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commit/galaxy-central: greg: Apply a corrected version of the patch from Peter Cock that flips the ¬†"Preserve directory structure?" setting when uploading library datasets from filesystem paths.
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/74c4dd43485a/ changeset: r5215:74c4dd43485a user: greg date: 2011-03-11 16:01:54 summary: Apply a corrected version of the patch from Peter Cock that flips the ¬†"Preserve directory structure?" setting when uploading library datasets from filesystem paths. affected #: 3 files (194 bytes) --- a/lib/galaxy/web/controllers/library_common.py Fri Mar 11 09:16:16 2011 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Fri Mar 11 10:01:54 2011 -0500 @@ -1097,9 +1097,7 @@ message = "No paths entered in the upload form" response_code = 400 return None, response_code, message - preserve_dirs = True - if params.get( 'dont_preserve_dirs', False ): - preserve_dirs = False + preserve_dirs = util.string_as_bool( params.get( 'preserve_dirs', False ) ) # locate files bad_paths = [] uploaded_datasets = [] --- a/templates/library/common/common.mako Fri Mar 11 09:16:16 2011 -0500 +++ b/templates/library/common/common.mako Fri Mar 11 10:01:54 2011 -0500 @@ -215,10 +215,11 @@ <div class="form-row"><label>Preserve directory structure?</label><div class="form-row-input"> - <input type="checkbox" name="dont_preserve_dirs" value="No"/>No + <input type="checkbox" name="preserve_dirs" value="Yes" checked="true" />Yes </div><div class="toolParamHelp" style="clear: both;"> - If checked, all files in subdirectories on the filesystem will be placed at the top level of the folder, instead of into subfolders. + If checked (default), library subfolders will be used to preserve any subdirectories on the filesystem.<br /> + If unchecked, any files in subdirectories on the filesystem will be placed directly in the library folder. </div></div> %endif --- a/test/base/twilltestcase.py Fri Mar 11 09:16:16 2011 -0500 +++ b/test/base/twilltestcase.py Fri Mar 11 10:01:54 2011 -0500 @@ -2004,7 +2004,7 @@ # Library dataset stuff def upload_library_dataset( self, cntrller, library_id, folder_id, filename='', server_dir='', replace_id='', upload_option='upload_file', file_type='auto', dbkey='hg18', space_to_tab='', - link_data_only='', dont_preserve_dirs='', roles=[], ldda_message='', hda_ids='', + link_data_only='', preserve_dirs='Yes', roles=[], ldda_message='', hda_ids='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], show_deleted='False', strings_displayed=[] ): """Add datasets to library using any upload_option""" @@ -2033,8 +2033,8 @@ tc.fv( "1", "space_to_tab", space_to_tab ) if link_data_only: tc.fv( "1", "link_data_only", link_data_only ) - if dont_preserve_dirs: - tc.fv( "1", "dont_preserve_dirs", dont_preserve_dirs ) + if upload_option == 'filesystem_paths' and preserve_dirs == 'Yes': + tc.fv( "1", "preserve_dirs", preserve_dirs ) for role_id in roles: tc.fv( "1", "roles", role_id ) # Refresh the form by selecting the upload_option - we do this here to ensure 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: greg: Apply patch from Ry4an Brase to correct "NoneType dereference on the jobs view" issue.
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0b9bba943c8f/ changeset: r5214:0b9bba943c8f user: greg date: 2011-03-11 15:16:16 summary: Apply patch from Ry4an Brase to correct "NoneType dereference on the jobs view" issue. affected #: 1 file (16 bytes) --- a/templates/admin/jobs.mako Thu Mar 10 17:30:35 2011 -0500 +++ b/templates/admin/jobs.mako Fri Mar 11 09:16:16 2011 -0500 @@ -47,7 +47,7 @@ %endif </td><td>${job.id}</td> - %if job.history.user: + %if job.history and job.history.user: <td>${job.history.user.email}</td> %else: <td>anonymous</td> 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: jgoecks: Trackster: access to datasets is based on accessibility, not ownership.
