPainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq, base_color_fn); -}; - -extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, { - /** * Draw a single read from reference-based read sequence and cigar. */ @@ -1255,6 +964,73 @@ drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]); } } + }, + + /** + * Draw a complete read pair + */ + draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) { + // All features need a start, end, and vertical center. + var feature_uid = feature[0], + feature_start = feature[1], + feature_end = feature[2], + feature_name = feature[3], + // -0.5 to put element between bases. + f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ), + f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ), + y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, + label_color = this.prefs.label_color; + + // Draw read. + if (feature[5] instanceof Array) { + // Read is paired. + var connector = true; + + // Draw left/forward read. + if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { + this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]); + } + else { + connector = false; + } + + // Draw right/reverse read. + if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) { + this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]); + } + else { + connector = false; + } + + // Draw connector if both reads were drawn. + // TODO: currently, there is no way to connect reads drawn on different tiles; to connect reads on different tiles, data manager + // code is needed to join mate pairs from different regions. Alternatively, requesting multiple regions of data at once would + // make it possible to put together more easily. + // -0.5 to position connector correctly between reads. + var b1_end = Math.ceil( Math.min(width, Math.max(-0.5 * w_scale, (feature[4][1] - tile_low - 0.5) * w_scale)) ), + b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) ); + if (connector && b2_start > b1_end) { + ctx.fillStyle = CONNECTOR_COLOR; + dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5); + } + } else { + // Read is single. + this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]); + } + if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") { + // Draw label. + ctx.fillStyle = this.prefs.label_color; + if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { + ctx.textAlign = "left"; + ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8); + } else { + ctx.textAlign = "right"; + ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8); + } + } + + // FIXME: provide actual coordinates for drawn read. + return [0,0]; } }); @@ -1775,7 +1551,6 @@ LinePainter: LinePainter, LinkedFeaturePainter: LinkedFeaturePainter, ReadPainter: ReadPainter, - RefBasedReadPainter: RefBasedReadPainter, ArcLinkedFeaturePainter: ArcLinkedFeaturePainter, DiagonalHeatmapPainter: DiagonalHeatmapPainter, VariantPainter: VariantPainter diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 9e7f9282deba9d383e708e210acea5dea8eb7673 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4163,8 +4163,7 @@ */ var ReadTrack = function (view, container, obj_dict) { FeatureTrack.call(this, view, container, obj_dict); - // Choose painter based on whether there is reference data. - this.painter = (view.reference_track ? painters.RefBasedReadPainter : painters.ReadPainter); + this.painter = painters.ReadPainter; this.update_icons(); }; https://bitbucket.org/galaxy/galaxy-central/commits/09676399640d/ Changeset: 09676399640d User: Jeremy Goecks Date: 2014-03-26 19:46:29 Summary: Trackster: remove reference to left_offset in painters because it is not needed. Affected #: 1 file diff -r 9e7f9282deba9d383e708e210acea5dea8eb7673 -r 09676399640d304d45dfeb81a32ed30d7314d855 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -127,9 +127,7 @@ Painter.prototype.default_prefs = {}; /** - * Draw on the context using a rectangle of width x height. w_scale is - * needed because it cannot be computed from width and view size alone - * as a left_offset may be present. + * Draw on the context using a rectangle of width x height using scale w_scale. */ Painter.prototype.draw = function(ctx, width, height, w_scale) {}; @@ -869,7 +867,6 @@ case "N": // Skipped bases. ctx.fillStyle = CONNECTOR_COLOR; ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1); - //ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5); // No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; @@ -1357,9 +1354,7 @@ }, /** - * Draw on the context using a rectangle of width x height. w_scale is - * needed because it cannot be computed from width and view size alone - * as a left_offset may be present. + * Draw on the context using a rectangle of width x height with scale w_scale. */ draw: function(ctx, width, height, w_scale) { ctx.save(); https://bitbucket.org/galaxy/galaxy-central/commits/ff91d665fb8e/ Changeset: ff91d665fb8e User: Jeremy Goecks Date: 2014-03-26 20:12:39 Summary: Trackster: set maximum label length. Affected #: 1 file diff -r 09676399640d304d45dfeb81a32ed30d7314d855 -r ff91d665fb8e211c0bea4c02d9c046f32be7005c static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -341,6 +341,7 @@ Painter.call(this, data, view_start, view_end, prefs, mode); this.alpha_scaler = (alpha_scaler ? alpha_scaler : new Scaler()); this.height_scaler = (height_scaler ? height_scaler : new Scaler()); + this.max_label_length = 200; }; FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" }; @@ -399,6 +400,7 @@ feature_mapper.y_translation = this.get_top_padding(width); return feature_mapper; }, + /** * Abstract function for drawing an individual feature. */ @@ -645,11 +647,11 @@ // FIXME: assumption here that the entire view starts at 0 if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8); + ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8, this.max_label_length); draw_end += ctx.measureText(feature_name).width + LABEL_SPACING; } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8); + ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8, this.max_label_length); draw_start -= ctx.measureText(feature_name).width + LABEL_SPACING; } //ctx.fillStyle = block_color; @@ -1019,10 +1021,10 @@ ctx.fillStyle = this.prefs.label_color; if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8); + ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8, this.max_label_length); } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8); + ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8, this.max_label_length); } } https://bitbucket.org/galaxy/galaxy-central/commits/cc7b0f0be551/ Changeset: cc7b0f0be551 User: Jeremy Goecks Date: 2014-03-26 20:39:14 Summary: Fix initialization of boolean values in client-side config object. Affected #: 1 file diff -r ff91d665fb8e211c0bea4c02d9c046f32be7005c -r cc7b0f0be551dd1c0564c1fd7b95b6a2aaa7ee39 static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -16,7 +16,7 @@ this.set(_.extend({}, defaults, options)); } - if (!this.get('value')) { + if (this.get('value') === undefined) { // Use default to set value. this.set_value(this.get('default_value')); https://bitbucket.org/galaxy/galaxy-central/commits/e298d0294721/ Changeset: e298d0294721 User: Jeremy Goecks Date: 2014-03-26 22:37:03 Summary: Trackster: fix offset bug that was rendering bases incorrectly. Affected #: 1 file diff -r cc7b0f0be551dd1c0564c1fd7b95b6a2aaa7ee39 -r e298d029472150df08bfae9b6ec311c78cb63dfd static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -740,6 +740,20 @@ * Draw a single read from reference-based read sequence and cigar. */ draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) { + // Helper function to update base and sequnence offsets. + var update_base_offset = function(offset, cig_op, cig_len) { + if ('M=NXD'.indexOf(cig_op) !== -1) { + offset += cig_len; + } + return offset; + }, + update_seq_offset = function(offset, cig_op, cig_len) { + if ('IX'.indexOf(cig_op) !== -1) { + offset += cig_len; + } + return offset; + }; + ctx.textAlign = "center"; var tile_region = [tile_low, tile_high], base_offset = 0, @@ -770,7 +784,7 @@ // Make sure that block is drawn even if it too small to be rendered officially; in this case, // read is drawn at 1px. - // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting + // TODO: need to ensure that s_start, s_end are calculated the same for both slotting // and drawing. if (s_start === s_end) { s_end += 1; @@ -793,21 +807,26 @@ var seq_start = feature_start + base_offset, // -0.5 to offset sequence between bases. - s_start = Math.floor( Math.max(0, -0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), + s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) ); + // Skip feature if it's not in tile. if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) { + // Update offsets. + base_offset = update_base_offset(base_offset, cig_op, cig_len); + seq_offset = update_seq_offset(seq_offset, cig_op, cig_len); continue; } // Make sure that read is drawn even if it too small to be rendered officially; in this case, // read is drawn at 1px. - // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting + // TODO: need to ensure that s_start, s_end are calculated the same for both slotting // and drawing. if (s_start === s_end) { s_end += 1; } - + + // Draw read feature. switch (cig_op) { case "H": // Hard clipping. case "S": // Soft clipping. https://bitbucket.org/galaxy/galaxy-central/commits/bc739e4b5bdf/ Changeset: bc739e4b5bdf User: Jeremy Goecks Date: 2014-03-26 22:38:22 Summary: Automated merge of local changesets with -default Affected #: 24 files diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -56,6 +56,7 @@ python_openid = 2.2.5 python_daemon = 1.5.5 pytz = 2013.9 +requests = 2.2.1 Routes = 1.12.3 sqlalchemy_migrate = 0.7.2 ssh = 1.7.14 diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -41,6 +41,7 @@ from galaxy.tools.parameters.basic import DataToolParameter from galaxy.util.json import to_json_string from galaxy.workflow.modules import ToolModule +from galaxy.workflow.steps import attach_ordered_steps log = logging.getLogger( __name__ ) @@ -1676,7 +1677,6 @@ """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ - from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps # Put parameters in workflow mode trans.workflow_building_mode = True diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -11,8 +11,10 @@ from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke +from galaxy.workflow.extract import extract_workflow log = logging.getLogger(__name__) @@ -51,7 +53,7 @@ step.state.inputs.update(param_dict) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin): @web.expose_api def index(self, trans, **kwd): @@ -141,9 +143,11 @@ """ POST /api/workflows - We're not creating workflows from the api. Just execute for now. + Run or create workflows from the api. - However, we will import them if installed_repository_file is specified. + If installed_repository_file or from_history_id is specified a new + workflow will be created for this user. Otherwise, workflow_id must be + specified and this API method will cause a workflow to execute. :param installed_repository_file The path of a workflow to import. Either workflow_id or installed_repository_file must be specified :type installed_repository_file str @@ -165,6 +169,15 @@ :param replacement_params: A dictionary used when renaming datasets :type replacement_params: dict + + :param from_history_id: Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file. + :type from_history_id: str + + :param job_ids: If from_history_id is set - this should be a list of jobs to include when extracting workflow from history. + :type job_ids: str + + :param dataset_ids: If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history. + :type dataset_ids: str """ # Pull parameters out of payload. @@ -183,6 +196,24 @@ cntrller='api', **payload) return result + if 'from_history_id' in payload: + from_history_id = payload.get( 'from_history_id' ) + history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True ) + job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) ) + dataset_ids = map( trans.security.decode_id, payload.get( "dataset_ids", [] ) ) + workflow_name = payload[ "workflow_name" ] + stored_workflow = extract_workflow( + trans=trans, + user=trans.get_user(), + history=history, + job_ids=job_ids, + dataset_ids=dataset_ids, + workflow_name=workflow_name, + ) + item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } ) + item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] ) + return item + trans.response.status = 403 return "Either workflow_id or installed_repository_file must be specified" if 'installed_repository_file' in payload: diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -201,9 +201,13 @@ repository_id = kwd.get( 'id', None ) repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) + params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ + ( web.url_for( '/', qualified=True ), + str( repository.name ), + str( repository.owner ), + str( repository.changeset_revision ) ) url = suc.url_join( tool_shed_url, - 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ - ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) + 'repository/check_for_updates%s' % params ) return trans.response.send_redirect( url ) @web.expose @@ -367,9 +371,10 @@ @web.require_admin def get_tool_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): """ - Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name, - owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need - it so that we can derive the tool shed from which it was installed. + Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for + the received repository name, owner and changeset revision. The received repository_id is the encoded id + of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which + it was installed. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) @@ -388,8 +393,8 @@ @web.require_admin def get_updated_repository_information( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): """ - Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an - uninstalled tool shed repository. + Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall + an updated revision of an uninstalled tool shed repository. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) @@ -436,13 +441,16 @@ @web.expose @web.require_admin - def initiate_tool_dependency_installation( self, trans, tool_dependencies ): + def initiate_tool_dependency_installation( self, trans, tool_dependencies, **kwd ): """Install specified dependencies for repository tools.""" # Get the tool_shed_repository from one of the tool_dependencies. - message = '' + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + err_msg = '' tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. - tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) + tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, + tool_shed_repository.repo_path( trans.app ) ) installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, @@ -452,13 +460,12 @@ if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) if text is not None: - message += ' %s' % text + err_msg += ' %s' % text tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies ] - if message: + if err_msg: + message += err_msg status = 'error' - else: - message = "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies ) - status = 'done' + message += "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies ) td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_tool_dependencies', @@ -506,9 +513,10 @@ status = 'error' else: # Install the latest downloadable revision of the repository. + params = '?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ + ( name, owner, str( latest_downloadable_revision ), web.url_for( '/', qualified=True ) ) url = suc.url_join( tool_shed_url, - 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ - ( name, owner, latest_downloadable_revision, web.url_for( '/', qualified=True ) ) ) + 'repository/install_repositories_by_revision%s' % params ) return trans.response.send_redirect( url ) else: message = 'Cannot locate installed tool shed repository with encoded id <b>%s</b>.' % str( repository_id ) @@ -521,43 +529,74 @@ message=message, status=status ) ) - @web.expose @web.require_admin - def install_tool_dependencies( self, trans, **kwd ): + def install_tool_dependencies_with_update( self, trans, **kwd ): + """ + Updating an installed tool shed repository where new tool dependencies but no new repository + dependencies are included in the updated revision. + """ + updating_repository_id = kwd.get( 'updating_repository_id', None ) + repository = suc.get_installed_tool_shed_repository( trans, updating_repository_id ) + # All received dependencies need to be installed - confirmed by the caller. + encoded_tool_dependencies_dict = kwd.get( 'encoded_tool_dependencies_dict', None ) + if encoded_tool_dependencies_dict is not None: + tool_dependencies_dict = encoding_util.tool_shed_decode( encoded_tool_dependencies_dict ) + else: + tool_dependencies_dict = {} + encoded_relative_install_dir = kwd.get( 'encoded_relative_install_dir', None ) + if encoded_relative_install_dir is not None: + relative_install_dir = encoding_util.tool_shed_decode( encoded_relative_install_dir ) + else: + relative_install_dir = '' + updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None ) + updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None ) + encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) - tool_dependencies = [] - for tool_dependency_id in tool_dependency_ids: - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) - tool_dependencies.append( tool_dependency ) - if kwd.get( 'install_tool_dependencies_button', False ): - # Filter tool dependencies to only those that are installed. - tool_dependencies_for_installation = [] - for tool_dependency in tool_dependencies: - if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.UNINSTALLED, - trans.install_model.ToolDependency.installation_status.ERROR ]: - tool_dependencies_for_installation.append( tool_dependency ) - if tool_dependencies_for_installation: - # Redirect back to the ToolDependencyGrid before initiating installation. - encoded_tool_dependency_for_installation_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies_for_installation ] - new_kwd = dict( action='manage_tool_dependencies', - operation='initiate_tool_dependency_installation', - tool_dependency_ids=encoded_tool_dependency_for_installation_ids, - message=message, - status=status ) - return self.tool_dependency_grid( trans, **new_kwd ) + install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) + if 'install_tool_dependencies_with_update_button' in kwd: + # Now that the user has chosen whether to install tool dependencies or not, we can + # update the repository record with the changes in the updated revision. + if encoded_updated_metadata: + updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) else: - message = 'All of the selected tool dependencies are already installed.' - status = 'error' - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repository_tool_dependencies', - tool_dependency_ids=tool_dependency_ids, - status=status, - message=message ) ) - return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies.mako', - tool_dependencies=tool_dependencies, + updated_metadata = None + repository = repository_util.update_repository_record( trans, + repository=repository, + updated_metadata_dict=updated_metadata, + updated_changeset_revision=updating_to_changeset_revision, + updated_ctx_rev=updating_to_ctx_rev ) + if install_tool_dependencies: + tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, + repository, + relative_install_dir, + set_status=False ) + message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ + ( str( repository.name ), updating_to_changeset_revision ) + self.initiate_tool_dependency_installation( trans, tool_dependencies, message=message, status=status ) + # Handle tool dependencies check box. + if trans.app.config.tool_dependency_dir is None: + if includes_tool_dependencies: + message = "Tool dependencies defined in this repository can be automatically installed if you set " + message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " + message += "(universe_wsgi.ini) and restart your Galaxy server." + status = "warning" + install_tool_dependencies_check_box_checked = False + else: + install_tool_dependencies_check_box_checked = True + install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', + checked=install_tool_dependencies_check_box_checked ) + return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies_with_update.mako', + repository=repository, + updating_repository_id=updating_repository_id, + updating_to_ctx_rev=updating_to_ctx_rev, + updating_to_changeset_revision=updating_to_changeset_revision, + encoded_updated_metadata=encoded_updated_metadata, + encoded_relative_install_dir=encoded_relative_install_dir, + encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, + install_tool_dependencies_check_box=install_tool_dependencies_check_box, + tool_dependencies_dict=tool_dependencies_dict, message=message, status=status ) @@ -611,7 +650,8 @@ # TODO: I believe this block should be removed, but make sure.. repositories_for_uninstallation = [] for repository_id in tsridslist: - repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( repository_id ) ) + repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ + .get( trans.security.decode_id( repository_id ) ) if repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLED, trans.install_model.ToolShedRepository.installation_status.ERROR ]: repositories_for_uninstallation.append( repository ) @@ -632,28 +672,34 @@ filtered_repo_info_dicts = [] filtered_tool_panel_section_keys = [] repositories_for_installation = [] - # Some repositories may have repository dependencies that are required to be installed before the dependent repository, so we'll - # order the list of tsr_ids to ensure all repositories install in the required order. + # Some repositories may have repository dependencies that are required to be installed before the + # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the + # required order. ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ repository_util.order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) for tsr_id in ordered_tsr_ids: - repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) + repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ + .get( trans.security.decode_id( tsr_id ) ) if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW, trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: repositories_for_installation.append( repository ) - repo_info_dict, tool_panel_section_key = repository_util.get_repository_components_for_installation( tsr_id, - ordered_tsr_ids, - ordered_repo_info_dicts, - ordered_tool_panel_section_keys ) + repo_info_dict, tool_panel_section_key = \ + repository_util.get_repository_components_for_installation( tsr_id, + ordered_tsr_ids, + ordered_repo_info_dicts, + ordered_tool_panel_section_keys ) filtered_repo_info_dicts.append( repo_info_dict ) filtered_tool_panel_section_keys.append( tool_panel_section_key ) if repositories_for_installation: decoded_kwd[ 'repo_info_dicts' ] = filtered_repo_info_dicts decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys - self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) + self.install_tool_shed_repositories( trans, + repositories_for_installation, + reinstalling=reinstalling, + **decoded_kwd ) else: kwd[ 'message' ] = 'All selected tool shed repositories are already installed.' kwd[ 'status' ] = 'error' @@ -772,7 +818,10 @@ trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) if tool_dependencies_for_installation: - self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) + self.initiate_tool_dependency_installation( trans, + tool_dependencies_for_installation, + message=message, + status=status ) else: message = 'All selected tool dependencies are already installed.' status = 'error' @@ -780,14 +829,16 @@ message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) ' message += ' and restart your Galaxy server to install tool dependencies.' status = 'error' - installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, - tool_shed_repository=tool_shed_repository, - name='inst_td_ids', - uninstalled_only=False ) - uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, - tool_shed_repository=tool_shed_repository, - name='uninstalled_tool_dependency_ids', - uninstalled_only=True ) + installed_tool_dependencies_select_field = \ + suc.build_tool_dependencies_select_field( trans, + tool_shed_repository=tool_shed_repository, + name='inst_td_ids', + uninstalled_only=False ) + uninstalled_tool_dependencies_select_field = \ + suc.build_tool_dependencies_select_field( trans, + tool_shed_repository=tool_shed_repository, + name='uninstalled_tool_dependency_ids', + uninstalled_only=True ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako', repository=tool_shed_repository, installed_tool_dependencies_select_field=installed_tool_dependencies_select_field, @@ -836,7 +887,10 @@ trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) if tool_dependencies_for_installation: - self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) + self.initiate_tool_dependency_installation( trans, + tool_dependencies_for_installation, + message=message, + status=status ) else: kwd[ 'message' ] = 'All selected tool dependencies are already installed.' kwd[ 'status' ] = 'error' @@ -876,18 +930,21 @@ @web.require_admin def prepare_for_install( self, trans, **kwd ): if not suc.have_shed_tool_conf_for_install( trans ): - message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a ' - message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation ' - message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose ' - message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' - message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation of Galaxy tool shed repository tools ' - message += 'into a local Galaxy instance</a> section of the Galaxy tool shed wiki for all of the details.' + message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one ' + message += 'shed tool configuration file name with a <b><toolbox></b> tag that includes a <b>tool_path</b> ' + message += 'attribute value which is a directory relative to the Galaxy installation directory in order ' + message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> ' + message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' + message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation ' + message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool ' + message += 'Shed wiki for all of the details.' return trans.show_error_message( message ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) shed_tool_conf = kwd.get( 'shed_tool_conf', None ) tool_shed_url = kwd.get( 'tool_shed_url', None ) - # Handle repository dependencies, which do not include those that are required only for compiling a dependent repository's tool dependencies. + # Handle repository dependencies, which do not include those that are required only for compiling a dependent + # repository's tool dependencies. has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) ) install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' ) # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. @@ -900,13 +957,36 @@ includes_tools_for_display_in_tool_panel = util.string_as_bool( kwd.get( 'includes_tools_for_display_in_tool_panel', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' ) + # In addition to installing new repositories, this method is called when updating an installed repository + # to a new changeset_revision where the update includes newly defined repository dependencies. + updating = util.asbool( kwd.get( 'updating', False ) ) + updating_repository_id = kwd.get( 'updating_repository_id', None ) + updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None ) + updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None ) + encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None ) encoded_repo_info_dicts = kwd.get( 'encoded_repo_info_dicts', '' ) if encoded_repo_info_dicts: encoded_repo_info_dicts = encoded_repo_info_dicts.split( encoding_util.encoding_sep ) if not encoded_repo_info_dicts: - # The request originated in the tool shed via a tool search. + # The request originated in the tool shed via a tool search or from this controller's + # update_to_changeset_revision() method. repository_ids = kwd.get( 'repository_ids', None ) - changeset_revisions = kwd.get( 'changeset_revisions', None ) + if updating: + # We have updated an installed repository where the updates included newly defined repository + # and possibly tool dependencies. We will have arrived here only if the updates include newly + # defined repository dependencies. We're preparing to allow the user to elect to install these + # dependencies. At this point, the repository has been updated to the latest changeset revision, + # but the received repository id is from the Galaxy side (the caller is this controller's + # update_to_changeset_revision() method. We need to get the id of the same repository from the + # Tool Shed side. + repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id ) + url = suc.url_join( tool_shed_url, + 'repository/get_repository_id?name=%s&owner=%s' % \ + ( str( repository.name ), str( repository.owner ) ) ) + repository_ids = common_util.tool_shed_get( trans.app, tool_shed_url, url ) + changeset_revisions = updating_to_changeset_revision + else: + changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. url = suc.url_join( tool_shed_url, 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \ @@ -918,7 +998,8 @@ if not includes_tools: includes_tools = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools', False ) ) if not includes_tools_for_display_in_tool_panel: - includes_tools_for_display_in_tool_panel = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) ) + includes_tools_for_display_in_tool_panel = \ + util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) ) if not has_repository_dependencies: has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) ) if not includes_tool_dependencies: @@ -927,6 +1008,19 @@ repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] if ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \ ( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ): + if updating: + encoded_updated_metadata_dict = kwd.get( 'encoded_updated_metadata_dict', None ) + updated_changeset_revision = kwd.get( 'updated_changeset_revision', None ) + updated_ctx_rev = kwd.get( 'updated_ctx_rev', None ) + repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id ) + decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) + # Now that the user has decided whether they will handle dependencies, we can update + # the repository to the latest revision. + repository = repository_util.update_repository_record( trans, + repository=repository, + updated_metadata_dict=decoded_updated_metadata, + updated_changeset_revision=updating_to_changeset_revision, + updated_ctx_rev=updating_to_ctx_rev ) install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) @@ -959,7 +1053,8 @@ tool_panel_section_keys=tool_panel_section_keys, tool_path=tool_path, tool_shed_url=tool_shed_url ) - encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = repository_util.initiate_repository_installation( trans, installation_dict ) + encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ + repository_util.initiate_repository_installation( trans, installation_dict ) return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', encoded_kwd=encoded_kwd, query=query, @@ -976,12 +1071,14 @@ tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans ) if len( repo_info_dicts ) == 1: - # If we're installing a single repository, see if it contains a readme or dependencies that we can display. + # If we're installing or updating a single repository, see if it contains a readme or + # dependencies that we can display. repo_info_dict = repo_info_dicts[ 0 ] dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, - includes_tool_dependencies ) + includes_tool_dependencies, + updating=updating ) changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None ) if not has_repository_dependencies: has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) @@ -990,7 +1087,8 @@ if not includes_tools: includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False ) if not includes_tools_for_display_in_tool_panel: - includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) + includes_tools_for_display_in_tool_panel = \ + dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None ) installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None ) missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None ) @@ -998,19 +1096,25 @@ name = dependencies_for_repository_dict.get( 'name', None ) repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None ) readme_files_dict = readme_util.