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/620da901f5b1/ changeset: r5213:620da901f5b1 user: jgoecks date: 2011-03-10 23:30:35 summary: Trackster: access to datasets is based on accessibility, not ownership. affected #: 1 file (230 bytes) --- a/lib/galaxy/web/controllers/tracks.py Thu Mar 10 16:42:34 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Thu Mar 10 17:30:35 2011 -0500 @@ -408,7 +408,7 @@ """ # Dataset check. - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) msg = self._check_dataset_state( trans, dataset ) if msg: return msg @@ -426,7 +426,7 @@ # TODO: this code is copied from data() -- should refactor. # Dataset check. - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) msg = self._check_dataset_state( trans, dataset ) if not msg: msg = messages.DATA @@ -443,7 +443,7 @@ # Dataset check. if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) msg = self._check_dataset_state( trans, dataset ) @@ -488,7 +488,7 @@ # Dataset check. if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) msg = self._check_dataset_state( trans, dataset ) @@ -656,7 +656,7 @@ low, high = int( low ), int( high ) # Dataset check. - original_dataset = self.get_dataset( trans, dataset_id ) + original_dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) msg = self._check_dataset_state( trans, original_dataset ) if msg: return to_json_string( msg ) 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: jgoecks: Make shared visualizations work again and pack trackster.js
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/52ead6780d84/ changeset: r5212:52ead6780d84 user: jgoecks date: 2011-03-10 22:42:34 summary: Make shared visualizations work again and pack trackster.js affected #: 4 files (4.0 KB) --- a/lib/galaxy/web/controllers/visualization.py Thu Mar 10 16:11:49 2011 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Thu Mar 10 16:42:34 2011 -0500 @@ -68,7 +68,9 @@ return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) -class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVisualization, UsesItemRatings ): +class VisualizationController( BaseController, Sharable, UsesAnnotations, + UsesHistoryDatasetAssociation, UsesVisualization, + UsesItemRatings ): _user_list_grid = VisualizationListGrid() _published_list_grid = VisualizationAllPublishedGrid() --- a/static/scripts/packed/trackster.js Thu Mar 10 16:11:49 2011 -0500 +++ b/static/scripts/packed/trackster.js Thu Mar 10 16:42:34 2011 -0500 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}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=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. 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g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!==null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},tile_data:function(d,a,g,k,j){var b=this,h=a*DENSITY*d,f=(a+1)*DENSITY*d,e={chrom:this.view.chrom,low:h,high:f,dbkey:this.view.dbkey};if(j===undefined){j=d+"_"+a}var c=b.data_cache.get(j);if(c){return k(c)}$.extend(e,g);$.ajax({url:this.data_url,dataType:"json",data:e,success:function(l){b.data_cache.set(j,l);return k(l)},error:function(m,l,n){console.log(m,l,n)}})},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){console.log("draw_tile_dict_length:",obj_length(c));if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,h,l,c,e,k,m,f){var d=this;var g=function(n){d.tile_cache.set(j,n);d.show_tile(n,k,h,m)};var a=setTimeout(function(){if(h<=d.view.high&&l>=d.view.low){var n;if(!b){n=d.tile_cache.get(j)}if(!n){d.draw_tile(e,c,k,m,function(p){if(p){var o=$("<div class='track-tile'>").prepend(p);n=o}g(n)})}if(n){g(n)}}delete f[a]},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(c,b,e,g,f){var a=this,d=DENSITY*c;if(g>CHAR_WIDTH_PX){a.tile_data(c,b,{},function(j){if(j===null){a.content_div.css("height","0px");return}var k=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(k)}k=$(k);var h=k.get(0).getContext("2d");k.get(0).width=Math.ceil(d*g+a.left_offset);k.get(0).height=a.height_px;h.font=DEFAULT_FONT;h.textAlign="center";for(var n=0,l=j.length;n<l;n++){var m=Math.round(n*g);h.fillText(j[n],m+a.left_offset,10)}return f(k)})}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(d,a,j,k,h){if(this.vertical_range===undefined){return}var c=this,f=a*DENSITY*d,b=DENSITY*d,g=d+"_"+a,e={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};this.tile_data(d,a,e,function(C){var l=document.createElement("canvas"),q=C.