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ) - # We're handling 1 of 2 scenarios here: (1) we're installing a tool shed repository for the first time, so we've retrieved the list of installed - # and missing repository dependencies from the database (2) we're handling the scenario where an error occurred during the installation process, - # so we have a tool_shed_repository record in the database with associated repository dependency records. Since we have the repository - # dependencies in either case, we'll merge the list of missing repository dependencies into the list of installed repository dependencies since - # each displayed repository dependency will display a status, whether installed or missing. - containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + # We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've + # retrieved the list of installed and missing repository dependencies from the database (2) we're handling the + # scenario where an error occurred during the installation process, so we have a tool_shed_repository record in + # the database with associated repository dependency records. Since we have the repository dependencies in both + # of the above 2 cases, we'll merge the list of missing repository dependencies into the list of installed + # repository dependencies since each displayed repository dependency will display a status, whether installed or + # missing. The 3rd scenario is where we're updating an installed repository and the updates include newly + # defined repository (and possibly tool) dependencies. In this case, merging will result in newly defined + # dependencies to be lost. We pass the updating parameter to make sure merging occurs only when appropriate. + containers_dict = \ + repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=updating ) else: # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies. containers_dicts = [] @@ -1018,7 +1122,8 @@ dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, - includes_tool_dependencies ) + includes_tool_dependencies, + updating=updating ) changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None ) if not has_repository_dependencies: has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) @@ -1027,34 +1132,39 @@ if not includes_tools: includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False ) if not includes_tools_for_display_in_tool_panel: - includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) + includes_tools_for_display_in_tool_panel = \ + dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None ) installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None ) missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None ) missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None ) name = dependencies_for_repository_dict.get( 'name', None ) repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None ) - containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=None, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + containers_dict = \ + repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=None, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=updating ) containers_dicts.append( containers_dict ) # Merge all containers into a single container. containers_dict = repository_util.merge_containers_dicts_for_new_install( containers_dicts ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: - message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " - message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository." + message = "Tool dependencies defined in this repository can be automatically installed if you set " + message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " + message += "(universe_wsgi.ini) and restart your Galaxy server before installing the repository." status = "warning" install_tool_dependencies_check_box_checked = False else: install_tool_dependencies_check_box_checked = True - install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) + install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', + checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts ) @@ -1062,6 +1172,11 @@ if includes_tools_for_display_in_tool_panel: return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, + updating=updating, + updating_repository_id=updating_repository_id, + updating_to_ctx_rev=updating_to_ctx_rev, + updating_to_changeset_revision=updating_to_changeset_revision, + encoded_updated_metadata=encoded_updated_metadata, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, @@ -1077,10 +1192,16 @@ message=message, status=status ) else: - # If installing repositories that includes no tools and has no repository dependencies, display a page allowing the Galaxy administrator to - # select a shed-related tool panel configuration file whose tool_path setting will be the location the repositories will be installed. + # If installing repositories that includes no tools and has no repository dependencies, display a page + # allowing the Galaxy administrator to select a shed-related tool panel configuration file whose tool_path + # setting will be the location the repositories will be installed. return trans.fill_template( '/admin/tool_shed_repository/select_shed_tool_panel_config.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, + updating=updating, + updating_repository_id=updating_repository_id, + updating_to_ctx_rev=updating_to_ctx_rev, + updating_to_changeset_revision=updating_to_changeset_revision, + encoded_updated_metadata=encoded_updated_metadata, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, @@ -1400,7 +1521,8 @@ dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, - includes_tool_dependencies ) + includes_tool_dependencies, + updating=False ) changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None ) has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False ) @@ -1449,14 +1571,16 @@ original_section_name = '' tool_panel_section_select_field = None shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) - containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + containers_dict = \ + repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=False ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed # repository dependency will display a status, whether installed or missing. containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) @@ -1574,8 +1698,8 @@ @web.require_admin def set_tool_versions( self, trans, **kwd ): """ - Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the - metadata for the repository's revision in the Galaxy database. + Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed + repository and update the metadata for the repository's revision in the Galaxy database. """ repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) @@ -1720,29 +1844,17 @@ resetting_all_metadata_on_repository=False, updating_installed_repository=True, persist=True ) - repository.metadata = metadata_dict - # Update the repository.changeset_revision column in the database. - repository.changeset_revision = latest_changeset_revision - repository.ctx_rev = latest_ctx_rev - # Update the repository.tool_shed_status column in the database. - tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository ) - if tool_shed_status_dict: - repository.tool_shed_status = tool_shed_status_dict - else: - repository.tool_shed_status = None - trans.install_model.context.add( repository ) - trans.install_model.context.flush() if 'tools' in metadata_dict: tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) tool_util.add_to_tool_panel( app=trans.app, - repository_name=repository.name, + repository_name=str( repository.name ), repository_clone_url=repository_clone_url, - changeset_revision=repository.installed_changeset_revision, + changeset_revision=str( repository.installed_changeset_revision ), repository_tools_tups=repository_tools_tups, - owner=repository.owner, + owner=str( repository.owner ), shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=False ) @@ -1755,19 +1867,40 @@ os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - # Create tool_dependency records if necessary. - if 'tool_dependencies' in metadata_dict: - tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, - repository, - relative_install_dir, - set_status=False ) + if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: + if 'repository_dependencies' in metadata_dict: + # Updates received include newly defined repository dependencies, so allow the user + # the option of installting them. We cannot update the repository with the changes + # until that happens, so we have to send them along. + new_kwd = dict( tool_shed_url=tool_shed_url, + updating_repository_id=trans.security.encode_id( repository.id ), + updating_to_ctx_rev=latest_ctx_rev, + updating_to_changeset_revision=latest_changeset_revision, + encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + updating=True ) + return self.prepare_for_install( trans, **new_kwd ) + # Updates received did not include any newly defined repository dependencies but did include + # newly defined tool dependencies. + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) + new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), + updating_to_ctx_rev=latest_ctx_rev, + updating_to_changeset_revision=latest_changeset_revision, + encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_relative_install_dir=encoded_relative_install_dir, + encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, + message=message, + status = status ) + return self.install_tool_dependencies_with_update( trans, **new_kwd ) + # Updates received did not include any newly defined repository dependencies or newly defined + # tool dependencies. + repository = repository_util.update_repository_record( trans, + repository=repository, + updated_metadata_dict=metadata_dict, + updated_changeset_revision=latest_changeset_revision, + updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ ( name, latest_changeset_revision ) - # See if any tool dependencies can be installed. - shed_tool_conf, tool_path, relative_install_dir = \ - suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - if repository.missing_tool_dependencies: - message += "Click the name of one of the missing tool dependencies listed below to install tool dependencies." else: message = "The directory containing the installed repository named '%s' cannot be found. " % name status = 'error' diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -4,7 +4,6 @@ import base64 import httplib import json -import math import os import sgmllib import svgfig @@ -20,12 +19,9 @@ from galaxy.datatypes.data import Data from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc +from galaxy.tools.parameters.basic import DataToolParameter from galaxy.tools.parameters import visit_input_values -from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue -from galaxy.tools.parameters.grouping import Conditional, Repeat -from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html -from galaxy.util.topsort import CycleError, topsort, topsort_levels from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework import form @@ -33,6 +29,14 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke +from galaxy.workflow.extract import summarize +from galaxy.workflow.extract import extract_workflow +from galaxy.workflow.steps import ( + attach_ordered_steps, + order_workflow_steps, + edgelist_for_workflow_steps, + order_workflow_steps_with_levels, +) class StoredWorkflowListGrid( grids.Grid ): @@ -1188,7 +1192,7 @@ if not user: return trans.show_error_message( "Must be logged in to create workflows" ) if ( job_ids is None and dataset_ids is None ) or workflow_name is None: - jobs, warnings = get_job_dict( trans ) + jobs, warnings = summarize( trans ) # Render return trans.fill_template( "workflow/build_from_current_history.mako", @@ -1197,82 +1201,13 @@ history=history ) else: - # Ensure job_ids and dataset_ids are lists (possibly empty) - if job_ids is None: - job_ids = [] - elif type( job_ids ) is not list: - job_ids = [ job_ids ] - if dataset_ids is None: - dataset_ids = [] - elif type( dataset_ids ) is not list: - dataset_ids = [ dataset_ids ] - # Convert both sets of ids to integers - job_ids = [ int( id ) for id in job_ids ] - dataset_ids = [ int( id ) for id in dataset_ids ] - # Find each job, for security we (implicately) check that they are - # associated witha job in the current history. - jobs, warnings = get_job_dict( trans ) - jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) - steps = [] - steps_by_job_id = {} - hid_to_output_pair = {} - # Input dataset steps - for hid in dataset_ids: - step = model.WorkflowStep() - step.type = 'data_input' - step.tool_inputs = dict( name="Input Dataset" ) - hid_to_output_pair[ hid ] = ( step, 'output' ) - steps.append( step ) - # Tool steps - for job_id in job_ids: - assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" - job = jobs_by_id[ job_id ] - tool = trans.app.toolbox.get_tool( job.tool_id ) - param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here - associations = cleanup_param_values( tool.inputs, param_values ) - step = model.WorkflowStep() - step.type = 'tool' - step.tool_id = job.tool_id - step.tool_inputs = tool.params_to_strings( param_values, trans.app ) - # NOTE: We shouldn't need to do two passes here since only - # an earlier job can be used as an input to a later - # job. - for other_hid, input_name in associations: - if other_hid in hid_to_output_pair: - other_step, other_name = hid_to_output_pair[ other_hid ] - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - # Should always be connected to an earlier step - conn.output_step = other_step - conn.output_name = other_name - steps.append( step ) - steps_by_job_id[ job_id ] = step - # Store created dataset hids - for assoc in job.output_datasets: - hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) - # Workflow to populate - workflow = model.Workflow() - workflow.name = workflow_name - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - # And let's try to set up some reasonable locations on the canvas - # (these are pretty arbitrary values) - levorder = order_workflow_steps_with_levels( steps ) - base_pos = 10 - for i, steps_at_level in enumerate( levorder ): - for j, index in enumerate( steps_at_level ): - step = steps[ index ] - step.position = dict( top=( base_pos + 120 * j ), - left=( base_pos + 220 * i ) ) - # Store it - stored = model.StoredWorkflow() - stored.user = user - stored.name = workflow_name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - trans.sa_session.add( stored ) - trans.sa_session.flush() + extract_workflow( + trans, + user=user, + job_ids=job_ids, + dataset_ids=dataset_ids, + workflow_name=workflow_name + ) # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" @@ -1692,148 +1627,6 @@ ## ---- Utility methods ------------------------------------------------------- -def attach_ordered_steps( workflow, steps ): - ordered_steps = order_workflow_steps( steps ) - if ordered_steps: - workflow.has_cycles = False - for i, step in enumerate( ordered_steps ): - step.order_index = i - workflow.steps.append( step ) - else: - workflow.has_cycles = True - workflow.steps = steps - - -def edgelist_for_workflow_steps( steps ): - """ - Create a list of tuples representing edges between ``WorkflowSteps`` based - on associated ``WorkflowStepConnection``s - """ - edges = [] - steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) - for step in steps: - edges.append( ( steps_to_index[step], steps_to_index[step] ) ) - for conn in step.input_connections: - edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) ) - return edges - - -def order_workflow_steps( steps ): - """ - Perform topological sort of the steps, return ordered or None - """ - position_data_available = True - for step in steps: - if not step.position or not 'left' in step.position or not 'top' in step.position: - position_data_available = False - if position_data_available: - steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2))) - try: - edges = edgelist_for_workflow_steps( steps ) - node_order = topsort( edges ) - return [ steps[i] for i in node_order ] - except CycleError: - return None - - -def order_workflow_steps_with_levels( steps ): - try: - return topsort_levels( edgelist_for_workflow_steps( steps ) ) - except CycleError: - return None - - -class FakeJob( object ): - """ - Fake job object for datasets that have no creating_job_associations, - they will be treated as "input" datasets. - """ - def __init__( self, dataset ): - self.is_fake = True - self.id = "fake_%s" % dataset.id - - -def get_job_dict( trans ): - """ - Return a dictionary of Job -> [ Dataset ] mappings, for all finished - active Datasets in the current history and the jobs that created them. - """ - history = trans.get_history() - # Get the jobs that created the datasets - warnings = set() - jobs = odict() - for dataset in history.active_datasets: - # FIXME: Create "Dataset.is_finished" - if dataset.state in ( 'new', 'running', 'queued' ): - warnings.add( "Some datasets still queued or running were ignored" ) - continue - - #if this hda was copied from another, we need to find the job that created the origial hda - job_hda = dataset - while job_hda.copied_from_history_dataset_association: - job_hda = job_hda.copied_from_history_dataset_association - - if not job_hda.creating_job_associations: - jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - - for assoc in job_hda.creating_job_associations: - job = assoc.job - if job in jobs: - jobs[ job ].append( ( assoc.name, dataset ) ) - else: - jobs[ job ] = [ ( assoc.name, dataset ) ] - return jobs, warnings - - -def cleanup_param_values( inputs, values ): - """ - Remove 'Data' values from `param_values`, along with metadata cruft, - but track the associations. - """ - associations = [] - # dbkey is pushed in by the framework - if 'dbkey' in values: - del values['dbkey'] - root_values = values - - # Recursively clean data inputs and dynamic selects - def cleanup( prefix, inputs, values ): - for key, input in inputs.items(): - if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ): - if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ): - values[key] = UnvalidatedValue( values[key] ) - if isinstance( input, DataToolParameter ): - tmp = values[key] - values[key] = None - # HACK: Nested associations are not yet working, but we - # still need to clean them up so we can serialize - # if not( prefix ): - if tmp: # this is false for a non-set optional dataset - if not isinstance(tmp, list): - associations.append( ( tmp.hid, prefix + key ) ) - else: - associations.extend( [ (t.hid, prefix + key) for t in tmp] ) - - # Cleanup the other deprecated crap associated with datasets - # as well. Worse, for nested datasets all the metadata is - # being pushed into the root. FIXME: MUST REMOVE SOON - key = prefix + key + "_" - for k in root_values.keys(): - if k.startswith( key ): - del root_values[k] - elif isinstance( input, Repeat ): - group_values = values[key] - for i, rep_values in enumerate( group_values ): - rep_index = rep_values['__index__'] - cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] ) - elif isinstance( input, Conditional ): - group_values = values[input.name] - current_case = group_values['__current_case__'] - cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values ) - cleanup( "", inputs, values ) - return associations - - def _build_workflow_on_str(instance_ds_names): # Returns suffix for new histories based on multi input iteration num_multi_inputs = len(instance_ds_names) diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -866,11 +866,13 @@ no_update = 'false' elif galaxy_url: # Start building up the url to redirect back to the calling Galaxy instance. + params = '?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ + ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) url = suc.url_join( galaxy_url, - 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ - ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) + 'admin_toolshed/update_to_changeset_revision%s' % params ) else: - message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url + message += 'You may need to enable third-party cookies in your browser. ' return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. @@ -883,15 +885,17 @@ trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: - # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. + # If changeset_revision is in the repository_metadata table for this repository, there are no + # additional updates. if from_update_manager: return no_update else: # Return the same value for changeset_revision and latest_changeset_revision. url += latest_changeset_revision else: - # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the - # repository was installed. We need to find the changeset_revision to which we need to update. + # The changeset_revision column in the repository_metadata table has been updated with a new + # changeset_revision value since the repository was installed. We need to find the changeset_revision + # to which we need to update. update_to_changeset_hash = None for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) @@ -1680,6 +1684,16 @@ return encoding_util.tool_shed_encode( repository_dependencies ) return '' + @web.expose + def get_repository_id( self, trans, **kwd ): + """Given a repository name and owner, return the encoded repository id.""" + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] + repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) + if repository: + return trans.security.encode_id( repository.id ) + return '' + @web.json def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ): """ @@ -1824,7 +1838,9 @@ if not repository_metadata: # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository # changelog that is associated with metadata. - changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision=changeset_revision ) + changeset_revision = suc.get_next_downloadable_changeset_revision( repository, + repo, + after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = repository_util.create_repo_info_dict( trans=trans, @@ -2039,11 +2055,12 @@ galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if galaxy_url: # Redirect back to local Galaxy to perform install. + params = '?