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(l)}l=$(l);l.get(0).width=Math.ceil(b*k);l.get(0).height=c.height_px;var z=l.get(0).getContext("2d"),n=false,B=c.prefs.min_value,v=c.prefs.max_value,A=c.vertical_range,m=c.total_frequency,u=c.height_px,s=c.mode;var r=Math.round(u+B/A*u);z.beginPath();z.moveTo(0,r);z.lineTo(b*k,r);z.fillStyle="#aaa";z.stroke();z.beginPath();z.fillStyle=c.prefs.color;var p,w,x;if(q.length>1){x=Math.ceil((q[1][0]-q[0][0])*k)}else{x=10}for(var o=0,t=q.length;o<t;o++){p=Math.round((q[o][0]-f)*k);w=q[o][1];if(w===null){if(n&&s==="Filled"){z.lineTo(p,u)}n=false;continue}if(w<B){w=B}else{if(w>v){w=v}}if(s==="Histogram"){w=Math.round(w/A*u);z.fillRect(p,r,x,-w)}else{if(s==="Intensity"){w=255-Math.floor((w-B)/A*255);z.fillStyle="rgb("+w+","+w+","+w+")";z.fillRect(p,0,x,u)}else{w=Math.round(u-(w-B)/A*u);if(n){z.lineTo(p,w)}else{n=true;if(s==="Filled"){z.moveTo(p,u);z.lineTo(p,w)}else{z.moveTo(p,w)}}}}}if(s==="Filled"){if(n){z.lineTo(p,r);z.lineTo(0,r)}z.fill()}else{z.stroke()}h(l)})}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2],s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O-1);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(z,E,l,n,j,d,p){var v=this;if(v.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return v.view.reference_track.tile_data(z,E,{},function(f){v.draw_tile(z,E,l,n,j,f)})}var G=E*DENSITY*z,a=(E+1)*DENSITY*z,s=a-G,H={hda_ldda:v.hda_ldda,dataset_id:v.dataset_id,resolution:this.view.resolution,mode:this.mode};if(p===undefined){var q=this.data_cache.get_data(G,a,this.mode),J=z+"_"+E+"_"+this.mode;if(q===undefined){return v.tile_data(z,E,H,function(f){v.data_cache.set_data(G,a,this.mode,f);v.draw_tile(z,E,l,n,j,d,f)},J)}p=q}var x=Math.ceil(s*n),u=this.mode,K=25,g=this.left_offset,r,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(u==="Auto"){if(p.dataset_type==="summary_tree"){u=p.dataset_type}else{if(p.extra_info==="no_detail"){u="no_detail"}else{var I=p.data;if((I.length&&I.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){u="Squish"}else{u="Pack"}}}}var A=this.get_y_scale(u);if(u==="summary_tree"){h=this.summary_draw_height}if(u==="Dense"){h=K}else{if(u==="no_detail"||u==="Squish"||u==="Pack"){h=this.incremental_slots(n,p.data,u)*A+K;r=this.inc_slots[n]}}c.get(0).width=x+g;c.get(0).height=h;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,h)+"px");var y=c.get(0).getContext("2d");y.fillStyle=this.prefs.block_color;y.font=this.default_font;y.textAlign="right";this.container_div.find(".yaxislabel").remove();if(u==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,h,G,g);return j(c)}if(p.message){c.css({"border-top":"1px solid red"});y.fillStyle="red";y.textAlign="left";var t=y.textBaseline;y.textBaseline="top";y.fillText(p.message,g,0);y.textBaseline=t;if(!p.data){return j(c)}}this.example_feature=(p.data.length?p.data[0]:undefined);var I=p.data;for(var B=0,D=I.length;B<D;B++){var k=I[B],m=k[0],w=k[1],b=k[2],e=(r&&r[m]!==undefined?r[m]:null);var C=false;var o;for(var F=0;F<this.filters.length;F++){o=this.filters[F];o.update_attrs(k);if(!o.keep(k)){C=true;break}}if(C){continue}if(is_overlap([w,b],[G,a])&&(u=="Dense"||e!==null)){this.draw_element(y,E,u,k,e,G,a,n,A,x,g,d)}}j(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}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=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!==null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},tile_data:function(d,a,g,k,j){var b=this,h=a*DENSITY*d,f=(a+1)*DENSITY*d,e={chrom:this.view.chrom,low:h,high:f,dbkey:this.view.dbkey};if(j===undefined){j=d+"_"+a}var c=b.data_cache.get(j);if(c){return k(c)}$.extend(e,g);$.ajax({url:this.data_url,dataType:"json",data:e,success:function(l){b.data_cache.set(j,l);return k(l)},error:function(m,l,n){console.log(m,l,n)}})},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,h,l,c,e,k,m,f){var d=this;var g=function(n){d.tile_cache.set(j,n);d.show_tile(n,k,h,m)};var a=setTimeout(function(){if(h<=d.view.high&&l>=d.view.low){var n;if(!b){n=d.tile_cache.get(j)}if(!n){d.draw_tile(e,c,k,m,function(p){if(p){var o=$("<div