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ + ( web.url_for( '/', qualified=True ), + ','.join( util.listify( repository_ids ) ), + ','.join( util.listify( changeset_revisions ) ) ) url = suc.url_join( galaxy_url, - 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ - ( web.url_for( '/', qualified=True ), - ','.join( util.listify( repository_ids ) ), - ','.join( util.listify( changeset_revisions ) ) ) ) + 'admin_toolshed/prepare_for_install%s' % params ) return trans.response.send_redirect( url ) else: message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url @@ -2477,9 +2494,10 @@ @web.expose def next_installable_changeset_revision( self, trans, **kwd ): """ - Handle a request from a Galaxy instance where the changeset_revision defined for a repository in a dependency definition file is older - than the changeset_revision associated with the installed repository. This will occur with repository's of type tool_dependency_definition, - and this scenario will occur while repository dependency hierarchies are bing installed. + Handle a request from a Galaxy instance where the changeset_revision defined for a repository + in a dependency definition file is older than the changeset_revision associated with the installed + repository. This will occur with repository's of type tool_dependency_definition, and this scenario + will occur while repository dependency hierarchies are bing installed. """ name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) @@ -2981,12 +2999,13 @@ @web.expose def updated_changeset_revisions( self, trans, **kwd ): """ - Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an installed repository can be updated. This - method will return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision. Among - other things , this method handles the scenario where an installed tool shed repository's tool_dependency definition file defines a changeset - revision for a complex repository dependency that is outdated. In other words, a defined changeset revision is older than the current changeset - revision for the required repository, making it impossible to discover the repository without knowledge of revisions to which it could have been - updated. + Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an + installed repository can be updated. This method will return a string of comma-separated changeset revision + hashes for all available updates to the received changeset revision. Among other things , this method + handles the scenario where an installed tool shed repository's tool_dependency definition file defines a + changeset revision for a complex repository dependency that is outdated. In other words, a defined changeset + revision is older than the current changeset revision for the required repository, making it impossible to + discover the repository without knowledge of revisions to which it could have been updated. """ name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/workflow/extract.py --- /dev/null +++ b/lib/galaxy/workflow/extract.py @@ -0,0 +1,209 @@ +""" This module contains functionality to aid in extracting workflows from +histories. +""" +from galaxy.util.odict import odict +from galaxy import model +from galaxy.tools.parameters.basic import ( + DataToolParameter, + DrillDownSelectToolParameter, + SelectToolParameter, + UnvalidatedValue +) +from galaxy.tools.parameters.grouping import ( + Conditional, + Repeat +) +from .steps import ( + attach_ordered_steps, + order_workflow_steps_with_levels +) + +WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored" + + +def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, workflow_name=None ): + steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids ) + # Workflow to populate + workflow = model.Workflow() + workflow.name = workflow_name + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + # And let's try to set up some reasonable locations on the canvas + # (these are pretty arbitrary values) + levorder = order_workflow_steps_with_levels( steps ) + base_pos = 10 + for i, steps_at_level in enumerate( levorder ): + for j, index in enumerate( steps_at_level ): + step = steps[ index ] + step.position = dict( top=( base_pos + 120 * j ), + left=( base_pos + 220 * i ) ) + # Store it + stored = model.StoredWorkflow() + stored.user = user + stored.name = workflow_name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + trans.sa_session.add( stored ) + trans.sa_session.flush() + return stored + + +def extract_steps( trans, history=None, job_ids=None, dataset_ids=None ): + # Ensure job_ids and dataset_ids are lists (possibly empty) + if job_ids is None: + job_ids = [] + elif type( job_ids ) is not list: + job_ids = [ job_ids ] + if dataset_ids is None: + dataset_ids = [] + elif type( dataset_ids ) is not list: + dataset_ids = [ dataset_ids ] + # Convert both sets of ids to integers + job_ids = [ int( id ) for id in job_ids ] + dataset_ids = [ int( id ) for id in dataset_ids ] + # Find each job, for security we (implicately) check that they are + # associated witha job in the current history. + jobs, warnings = summarize( trans, history=history ) + jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) + steps = [] + steps_by_job_id = {} + hid_to_output_pair = {} + # Input dataset steps + for hid in dataset_ids: + step = model.WorkflowStep() + step.type = 'data_input' + step.tool_inputs = dict( name="Input Dataset" ) + hid_to_output_pair[ hid ] = ( step, 'output' ) + steps.append( step ) + # Tool steps + for job_id in job_ids: + assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" + job = jobs_by_id[ job_id ] + tool_inputs, associations = step_inputs( trans, job ) + step = model.WorkflowStep() + step.type = 'tool' + step.tool_id = job.tool_id + step.tool_inputs = tool_inputs + # NOTE: We shouldn't need to do two passes here since only + # an earlier job can be used as an input to a later + # job. + for other_hid, input_name in associations: + if other_hid in hid_to_output_pair: + other_step, other_name = hid_to_output_pair[ other_hid ] + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + # Should always be connected to an earlier step + conn.output_step = other_step + conn.output_name = other_name + steps.append( step ) + steps_by_job_id[ job_id ] = step + # Store created dataset hids + for assoc in job.output_datasets: + hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) + return steps + + +class FakeJob( object ): + """ + Fake job object for datasets that have no creating_job_associations, + they will be treated as "input" datasets. + """ + def __init__( self, dataset ): + self.is_fake = True + self.id = "fake_%s" % dataset.id + + +def summarize( trans, history=None ): + """ Return mapping of job description to datasets for active items in + supplied history - needed for building workflow from a history. + + Formerly call get_job_dict in workflow web controller. + """ + if not history: + history = trans.get_history() + + # Get the jobs that created the datasets + warnings = set() + jobs = odict() + for dataset in history.active_datasets: + # FIXME: Create "Dataset.is_finished" + if dataset.state in ( 'new', 'running', 'queued' ): + warnings.add( WARNING_SOME_DATASETS_NOT_READY ) + continue + + #if this hda was copied from another, we need to find the job that created the origial hda + job_hda = dataset + while job_hda.copied_from_history_dataset_association: + job_hda = job_hda.copied_from_history_dataset_association + + if not job_hda.creating_job_associations: + jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] + + for assoc in job_hda.creating_job_associations: + job = assoc.job + if job in jobs: + jobs[ job ].append( ( assoc.name, dataset ) ) + else: + jobs[ job ] = [ ( assoc.name, dataset ) ] + + return jobs, warnings + + +def step_inputs( trans, job ): + tool = trans.app.toolbox.get_tool( job.tool_id ) + param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here + associations = __cleanup_param_values( tool.inputs, param_values ) + tool_inputs = tool.params_to_strings( param_values, trans.app ) + return tool_inputs, associations + + +def __cleanup_param_values( inputs, values ): + """ + Remove 'Data' values from `param_values`, along with metadata cruft, + but track the associations. + """ + associations = [] + # dbkey is pushed in by the framework + if 'dbkey' in values: + del values['dbkey'] + root_values = values + + # Recursively clean data inputs and dynamic selects + def cleanup( prefix, inputs, values ): + for key, input in inputs.items(): + if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ): + if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ): + values[key] = UnvalidatedValue( values[key] ) + if isinstance( input, DataToolParameter ): + tmp = values[key] + values[key] = None + # HACK: Nested associations are not yet working, but we + # still need to clean them up so we can serialize + # if not( prefix ): + if tmp: # this is false for a non-set optional dataset + if not isinstance(tmp, list): + associations.append( ( tmp.hid, prefix + key ) ) + else: + associations.extend( [ (t.hid, prefix + key) for t in tmp] ) + + # Cleanup the other deprecated crap associated with datasets + # as well. Worse, for nested datasets all the metadata is + # being pushed into the root. FIXME: MUST REMOVE SOON + key = prefix + key + "_" + for k in root_values.keys(): + if k.startswith( key ): + del root_values[k] + elif isinstance( input, Repeat ): + group_values = values[key] + for i, rep_values in enumerate( group_values ): + rep_index = rep_values['__index__'] + cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] ) + elif isinstance( input, Conditional ): + group_values = values[input.name] + current_case = group_values['__current_case__'] + cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values ) + cleanup( "", inputs, values ) + return associations + +__all__ = [ summarize, extract_workflow ] diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/workflow/steps.py --- /dev/null +++ b/lib/galaxy/workflow/steps.py @@ -0,0 +1,63 @@ +""" This module contains utility methods for reasoning about and ordering +workflow steps. +""" +import math +from galaxy.util.topsort import ( + CycleError, + topsort, + topsort_levels +) + + +def attach_ordered_steps( workflow, steps ): + """ Attempt to topologically order steps and attach to workflow. If this + fails - the workflow contains cycles so it mark it as such. + """ + ordered_steps = order_workflow_steps( steps ) + if ordered_steps: + workflow.has_cycles = False + for i, step in enumerate( ordered_steps ): + step.order_index = i + workflow.steps.append( step ) + else: + workflow.has_cycles = True + workflow.steps = steps + + +def order_workflow_steps( steps ): + """ + Perform topological sort of the steps, return ordered or None + """ + position_data_available = True + for step in steps: + if not step.position or not 'left' in step.position or not 'top' in step.position: + position_data_available = False + if position_data_available: + steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2))) + try: + edges = edgelist_for_workflow_steps( steps ) + node_order = topsort( edges ) + return [ steps[i] for i in node_order ] + except CycleError: + return None + + +def edgelist_for_workflow_steps( steps ): + """ + Create a list of tuples representing edges between ``WorkflowSteps`` based + on associated ``WorkflowStepConnection``s + """ + edges = [] + steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) + for step in steps: + edges.append( ( steps_to_index[step], steps_to_index[step] ) ) + for conn in step.input_connections: + edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) ) + return edges + + +def order_workflow_steps_with_levels( steps ): + try: + return topsort_levels( edgelist_for_workflow_steps( steps ) ) + except CycleError: + return None diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -37,15 +37,19 @@ Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. - This method is called from Galaxy under three scenarios: + This method is called from Galaxy under four scenarios: 1. During the tool shed repository installation process via the tool shed's get_repository_information() - method. In this case both the received repository and repository_metadata will be objects., but + method. In this case both the received repository and repository_metadata will be objects, but tool_dependencies and repository_dependencies will be None. - 2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no + 2. When getting updates for an install repository where the updates include newly defined repository + dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information() + method is the caller, and both the received repository and repository_metadata will be objects, but + tool_dependencies and repository_dependencies will be None. + 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes definitions for them. - 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates + 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates available. In this case, this method is reached via the tool shed's get_updated_repository_information() method, and both repository and repository_metadata will be objects but tool_dependencies and repository_dependencies will be None. @@ -184,16 +188,22 @@ repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + repository_id, + changeset_revision ) if not repository_metadata: - # The received changeset_revision is no longer installable, so get the next changeset_revision in the repository's changelog. - # This generally occurs only with repositories of type tool_dependency_definition. - next_downloadable_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + # The received changeset_revision is no longer installable, so get the next changeset_revision + # in the repository's changelog. This generally occurs only with repositories of type + # tool_dependency_definition. + next_downloadable_changeset_revision = \ + suc.get_next_downloadable_changeset_revision( repository,repo, changeset_revision ) if next_downloadable_changeset_revision: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision ) + repository_metadata = \ + suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision ) if repository_metadata: - # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption is not valid we'll have to - # enhance the callers to handle repository_metadata values of None in the returned repo_info_dict. + # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption + # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the + # returned repo_info_dict. metadata = repository_metadata.metadata if 'tools' in metadata: includes_tools = True @@ -743,9 +753,13 @@ ordered_tool_panel_section_keys.append( tool_panel_section_key ) return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys -def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies, - installed_tool_dependencies, missing_tool_dependencies ): - """Return the populated containers for a repository being installed for the first time.""" +def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, + missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies, + updating=False ): + """ + Return the populated containers for a repository being installed for the first time or for an installed repository + that is being updated and the updates include newly defined repository (and possibly tool) dependencies. + """ installed_tool_dependencies, missing_tool_dependencies = \ tool_dependency_util.populate_tool_dependencies_dicts( trans=trans, tool_shed_url=tool_shed_url, @@ -753,27 +767,32 @@ repository_installed_tool_dependencies=installed_tool_dependencies, repository_missing_tool_dependencies=missing_tool_dependencies, required_repo_info_dicts=None ) - # Since we are installing a new repository, most of the repository contents are set to None since we don't yet know what they are. - containers_dict = container_util.build_repository_containers_for_galaxy( trans=trans, - repository=None, - datatypes=None, - invalid_tools=None, - missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=installed_repository_dependencies, - tool_dependencies=installed_tool_dependencies, - valid_tools=None, - workflows=None, - valid_data_managers=None, - invalid_data_managers=None, - data_managers_errors=None, - new_install=True, - reinstalling=False ) - # Merge the missing_repository_dependencies container contents to the installed_repository_dependencies container. - containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) - # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container. - containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict ) + # Most of the repository contents are set to None since we don't yet know what they are. + containers_dict = \ + container_util.build_repository_containers_for_galaxy( trans=trans, + repository=None, + datatypes=None, + invalid_tools=None, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None, + data_managers_errors=None, + new_install=True, + reinstalling=False ) + if not updating: + # If we installing a new repository and not updaing an installed repository, we can merge + # the missing_repository_dependencies container contents to the installed_repository_dependencies + # container. When updating an installed repository, merging will result in losing newly defined + # dependencies included in the updates. + containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container. + containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict ) return containers_dict def pull_repository( repo, repository_clone_url, ctx_rev ): @@ -875,3 +894,23 @@ repository.uninstalled = uninstalled trans.install_model.context.add( repository ) trans.install_model.context.flush() + +def update_repository_record( trans, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ): + """ + Update a tool_shed_repository database record with new information retrieved from the + Tool Shed. This happens when updating an installed repository to a new changeset revision. + """ + repository.metadata = updated_metadata_dict + # Update the repository.changeset_revision column in the database. + repository.changeset_revision = updated_changeset_revision + repository.ctx_rev = updated_ctx_rev + # Update the repository.tool_shed_status column in the database. + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository ) + if tool_shed_status_dict: + repository.tool_shed_status = tool_shed_status_dict + else: + repository.tool_shed_status = None + trans.install_model.context.add( repository ) + trans.install_model.context.flush() + trans.install_model.context.refresh( repository ) + return repository diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -359,13 +359,14 @@ can_install_tool_dependency = True if can_install_tool_dependency: package_install_version = package_elem.get( 'version', '1.0' ) - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.install_model.ToolDependency.installation_status.INSTALLING, - set_status=True ) + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.install_model.ToolDependency.installation_status.INSTALLING, + set_status=True ) # Get the information about the current platform in case the tool dependency definition includes tag sets # for installing compiled binaries. platform_info_dict = tool_dependency_util.get_platform_info_dict() @@ -879,25 +880,28 @@ # Tool dependencies of type "set_environmnet" always have the version attribute set to None. attr_tup = ( env_var_name, None, 'set_environment' ) if attr_tup in attr_tups_of_dependencies_for_install: - install_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - repository_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dependency_type='set_environment', - tool_dependency_name=env_var_name, - tool_dependency_version=None ) + install_dir = \ + tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='set_environment', + tool_dependency_name=env_var_name, + tool_dependency_version=None ) tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository ) env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir ) if env_var_dict: if not os.path.exists( install_dir ): os.makedirs( install_dir ) - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=env_var_name, - version=None, - type='set_environment', - status=app.install_model.ToolDependency.installation_status.INSTALLING, - set_status=True ) + status = app.install_model.ToolDependency.installation_status.INSTALLING + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=env_var_name, + version=None, + type='set_environment', + status=status, + set_status=True ) if env_var_version == '1.0': # Create this tool dependency's env.sh file. env_file_builder = fabric_util.EnvFileBuilder( install_dir ) @@ -906,28 +910,34 @@ error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ ( str( tool_dependency.name ), str( return_code ) ) log.debug( error_message ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.ERROR, - error_message=error_message, - remove_from_disk=False ) + status = app.install_model.ToolDependency.installation_status.ERROR + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) else: if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR, app.install_model.ToolDependency.installation_status.INSTALLED ]: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.INSTALLED, - error_message=None, - remove_from_disk=False ) + status = app.install_model.ToolDependency.installation_status.INSTALLED + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=None, + remove_from_disk=False ) log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \ ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) ) else: error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.ERROR, - error_message=error_message, - remove_from_disk=False ) + status = app.install_model.ToolDependency.installation_status.ERROR + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) return tool_dependency def strip_path( fpath ): diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -70,7 +70,7 @@ if display_path is not None: datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False ) -def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): +def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=False ): """ Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined by the received repo_info_dict. @@ -90,7 +90,7 @@ # Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies. # We don't add to installed_td and missing_td here because at this point they are empty. installed_td, missing_td = \ - get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies ) + get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies ) # In cases where a repository dependency is required only for compiling a dependent repository's # tool dependency, the value of repository_dependencies will be an empty dictionary here. if repository_dependencies: @@ -101,10 +101,11 @@ name, repository_owner, changeset_revision ) - if repository and repository.metadata: + if not updating and repository and repository.metadata: installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository ) else: - installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) + installed_rd, missing_rd = \ + get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple ) # Discover all repository dependencies and retrieve information for installing them. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) @@ -119,7 +120,8 @@ required_tool_dependencies = {} for rid in required_repo_info_dicts: for name, repo_info_tuple in rid.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, rid_repository_dependencies, rid_tool_dependencies = \ + description, repository_clone_url, changeset_revision, ctx_rev, \ + repository_owner, rid_repository_dependencies, rid_tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) if rid_tool_dependencies: for td_key, td_dict in rid_tool_dependencies.items(): @@ -128,7 +130,9 @@ if required_tool_dependencies: # Discover and categorize all tool dependencies defined for this repository's repository dependencies. required_installed_td, required_missing_td = \ - get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, required_tool_dependencies ) + get_installed_and_missing_tool_dependencies_for_repository( trans, + tool_shed_url, + required_tool_dependencies ) if required_installed_td: if not includes_tool_dependencies: includes_tool_dependencies = True @@ -168,11 +172,12 @@ def get_installed_and_missing_repository_dependencies( trans, repository ): """ - Return the installed and missing repository dependencies for a tool shed repository that has a record in the Galaxy database, but - may or may not be installed. In this case, the repository dependencies are associated with the repository in the database. Do not - include a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since these - special kinds of repository dependencies are really a dependency of the dependent repository's contained tool dependency, and only if - that tool dependency requires compilation. + Return the installed and missing repository dependencies for a tool shed repository that has a record + in the Galaxy database, but may or may not be installed. In this case, the repository dependencies are + associated with the repository in the database. Do not include a repository dependency if it is required + only to compile a tool dependency defined for the dependent repository since these special kinds of repository + dependencies are really a dependency of the dependent repository's contained tool dependency, and only + if that tool dependency requires compilation. """ missing_repository_dependencies = {} installed_repository_dependencies = {} @@ -228,7 +233,7 @@ missing_repository_dependencies[ 'description' ] = description return installed_repository_dependencies, missing_repository_dependencies -def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ): +def get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple ): """ Parse the received repository_dependencies dictionary that is associated with a repository being installed into Galaxy for the first time and attempt to determine repository dependencies that are @@ -264,13 +269,13 @@ tmp_repo_info_tuple ) if repository: new_rd_tup = [ tool_shed, - name, - owner, - changeset_revision, - prior_installation_required, - only_if_compiling_contained_td, - repository.id, - repository.status ] + name, + owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, + repository.id, + repository.status ] if repository.status == trans.install_model.ToolShedRepository.installation_status.INSTALLED: if new_rd_tup not in installed_rd_tups: installed_rd_tups.append( new_rd_tup ) @@ -285,12 +290,12 @@ missing_rd_tups.append( new_rd_tup ) else: new_rd_tup = [ tool_shed, - name, - owner, - changeset_revision, - prior_installation_required, - only_if_compiling_contained_td, - None, + name, + owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, + None, 'Never installed' ] if not util.asbool( only_if_compiling_contained_td ): # A repository dependency that is not installed will not be considered missing if it's value for @@ -307,11 +312,17 @@ missing_repository_dependencies[ 'description' ] = description return installed_repository_dependencies, missing_repository_dependencies -def get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies_dict ): +def get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies_dict ): """ Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories being installed into Galaxy. """ + # FIXME: This implementation breaks when updates to a repository contain dependencies that result in + # multiple entries for a specific tool dependency. A scenario where this can happen is where 2 repositories + # define the same dependency internally (not using the complex repository dependency definition to a separate + # package repository approach). If 2 repositories contain the same tool_dependencies.xml file, one dependency + # will be lost since the values in these returned dictionaries are not lists. All tool dependency dictionaries + # should have lists as values. These scenarios are probably extreme corner cases, but still should be handled. installed_tool_dependencies = {} missing_tool_dependencies = {} if tool_dependencies_dict: diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -821,8 +821,8 @@ tool_dependencies = metadata[ 'tool_dependencies' ] if trans.webapp.name == 'tool_shed': if 'orphan_tool_dependencies' in metadata: - # The use of the orphan_tool_dependencies category in metadata has been deprecated, but we still need to check in case - # the metadata is out of date. + # The use of the orphan_tool_dependencies category in metadata has been deprecated, + # but we still need to check in case the metadata is out of date. orphan_tool_dependencies = metadata[ 'orphan_tool_dependencies' ] tool_dependencies.update( orphan_tool_dependencies ) # Tool dependencies can be categorized as orphans only if the repository contains tools. diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/tool_shed/util/encoding_util.py --- a/lib/tool_shed/util/encoding_util.py +++ b/lib/tool_shed/util/encoding_util.py @@ -21,7 +21,6 @@ try: values = json.loads( value ) except Exception, e: - #log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) ) pass if values is not None: try: @@ -34,7 +33,7 @@ return values def tool_shed_encode( val ): - if isinstance( val, dict ): + if isinstance( val, dict ) or isinstance( val, list ): value = json.dumps( val ) else: value = val This diff is so big that we needed to truncate the remainder. 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: jmchilton: Fix broken import with workflow PR.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8af539a3006b/ Changeset: 8af539a3006b User: jmchilton Date: 2014-03-26 22:28:31 Summary: Fix broken import with workflow PR. Affected #: 1 file diff -r 46d4a48fcb7b6dd736f081f5d8b650b0a33a296c -r 8af539a3006b24e027215af4f270b5db0d07c5e6 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -41,7 +41,7 @@ from galaxy.tools.parameters.basic import DataToolParameter from galaxy.util.json import to_json_string from galaxy.workflow.modules import ToolModule -from galaxy.workflow.build_util import attach_ordered_steps +from galaxy.workflow.steps import attach_ordered_steps log = logging.getLogger( __name__ ) 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: 3 new changesets