class='track-tile'>").prepend(p);n=o}g(n)})}if(n){g(n)}}delete f[a]},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(c,b,e,g,f){var a=this,d=DENSITY*c;if(g>CHAR_WIDTH_PX){a.tile_data(c,b,{},function(j){if(j===null){a.content_div.css("height","0px");return}var k=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(k)}k=$(k);var h=k.get(0).getContext("2d");k.get(0).width=Math.ceil(d*g+a.left_offset);k.get(0).height=a.height_px;h.font=DEFAULT_FONT;h.textAlign="center";for(var n=0,l=j.length;n<l;n++){var m=Math.round(n*g);h.fillText(j[n],m+a.left_offset,10)}return f(k)})}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(d,a,j,k,h){if(this.vertical_range===undefined){return}var c=this,f=a*DENSITY*d,b=DENSITY*d,g=d+"_"+a,e={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};this.tile_data(d,a,e,function(C){var l=document.createElement("canvas"),q=C.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(l)}l=$(l);l.get(0).width=Math.ceil(b*k);l.get(0).height=c.height_px;var z=l.get(0).getContext("2d"),n=false,B=c.prefs.min_value,v=c.prefs.max_value,A=c.vertical_range,m=c.total_frequency,u=c.height_px,s=c.mode;var r=Math.round(u+B/A*u);z.beginPath();z.moveTo(0,r);z.lineTo(b*k,r);z.fillStyle="#aaa";z.stroke();z.beginPath();z.fillStyle=c.prefs.color;var p,w,x;if(q.length>1){x=Math.ceil((q[1][0]-q[0][0])*k)}else{x=10}for(var o=0,t=q.length;o<t;o++){p=Math.round((q[o][0]-f)*k);w=q[o][1];if(w===null){if(n&&s==="Filled"){z.lineTo(p,u)}n=false;continue}if(w<B){w=B}else{if(w>v){w=v}}if(s==="Histogram"){w=Math.round(w/A*u);z.fillRect(p,r,x,-w)}else{if(s==="Intensity"){w=255-Math.floor((w-B)/A*255);z.fillStyle="rgb("+w+","+w+","+w+")";z.fillRect(p,0,x,u)}else{w=Math.round(u-(w-B)/A*u);if(n){z.lineTo(p,w)}else{n=true;if(s==="Filled"){z.moveTo(p,u);z.lineTo(p,w)}else{z.moveTo(p,w)}}}}}if(s==="Filled"){if(n){z.lineTo(p,r);z.lineTo(0,r)}z.fill()}else{z.stroke()}h(l)})}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2],s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O-1);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(z,E,l,n,j,d,p){var v=this;if(v.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return v.view.reference_track.tile_data(z,E,{},function(f){v.draw_tile(z,E,l,n,j,f)})}var G=E*DENSITY*z,a=(E+1)*DENSITY*z,s=a-G,H={hda_ldda:v.hda_ldda,dataset_id:v.dataset_id,resolution:this.view.resolution,mode:this.mode};if(p===undefined){var q=this.data_cache.get_data(G,a,this.mode),J=z+"_"+E+"_"+this.mode;if(q===undefined){return v.tile_data(z,E,H,function(f){v.data_cache.set_data(G,a,this.mode,f);v.draw_tile(z,E,l,n,j,d,f)},J)}p=q}var x=Math.ceil(s*n),u=this.mode,K=25,g=this.left_offset,r,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(u==="Auto"){if(p.dataset_type==="summary_tree"){u=p.dataset_type}else{if(p.extra_info==="no_detail"){u="no_detail"}else{var I=p.data;if((I.length&&I.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){u="Squish"}else{u="Pack"}}}}var A=this.get_y_scale(u);if(u==="summary_tree"){h=this.summary_draw_height}if(u==="Dense"){h=K}else{if(u==="no_detail"||u==="Squish"||u==="Pack"){h=this.incremental_slots(n,p.data,u)*A+K;r=this.inc_slots[n]}}c.get(0).width=x+g;c.get(0).height=h;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,h)+"px");var y=c.get(0).getContext("2d");y.fillStyle=this.prefs.block_color;y.font=this.default_font;y.textAlign="right";this.container_div.find(".yaxislabel").remove();if(u==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,h,G,g);return j(c)}if(p.message){c.css({"border-top":"1px solid red"});y.fillStyle="red";y.textAlign="left";var t=y.textBaseline;y.textBaseline="top";y.fillText(p.message,g,0);y.textBaseline=t;if(!p.data){return j(c)}}this.example_feature=(p.data.length?p.data[0]:undefined);var I=p.data;for(var B=0,D=I.length;B<D;B++){var k=I[B],m=k[0],w=k[1],b=k[2],e=(r&&r[m]!==undefined?r[m]:null);var C=false;var o;for(var F=0;F<this.filters.length;F++){o=this.filters[F];o.update_attrs(k);if(!o.keep(k)){C=true;break}}if(C){continue}if(is_overlap([w,b],[G,a])&&(u=="Dense"||e!