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d5d2a3a7e244/ Changeset: d5d2a3a7e244 User: jmchilton Date: 2014-03-20 16:43:24 Summary: Add dependency on requests 2.2.1. Will improve and fix bugs in API testing and API driven tests of tools. Affected #: 1 file diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r d5d2a3a7e244a2ff91ca3392729ae7d58c4bb08b eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -56,6 +56,7 @@ python_openid = 2.2.5 python_daemon = 1.5.5 pytz = 2013.9 +requests = 2.2.1 Routes = 1.12.3 sqlalchemy_migrate = 0.7.2 ssh = 1.7.14 https://bitbucket.org/galaxy/galaxy-central/commits/1996ad824139/ Changeset: 1996ad824139 User: jmchilton Date: 2014-03-20 16:43:57 Summary: Force use of requests in API tests, eliminate hacked together compatibility layer. Affected #: 1 file diff -r d5d2a3a7e244a2ff91ca3392729ae7d58c4bb08b -r 1996ad824139dc5540a2844d90f0cd5cae0b0650 test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -1,6 +1,8 @@ import os from StringIO import StringIO from galaxy.tools.parameters import grouping +from galaxy import eggs +eggs.require( "requests" ) from galaxy.util import listify from galaxy.util.odict import odict import galaxy.model @@ -424,104 +426,7 @@ } -# Lets just try to use requests if it is available, but if not provide fallback -# on custom implementations of limited requests get, put, etc... functionality. -try: - from requests import get as get_request - from requests import post as post_request - from requests import put as put_request - from requests import delete as delete_request -except ImportError: - import urllib2 - import httplib - - class RequestsLikeResponse( object ): - - def __init__( self, content, status_code ): - self.content = content - self.status_code = status_code - - def json( self ): - return loads( self.content ) - - def get_request( url, params={} ): - argsep = '&' - if '?' not in url: - argsep = '?' - param_pairs = [] - for key, value in params.iteritems(): - # Handle single parameters or lists and tuples of them. - if isinstance( value, tuple ): - value = list( value ) - elif not isinstance( value, list ): - value = [ value ] - for val in value: - param_pairs.append( "%s=%s" % ( key, val ) ) - url = url + argsep + '&'.join( param_pairs ) - #req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' } ) - try: - response = urllib2.urlopen( url ) - return RequestsLikeResponse( response.read(), status_code=response.getcode() ) - except urllib2.HTTPError as e: - return RequestsLikeResponse( e.read(), status_code=e.code ) - - def post_request( url, data, files={} ): - return __multipart_request( url, data, files, verb="POST" ) - - def put_request( url, data=None ): - if isinstance( data, dict ): - assert False, "This test will fail, Galaxy's webob dependency does not parse out urlencoded PUT/PATCH entity data, API will receive empty payload." - return __urllib_request( url, 'PUT', json_str=data ) - - def delete_request( url ): - return __urllib_request( url, 'DELETE' ) - - def __urllib_request( url, verb, json_str=None ): - opener = urllib2.build_opener(urllib2.HTTPHandler) - request = urllib2.Request(url) - request.get_method = lambda: verb - if json_str: - request.add_header( "content-type", "application/json" ) - request.add_data(json_str) - try: - response = opener.open(request) - return RequestsLikeResponse( response.read(), status_code=response.getcode() ) - except urllib2.HTTPError as e: - return RequestsLikeResponse( e.read(), status_code=e.code ) - - def __multipart_request( url, data, files={}, verb="POST" ): - parsed_url = urllib2.urlparse.urlparse( url ) - return __multipart( host=parsed_url.netloc, selector=parsed_url.path, fields=data.iteritems(), files=(files or {}).iteritems(), verb=verb ) - - # http://stackoverflow.com/a/681182 - def __multipart(host, selector, fields, files, verb="POST"): - h = httplib.HTTP(host) - h.putrequest(verb, selector) - content_type, body = __encode_multipart_formdata(fields, files) - h.putheader('content-type', content_type) - h.putheader('content-length', str(len(body))) - h.endheaders() - h.send(body) - errcode, errmsg, headers = h.getreply() - return RequestsLikeResponse(h.file.read(), status_code=errcode) - - def __encode_multipart_formdata(fields, files): - LIMIT = '----------lImIt_of_THE_fIle_eW_$' - CRLF = '\r\n' - L = [] - for (key, value) in fields: - L.append('--' + LIMIT) - L.append('Content-Disposition: form-data; name="%s"' % key) - L.append('') - L.append(value) - for (key, value) in files: - L.append('--' + LIMIT) - L.append('Content-Disposition: form-data; name="%s"; filename="%s";' % (key, key)) - L.append('Content-Type: application/octet-stream') - L.append('') - L.append(value.read()) - L.append('--' + LIMIT + '--') - L.append('') - body = CRLF.join(L) - content_type = 'multipart/form-data; boundary=%s' % LIMIT - return content_type, body +from requests import get as get_request +from requests import post as post_request +from requests import put as put_request +from requests import delete as delete_request https://bitbucket.org/galaxy/galaxy-central/commits/46d4a48fcb7b/ Changeset: 46d4a48fcb7b User: jmchilton Date: 2014-03-26 22:22:34 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #350) Make requests dependency mandatory for testing Affected #: 2 files diff -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 -r 46d4a48fcb7b6dd736f081f5d8b650b0a33a296c eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -56,6 +56,7 @@ python_openid = 2.2.5 python_daemon = 1.5.5 pytz = 2013.9 +requests = 2.2.1 Routes = 1.12.3 sqlalchemy_migrate = 0.7.2 ssh = 1.7.14 diff -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 -r 46d4a48fcb7b6dd736f081f5d8b650b0a33a296c test/base/interactor.py --- a/test/base/interactor.py +++ b/test/base/interactor.py @@ -1,6 +1,8 @@ import os from StringIO import StringIO from galaxy.tools.parameters import grouping +from galaxy import eggs +eggs.require( "requests" ) from galaxy.util import listify from galaxy.util.odict import odict import galaxy.model @@ -424,104 +426,7 @@ } -# Lets just try to use requests if it is available, but if not provide fallback -# on custom implementations of limited requests get, put, etc... functionality. -try: - from requests import get as get_request - from requests import post as post_request - from requests import put as put_request - from requests import delete as delete_request -except ImportError: - import urllib2 - import httplib - - class RequestsLikeResponse( object ): - - def __init__( self, content, status_code ): - self.content = content - self.status_code = status_code - - def json( self ): - return loads( self.content ) - - def get_request( url, params={} ): - argsep = '&' - if '?' not in url: - argsep = '?' - param_pairs = [] - for key, value in params.iteritems(): - # Handle single parameters or lists and tuples of them. - if isinstance( value, tuple ): - value = list( value ) - elif not isinstance( value, list ): - value = [ value ] - for val in value: - param_pairs.append( "%s=%s" % ( key, val ) ) - url = url + argsep + '&'.join( param_pairs ) - #req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' } ) - try: - response = urllib2.urlopen( url ) - return RequestsLikeResponse( response.read(), status_code=response.getcode() ) - except urllib2.HTTPError as e: - return RequestsLikeResponse( e.read(), status_code=e.code ) - - def post_request( url, data, files={} ): - return __multipart_request( url, data, files, verb="POST" ) - - def put_request( url, data=None ): - if isinstance( data, dict ): - assert False, "This test will fail, Galaxy's webob dependency does not parse out urlencoded PUT/PATCH entity data, API will receive empty payload." - return __urllib_request( url, 'PUT', json_str=data ) - - def delete_request( url ): - return __urllib_request( url, 'DELETE' ) - - def __urllib_request( url, verb, json_str=None ): - opener = urllib2.build_opener(urllib2.HTTPHandler) - request = urllib2.Request(url) - request.get_method = lambda: verb - if json_str: - request.add_header( "content-type", "application/json" ) - request.add_data(json_str) - try: - response = opener.open(request) - return RequestsLikeResponse( response.read(), status_code=response.getcode() ) - except urllib2.HTTPError as e: - return RequestsLikeResponse( e.read(), status_code=e.code ) - - def __multipart_request( url, data, files={}, verb="POST" ): - parsed_url = urllib2.urlparse.urlparse( url ) - return __multipart( host=parsed_url.netloc, selector=parsed_url.path, fields=data.iteritems(), files=(files or {}).iteritems(), verb=verb ) - - # http://stackoverflow.com/a/681182 - def __multipart(host, selector, fields, files, verb="POST"): - h = httplib.HTTP(host) - h.putrequest(verb, selector) - content_type, body = __encode_multipart_formdata(fields, files) - h.putheader('content-type', content_type) - h.putheader('content-length', str(len(body))) - h.endheaders() - h.send(body) - errcode, errmsg, headers = h.getreply() - return RequestsLikeResponse(h.file.read(), status_code=errcode) - - def __encode_multipart_formdata(fields, files): - LIMIT = '----------lImIt_of_THE_fIle_eW_$' - CRLF = '\r\n' - L = [] - for (key, value) in fields: - L.append('--' + LIMIT) - L.append('Content-Disposition: form-data; name="%s"' % key) - L.append('') - L.append(value) - for (key, value) in files: - L.append('--' + LIMIT) - L.append('Content-Disposition: form-data; name="%s"; filename="%s";' % (key, key)) - L.append('Content-Type: application/octet-stream') - L.append('') - L.append(value.read()) - L.append('--' + LIMIT + '--') - L.append('') - body = CRLF.join(L) - content_type = 'multipart/form-data; boundary=%s' % LIMIT - return content_type, body +from requests import get as get_request +from requests import post as post_request +from requests import put as put_request +from requests import delete as delete_request 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: 5 new changesets
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6c786abce7e2/ Changeset: 6c786abce7e2 User: jmchilton Date: 2014-03-17 16:44:09 Summary: Start work on stand-alone module for extracting workflows from histories. In particular, this moves get_job_dict out of workflow controller. I am making big changes to this downstream in dataset collection work so I want unit tests - additionally get_job_dict isn't really a great name for what this becomes - so I am renaming it to summarize. Affected #: 3 files diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -23,7 +23,6 @@ from galaxy.tools.parameters import visit_input_values from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue from galaxy.tools.parameters.grouping import Conditional, Repeat -from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html from galaxy.util.topsort import CycleError, topsort, topsort_levels from galaxy.web import error, url_for @@ -33,6 +32,7 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke +from galaxy.workflow.extract import summarize class StoredWorkflowListGrid( grids.Grid ): @@ -1188,7 +1188,7 @@ if not user: return trans.show_error_message( "Must be logged in to create workflows" ) if ( job_ids is None and dataset_ids is None ) or workflow_name is None: - jobs, warnings = get_job_dict( trans ) + jobs, warnings = summarize( trans ) # Render return trans.fill_template( "workflow/build_from_current_history.mako", @@ -1211,7 +1211,7 @@ dataset_ids = [ int( id ) for id in dataset_ids ] # Find each job, for security we (implicately) check that they are # associated witha job in the current history. - jobs, warnings = get_job_dict( trans ) + jobs, warnings = summarize( trans ) jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) steps = [] steps_by_job_id = {} @@ -1743,48 +1743,6 @@ return None -class FakeJob( object ): - """ - Fake job object for datasets that have no creating_job_associations, - they will be treated as "input" datasets. - """ - def __init__( self, dataset ): - self.is_fake = True - self.id = "fake_%s" % dataset.id - - -def get_job_dict( trans ): - """ - Return a dictionary of Job -> [ Dataset ] mappings, for all finished - active Datasets in the current history and the jobs that created them. - """ - history = trans.get_history() - # Get the jobs that created the datasets - warnings = set() - jobs = odict() - for dataset in history.active_datasets: - # FIXME: Create "Dataset.is_finished" - if dataset.state in ( 'new', 'running', 'queued' ): - warnings.add( "Some datasets still queued or running were ignored" ) - continue - - #if this hda was copied from another, we need to find the job that created the origial hda - job_hda = dataset - while job_hda.copied_from_history_dataset_association: - job_hda = job_hda.copied_from_history_dataset_association - - if not job_hda.creating_job_associations: - jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - - for assoc in job_hda.creating_job_associations: - job = assoc.job - if job in jobs: - jobs[ job ].append( ( assoc.name, dataset ) ) - else: - jobs[ job ] = [ ( assoc.name, dataset ) ] - return jobs, warnings - - def cleanup_param_values( inputs, values ): """ Remove 'Data' values from `param_values`, along with metadata cruft, diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 lib/galaxy/workflow/extract.py --- /dev/null +++ b/lib/galaxy/workflow/extract.py @@ -0,0 +1,54 @@ +""" This module contains functionality to aid in extracting workflows from +histories. +""" +from galaxy.util.odict import odict + +WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored" + + +class FakeJob( object ): + """ + Fake job object for datasets that have no creating_job_associations, + they will be treated as "input" datasets. + """ + def __init__( self, dataset ): + self.is_fake = True + self.id = "fake_%s" % dataset.id + + +def summarize( trans, history=None ): + """ Return mapping of job description to datasets for active items in + supplied history - needed for building workflow from a history. + + Formerly call get_job_dict in workflow web controller. + """ + if not history: + history = trans.get_history() + + # Get the jobs that created the datasets + warnings = set() + jobs = odict() + for dataset in history.active_datasets: + # FIXME: Create "Dataset.is_finished" + if dataset.state in ( 'new', 'running', 'queued' ): + warnings.add( WARNING_SOME_DATASETS_NOT_READY ) + continue + + #if this hda was copied from another, we need to find the job that created the origial hda + job_hda = dataset + while job_hda.copied_from_history_dataset_association: + job_hda = job_hda.copied_from_history_dataset_association + + if not job_hda.creating_job_associations: + jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] + + for assoc in job_hda.creating_job_associations: + job = assoc.job + if job in jobs: + jobs[ job ].append( ( assoc.name, dataset ) ) + else: + jobs[ job ] = [ ( assoc.name, dataset ) ] + + return jobs, warnings + +__all__ = [ summarize ] diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 test/unit/workflows/test_extract_summary.py --- /dev/null +++ b/test/unit/workflows/test_extract_summary.py @@ -0,0 +1,98 @@ +import unittest + +from galaxy import model +from galaxy.workflow import extract + +UNDEFINED_JOB = object() + + +class TestWorkflowExtractSummary( unittest.TestCase ): + + def setUp( self ): + self.history = MockHistory() + self.trans = MockTrans( self.history ) + + def test_empty_history( self ): + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert not job_dict + + def test_summarize_returns_name_and_dataset_list( self ): + # Create two jobs and three datasets, test they are groupped + # by job correctly with correct output names. + hda1 = MockHda() + self.history.active_datasets.append( hda1 ) + hda2 = MockHda( job=hda1.job, output_name="out2" ) + self.history.active_datasets.append( hda2 ) + hda3 = MockHda( output_name="out3" ) + self.history.active_datasets.append( hda3 ) + + job_dict, warnings = extract.summarize( trans=self.trans ) + assert len( job_dict ) == 2 + assert not warnings + self.assertEquals( job_dict[ hda1.job ], [ ( 'out1', hda1 ), ( 'out2', hda2 ) ] ) + self.assertEquals( job_dict[ hda3.job ], [ ( 'out3', hda3 ) ] ) + + def test_finds_original_job_if_copied( self ): + hda = MockHda() + derived_hda_1 = MockHda() + derived_hda_1.copied_from_history_dataset_association = hda + derived_hda_2 = MockHda() + derived_hda_2.copied_from_history_dataset_association = derived_hda_1 + self.history.active_datasets.append( derived_hda_2 ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert len( job_dict ) == 1 + self.assertEquals( job_dict[ hda.job ], [ ('out1', derived_hda_2 ) ] ) + + def test_fake_job( self ): + """ Fakes job if creating_job_associations is empty. + """ + hda = MockHda( job=UNDEFINED_JOB ) + self.history.active_datasets.append( hda ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert len( job_dict ) == 1 + fake_job = job_dict.keys()[ 0 ] + assert fake_job.id.startswith( "fake_" ) + datasets = job_dict.values()[ 0 ] + assert datasets == [ ( None, hda ) ] + + def test_warns_and_skips_datasets_if_not_finished( self ): + hda = MockHda( state='queued' ) + self.history.active_datasets.append( hda ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert warnings + assert len( job_dict ) == 0 + + +class MockHistory( object ): + + def __init__( self ): + self.active_datasets = [] + + +class MockTrans( object ): + + def __init__( self, history ): + self.history = history + + def get_history( self ): + return self.history + + +class MockHda( object ): + + def __init__( self, state='ok', output_name='out1', job=None ): + self.id = 123 + self.state = state + self.copied_from_history_dataset_association = None + if job is not UNDEFINED_JOB: + if not job: + job = model.Job() + self.job = job + assoc = model.JobToOutputDatasetAssociation( output_name, self ) + assoc.job = job + self.creating_job_associations = [ assoc ] + else: + self.creating_job_associations = [] https://bitbucket.org/galaxy/galaxy-central/commits/69e29134e64c/ Changeset: 69e29134e64c User: jmchilton Date: 2014-03-17 16:44:09 Summary: Refactor workflow controller step utilities into new module. This will allow for cleaner reuse outside of web controller, clean up API import of attach_steps accordingly. Affected #: 3 files diff -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 -r 69e29134e64c08c09e94a9f69d59329eb2f52107 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -41,6 +41,7 @@ from galaxy.tools.parameters.basic import DataToolParameter from galaxy.util.json import to_json_string from galaxy.workflow.modules import ToolModule +from galaxy.workflow.build_util import attach_ordered_steps log = logging.getLogger( __name__ ) @@ -1626,7 +1627,6 @@ """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ - from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps # Put parameters in workflow mode trans.workflow_building_mode = True diff -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 -r 69e29134e64c08c09e94a9f69d59329eb2f52107 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -4,7 +4,6 @@ import base64 import httplib import json -import math import os import sgmllib import svgfig @@ -24,7 +23,6 @@ from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue from galaxy.tools.parameters.grouping import Conditional, Repeat from galaxy.util.sanitize_html import sanitize_html -from galaxy.util.topsort import CycleError, topsort, topsort_levels from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework import form @@ -33,6 +31,12 @@ from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke from galaxy.workflow.extract import summarize +from galaxy.workflow.steps import ( + attach_ordered_steps, + order_workflow_steps, + edgelist_for_workflow_steps, + order_workflow_steps_with_levels, +) class StoredWorkflowListGrid( grids.Grid ): @@ -1692,57 +1696,6 @@ ## ---- Utility methods ------------------------------------------------------- -def attach_ordered_steps( workflow, steps ): - ordered_steps = order_workflow_steps( steps ) - if ordered_steps: - workflow.has_cycles = False - for i, step in enumerate( ordered_steps ): - step.order_index = i - workflow.steps.append( step ) - else: - workflow.has_cycles = True - workflow.steps = steps - - -def edgelist_for_workflow_steps( steps ): - """ - Create a list of tuples representing edges between ``WorkflowSteps`` based - on associated ``WorkflowStepConnection``s - """ - edges = [] - steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) - for step in steps: - edges.append( ( steps_to_index[step], steps_to_index[step] ) ) - for conn in step.input_connections: - edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) ) - return edges - - -def order_workflow_steps( steps ): - """ - Perform topological sort of the steps, return ordered or None - """ - position_data_available = True - for step in steps: - if not step.position or not 'left' in step.position or not 'top' in step.position: - position_data_available = False - if position_data_available: - steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2))) - try: - edges = edgelist_for_workflow_steps( steps ) - node_order = topsort( edges ) - return [ steps[i] for i in node_order ] - except CycleError: - return None - - -def order_workflow_steps_with_levels( steps ): - try: - return topsort_levels( edgelist_for_workflow_steps( steps ) ) - except CycleError: - return None - - def cleanup_param_values( inputs, values ): """ Remove 'Data' values from `param_values`, along with metadata cruft, diff -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 -r 69e29134e64c08c09e94a9f69d59329eb2f52107 lib/galaxy/workflow/steps.py --- /dev/null +++ b/lib/galaxy/workflow/steps.py @@ -0,0 +1,63 @@ +""" This module contains utility methods for reasoning about and ordering +workflow steps. +""" +import math +from galaxy.util.topsort import ( + CycleError, + topsort, + topsort_levels +) + + +def attach_ordered_steps( workflow, steps ): + """ Attempt to topologically order steps and attach to workflow. If this + fails - the workflow contains cycles so it mark it as such. + """ + ordered_steps = order_workflow_steps( steps ) + if ordered_steps: + workflow.has_cycles = False + for i, step in enumerate( ordered_steps ): + step.order_index = i + workflow.steps.append( step ) + else: + workflow.has_cycles = True + workflow.steps = steps + + +def order_workflow_steps( steps ): + """ + Perform topological sort of the steps, return ordered or None + """ + position_data_available = True + for step in steps: + if not step.position or not 'left' in step.position or not 'top' in step.position: + position_data_available = False + if position_data_available: + steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2))) + try: + edges = edgelist_for_workflow_steps( steps ) + node_order = topsort( edges ) + return [ steps[i] for i in node_order ] + except CycleError: + return None + + +def edgelist_for_workflow_steps( steps ): + """ + Create a list of tuples representing edges between ``WorkflowSteps`` based + on associated ``WorkflowStepConnection``s + """ + edges = [] + steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) + for step in steps: + edges.append( ( steps_to_index[step], steps_to_index[step] ) ) + for conn in step.input_connections: + edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) ) + return edges + + +def order_workflow_steps_with_levels( steps ): + try: + return topsort_levels( edgelist_for_workflow_steps( steps ) ) + except CycleError: + return None https://bitbucket.org/galaxy/galaxy-central/commits/0eb7631a6d67/ Changeset: 0eb7631a6d67 User: jmchilton Date: 2014-03-17 16:44:09 Summary: Refactor code for extracting workflow from history into workflow extract module. Will allow reuse with API controller. Affected #: 2 files diff -r 69e29134e64c08c09e94a9f69d59329eb2f52107 -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -19,9 +19,8 @@ from galaxy.datatypes.data import Data from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc +from galaxy.tools.parameters.basic import DataToolParameter from galaxy.tools.parameters import visit_input_values -from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue -from galaxy.tools.parameters.grouping import Conditional, Repeat from galaxy.util.sanitize_html import sanitize_html from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin @@ -31,6 +30,7 @@ from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke from galaxy.workflow.extract import summarize +from galaxy.workflow.extract import extract_workflow from galaxy.workflow.steps import ( attach_ordered_steps, order_workflow_steps, @@ -1201,82 +1201,13 @@ history=history ) else: - # Ensure job_ids and dataset_ids are lists (possibly empty) - if job_ids is None: - job_ids = [] - elif type( job_ids ) is not list: - job_ids = [ job_ids ] - if dataset_ids is None: - dataset_ids = [] - elif type( dataset_ids ) is not list: - dataset_ids = [ dataset_ids ] - # Convert both sets of ids to integers - job_ids = [ int( id ) for id in job_ids ] - dataset_ids = [ int( id ) for id in dataset_ids ] - # Find each job, for security we (implicately) check that they are - # associated witha job in the current history. - jobs, warnings = summarize( trans ) - jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) - steps = [] - steps_by_job_id = {} - hid_to_output_pair = {} - # Input dataset steps - for hid in dataset_ids: - step = model.WorkflowStep() - step.type = 'data_input' - step.tool_inputs = dict( name="Input Dataset" ) - hid_to_output_pair[ hid ] = ( step, 'output' ) - steps.append( step ) - # Tool steps - for job_id in job_ids: - assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" - job = jobs_by_id[ job_id ] - tool = trans.app.toolbox.get_tool( job.tool_id ) - param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here - associations = cleanup_param_values( tool.inputs, param_values ) - step = model.WorkflowStep() - step.type = 'tool' - step.tool_id = job.tool_id - step.tool_inputs = tool.params_to_strings( param_values, trans.app ) - # NOTE: We shouldn't need to do two passes here since only - # an earlier job can be used as an input to a later - # job. - for other_hid, input_name in associations: - if other_hid in hid_to_output_pair: - other_step, other_name = hid_to_output_pair[ other_hid ] - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - # Should always be connected to an earlier step - conn.output_step = other_step - conn.output_name = other_name - steps.append( step ) - steps_by_job_id[ job_id ] = step - # Store created dataset hids - for assoc in job.output_datasets: - hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) - # Workflow to populate - workflow = model.Workflow() - workflow.name = workflow_name - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - # And let's try to set up some reasonable locations on the canvas - # (these are pretty arbitrary values) - levorder = order_workflow_steps_with_levels( steps ) - base_pos = 10 - for i, steps_at_level in enumerate( levorder ): - for j, index in enumerate( steps_at_level ): - step = steps[ index ] - step.position = dict( top=( base_pos + 120 * j ), - left=( base_pos + 220 * i ) ) - # Store it - stored = model.StoredWorkflow() - stored.user = user - stored.name = workflow_name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - trans.sa_session.add( stored ) - trans.sa_session.flush() + extract_workflow( + trans, + user=user, + job_ids=job_ids, + dataset_ids=dataset_ids, + workflow_name=workflow_name + ) # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" @@ -1696,55 +1627,6 @@ ## ---- Utility methods ------------------------------------------------------- -def cleanup_param_values( inputs, values ): - """ - Remove 'Data' values from `param_values`, along with metadata cruft, - but track the associations. - """ - associations = [] - # dbkey is pushed in by the framework - if 'dbkey' in values: - del values['dbkey'] - root_values = values - - # Recursively clean data inputs and dynamic selects - def cleanup( prefix, inputs, values ): - for key, input in inputs.items(): - if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ): - if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ): - values[key] = UnvalidatedValue( values[key] ) - if isinstance( input, DataToolParameter ): - tmp = values[key] - values[key] = None - # HACK: Nested associations are not yet working, but we - # still need to clean them up so we can serialize - # if not( prefix ): - if tmp: # this is false for a non-set optional dataset - if not isinstance(tmp, list): - associations.append( ( tmp.hid, prefix + key ) ) - else: - associations.extend( [ (t.hid, prefix + key) for t in tmp] ) - - # Cleanup the other deprecated crap associated with datasets - # as well. Worse, for nested datasets all the metadata is - # being pushed into the root. FIXME: MUST REMOVE SOON - key = prefix + key + "_" - for k in root_values.keys(): - if k.startswith( key ): - del root_values[k] - elif isinstance( input, Repeat ): - group_values = values[key] - for i, rep_values in enumerate( group_values ): - rep_index = rep_values['__index__'] - cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] ) - elif isinstance( input, Conditional ): - group_values = values[input.name] - current_case = group_values['__current_case__'] - cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values ) - cleanup( "", inputs, values ) - return associations - - def _build_workflow_on_str(instance_ds_names): # Returns suffix for new histories based on multi input iteration num_multi_inputs = len(instance_ds_names) diff -r 69e29134e64c08c09e94a9f69d59329eb2f52107 -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda lib/galaxy/workflow/extract.py --- a/lib/galaxy/workflow/extract.py +++ b/lib/galaxy/workflow/extract.py @@ -2,10 +2,108 @@ histories. """ from galaxy.util.odict import odict +from galaxy import model +from galaxy.tools.parameters.basic import ( + DataToolParameter, + DrillDownSelectToolParameter, + SelectToolParameter, + UnvalidatedValue +) +from galaxy.tools.parameters.grouping import ( + Conditional, + Repeat +) +from .steps import ( + attach_ordered_steps, + order_workflow_steps_with_levels +) WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored" +def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, workflow_name=None ): + steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids ) + # Workflow to populate + workflow = model.Workflow() + workflow.name = workflow_name + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + # And let's try to set up some reasonable locations on the canvas + # (these are pretty arbitrary values) + levorder = order_workflow_steps_with_levels( steps ) + base_pos = 10 + for i, steps_at_level in enumerate( levorder ): + for j, index in enumerate( steps_at_level ): + step = steps[ index ] + step.position = dict( top=( base_pos + 120 * j ), + left=( base_pos + 220 * i ) ) + # Store it + stored = model.StoredWorkflow() + stored.user = user + stored.name = workflow_name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + trans.sa_session.add( stored ) + trans.sa_session.flush() + return stored + + +def extract_steps( trans, history=None, job_ids=None, dataset_ids=None ): + # Ensure job_ids and dataset_ids are lists (possibly empty) + if job_ids is None: + job_ids = [] + elif type( job_ids ) is not list: + job_ids = [ job_ids ] + if dataset_ids is None: + dataset_ids = [] + elif type( dataset_ids ) is not list: + dataset_ids = [ dataset_ids ] + # Convert both sets of ids to integers + job_ids = [ int( id ) for id in job_ids ] + dataset_ids = [ int( id ) for id in dataset_ids ] + # Find each job, for security we (implicately) check that they are + # associated witha job in the current history. + jobs, warnings = summarize( trans, history=history ) + jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) + steps = [] + steps_by_job_id = {} + hid_to_output_pair = {} + # Input dataset steps + for hid in dataset_ids: + step = model.WorkflowStep() + step.type = 'data_input' + step.tool_inputs = dict( name="Input Dataset" ) + hid_to_output_pair[ hid ] = ( step, 'output' ) + steps.append( step ) + # Tool steps + for job_id in job_ids: + assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" + job = jobs_by_id[ job_id ] + tool_inputs, associations = step_inputs( trans, job ) + step = model.WorkflowStep() + step.type = 'tool' + step.tool_id = job.tool_id + step.tool_inputs = tool_inputs + # NOTE: We shouldn't need to do two passes here since only + # an earlier job can be used as an input to a later + # job. + for other_hid, input_name in associations: + if other_hid in hid_to_output_pair: + other_step, other_name = hid_to_output_pair[ other_hid ] + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + # Should always be connected to an earlier step + conn.output_step = other_step + conn.output_name = other_name + steps.append( step ) + steps_by_job_id[ job_id ] = step + # Store created dataset hids + for assoc in job.output_datasets: + hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) + return steps + + class FakeJob( object ): """ Fake job object for datasets that have no creating_job_associations, @@ -51,4 +149,61 @@ return jobs, warnings -__all__ = [ summarize ] + +def step_inputs( trans, job ): + tool = trans.app.toolbox.get_tool( job.tool_id ) + param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here + associations = __cleanup_param_values( tool.inputs, param_values ) + tool_inputs = tool.params_to_strings( param_values, trans.app ) + return tool_inputs, associations + + +def __cleanup_param_values( inputs, values ): + """ + Remove 'Data' values from `param_values`, along with metadata cruft, + but track the associations. + """ + associations = [] + # dbkey is pushed in by the framework + if 'dbkey' in values: + del values['dbkey'] + root_values = values + + # Recursively clean data inputs and dynamic selects + def cleanup( prefix, inputs, values ): + for key, input in inputs.items(): + if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ): + if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ): + values[key] = UnvalidatedValue( values[key] ) + if isinstance( input, DataToolParameter ): + tmp = values[key] + values[key] = None + # HACK: Nested associations are not yet working, but we + # still need to clean them up so we can serialize + # if not( prefix ): + if tmp: # this is false for a non-set optional dataset + if not isinstance(tmp, list): + associations.append( ( tmp.hid, prefix + key ) ) + else: + associations.extend( [ (t.hid, prefix + key) for t in tmp] ) + + # Cleanup the other deprecated crap associated with datasets + # as well. Worse, for nested datasets all the metadata is + # being pushed into the root. FIXME: MUST REMOVE SOON + key = prefix + key + "_" + for k in root_values.keys(): + if k.startswith( key ): + del root_values[k] + elif isinstance( input, Repeat ): + group_values = values[key] + for i, rep_values in enumerate( group_values ): + rep_index = rep_values['__index__'] + cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] ) + elif isinstance( input, Conditional ): + group_values = values[input.name] + current_case = group_values['__current_case__'] + cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values ) + cleanup( "", inputs, values ) + return associations + +__all__ = [ summarize, extract_workflow ] https://bitbucket.org/galaxy/galaxy-central/commits/17a2dc7d3902/ Changeset: 17a2dc7d3902 User: jmchilton Date: 2014-03-17 16:44:09 Summary: Add ability to extract workflow from a history to workflows API. Affected #: 2 files diff -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda -r 17a2dc7d39027d97a4185adbd03944b4bb1642cf lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -11,8 +11,10 @@ from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke +from galaxy.workflow.extract import extract_workflow log = logging.getLogger(__name__) @@ -51,7 +53,7 @@ step.state.inputs.update(param_dict) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin): @web.expose_api def index(self, trans, **kwd): @@ -141,9 +143,11 @@ """ POST /api/workflows - We're not creating workflows from the api. Just execute for now. + Run or create workflows from the api. - However, we will import them if installed_repository_file is specified. + If installed_repository_file or from_history_id is specified a new + workflow will be created for this user. Otherwise, workflow_id must be + specified and this API method will cause a workflow to execute. :param installed_repository_file The path of a workflow to import. Either workflow_id or installed_repository_file must be specified :type installed_repository_file str @@ -165,6 +169,15 @@ :param replacement_params: A dictionary used when renaming datasets :type replacement_params: dict + + :param from_history_id: Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file. + :type from_history_id: str + + :param job_ids: If from_history_id is set - this should be a list of jobs to include when extracting workflow from history. + :type job_ids: str + + :param dataset_ids: If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history. + :type dataset_ids: str """ # Pull parameters out of payload. @@ -183,6 +196,24 @@ cntrller='api', **payload) return result + if 'from_history_id' in payload: + from_history_id = payload.get( 'from_history_id' ) + history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True ) + job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) ) + dataset_ids = map( trans.security.decode_id, payload.get( "dataset_ids", [] ) ) + workflow_name = payload[ "workflow_name" ] + stored_workflow = extract_workflow( + trans=trans, + user=trans.get_user(), + history=history, + job_ids=job_ids, + dataset_ids=dataset_ids, + workflow_name=workflow_name, + ) + item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } ) + item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] ) + return item + trans.response.status = 403 return "Either workflow_id or installed_repository_file must be specified" if 'installed_repository_file' in payload: diff -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda -r 17a2dc7d39027d97a4185adbd03944b4bb1642cf test/functional/api/test_workflows.py --- a/test/functional/api/test_workflows.py +++ b/test/functional/api/test_workflows.py @@ -67,6 +67,39 @@ self._assert_status_code_is( run_workflow_response, 200 ) self._wait_for_history( history_id, assert_ok=True ) + def test_extract_from_history( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + contents_response = self._get( "histories/%s/contents" % history_id ) + self._assert_status_code_is( contents_response, 200 ) + hda_ids = map( lambda c: c[ "id" ], contents_response.json() ) + + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + + self._wait_for_history( history_id, assert_ok=True ) + data = dict( history_id=history_id, tool_id="cat1" ) + jobs_response = self._get( "jobs", data=data ) + self._assert_status_code_is( jobs_response, 200 ) + cat1_job_id = jobs_response.json()[ 0 ][ "id" ] + + contents_response = self._get( "history/%s/contents", data=data ) + create_from_data = dict( + from_history_id=history_id, + dataset_ids=dumps( hda_ids ), + job_ids=dumps( [ cat1_job_id ] ), + workflow_name="test import from history", + ) + run_workflow_response = self._post( "workflows", data=create_from_data ) + self._assert_status_code_is( run_workflow_response, 200 ) + + new_workflow_id = run_workflow_response.json()[ "id" ] + download_response = self._get( "workflows/%s/download" % new_workflow_id ) + self._assert_status_code_is( download_response, 200 ) + downloaded_workflow = download_response.json() + self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) + assert len( downloaded_workflow[ "steps" ] ) == 3 + def test_run_replace_params_by_tool( self ): workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" ) workflow_request[ "parameters" ] = dumps( dict( random_lines1=dict( num_lines=5 ) ) ) https://bitbucket.org/galaxy/galaxy-central/commits/6d0c89fc3558/ Changeset: 6d0c89fc3558 User: jmchilton Date: 2014-03-26 22:21:15 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #348) Enhance workflows API to allow extracting workflow from history. Affected #: 7 files diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -41,6 +41,7 @@ from galaxy.tools.parameters.basic import DataToolParameter from galaxy.util.json import to_json_string from galaxy.workflow.modules import ToolModule +from galaxy.workflow.build_util import attach_ordered_steps log = logging.getLogger( __name__ ) @@ -1676,7 +1677,6 @@ """ Creates a workflow from a dict. Created workflow is stored in the database and returned. """ - from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps # Put parameters in workflow mode trans.workflow_building_mode = True diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -11,8 +11,10 @@ from galaxy import web from galaxy.web import _future_expose_api as expose_api from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke +from galaxy.workflow.extract import extract_workflow log = logging.getLogger(__name__) @@ -51,7 +53,7 @@ step.state.inputs.update(param_dict) -class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin): @web.expose_api def index(self, trans, **kwd): @@ -141,9 +143,11 @@ """ POST /api/workflows - We're not creating workflows from the api. Just execute for now. + Run or create workflows from the api. - However, we will import them if installed_repository_file is specified. + If installed_repository_file or from_history_id is specified a new + workflow will be created for this user. Otherwise, workflow_id must be + specified and this API method will cause a workflow to execute. :param installed_repository_file The path of a workflow to import. Either workflow_id or installed_repository_file must be specified :type installed_repository_file str @@ -165,6 +169,15 @@ :param replacement_params: A dictionary used when renaming datasets :type replacement_params: dict + + :param from_history_id: Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file. + :type from_history_id: str + + :param job_ids: If from_history_id is set - this should be a list of jobs to include when extracting workflow from history. + :type job_ids: str + + :param dataset_ids: If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history. + :type dataset_ids: str """ # Pull parameters out of payload. @@ -183,6 +196,24 @@ cntrller='api', **payload) return result + if 'from_history_id' in payload: + from_history_id = payload.get( 'from_history_id' ) + history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True ) + job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) ) + dataset_ids = map( trans.security.decode_id, payload.get( "dataset_ids", [] ) ) + workflow_name = payload[ "workflow_name" ] + stored_workflow = extract_workflow( + trans=trans, + user=trans.get_user(), + history=history, + job_ids=job_ids, + dataset_ids=dataset_ids, + workflow_name=workflow_name, + ) + item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } ) + item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] ) + return item + trans.response.status = 403 return "Either workflow_id or installed_repository_file must be specified" if 'installed_repository_file' in payload: diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -4,7 +4,6 @@ import base64 import httplib import json -import math import os import sgmllib import svgfig @@ -20,12 +19,9 @@ from galaxy.datatypes.data import Data from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc +from galaxy.tools.parameters.basic import DataToolParameter from galaxy.tools.parameters import visit_input_values -from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue -from galaxy.tools.parameters.grouping import Conditional, Repeat -from galaxy.util.odict import odict from galaxy.util.sanitize_html import sanitize_html -from galaxy.util.topsort import CycleError, topsort, topsort_levels from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework import form @@ -33,6 +29,14 @@ from galaxy.web.framework.helpers import to_unicode from galaxy.workflow.modules import module_factory from galaxy.workflow.run import invoke +from galaxy.workflow.extract import summarize +from galaxy.workflow.extract import extract_workflow +from galaxy.workflow.steps import ( + attach_ordered_steps, + order_workflow_steps, + edgelist_for_workflow_steps, + order_workflow_steps_with_levels, +) class StoredWorkflowListGrid( grids.Grid ): @@ -1188,7 +1192,7 @@ if not user: return trans.show_error_message( "Must be logged in to create workflows" ) if ( job_ids is None and dataset_ids is None ) or workflow_name is None: - jobs, warnings = get_job_dict( trans ) + jobs, warnings = summarize( trans ) # Render return trans.fill_template( "workflow/build_from_current_history.mako", @@ -1197,82 +1201,13 @@ history=history ) else: - # Ensure job_ids and dataset_ids are lists (possibly empty) - if job_ids is None: - job_ids = [] - elif type( job_ids ) is not list: - job_ids = [ job_ids ] - if dataset_ids is None: - dataset_ids = [] - elif type( dataset_ids ) is not list: - dataset_ids = [ dataset_ids ] - # Convert both sets of ids to integers - job_ids = [ int( id ) for id in job_ids ] - dataset_ids = [ int( id ) for id in dataset_ids ] - # Find each job, for security we (implicately) check that they are - # associated witha job in the current history. - jobs, warnings = get_job_dict( trans ) - jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) - steps = [] - steps_by_job_id = {} - hid_to_output_pair = {} - # Input dataset steps - for hid in dataset_ids: - step = model.WorkflowStep() - step.type = 'data_input' - step.tool_inputs = dict( name="Input Dataset" ) - hid_to_output_pair[ hid ] = ( step, 'output' ) - steps.append( step ) - # Tool steps - for job_id in job_ids: - assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" - job = jobs_by_id[ job_id ] - tool = trans.app.toolbox.get_tool( job.tool_id ) - param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here - associations = cleanup_param_values( tool.inputs, param_values ) - step = model.WorkflowStep() - step.type = 'tool' - step.tool_id = job.tool_id - step.tool_inputs = tool.params_to_strings( param_values, trans.app ) - # NOTE: We shouldn't need to do two passes here since only - # an earlier job can be used as an input to a later - # job. - for other_hid, input_name in associations: - if other_hid in hid_to_output_pair: - other_step, other_name = hid_to_output_pair[ other_hid ] - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - # Should always be connected to an earlier step - conn.output_step = other_step - conn.output_name = other_name - steps.append( step ) - steps_by_job_id[ job_id ] = step - # Store created dataset hids - for assoc in job.output_datasets: - hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) - # Workflow to populate - workflow = model.Workflow() - workflow.name = workflow_name - # Order the steps if possible - attach_ordered_steps( workflow, steps ) - # And let's try to set up some reasonable locations on the canvas - # (these are pretty arbitrary values) - levorder = order_workflow_steps_with_levels( steps ) - base_pos = 10 - for i, steps_at_level in enumerate( levorder ): - for j, index in enumerate( steps_at_level ): - step = steps[ index ] - step.position = dict( top=( base_pos + 120 * j ), - left=( base_pos + 220 * i ) ) - # Store it - stored = model.StoredWorkflow() - stored.user = user - stored.name = workflow_name - workflow.stored_workflow = stored - stored.latest_workflow = workflow - trans.sa_session.add( stored ) - trans.sa_session.flush() + extract_workflow( + trans, + user=user, + job_ids=job_ids, + dataset_ids=dataset_ids, + workflow_name=workflow_name + ) # Index page with message return trans.show_message( "Workflow '%s' created from current history." % workflow_name ) ## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>" @@ -1692,148 +1627,6 @@ ## ---- Utility methods ------------------------------------------------------- -def attach_ordered_steps( workflow, steps ): - ordered_steps = order_workflow_steps( steps ) - if ordered_steps: - workflow.has_cycles = False - for i, step in enumerate( ordered_steps ): - step.order_index = i - workflow.steps.append( step ) - else: - workflow.has_cycles = True - workflow.steps = steps - - -def edgelist_for_workflow_steps( steps ): - """ - Create a list of tuples representing edges between ``WorkflowSteps`` based - on associated ``WorkflowStepConnection``s - """ - edges = [] - steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) - for step in steps: - edges.append( ( steps_to_index[step], steps_to_index[step] ) ) - for conn in step.input_connections: - edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) ) - return edges - - -def order_workflow_steps( steps ): - """ - Perform topological sort of the steps, return ordered or None - """ - position_data_available = True - for step in steps: - if not step.position or not 'left' in step.position or not 'top' in step.position: - position_data_available = False - if position_data_available: - steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2))) - try: - edges = edgelist_for_workflow_steps( steps ) - node_order = topsort( edges ) - return [ steps[i] for i in node_order ] - except CycleError: - return None - - -def order_workflow_steps_with_levels( steps ): - try: - return topsort_levels( edgelist_for_workflow_steps( steps ) ) - except CycleError: - return None - - -class FakeJob( object ): - """ - Fake job object for datasets that have no creating_job_associations, - they will be treated as "input" datasets. - """ - def __init__( self, dataset ): - self.is_fake = True - self.id = "fake_%s" % dataset.id - - -def get_job_dict( trans ): - """ - Return a dictionary of Job -> [ Dataset ] mappings, for all finished - active Datasets in the current history and the jobs that created them. - """ - history = trans.get_history() - # Get the jobs that created the datasets - warnings = set() - jobs = odict() - for dataset in history.active_datasets: - # FIXME: Create "Dataset.is_finished" - if dataset.state in ( 'new', 'running', 'queued' ): - warnings.add( "Some datasets still queued or running were ignored" ) - continue - - #if this hda was copied from another, we need to find the job that created the origial hda - job_hda = dataset - while job_hda.copied_from_history_dataset_association: - job_hda = job_hda.copied_from_history_dataset_association - - if not job_hda.creating_job_associations: - jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - - for assoc in job_hda.creating_job_associations: - job = assoc.job - if job in jobs: - jobs[ job ].append( ( assoc.name, dataset ) ) - else: - jobs[ job ] = [ ( assoc.name, dataset ) ] - return jobs, warnings - - -def cleanup_param_values( inputs, values ): - """ - Remove 'Data' values from `param_values`, along with metadata cruft, - but track the associations. - """ - associations = [] - # dbkey is pushed in by the framework - if 'dbkey' in values: - del values['dbkey'] - root_values = values - - # Recursively clean data inputs and dynamic selects - def cleanup( prefix, inputs, values ): - for key, input in inputs.items(): - if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ): - if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ): - values[key] = UnvalidatedValue( values[key] ) - if isinstance( input, DataToolParameter ): - tmp = values[key] - values[key] = None - # HACK: Nested associations are not yet working, but we - # still need to clean them up so we can serialize - # if not( prefix ): - if tmp: # this is false for a non-set optional dataset - if not isinstance(tmp, list): - associations.append( ( tmp.hid, prefix + key ) ) - else: - associations.extend( [ (t.hid, prefix + key) for t in tmp] ) - - # Cleanup the other deprecated crap associated with datasets - # as well. Worse, for nested datasets all the metadata is - # being pushed into the root. FIXME: MUST REMOVE SOON - key = prefix + key + "_" - for k in root_values.keys(): - if k.startswith( key ): - del root_values[k] - elif isinstance( input, Repeat ): - group_values = values[key] - for i, rep_values in enumerate( group_values ): - rep_index = rep_values['__index__'] - cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] ) - elif isinstance( input, Conditional ): - group_values = values[input.name] - current_case = group_values['__current_case__'] - cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values ) - cleanup( "", inputs, values ) - return associations - - def _build_workflow_on_str(instance_ds_names): # Returns suffix for new histories based on multi input iteration num_multi_inputs = len(instance_ds_names) diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/workflow/extract.py --- /dev/null +++ b/lib/galaxy/workflow/extract.py @@ -0,0 +1,209 @@ +""" This module contains functionality to aid in extracting workflows from +histories. +""" +from galaxy.util.odict import odict +from galaxy import model +from galaxy.tools.parameters.basic import ( + DataToolParameter, + DrillDownSelectToolParameter, + SelectToolParameter, + UnvalidatedValue +) +from galaxy.tools.parameters.grouping import ( + Conditional, + Repeat +) +from .steps import ( + attach_ordered_steps, + order_workflow_steps_with_levels +) + +WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored" + + +def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, workflow_name=None ): + steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids ) + # Workflow to populate + workflow = model.Workflow() + workflow.name = workflow_name + # Order the steps if possible + attach_ordered_steps( workflow, steps ) + # And let's try to set up some reasonable locations on the canvas + # (these are pretty arbitrary values) + levorder = order_workflow_steps_with_levels( steps ) + base_pos = 10 + for i, steps_at_level in enumerate( levorder ): + for j, index in enumerate( steps_at_level ): + step = steps[ index ] + step.position = dict( top=( base_pos + 120 * j ), + left=( base_pos + 220 * i ) ) + # Store it + stored = model.StoredWorkflow() + stored.user = user + stored.name = workflow_name + workflow.stored_workflow = stored + stored.latest_workflow = workflow + trans.sa_session.add( stored ) + trans.sa_session.flush() + return stored + + +def extract_steps( trans, history=None, job_ids=None, dataset_ids=None ): + # Ensure job_ids and dataset_ids are lists (possibly empty) + if job_ids is None: + job_ids = [] + elif type( job_ids ) is not list: + job_ids = [ job_ids ] + if dataset_ids is None: + dataset_ids = [] + elif type( dataset_ids ) is not list: + dataset_ids = [ dataset_ids ] + # Convert both sets of ids to integers + job_ids = [ int( id ) for id in job_ids ] + dataset_ids = [ int( id ) for id in dataset_ids ] + # Find each job, for security we (implicately) check that they are + # associated witha job in the current history. + jobs, warnings = summarize( trans, history=history ) + jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() ) + steps = [] + steps_by_job_id = {} + hid_to_output_pair = {} + # Input dataset steps + for hid in dataset_ids: + step = model.WorkflowStep() + step.type = 'data_input' + step.tool_inputs = dict( name="Input Dataset" ) + hid_to_output_pair[ hid ] = ( step, 'output' ) + steps.append( step ) + # Tool steps + for job_id in job_ids: + assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" + job = jobs_by_id[ job_id ] + tool_inputs, associations = step_inputs( trans, job ) + step = model.WorkflowStep() + step.type = 'tool' + step.tool_id = job.tool_id + step.tool_inputs = tool_inputs + # NOTE: We shouldn't need to do two passes here since only + # an earlier job can be used as an input to a later + # job. + for other_hid, input_name in associations: + if other_hid in hid_to_output_pair: + other_step, other_name = hid_to_output_pair[ other_hid ] + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + # Should always be connected to an earlier step + conn.output_step = other_step + conn.output_name = other_name + steps.append( step ) + steps_by_job_id[ job_id ] = step + # Store created dataset hids + for assoc in job.output_datasets: + hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name ) + return steps + + +class FakeJob( object ): + """ + Fake job object for datasets that have no creating_job_associations, + they will be treated as "input" datasets. + """ + def __init__( self, dataset ): + self.is_fake = True + self.id = "fake_%s" % dataset.id + + +def summarize( trans, history=None ): + """ Return mapping of job description to datasets for active items in + supplied history - needed for building workflow from a history. + + Formerly call get_job_dict in workflow web controller. + """ + if not history: + history = trans.get_history() + + # Get the jobs that created the datasets + warnings = set() + jobs = odict() + for dataset in history.active_datasets: + # FIXME: Create "Dataset.is_finished" + if dataset.state in ( 'new', 'running', 'queued' ): + warnings.add( WARNING_SOME_DATASETS_NOT_READY ) + continue + + #if this hda was copied from another, we need to find the job that created the origial hda + job_hda = dataset + while job_hda.copied_from_history_dataset_association: + job_hda = job_hda.copied_from_history_dataset_association + + if not job_hda.creating_job_associations: + jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] + + for assoc in job_hda.creating_job_associations: + job = assoc.job + if job in jobs: + jobs[ job ].append( ( assoc.name, dataset ) ) + else: + jobs[ job ] = [ ( assoc.name, dataset ) ] + + return jobs, warnings + + +def step_inputs( trans, job ): + tool = trans.app.toolbox.get_tool( job.tool_id ) + param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here + associations = __cleanup_param_values( tool.inputs, param_values ) + tool_inputs = tool.params_to_strings( param_values, trans.app ) + return tool_inputs, associations + + +def __cleanup_param_values( inputs, values ): + """ + Remove 'Data' values from `param_values`, along with metadata cruft, + but track the associations. + """ + associations = [] + # dbkey is pushed in by the framework + if 'dbkey' in values: + del values['dbkey'] + root_values = values + + # Recursively clean data inputs and dynamic selects + def cleanup( prefix, inputs, values ): + for key, input in inputs.items(): + if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ): + if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ): + values[key] = UnvalidatedValue( values[key] ) + if isinstance( input, DataToolParameter ): + tmp = values[key] + values[key] = None + # HACK: Nested associations are not yet working, but we + # still need to clean them up so we can serialize + # if not( prefix ): + if tmp: # this is false for a non-set optional dataset + if not isinstance(tmp, list): + associations.append( ( tmp.hid, prefix + key ) ) + else: + associations.extend( [ (t.hid, prefix + key) for t in tmp] ) + + # Cleanup the other deprecated crap associated with datasets + # as well. Worse, for nested datasets all the metadata is + # being pushed into the root. FIXME: MUST REMOVE SOON + key = prefix + key + "_" + for k in root_values.keys(): + if k.startswith( key ): + del root_values[k] + elif isinstance( input, Repeat ): + group_values = values[key] + for i, rep_values in enumerate( group_values ): + rep_index = rep_values['__index__'] + cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] ) + elif isinstance( input, Conditional ): + group_values = values[input.name] + current_case = group_values['__current_case__'] + cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values ) + cleanup( "", inputs, values ) + return associations + +__all__ = [ summarize, extract_workflow ] diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/workflow/steps.py --- /dev/null +++ b/lib/galaxy/workflow/steps.py @@ -0,0 +1,63 @@ +""" This module contains utility methods for reasoning about and ordering +workflow steps. +""" +import math +from galaxy.util.topsort import ( + CycleError, + topsort, + topsort_levels +) + + +def attach_ordered_steps( workflow, steps ): + """ Attempt to topologically order steps and attach to workflow. If this + fails - the workflow contains cycles so it mark it as such. + """ + ordered_steps = order_workflow_steps( steps ) + if ordered_steps: + workflow.has_cycles = False + for i, step in enumerate( ordered_steps ): + step.order_index = i + workflow.steps.append( step ) + else: + workflow.has_cycles = True + workflow.steps = steps + + +def order_workflow_steps( steps ): + """ + Perform topological sort of the steps, return ordered or None + """ + position_data_available = True + for step in steps: + if not step.position or not 'left' in step.position or not 'top' in step.position: + position_data_available = False + if position_data_available: + steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2))) + try: + edges = edgelist_for_workflow_steps( steps ) + node_order = topsort( edges ) + return [ steps[i] for i in node_order ] + except CycleError: + return None + + +def edgelist_for_workflow_steps( steps ): + """ + Create a list of tuples representing edges between ``WorkflowSteps`` based + on associated ``WorkflowStepConnection``s + """ + edges = [] + steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) ) + for step in steps: + edges.append( ( steps_to_index[step], steps_to_index[step] ) ) + for conn in step.input_connections: + edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) ) + return edges + + +def order_workflow_steps_with_levels( steps ): + try: + return topsort_levels( edgelist_for_workflow_steps( steps ) ) + except CycleError: + return None diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 test/functional/api/test_workflows.py --- a/test/functional/api/test_workflows.py +++ b/test/functional/api/test_workflows.py @@ -67,6 +67,39 @@ self._assert_status_code_is( run_workflow_response, 200 ) self._wait_for_history( history_id, assert_ok=True ) + def test_extract_from_history( self ): + workflow = self.workflow_populator.load_workflow( name="test_for_extract" ) + workflow_request, history_id = self._setup_workflow_run( workflow ) + contents_response = self._get( "histories/%s/contents" % history_id ) + self._assert_status_code_is( contents_response, 200 ) + hda_ids = map( lambda c: c[ "id" ], contents_response.json() ) + + run_workflow_response = self._post( "workflows", data=workflow_request ) + self._assert_status_code_is( run_workflow_response, 200 ) + + self._wait_for_history( history_id, assert_ok=True ) + data = dict( history_id=history_id, tool_id="cat1" ) + jobs_response = self._get( "jobs", data=data ) + self._assert_status_code_is( jobs_response, 200 ) + cat1_job_id = jobs_response.json()[ 0 ][ "id" ] + + contents_response = self._get( "history/%s/contents", data=data ) + create_from_data = dict( + from_history_id=history_id, + dataset_ids=dumps( hda_ids ), + job_ids=dumps( [ cat1_job_id ] ), + workflow_name="test import from history", + ) + run_workflow_response = self._post( "workflows", data=create_from_data ) + self._assert_status_code_is( run_workflow_response, 200 ) + + new_workflow_id = run_workflow_response.json()[ "id" ] + download_response = self._get( "workflows/%s/download" % new_workflow_id ) + self._assert_status_code_is( download_response, 200 ) + downloaded_workflow = download_response.json() + self.assertEquals( downloaded_workflow[ "name" ], "test import from history" ) + assert len( downloaded_workflow[ "steps" ] ) == 3 + def test_run_replace_params_by_tool( self ): workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" ) workflow_request[ "parameters" ] = dumps( dict( random_lines1=dict( num_lines=5 ) ) ) diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 test/unit/workflows/test_extract_summary.py --- /dev/null +++ b/test/unit/workflows/test_extract_summary.py @@ -0,0 +1,98 @@ +import unittest + +from galaxy import model +from galaxy.workflow import extract + +UNDEFINED_JOB = object() + + +class TestWorkflowExtractSummary( unittest.TestCase ): + + def setUp( self ): + self.history = MockHistory() + self.trans = MockTrans( self.history ) + + def test_empty_history( self ): + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert not job_dict + + def test_summarize_returns_name_and_dataset_list( self ): + # Create two jobs and three datasets, test they are groupped + # by job correctly with correct output names. + hda1 = MockHda() + self.history.active_datasets.append( hda1 ) + hda2 = MockHda( job=hda1.job, output_name="out2" ) + self.history.active_datasets.append( hda2 ) + hda3 = MockHda( output_name="out3" ) + self.history.active_datasets.append( hda3 ) + + job_dict, warnings = extract.summarize( trans=self.trans ) + assert len( job_dict ) == 2 + assert not warnings + self.assertEquals( job_dict[ hda1.job ], [ ( 'out1', hda1 ), ( 'out2', hda2 ) ] ) + self.assertEquals( job_dict[ hda3.job ], [ ( 'out3', hda3 ) ] ) + + def test_finds_original_job_if_copied( self ): + hda = MockHda() + derived_hda_1 = MockHda() + derived_hda_1.copied_from_history_dataset_association = hda + derived_hda_2 = MockHda() + derived_hda_2.copied_from_history_dataset_association = derived_hda_1 + self.history.active_datasets.append( derived_hda_2 ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert len( job_dict ) == 1 + self.assertEquals( job_dict[ hda.job ], [ ('out1', derived_hda_2 ) ] ) + + def test_fake_job( self ): + """ Fakes job if creating_job_associations is empty. + """ + hda = MockHda( job=UNDEFINED_JOB ) + self.history.active_datasets.append( hda ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert not warnings + assert len( job_dict ) == 1 + fake_job = job_dict.keys()[ 0 ] + assert fake_job.id.startswith( "fake_" ) + datasets = job_dict.values()[ 0 ] + assert datasets == [ ( None, hda ) ] + + def test_warns_and_skips_datasets_if_not_finished( self ): + hda = MockHda( state='queued' ) + self.history.active_datasets.append( hda ) + job_dict, warnings = extract.summarize( trans=self.trans ) + assert warnings + assert len( job_dict ) == 0 + + +class MockHistory( object ): + + def __init__( self ): + self.active_datasets = [] + + +class MockTrans( object ): + + def __init__( self, history ): + self.history = history + + def get_history( self ): + return self.history + + +class MockHda( object ): + + def __init__( self, state='ok', output_name='out1', job=None ): + self.id = 123 + self.state = state + self.copied_from_history_dataset_association = None + if job is not UNDEFINED_JOB: + if not job: + job = model.Job() + self.job = job + assoc = model.JobToOutputDatasetAssociation( output_name, self ) + assoc.job = job + self.creating_job_associations = [ assoc ] + else: + self.creating_job_associations = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Handle combinations of newly defined tool dependencies and repository dependencies that are included in updates being pulled to tool shed repositories installed into Galaxy.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/90b4baa5c2b1/ Changeset: 90b4baa5c2b1 User: greg Date: 2014-03-26 19:58:08 Summary: Handle combinations of newly defined tool dependencies and repository dependencies that are included in updates being pulled to tool shed repositories installed into Galaxy. Affected #: 15 files diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -201,9 +201,13 @@ repository_id = kwd.get( 'id', None ) repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) + params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ + ( web.url_for( '/', qualified=True ), + str( repository.name ), + str( repository.owner ), + str( repository.changeset_revision ) ) url = suc.url_join( tool_shed_url, - 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ - ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) ) + 'repository/check_for_updates%s' % params ) return trans.response.send_redirect( url ) @web.expose @@ -367,9 +371,10 @@ @web.require_admin def get_tool_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): """ - Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name, - owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need - it so that we can derive the tool shed from which it was installed. + Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for + the received repository name, owner and changeset revision. The received repository_id is the encoded id + of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which + it was installed. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) @@ -388,8 +393,8 @@ @web.require_admin def get_updated_repository_information( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): """ - Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an - uninstalled tool shed repository. + Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall + an updated revision of an uninstalled tool shed repository. """ repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) @@ -436,13 +441,16 @@ @web.expose @web.require_admin - def initiate_tool_dependency_installation( self, trans, tool_dependencies ): + def initiate_tool_dependency_installation( self, trans, tool_dependencies, **kwd ): """Install specified dependencies for repository tools.""" # Get the tool_shed_repository from one of the tool_dependencies. - message = '' + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + err_msg = '' tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. - tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) + tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, + tool_shed_repository.repo_path( trans.app ) ) installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, @@ -452,13 +460,12 @@ if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) if text is not None: - message += ' %s' % text + err_msg += ' %s' % text tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies ] - if message: + if err_msg: + message += err_msg status = 'error' - else: - message = "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies ) - status = 'done' + message += "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies ) td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_tool_dependencies', @@ -506,9 +513,10 @@ status = 'error' else: # Install the latest downloadable revision of the repository. + params = '?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ + ( name, owner, str( latest_downloadable_revision ), web.url_for( '/', qualified=True ) ) url = suc.url_join( tool_shed_url, - 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ - ( name, owner, latest_downloadable_revision, web.url_for( '/', qualified=True ) ) ) + 'repository/install_repositories_by_revision%s' % params ) return trans.response.send_redirect( url ) else: message = 'Cannot locate installed tool shed repository with encoded id <b>%s</b>.' % str( repository_id ) @@ -521,43 +529,74 @@ message=message, status=status ) ) - @web.expose @web.require_admin - def install_tool_dependencies( self, trans, **kwd ): + def install_tool_dependencies_with_update( self, trans, **kwd ): + """ + Updating an installed tool shed repository where new tool dependencies but no new repository + dependencies are included in the updated revision. + """ + updating_repository_id = kwd.get( 'updating_repository_id', None ) + repository = suc.get_installed_tool_shed_repository( trans, updating_repository_id ) + # All received dependencies need to be installed - confirmed by the caller. + encoded_tool_dependencies_dict = kwd.get( 'encoded_tool_dependencies_dict', None ) + if encoded_tool_dependencies_dict is not None: + tool_dependencies_dict = encoding_util.tool_shed_decode( encoded_tool_dependencies_dict ) + else: + tool_dependencies_dict = {} + encoded_relative_install_dir = kwd.get( 'encoded_relative_install_dir', None ) + if encoded_relative_install_dir is not None: + relative_install_dir = encoding_util.tool_shed_decode( encoded_relative_install_dir ) + else: + relative_install_dir = '' + updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None ) + updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None ) + encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) - tool_dependencies = [] - for tool_dependency_id in tool_dependency_ids: - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) - tool_dependencies.append( tool_dependency ) - if kwd.get( 'install_tool_dependencies_button', False ): - # Filter tool dependencies to only those that are installed. - tool_dependencies_for_installation = [] - for tool_dependency in tool_dependencies: - if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.UNINSTALLED, - trans.install_model.ToolDependency.installation_status.ERROR ]: - tool_dependencies_for_installation.append( tool_dependency ) - if tool_dependencies_for_installation: - # Redirect back to the ToolDependencyGrid before initiating installation. - encoded_tool_dependency_for_installation_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies_for_installation ] - new_kwd = dict( action='manage_tool_dependencies', - operation='initiate_tool_dependency_installation', - tool_dependency_ids=encoded_tool_dependency_for_installation_ids, - message=message, - status=status ) - return self.tool_dependency_grid( trans, **new_kwd ) + install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) + if 'install_tool_dependencies_with_update_button' in kwd: + # Now that the user has chosen whether to install tool dependencies or not, we can + # update the repository record with the changes in the updated revision. + if encoded_updated_metadata: + updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) else: - message = 'All of the selected tool dependencies are already installed.' - status = 'error' - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repository_tool_dependencies', - tool_dependency_ids=tool_dependency_ids, - status=status, - message=message ) ) - return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies.mako', - tool_dependencies=tool_dependencies, + updated_metadata = None + repository = repository_util.update_repository_record( trans, + repository=repository, + updated_metadata_dict=updated_metadata, + updated_changeset_revision=updating_to_changeset_revision, + updated_ctx_rev=updating_to_ctx_rev ) + if install_tool_dependencies: + tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, + repository, + relative_install_dir, + set_status=False ) + message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ + ( str( repository.name ), updating_to_changeset_revision ) + self.initiate_tool_dependency_installation( trans, tool_dependencies, message=message, status=status ) + # Handle tool dependencies check box. + if trans.app.config.tool_dependency_dir is None: + if includes_tool_dependencies: + message = "Tool dependencies defined in this repository can be automatically installed if you set " + message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " + message += "(universe_wsgi.ini) and restart your Galaxy server." + status = "warning" + install_tool_dependencies_check_box_checked = False + else: + install_tool_dependencies_check_box_checked = True + install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', + checked=install_tool_dependencies_check_box_checked ) + return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies_with_update.mako', + repository=repository, + updating_repository_id=updating_repository_id, + updating_to_ctx_rev=updating_to_ctx_rev, + updating_to_changeset_revision=updating_to_changeset_revision, + encoded_updated_metadata=encoded_updated_metadata, + encoded_relative_install_dir=encoded_relative_install_dir, + encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, + install_tool_dependencies_check_box=install_tool_dependencies_check_box, + tool_dependencies_dict=tool_dependencies_dict, message=message, status=status ) @@ -611,7 +650,8 @@ # TODO: I believe this block should be removed, but make sure.. repositories_for_uninstallation = [] for repository_id in tsridslist: - repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( repository_id ) ) + repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ + .get( trans.security.decode_id( repository_id ) ) if repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLED, trans.install_model.ToolShedRepository.installation_status.ERROR ]: repositories_for_uninstallation.append( repository ) @@ -632,28 +672,34 @@ filtered_repo_info_dicts = [] filtered_tool_panel_section_keys = [] repositories_for_installation = [] - # Some repositories may have repository dependencies that are required to be installed before the dependent repository, so we'll - # order the list of tsr_ids to ensure all repositories install in the required order. + # Some repositories may have repository dependencies that are required to be installed before the + # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the + # required order. ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ repository_util.order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) for tsr_id in ordered_tsr_ids: - repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) + repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ + .get( trans.security.decode_id( tsr_id ) ) if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW, trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: repositories_for_installation.append( repository ) - repo_info_dict, tool_panel_section_key = repository_util.get_repository_components_for_installation( tsr_id, - ordered_tsr_ids, - ordered_repo_info_dicts, - ordered_tool_panel_section_keys ) + repo_info_dict, tool_panel_section_key = \ + repository_util.get_repository_components_for_installation( tsr_id, + ordered_tsr_ids, + ordered_repo_info_dicts, + ordered_tool_panel_section_keys ) filtered_repo_info_dicts.append( repo_info_dict ) filtered_tool_panel_section_keys.append( tool_panel_section_key ) if repositories_for_installation: decoded_kwd[ 'repo_info_dicts' ] = filtered_repo_info_dicts decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys - self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) + self.install_tool_shed_repositories( trans, + repositories_for_installation, + reinstalling=reinstalling, + **decoded_kwd ) else: kwd[ 'message' ] = 'All selected tool shed repositories are already installed.' kwd[ 'status' ] = 'error' @@ -772,7 +818,10 @@ trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) if tool_dependencies_for_installation: - self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) + self.initiate_tool_dependency_installation( trans, + tool_dependencies_for_installation, + message=message, + status=status ) else: message = 'All selected tool dependencies are already installed.' status = 'error' @@ -780,14 +829,16 @@ message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) ' message += ' and restart your Galaxy server to install tool dependencies.' status = 'error' - installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, - tool_shed_repository=tool_shed_repository, - name='inst_td_ids', - uninstalled_only=False ) - uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, - tool_shed_repository=tool_shed_repository, - name='uninstalled_tool_dependency_ids', - uninstalled_only=True ) + installed_tool_dependencies_select_field = \ + suc.build_tool_dependencies_select_field( trans, + tool_shed_repository=tool_shed_repository, + name='inst_td_ids', + uninstalled_only=False ) + uninstalled_tool_dependencies_select_field = \ + suc.build_tool_dependencies_select_field( trans, + tool_shed_repository=tool_shed_repository, + name='uninstalled_tool_dependency_ids', + uninstalled_only=True ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako', repository=tool_shed_repository, installed_tool_dependencies_select_field=installed_tool_dependencies_select_field, @@ -836,7 +887,10 @@ trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) if tool_dependencies_for_installation: - self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) + self.initiate_tool_dependency_installation( trans, + tool_dependencies_for_installation, + message=message, + status=status ) else: kwd[ 'message' ] = 'All selected tool dependencies are already installed.' kwd[ 'status' ] = 'error' @@ -876,18 +930,21 @@ @web.require_admin def prepare_for_install( self, trans, **kwd ): if not suc.have_shed_tool_conf_for_install( trans ): - message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a ' - message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation ' - message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose ' - message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' - message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation of Galaxy tool shed repository tools ' - message += 'into a local Galaxy instance</a> section of the Galaxy tool shed wiki for all of the details.' + message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one ' + message += 'shed tool configuration file name with a <b><toolbox></b> tag that includes a <b>tool_path</b> ' + message += 'attribute value which is a directory relative to the Galaxy installation directory in order ' + message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> ' + message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' + message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation ' + message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool ' + message += 'Shed wiki for all of the details.' return trans.show_error_message( message ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) shed_tool_conf = kwd.get( 'shed_tool_conf', None ) tool_shed_url = kwd.get( 'tool_shed_url', None ) - # Handle repository dependencies, which do not include those that are required only for compiling a dependent repository's tool dependencies. + # Handle repository dependencies, which do not include those that are required only for compiling a dependent + # repository's tool dependencies. has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) ) install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' ) # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. @@ -900,13 +957,36 @@ includes_tools_for_display_in_tool_panel = util.string_as_bool( kwd.get( 'includes_tools_for_display_in_tool_panel', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' ) + # In addition to installing new repositories, this method is called when updating an installed repository + # to a new changeset_revision where the update includes newly defined repository dependencies. + updating = util.asbool( kwd.get( 'updating', False ) ) + updating_repository_id = kwd.get( 'updating_repository_id', None ) + updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None ) + updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None ) + encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None ) encoded_repo_info_dicts = kwd.get( 'encoded_repo_info_dicts', '' ) if encoded_repo_info_dicts: encoded_repo_info_dicts = encoded_repo_info_dicts.split( encoding_util.encoding_sep ) if not encoded_repo_info_dicts: - # The request originated in the tool shed via a tool search. + # The request originated in the tool shed via a tool search or from this controller's + # update_to_changeset_revision() method. repository_ids = kwd.get( 'repository_ids', None ) - changeset_revisions = kwd.get( 'changeset_revisions', None ) + if updating: + # We have updated an installed repository where the updates included newly defined repository + # and possibly tool dependencies. We will have arrived here only if the updates include newly + # defined repository dependencies. We're preparing to allow the user to elect to install these + # dependencies. At this point, the repository has been updated to the latest changeset revision, + # but the received repository id is from the Galaxy side (the caller is this controller's + # update_to_changeset_revision() method. We need to get the id of the same repository from the + # Tool Shed side. + repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id ) + url = suc.url_join( tool_shed_url, + 'repository/get_repository_id?name=%s&owner=%s' % \ + ( str( repository.name ), str( repository.owner ) ) ) + repository_ids = common_util.tool_shed_get( trans.app, tool_shed_url, url ) + changeset_revisions = updating_to_changeset_revision + else: + changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. url = suc.url_join( tool_shed_url, 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \ @@ -918,7 +998,8 @@ if not includes_tools: includes_tools = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools', False ) ) if not includes_tools_for_display_in_tool_panel: - includes_tools_for_display_in_tool_panel = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) ) + includes_tools_for_display_in_tool_panel = \ + util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) ) if not has_repository_dependencies: has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) ) if not includes_tool_dependencies: @@ -927,6 +1008,19 @@ repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] if ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \ ( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ): + if updating: + encoded_updated_metadata_dict = kwd.get( 'encoded_updated_metadata_dict', None ) + updated_changeset_revision = kwd.get( 'updated_changeset_revision', None ) + updated_ctx_rev = kwd.get( 'updated_ctx_rev', None ) + repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id ) + decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) + # Now that the user has decided whether they will handle dependencies, we can update + # the repository to the latest revision. + repository = repository_util.update_repository_record( trans, + repository=repository, + updated_metadata_dict=decoded_updated_metadata, + updated_changeset_revision=updating_to_changeset_revision, + updated_ctx_rev=updating_to_ctx_rev ) install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) @@ -959,7 +1053,8 @@ tool_panel_section_keys=tool_panel_section_keys, tool_path=tool_path, tool_shed_url=tool_shed_url ) - encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = repository_util.initiate_repository_installation( trans, installation_dict ) + encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ + repository_util.initiate_repository_installation( trans, installation_dict ) return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', encoded_kwd=encoded_kwd, query=query, @@ -976,12 +1071,14 @@ tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans ) if len( repo_info_dicts ) == 1: - # If we're installing a single repository, see if it contains a readme or dependencies that we can display. + # If we're installing or updating a single repository, see if it contains a readme or + # dependencies that we can display. repo_info_dict = repo_info_dicts[ 0 ] dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, - includes_tool_dependencies ) + includes_tool_dependencies, + updating=updating ) changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None ) if not has_repository_dependencies: has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) @@ -990,7 +1087,8 @@ if not includes_tools: includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False ) if not includes_tools_for_display_in_tool_panel: - includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) + includes_tools_for_display_in_tool_panel = \ + dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None ) installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None ) missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None ) @@ -998,19 +1096,25 @@ name = dependencies_for_repository_dict.get( 'name', None ) repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None ) readme_files_dict = readme_util.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict ) - # We're handling 1 of 2 scenarios here: (1) we're installing a tool shed repository for the first time, so we've retrieved the list of installed - # and missing repository dependencies from the database (2) we're handling the scenario where an error occurred during the installation process, - # so we have a tool_shed_repository record in the database with associated repository dependency records. Since we have the repository - # dependencies in either case, we'll merge the list of missing repository dependencies into the list of installed repository dependencies since - # each displayed repository dependency will display a status, whether installed or missing. - containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + # We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've + # retrieved the list of installed and missing repository dependencies from the database (2) we're handling the + # scenario where an error occurred during the installation process, so we have a tool_shed_repository record in + # the database with associated repository dependency records. Since we have the repository dependencies in both + # of the above 2 cases, we'll merge the list of missing repository dependencies into the list of installed + # repository dependencies since each displayed repository dependency will display a status, whether installed or + # missing. The 3rd scenario is where we're updating an installed repository and the updates include newly + # defined repository (and possibly tool) dependencies. In this case, merging will result in newly defined + # dependencies to be lost. We pass the updating parameter to make sure merging occurs only when appropriate. + containers_dict = \ + repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=updating ) else: # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies. containers_dicts = [] @@ -1018,7 +1122,8 @@ dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, - includes_tool_dependencies ) + includes_tool_dependencies, + updating=updating ) changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None ) if not has_repository_dependencies: has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) @@ -1027,34 +1132,39 @@ if not includes_tools: includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False ) if not includes_tools_for_display_in_tool_panel: - includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) + includes_tools_for_display_in_tool_panel = \ + dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None ) installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None ) missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None ) missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None ) name = dependencies_for_repository_dict.get( 'name', None ) repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None ) - containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=None, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + containers_dict = \ + repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=None, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=updating ) containers_dicts.append( containers_dict ) # Merge all containers into a single container. containers_dict = repository_util.merge_containers_dicts_for_new_install( containers_dicts ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: - message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " - message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository." + message = "Tool dependencies defined in this repository can be automatically installed if you set " + message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " + message += "(universe_wsgi.ini) and restart your Galaxy server before installing the repository." status = "warning" install_tool_dependencies_check_box_checked = False else: install_tool_dependencies_check_box_checked = True - install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) + install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', + checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts ) @@ -1062,6 +1172,11 @@ if includes_tools_for_display_in_tool_panel: return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, + updating=updating, + updating_repository_id=updating_repository_id, + updating_to_ctx_rev=updating_to_ctx_rev, + updating_to_changeset_revision=updating_to_changeset_revision, + encoded_updated_metadata=encoded_updated_metadata, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, @@ -1077,10 +1192,16 @@ message=message, status=status ) else: - # If installing repositories that includes no tools and has no repository dependencies, display a page allowing the Galaxy administrator to - # select a shed-related tool panel configuration file whose tool_path setting will be the location the repositories will be installed. + # If installing repositories that includes no tools and has no repository dependencies, display a page + # allowing the Galaxy administrator to select a shed-related tool panel configuration file whose tool_path + # setting will be the location the repositories will be installed. return trans.fill_template( '/admin/tool_shed_repository/select_shed_tool_panel_config.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, + updating=updating, + updating_repository_id=updating_repository_id, + updating_to_ctx_rev=updating_to_ctx_rev, + updating_to_changeset_revision=updating_to_changeset_revision, + encoded_updated_metadata=encoded_updated_metadata, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, @@ -1400,7 +1521,8 @@ dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, - includes_tool_dependencies ) + includes_tool_dependencies, + updating=False ) changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None ) has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False ) @@ -1449,14 +1571,16 @@ original_section_name = '' tool_panel_section_select_field = None shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) - containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans, - tool_shed_url=tool_shed_url, - tool_path=tool_path, - readme_files_dict=readme_files_dict, - installed_repository_dependencies=installed_repository_dependencies, - missing_repository_dependencies=missing_repository_dependencies, - installed_tool_dependencies=installed_tool_dependencies, - missing_tool_dependencies=missing_tool_dependencies ) + containers_dict = \ + repository_util.populate_containers_dict_for_new_install( trans=trans, + tool_shed_url=tool_shed_url, + tool_path=tool_path, + readme_files_dict=readme_files_dict, + installed_repository_dependencies=installed_repository_dependencies, + missing_repository_dependencies=missing_repository_dependencies, + installed_tool_dependencies=installed_tool_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + updating=False ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed # repository dependency will display a status, whether installed or missing. containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) @@ -1574,8 +1698,8 @@ @web.require_admin def set_tool_versions( self, trans, **kwd ): """ - Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the - metadata for the repository's revision in the Galaxy database. + Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed + repository and update the metadata for the repository's revision in the Galaxy database. """ repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) @@ -1720,29 +1844,17 @@ resetting_all_metadata_on_repository=False, updating_installed_repository=True, persist=True ) - repository.metadata = metadata_dict - # Update the repository.changeset_revision column in the database. - repository.changeset_revision = latest_changeset_revision - repository.ctx_rev = latest_ctx_rev - # Update the repository.tool_shed_status column in the database. - tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository ) - if tool_shed_status_dict: - repository.tool_shed_status = tool_shed_status_dict - else: - repository.tool_shed_status = None - trans.install_model.context.add( repository ) - trans.install_model.context.flush() if 'tools' in metadata_dict: tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) tool_util.add_to_tool_panel( app=trans.app, - repository_name=repository.name, + repository_name=str( repository.name ), repository_clone_url=repository_clone_url, - changeset_revision=repository.installed_changeset_revision, + changeset_revision=str( repository.installed_changeset_revision ), repository_tools_tups=repository_tools_tups, - owner=repository.owner, + owner=str( repository.owner ), shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=False ) @@ -1755,19 +1867,40 @@ os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - # Create tool_dependency records if necessary. - if 'tool_dependencies' in metadata_dict: - tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, - repository, - relative_install_dir, - set_status=False ) + if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: + if 'repository_dependencies' in metadata_dict: + # Updates received include newly defined repository dependencies, so allow the user + # the option of installting them. We cannot update the repository with the changes + # until that happens, so we have to send them along. + new_kwd = dict( tool_shed_url=tool_shed_url, + updating_repository_id=trans.security.encode_id( repository.id ), + updating_to_ctx_rev=latest_ctx_rev, + updating_to_changeset_revision=latest_changeset_revision, + encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + updating=True ) + return self.prepare_for_install( trans, **new_kwd ) + # Updates received did not include any newly defined repository dependencies but did include + # newly defined tool dependencies. + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) + new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), + updating_to_ctx_rev=latest_ctx_rev, + updating_to_changeset_revision=latest_changeset_revision, + encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_relative_install_dir=encoded_relative_install_dir, + encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, + message=message, + status = status ) + return self.install_tool_dependencies_with_update( trans, **new_kwd ) + # Updates received did not include any newly defined repository dependencies or newly defined + # tool dependencies. + repository = repository_util.update_repository_record( trans, + repository=repository, + updated_metadata_dict=metadata_dict, + updated_changeset_revision=latest_changeset_revision, + updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ ( name, latest_changeset_revision ) - # See if any tool dependencies can be installed. - shed_tool_conf, tool_path, relative_install_dir = \ - suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - if repository.missing_tool_dependencies: - message += "Click the name of one of the missing tool dependencies listed below to install tool dependencies." else: message = "The directory containing the installed repository named '%s' cannot be found. " % name status = 'error' diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -866,11 +866,13 @@ no_update = 'false' elif galaxy_url: # Start building up the url to redirect back to the calling Galaxy instance. + params = '?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ + ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) url = suc.url_join( galaxy_url, - 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ - ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) + 'admin_toolshed/update_to_changeset_revision%s' % params ) else: - message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url + message += 'You may need to enable third-party cookies in your browser. ' return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. @@ -883,15 +885,17 @@ trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: - # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. + # If changeset_revision is in the repository_metadata table for this repository, there are no + # additional updates. if from_update_manager: return no_update else: # Return the same value for changeset_revision and latest_changeset_revision. url += latest_changeset_revision else: - # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the - # repository was installed. We need to find the changeset_revision to which we need to update. + # The changeset_revision column in the repository_metadata table has been updated with a new + # changeset_revision value since the repository was installed. We need to find the changeset_revision + # to which we need to update. update_to_changeset_hash = None for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) @@ -1680,6 +1684,16 @@ return encoding_util.tool_shed_encode( repository_dependencies ) return '' + @web.expose + def get_repository_id( self, trans, **kwd ): + """Given a repository name and owner, return the encoded repository id.""" + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] + repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner ) + if repository: + return trans.security.encode_id( repository.id ) + return '' + @web.json def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ): """ @@ -1824,7 +1838,9 @@ if not repository_metadata: # The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository # changelog that is associated with metadata. - changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision=changeset_revision ) + changeset_revision = suc.get_next_downloadable_changeset_revision( repository, + repo, + after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) repo_info_dict = repository_util.create_repo_info_dict( trans=trans, @@ -2039,11 +2055,12 @@ galaxy_url = suc.handle_galaxy_url( trans, **kwd ) if galaxy_url: # Redirect back to local Galaxy to perform install. + params = '?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ + ( web.url_for( '/', qualified=True ), + ','.join( util.listify( repository_ids ) ), + ','.join( util.listify( changeset_revisions ) ) ) url = suc.url_join( galaxy_url, - 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ - ( web.url_for( '/', qualified=True ), - ','.join( util.listify( repository_ids ) ), - ','.join( util.listify( changeset_revisions ) ) ) ) + 'admin_toolshed/prepare_for_install%s' % params ) return trans.response.send_redirect( url ) else: message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url @@ -2477,9 +2494,10 @@ @web.expose def next_installable_changeset_revision( self, trans, **kwd ): """ - Handle a request from a Galaxy instance where the changeset_revision defined for a repository in a dependency definition file is older - than the changeset_revision associated with the installed repository. This will occur with repository's of type tool_dependency_definition, - and this scenario will occur while repository dependency hierarchies are bing installed. + Handle a request from a Galaxy instance where the changeset_revision defined for a repository + in a dependency definition file is older than the changeset_revision associated with the installed + repository. This will occur with repository's of type tool_dependency_definition, and this scenario + will occur while repository dependency hierarchies are bing installed. """ name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) @@ -2981,12 +2999,13 @@ @web.expose def updated_changeset_revisions( self, trans, **kwd ): """ - Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an installed repository can be updated. This - method will return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision. Among - other things , this method handles the scenario where an installed tool shed repository's tool_dependency definition file defines a changeset - revision for a complex repository dependency that is outdated. In other words, a defined changeset revision is older than the current changeset - revision for the required repository, making it impossible to discover the repository without knowledge of revisions to which it could have been - updated. + Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an + installed repository can be updated. This method will return a string of comma-separated changeset revision + hashes for all available updates to the received changeset revision. Among other things , this method + handles the scenario where an installed tool shed repository's tool_dependency definition file defines a + changeset revision for a complex repository dependency that is outdated. In other words, a defined changeset + revision is older than the current changeset revision for the required repository, making it impossible to + discover the repository without knowledge of revisions to which it could have been updated. """ name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -37,15 +37,19 @@ Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined for the repository, as well as the defined tool dependencies. - This method is called from Galaxy under three scenarios: + This method is called from Galaxy under four scenarios: 1. During the tool shed repository installation process via the tool shed's get_repository_information() - method. In this case both the received repository and repository_metadata will be objects., but + method. In this case both the received repository and repository_metadata will be objects, but tool_dependencies and repository_dependencies will be None. - 2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no + 2. When getting updates for an install repository where the updates include newly defined repository + dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information() + method is the caller, and both the received repository and repository_metadata will be objects, but + tool_dependencies and repository_dependencies will be None. + 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes definitions for them. - 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates + 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates available. In this case, this method is reached via the tool shed's get_updated_repository_information() method, and both repository and repository_metadata will be objects but tool_dependencies and repository_dependencies will be None. @@ -184,16 +188,22 @@ repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + repository_id, + changeset_revision ) if not repository_metadata: - # The received changeset_revision is no longer installable, so get the next changeset_revision in the repository's changelog. - # This generally occurs only with repositories of type tool_dependency_definition. - next_downloadable_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + # The received changeset_revision is no longer installable, so get the next changeset_revision + # in the repository's changelog. This generally occurs only with repositories of type + # tool_dependency_definition. + next_downloadable_changeset_revision = \ + suc.get_next_downloadable_changeset_revision( repository,repo, changeset_revision ) if next_downloadable_changeset_revision: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision ) + repository_metadata = \ + suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision ) if repository_metadata: - # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption is not valid we'll have to - # enhance the callers to handle repository_metadata values of None in the returned repo_info_dict. + # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption + # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the + # returned repo_info_dict. metadata = repository_metadata.metadata if 'tools' in metadata: includes_tools = True @@ -743,9 +753,13 @@ ordered_tool_panel_section_keys.append( tool_panel_section_key ) return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys -def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies, - installed_tool_dependencies, missing_tool_dependencies ): - """Return the populated containers for a repository being installed for the first time.""" +def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, + missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies, + updating=False ): + """ + Return the populated containers for a repository being installed for the first time or for an installed repository + that is being updated and the updates include newly defined repository (and possibly tool) dependencies. + """ installed_tool_dependencies, missing_tool_dependencies = \ tool_dependency_util.populate_tool_dependencies_dicts( trans=trans, tool_shed_url=tool_shed_url, @@ -753,27 +767,32 @@ repository_installed_tool_dependencies=installed_tool_dependencies, repository_missing_tool_dependencies=missing_tool_dependencies, required_repo_info_dicts=None ) - # Since we are installing a new repository, most of the repository contents are set to None since we don't yet know what they are. - containers_dict = container_util.build_repository_containers_for_galaxy( trans=trans, - repository=None, - datatypes=None, - invalid_tools=None, - missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=installed_repository_dependencies, - tool_dependencies=installed_tool_dependencies, - valid_tools=None, - workflows=None, - valid_data_managers=None, - invalid_data_managers=None, - data_managers_errors=None, - new_install=True, - reinstalling=False ) - # Merge the missing_repository_dependencies container contents to the installed_repository_dependencies container. - containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) - # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container. - containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict ) + # Most of the repository contents are set to None since we don't yet know what they are. + containers_dict = \ + container_util.build_repository_containers_for_galaxy( trans=trans, + repository=None, + datatypes=None, + invalid_tools=None, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None, + data_managers_errors=None, + new_install=True, + reinstalling=False ) + if not updating: + # If we installing a new repository and not updaing an installed repository, we can merge + # the missing_repository_dependencies container contents to the installed_repository_dependencies + # container. When updating an installed repository, merging will result in losing newly defined + # dependencies included in the updates. + containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict ) + # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container. + containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict ) return containers_dict def pull_repository( repo, repository_clone_url, ctx_rev ): @@ -875,3 +894,23 @@ repository.uninstalled = uninstalled trans.install_model.context.add( repository ) trans.install_model.context.flush() + +def update_repository_record( trans, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ): + """ + Update a tool_shed_repository database record with new information retrieved from the + Tool Shed. This happens when updating an installed repository to a new changeset revision. + """ + repository.metadata = updated_metadata_dict + # Update the repository.changeset_revision column in the database. + repository.changeset_revision = updated_changeset_revision + repository.ctx_rev = updated_ctx_rev + # Update the repository.tool_shed_status column in the database. + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository ) + if tool_shed_status_dict: + repository.tool_shed_status = tool_shed_status_dict + else: + repository.tool_shed_status = None + trans.install_model.context.add( repository ) + trans.install_model.context.flush() + trans.install_model.context.refresh( repository ) + return repository diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -359,13 +359,14 @@ can_install_tool_dependency = True if can_install_tool_dependency: package_install_version = package_elem.get( 'version', '1.0' ) - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=package_name, - version=package_version, - type='package', - status=app.install_model.ToolDependency.installation_status.INSTALLING, - set_status=True ) + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=package_name, + version=package_version, + type='package', + status=app.install_model.ToolDependency.installation_status.INSTALLING, + set_status=True ) # Get the information about the current platform in case the tool dependency definition includes tag sets # for installing compiled binaries. platform_info_dict = tool_dependency_util.get_platform_info_dict() @@ -879,25 +880,28 @@ # Tool dependencies of type "set_environmnet" always have the version attribute set to None. attr_tup = ( env_var_name, None, 'set_environment' ) if attr_tup in attr_tups_of_dependencies_for_install: - install_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app, - repository_name=tool_shed_repository.name, - repository_owner=tool_shed_repository.owner, - repository_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dependency_type='set_environment', - tool_dependency_name=env_var_name, - tool_dependency_version=None ) + install_dir = \ + tool_dependency_util.get_tool_dependency_install_dir( app=app, + repository_name=tool_shed_repository.name, + repository_owner=tool_shed_repository.owner, + repository_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dependency_type='set_environment', + tool_dependency_name=env_var_name, + tool_dependency_version=None ) tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository ) env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir ) if env_var_dict: if not os.path.exists( install_dir ): os.makedirs( install_dir ) - tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app, - tool_shed_repository=tool_shed_repository, - name=env_var_name, - version=None, - type='set_environment', - status=app.install_model.ToolDependency.installation_status.INSTALLING, - set_status=True ) + status = app.install_model.ToolDependency.installation_status.INSTALLING + tool_dependency = \ + tool_dependency_util.create_or_update_tool_dependency( app=app, + tool_shed_repository=tool_shed_repository, + name=env_var_name, + version=None, + type='set_environment', + status=status, + set_status=True ) if env_var_version == '1.0': # Create this tool dependency's env.sh file. env_file_builder = fabric_util.EnvFileBuilder( install_dir ) @@ -906,28 +910,34 @@ error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ ( str( tool_dependency.name ), str( return_code ) ) log.debug( error_message ) - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.ERROR, - error_message=error_message, - remove_from_disk=False ) + status = app.install_model.ToolDependency.installation_status.ERROR + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) else: if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR, app.install_model.ToolDependency.installation_status.INSTALLED ]: - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.INSTALLED, - error_message=None, - remove_from_disk=False ) + status = app.install_model.ToolDependency.installation_status.INSTALLED + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=None, + remove_from_disk=False ) log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \ ( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) ) else: error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).' - tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app, - tool_dependency=tool_dependency, - status=app.install_model.ToolDependency.installation_status.ERROR, - error_message=error_message, - remove_from_disk=False ) + status = app.install_model.ToolDependency.installation_status.ERROR + tool_dependency = \ + tool_dependency_util.set_tool_dependency_attributes( app, + tool_dependency=tool_dependency, + status=status, + error_message=error_message, + remove_from_disk=False ) return tool_dependency def strip_path( fpath ): diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -70,7 +70,7 @@ if display_path is not None: datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False ) -def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): +def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=False ): """ Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined by the received repo_info_dict. @@ -90,7 +90,7 @@ # Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies. # We don't add to installed_td and missing_td here because at this point they are empty. installed_td, missing_td = \ - get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies ) + get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies ) # In cases where a repository dependency is required only for compiling a dependent repository's # tool dependency, the value of repository_dependencies will be an empty dictionary here. if repository_dependencies: @@ -101,10 +101,11 @@ name, repository_owner, changeset_revision ) - if repository and repository.metadata: + if not updating and repository and repository.metadata: installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository ) else: - installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) + installed_rd, missing_rd = \ + get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple ) # Discover all repository dependencies and retrieve information for installing them. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) @@ -119,7 +120,8 @@ required_tool_dependencies = {} for rid in required_repo_info_dicts: for name, repo_info_tuple in rid.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, rid_repository_dependencies, rid_tool_dependencies = \ + description, repository_clone_url, changeset_revision, ctx_rev, \ + repository_owner, rid_repository_dependencies, rid_tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) if rid_tool_dependencies: for td_key, td_dict in rid_tool_dependencies.items(): @@ -128,7 +130,9 @@ if required_tool_dependencies: # Discover and categorize all tool dependencies defined for this repository's repository dependencies. required_installed_td, required_missing_td = \ - get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, required_tool_dependencies ) + get_installed_and_missing_tool_dependencies_for_repository( trans, + tool_shed_url, + required_tool_dependencies ) if required_installed_td: if not includes_tool_dependencies: includes_tool_dependencies = True @@ -168,11 +172,12 @@ def get_installed_and_missing_repository_dependencies( trans, repository ): """ - Return the installed and missing repository dependencies for a tool shed repository that has a record in the Galaxy database, but - may or may not be installed. In this case, the repository dependencies are associated with the repository in the database. Do not - include a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since these - special kinds of repository dependencies are really a dependency of the dependent repository's contained tool dependency, and only if - that tool dependency requires compilation. + Return the installed and missing repository dependencies for a tool shed repository that has a record + in the Galaxy database, but may or may not be installed. In this case, the repository dependencies are + associated with the repository in the database. Do not include a repository dependency if it is required + only to compile a tool dependency defined for the dependent repository since these special kinds of repository + dependencies are really a dependency of the dependent repository's contained tool dependency, and only + if that tool dependency requires compilation. """ missing_repository_dependencies = {} installed_repository_dependencies = {} @@ -228,7 +233,7 @@ missing_repository_dependencies[ 'description' ] = description return installed_repository_dependencies, missing_repository_dependencies -def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ): +def get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple ): """ Parse the received repository_dependencies dictionary that is associated with a repository being installed into Galaxy for the first time and attempt to determine repository dependencies that are @@ -264,13 +269,13 @@ tmp_repo_info_tuple ) if repository: new_rd_tup = [ tool_shed, - name, - owner, - changeset_revision, - prior_installation_required, - only_if_compiling_contained_td, - repository.id, - repository.status ] + name, + owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, + repository.id, + repository.status ] if repository.status == trans.install_model.ToolShedRepository.installation_status.INSTALLED: if new_rd_tup not in installed_rd_tups: installed_rd_tups.append( new_rd_tup ) @@ -285,12 +290,12 @@ missing_rd_tups.append( new_rd_tup ) else: new_rd_tup = [ tool_shed, - name, - owner, - changeset_revision, - prior_installation_required, - only_if_compiling_contained_td, - None, + name, + owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, + None, 'Never installed' ] if not util.asbool( only_if_compiling_contained_td ): # A repository dependency that is not installed will not be considered missing if it's value for @@ -307,11 +312,17 @@ missing_repository_dependencies[ 'description' ] = description return installed_repository_dependencies, missing_repository_dependencies -def get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies_dict ): +def get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies_dict ): """ Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories being installed into Galaxy. """ + # FIXME: This implementation breaks when updates to a repository contain dependencies that result in + # multiple entries for a specific tool dependency. A scenario where this can happen is where 2 repositories + # define the same dependency internally (not using the complex repository dependency definition to a separate + # package repository approach). If 2 repositories contain the same tool_dependencies.xml file, one dependency + # will be lost since the values in these returned dictionaries are not lists. All tool dependency dictionaries + # should have lists as values. These scenarios are probably extreme corner cases, but still should be handled. installed_tool_dependencies = {} missing_tool_dependencies = {} if tool_dependencies_dict: diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -821,8 +821,8 @@ tool_dependencies = metadata[ 'tool_dependencies' ] if trans.webapp.name == 'tool_shed': if 'orphan_tool_dependencies' in metadata: - # The use of the orphan_tool_dependencies category in metadata has been deprecated, but we still need to check in case - # the metadata is out of date. + # The use of the orphan_tool_dependencies category in metadata has been deprecated, + # but we still need to check in case the metadata is out of date. orphan_tool_dependencies = metadata[ 'orphan_tool_dependencies' ] tool_dependencies.update( orphan_tool_dependencies ) # Tool dependencies can be categorized as orphans only if the repository contains tools. diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/encoding_util.py --- a/lib/tool_shed/util/encoding_util.py +++ b/lib/tool_shed/util/encoding_util.py @@ -21,7 +21,6 @@ try: values = json.loads( value ) except Exception, e: - #log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) ) pass if values is not None: try: @@ -34,7 +33,7 @@ return values def tool_shed_encode( val ): - if isinstance( val, dict ): + if isinstance( val, dict ) or isinstance( val, list ): value = json.dumps( val ) else: value = val diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -662,9 +662,11 @@ # See if we have a repository dependencies defined. if name == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: path_to_repository_dependencies_config = os.path.join( root, name ) - metadata_dict, error_message = generate_repository_dependency_metadata( app, - path_to_repository_dependencies_config, - metadata_dict ) + metadata_dict, error_message = \ + generate_repository_dependency_metadata( app, + path_to_repository_dependencies_config, + metadata_dict, + updating_installed_repository=updating_installed_repository ) if error_message: invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. @@ -795,7 +797,10 @@ # is True, the tool dependency definition will be set as invalid. This is currently the only case # where a tool dependency definition is considered invalid. repository_dependency_tup, repository_dependency_is_valid, error_message = \ - handle_repository_elem( app=app, repository_elem=sub_elem, only_if_compiling_contained_td=False ) + handle_repository_elem( app=app, + repository_elem=sub_elem, + only_if_compiling_contained_td=False, + updating_installed_repository=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': @@ -829,7 +834,8 @@ repository_dependency_tup, repository_dependency_is_valid, error_message = \ handle_repository_elem( app=app, repository_elem=sub_action_elem, - only_if_compiling_contained_td=True ) + only_if_compiling_contained_td=True, + updating_installed_repository=False ) if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) if repository_dependency_is_valid: @@ -841,10 +847,10 @@ return valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, \ repository_dependency_is_valid, error_message -def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict ): +def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict, updating_installed_repository=False ): """ - Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method - is called from the tool shed as well as from Galaxy. + Generate a repository dependencies dictionary based on valid information defined in the received + repository_dependencies_config. This method is called from the tool shed as well as from Galaxy. """ error_message = '' # Make sure we're looking at a valid repository_dependencies.xml file. @@ -861,7 +867,10 @@ valid_repository_dependency_tups = [] for repository_elem in root.findall( 'repository' ): repository_dependency_tup, repository_dependency_is_valid, err_msg = \ - handle_repository_elem( app, repository_elem, only_if_compiling_contained_td=False ) + handle_repository_elem( app, + repository_elem, + only_if_compiling_contained_td=False, + updating_installed_repository=updating_installed_repository ) if repository_dependency_is_valid: valid_repository_dependency_tups.append( repository_dependency_tup ) else: @@ -885,11 +894,12 @@ metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict return metadata_dict, error_message -def generate_tool_dependency_metadata( app, repository, changeset_revision, repository_clone_url, tool_dependencies_config, metadata_dict, - original_repository_metadata=None ): +def generate_tool_dependency_metadata( app, repository, changeset_revision, repository_clone_url, tool_dependencies_config, + metadata_dict, original_repository_metadata=None ): """ - If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository, - then update the received metadata_dict with information from the parsed tool_dependencies_config. + If the combination of name, version and type of each element is defined in the <requirement> tag for + at least one tool in the repository, then update the received metadata_dict with information from the + parsed tool_dependencies_config. """ error_message = '' if original_repository_metadata: @@ -1171,7 +1181,7 @@ deleted_tool_dependency_names.append( original_dependency_val_dict[ 'name' ] ) return updated_tool_dependency_names, deleted_tool_dependency_names -def handle_repository_elem( app, repository_elem, only_if_compiling_contained_td=False ): +def handle_repository_elem( app, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ): """ Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, we're generating repository dependencies metadata for @@ -1187,14 +1197,17 @@ changeset_revision = repository_elem.get( 'changeset_revision', None ) prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) ) if app.name == 'galaxy': - # We're installing a repository into Galaxy, so make sure its contained repository dependency definition - # is valid. - if toolshed is None or name is None or owner is None or changeset_revision is None: - # Raise an exception here instead of returning an error_message to keep the installation from - # proceeding. Reaching here implies a bug in the Tool Shed framework. - error_message = 'Installation halted because the following repository dependency definition is invalid:\n' - error_message += xml_util.xml_to_string( repository_elem, use_indent=True ) - raise Exception( error_message ) + if updating_installed_repository: + pass + else: + # We're installing a repository into Galaxy, so make sure its contained repository dependency definition + # is valid. + if toolshed is None or name is None or owner is None or changeset_revision is None: + # Raise an exception here instead of returning an error_message to keep the installation from + # proceeding. Reaching here implies a bug in the Tool Shed framework. + error_message = 'Installation halted because the following repository dependency definition is invalid:\n' + error_message += xml_util.xml_to_string( repository_elem, use_indent=True ) + raise Exception( error_message ) if not toolshed: # Default to the current tool shed. toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) @@ -1230,6 +1243,14 @@ updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message + if updating_installed_repository: + # The repository dependency was included in an update to the installed repository, so it will + # not yet be installed. Return the tuple for later installation. + return repository_dependency_tup, is_valid, error_message + if updating_installed_repository: + # The repository dependency was included in an update to the installed repository, so it will not yet + # be installed. Return the tuple for later installation. + return repository_dependency_tup, is_valid, error_message # Don't generate an error message for missing repository dependencies that are required only if compiling the # dependent repository's tool dependency. if not only_if_compiling_contained_td: diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -90,7 +90,6 @@ if tree is None: return tool_dependency_objects root = tree.getroot() - fabric_version_checked = False for elem in root: tool_dependency_type = elem.tag if tool_dependency_type == 'package': @@ -574,8 +573,8 @@ sa_session.flush() return tool_dependency -def sync_database_with_file_system( app, tool_shed_repository, tool_dependency_name, tool_dependency_version, tool_dependency_install_dir, - tool_dependency_type='package' ): +def sync_database_with_file_system( app, tool_shed_repository, tool_dependency_name, tool_dependency_version, + tool_dependency_install_dir, tool_dependency_type='package' ): """ The installation directory defined by the received tool_dependency_install_dir exists, so check for the presence of fabric_util.INSTALLATION_LOG. If the files exists, we'll assume the tool dependency is installed, but not diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -90,6 +90,7 @@ return str( self.count ) repository_dependencies_root_folder = containers_dict.get( 'repository_dependencies', None ) + missing_repository_dependencies_root_folder = containers_dict.get( 'missing_repository_dependencies', None ) tool_dependencies_root_folder = containers_dict.get( 'tool_dependencies', None ) missing_tool_dependencies_root_folder = containers_dict.get( 'missing_tool_dependencies', None ) env_settings_heaader_row_displayed = False @@ -112,7 +113,7 @@ </p></div></div> - %if repository_dependencies_root_folder: + %if repository_dependencies_root_folder or missing_repository_dependencies_root_folder: %if repository_dependencies_check_box is not None: <div class="form-row"> %if export: @@ -131,14 +132,26 @@ </div><div style="clear: both"></div> %endif - <div class="form-row"> - <p/> - <% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table"> - ${render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} - </table> - <div style="clear: both"></div> - </div> + %if repository_dependencies_root_folder: + <div class="form-row"> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table"> + ${render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + <div style="clear: both"></div> + </div> + %endif + %if missing_repository_dependencies_root_folder: + <div class="form-row"> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table"> + ${render_folder( missing_repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table> + <div style="clear: both"></div> + </div> + %endif %endif %if tool_dependencies_root_folder or missing_tool_dependencies_root_folder: %if install_tool_dependencies_check_box is not None: diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/install_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/install_tool_dependencies.mako +++ /dev/null @@ -1,81 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<% import os %> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="warningmessage"> - <p> - The tool dependencies listed below can be automatically installed with the repository. Installing them provides significant - benefits and Galaxy includes various features to manage them. - </p> - <p> - Each of these dependencies may require their own build requirements (e.g., CMake, g++, etc). Galaxy will not attempt to install - these build requirements, so if any are missing from your environment tool dependency installation may partially fail. The - repository and all of it's contents will be installed in any case. - </p> - <p> - If tool dependency installation fails in any way, you can install the missing build requirements and have Galaxy attempt to install - the tool dependencies again using the <b>Install tool dependencies</b> pop-up menu option on the <b>Manage repository</b> page. - </p> -</div> - -<div class="toolForm"> - <div class="toolFormBody"> - <form name="install_tool_dependenceies" id="install_tool_dependenceies" action="${h.url_for( controller='admin_toolshed', action='install_tool_dependencies' )}" method="post" > - <div class="form-row"> - <table class="grid"> - <tr><td colspan="4" bgcolor="#D8D8D8"><b>Tool dependencies</b></td></tr> - <tr> - <th>Name</th> - <th>Version</th> - <th>Type</th> - <th>Install directory</th> - </tr> - <% tool_shed_repository = None %> - %for tool_dependency in tool_dependencies: - <input type="hidden" name="tool_dependency_ids" value="${trans.security.encode_id( tool_dependency.id )}"/> - <% - readme_text = None - if tool_shed_repository is None: - tool_shed_repository = tool_dependency.tool_shed_repository - metadata = tool_shed_repository.metadata - tool_dependencies_dict = metadata[ 'tool_dependencies' ] - for key, requirements_dict in tool_dependencies_dict.items(): - key_items = key.split( '/' ) - key_name = key_items[ 0 ] - key_version = key_items[ 1 ] - if key_name == tool_dependency.name and key_version == tool_dependency.version: - readme_text = requirements_dict.get( 'readme', None ) - install_dir = os.path.join( trans.app.config.tool_dependency_dir, - tool_dependency.name, - tool_dependency.version, - tool_shed_repository.owner, - tool_shed_repository.name, - tool_shed_repository.installed_changeset_revision ) - %> - %if not os.path.exists( install_dir ): - <tr> - <td>${tool_dependency.name}</td> - <td>${tool_dependency.version}</td> - <td>${tool_dependency.type}</td> - <td>${install_dir}</td> - </tr> - %if readme_text: - <tr><td colspan="4" bgcolor="#FFFFCC">${tool_dependency.name} ${tool_dependency.version} requirements and installation information</td></tr> - <tr><td colspan="4"><pre>${readme_text}</pre></td></tr> - %endif - %endif - %endfor - </table> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="install_tool_dependencies_button" value="Install"/> - </div> - </form> - </div> -</div> diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako @@ -0,0 +1,91 @@ +<%inherit file="/base.mako"/> +<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" /> +<%namespace file="/message.mako" import="render_msg" /> + +<% + import os + from tool_shed.util.common_util import parse_repository_dependency_tuple +%> + +${render_galaxy_repository_actions( repository )} + +%if message: + ${render_msg( message, status )} +%endif + +<div class="warningmessage"> + <p> + The updates to the <b>${repository.name}</b> repository require the following packages. Click the <b>Install</b> button to install them. + Installing some packages may take a while, but you can continue to use Galaxy during installation. + </p> +</div> + +<div class="toolForm"> + <div class="toolFormBody"> + <form name="install_tool_dependencies_with_update" id="install_tool_dependencies_with_update" action="${h.url_for( controller='admin_toolshed', action='install_tool_dependencies_with_update' )}" method="post" > + <input type="hidden" name="updating_repository_id" value="${updating_repository_id}"/> + <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}"/> + <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}"/> + <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}"/> + <input type="hidden" name="encoded_relative_install_dir" value="${encoded_relative_install_dir}"/> + <input type="hidden" name="encoded_tool_dependencies_dict" value="${encoded_tool_dependencies_dict}"/> + %if tool_dependencies_dict: + %if install_tool_dependencies_check_box is not None: + <div class="form-row"> + <label>Handle tool dependencies?</label> + <% disabled = trans.app.config.tool_dependency_dir is None %> + ${install_tool_dependencies_check_box.get_html( disabled=disabled )} + <div class="toolParamHelp" style="clear: both;"> + %if disabled: + Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies. + %else: + Un-check to skip automatic handling of these tool dependencies. + %endif + </div> + </div> + <div style="clear: both"></div> + %endif + <div class="form-row"> + <table class="grid"> + <tr><td colspan="4" bgcolor="#D8D8D8"><b>New tool dependencies included in update</b></td></tr> + <tr> + <th>Name</th> + <th>Version</th> + <th>Install directory</th> + </tr> + %for key, requirements_dict in tool_dependencies_dict.items(): + <% + readme_text = None + key_items = key.split( '/' ) + key_name = key_items[ 0 ] + key_version = key_items[ 1 ] + readme_text = requirements_dict.get( 'readme', None ) + install_dir = os.path.join( trans.app.config.tool_dependency_dir, + key_name, + key_version, + repository.owner, + repository.name, + repository.installed_changeset_revision ) + %> + %if not os.path.exists( install_dir ): + <tr> + <td>${key_name}</td> + <td>${key_version}</td> + <td>${install_dir}</td> + </tr> + %if readme_text: + <tr><td colspan="4" bgcolor="#FFFFCC">${key_name} ${key_version} requirements and installation information</td></tr> + <tr><td colspan="4"><pre>${readme_text}</pre></td></tr> + %endif + %endif + %endfor + </table> + <div style="clear: both"></div> + </div> + %endif + <div class="form-row"> + <input type="submit" name="install_tool_dependencies_with_update_button" value="Install"/> + </div> + </form> + </div> +</div> diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako @@ -30,8 +30,6 @@ <tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Version</th><th bgcolor="#D8D8D8">Type</th><th bgcolor="#D8D8D8">Status</th><th bgcolor="#D8D8D8">Error</th></tr> %for tool_dependency in repository.tool_dependencies: <% - # Tool dependencies cannot be uninstalled if they have a status of 'Installed'. Only the containing repository - # can be uninstalled (only if it has no dependent repositories) if a tool dependency has been successfully installed. if tool_dependency.error_message: error_message = tool_dependency.error_message else: @@ -41,8 +39,7 @@ trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: can_install = True if not can_uninstall: - if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.INSTALLED, - trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, + if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: can_uninstall = True %> diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -46,8 +46,8 @@ <div class="warningmessage"><p> - The core Galaxy development team does not maintain the contents of many Galaxy tool shed repositories. Some repository tools - may include code that produces malicious behavior, so be aware of what you are installing. + The Galaxy development team does not maintain the contents of many Galaxy Tool Shed repositories. Some + repository tools may include code that produces malicious behavior, so be aware of what you are installing. </p><p> If you discover a repository that causes problems after installation, contact <a href="http://wiki.g2.bx.psu.edu/Support" target="_blank">Galaxy support</a>, @@ -63,6 +63,11 @@ <form name="select_shed_tool_panel_config" id="select_shed_tool_panel_config" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install' )}" method="post" ><div class="form-row"><input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" /> + <input type="hidden" name="updating" value="${updating}" /> + <input type="hidden" name="updating_repository_id" value="${updating_repository_id}" /> + <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}" /> + <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}" /> + <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}" /><input type="hidden" name="includes_tools" value="${includes_tools}" /><input type="hidden" name="includes_tool_dependencies" value="${includes_tool_dependencies}" /><input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" /> diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -46,8 +46,8 @@ <div class="warningmessage"><p> - The core Galaxy development team does not maintain the contents of many Galaxy tool shed repositories. Some repository tools - may include code that produces malicious behavior, so be aware of what you are installing. + The Galaxy development team does not maintain the contents of many Galaxy Tool Shed repositories. Some + repository tools may include code that produces malicious behavior, so be aware of what you are installing. </p><p> If you discover a repository that causes problems after installation, contact <a href="http://wiki.g2.bx.psu.edu/Support" target="_blank">Galaxy support</a>, @@ -67,6 +67,11 @@ <input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" /><input type="hidden" name="tool_shed_url" value="${tool_shed_url}" /><input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" /> + <input type="hidden" name="updating" value="${updating}" /> + <input type="hidden" name="updating_repository_id" value="${updating_repository_id}" /> + <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}" /> + <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}" /> + <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}" /></div><div style="clear: both"></div><% readme_files_dict = containers_dict.get( 'readme_files', 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: jmchilton: Update LWR client through LWR commit 2fec198.
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc67550cf28a/ Changeset: dc67550cf28a User: jmchilton Date: 2014-03-26 16:00:22 Summary: Update LWR client through LWR commit 2fec198. Makes parsing LWR host more robust - auto-adding http to beginning and trailing / if needed. Also makes LWR runn compatible with forthcoming job metrics pull request and pulls in Python 3 fix for job_script module. Affected #: 3 files diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/interface.py --- a/lib/galaxy/jobs/runners/lwr_client/interface.py +++ b/lib/galaxy/jobs/runners/lwr_client/interface.py @@ -36,8 +36,13 @@ def __init__(self, destination_params, transport): self.transport = transport - self.remote_host = destination_params.get("url") - assert self.remote_host is not None, "Failed to determine url for LWR client." + remote_host = destination_params.get("url") + assert remote_host is not None, "Failed to determine url for LWR client." + if not remote_host.endswith("/"): + remote_host = "%s/" % remote_host + if not remote_host.startswith("http"): + remote_host = "http://%s" % remote_host + self.remote_host = remote_host self.private_key = destination_params.get("private_token", None) def execute(self, command, args={}, data=None, input_path=None, output_path=None): diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/staging/down.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py @@ -14,7 +14,7 @@ # this pattern picks up attiditional files to copy back - such as those # associated with multiple outputs and metadata configuration. Set to .* to just # copy everything -COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|dataset_\d+_files.+") +COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|__instrument_.*|dataset_\d+_files.+") def finish_job(client, cleanup_job, job_completed_normally, client_outputs, lwr_outputs): diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/util/job_script/__init__.py --- a/lib/galaxy/jobs/runners/util/job_script/__init__.py +++ b/lib/galaxy/jobs/runners/util/job_script/__init__.py @@ -2,11 +2,11 @@ from pkg_resources import resource_string DEFAULT_JOB_FILE_TEMPLATE = Template( - resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh') + resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh').decode('UTF-8') ) SLOTS_STATEMENT_CLUSTER_DEFAULT = \ - resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh') + resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh').decode('UTF-8') SLOTS_STATEMENT_SINGLE = """ GALAXY_SLOTS="1" 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: 2 new changesets
by commits-noreply＠bitbucket.org 26 Mar '14

26 Mar '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56be13c43a4e/ Changeset: 56be13c43a4e Branch: stable User: jmchilton Date: 2014-03-26 15:24:08 Summary: Fix NoneType exception when using LWR with old-style tool runner URLs. Affected #: 1 file diff -r 6007992cbcd3626cbed38b0e883f516b016f98be -r 56be13c43a4e8c1ad391eab212982659e4845d94 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -156,7 +156,8 @@ job_id = "%s_%s" % (job_id, job_wrapper.task_id) params = job_wrapper.job_destination.params.copy() for key, value in params.iteritems(): - params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + if value: + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) return self.get_client( params, job_id ) def get_client_from_state(self, job_state): https://bitbucket.org/galaxy/galaxy-central/commits/62146f92190c/ Changeset: 62146f92190c User: jmchilton Date: 2014-03-26 15:27:44 Summary: Merge latest stable. Affected #: 1 file diff -r 66c7385957303447c8f5bb96731945bba179c83a -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -220,7 +220,8 @@ job_id = "%s_%s" % (job_id, job_wrapper.task_id) params = job_wrapper.job_destination.params.copy() for key, value in params.iteritems(): - params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) + if value: + params[key] = model.User.expand_user_properties( job_wrapper.get_job().user, value ) return self.get_client( params, job_id ) def get_client_from_state(self, job_state): 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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