==null)){this.draw_element(y,E,u,k,e,G,a,n,A,x,g,d)}}j(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file --- a/templates/tracks/browser.mako Thu Mar 10 16:11:49 2011 -0500 +++ b/templates/tracks/browser.mako Thu Mar 10 16:42:34 2011 -0500 @@ -10,29 +10,29 @@ </%def><%def name="stylesheets()"> -${parent.stylesheets()} + ${parent.stylesheets()} -${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} + ${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} -<style type="text/css"> - #browser-container { - overflow: none; - } - .nav-container { - width: 100%; - ## Overriding styles from trackster.css to push nav up into title bar - height: 0; - text-align: center; - } - .nav { - ## Overriding styles from trackster.css to push nav up into title bar - position: relative; - display: inline-block; - top: -2em; - background: transparent; - border: none; - } -</style> + <style type="text/css"> + #browser-container { + overflow: none; + } + .nav-container { + width: 100%; + ## Overriding styles from trackster.css to push nav up into title bar + height: 0; + text-align: center; + } + .nav { + ## Overriding styles from trackster.css to push nav up into title bar + position: relative; + display: inline-block; + top: -2em; + background: transparent; + border: none; + } + </style></%def><%def name="center_panel()"> --- a/templates/visualization/display.mako Thu Mar 10 16:11:49 2011 -0500 +++ b/templates/visualization/display.mako Thu Mar 10 16:42:34 2011 -0500 @@ -8,17 +8,39 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> - ${h.js( "jquery.event.drag", "jquery.autocomplete", "trackster" )} + ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} </%def><%def name="stylesheets()"> ${parent.stylesheets()} - + + ## For page: <style type="text/css"> .page-body { padding: 0px; } + </style> + ## For visualization (TODO: copied from browser.mako): + ${h.css( "trackster", "overcast/jquery-ui-1.8.5.custom" )} + <style type="text/css"> + #browser-container { + overflow: none; + } + .nav-container { + width: 100%; + ## Overriding styles from trackster.css to push nav up into title bar + height: 0; + text-align: center; + } + .nav { + ## Overriding styles from trackster.css to push nav up into title bar + position: relative; + display: inline-block; + top: -2em; + background: transparent; + border: none; + } </style></%def> @@ -34,10 +56,19 @@ <div id="${visualization.id}" class="unified-panel-body" style="overflow:none;top:0px;"></div><script type="text/javascript"> - - var data_url = "${h.url_for( controller='/tracks', action='data' )}", + // TODO: much of this code is copied from browser.mako -- create shared base and use in both places. + + // + // Place URLs here so that url_for can be used to generate them. + // + var default_data_url = "${h.url_for( controller='/tracks', action='data' )}", + raw_data_url = "${h.url_for( controller='/tracks', action='raw_data' )}", + run_tool_url = "${h.url_for( controller='/tracks', action='run_tool' )}", reference_url = "${h.url_for( controller='/tracks', action='reference' )}", chrom_url = "${h.url_for( controller='/tracks', action='chroms' )}", + dataset_state_url = "${h.url_for( controller='/tracks', action='dataset_state' )}", + converted_datasets_state_url = "${h.url_for( controller='/tracks', action='converted_datasets_state' )}", + addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view, container_element = $("#${visualization.id}"); @@ -48,12 +79,60 @@ } else { // Viewing just one shared viz $("#right-border").live("click", function() { view.resize_window(); }); } - view = new View( container_element, "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); - %for track in config.get('tracks'): - view.add_track( - new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['prefs']} ) - ); - %endfor + + // Create view and add tracks. + var callback; + %if 'viewport' in config: + var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); } + %endif + view = new View(container_element, "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}", callback); + ## A little ugly and redundant, but it gets the job done moving the config from python to JS: + var tracks_config = JSON.parse('${ h.to_json_string( config.get('tracks') ) }'); + var track_config, track, parent_track, parent_obj; + for (var i = 0; i < tracks_config.length; i++) { + track_config = tracks_config[i]; + track = new addable_track_types[track_config["track_type"]]( + track_config['name'], + view, + track_config['hda_ldda'], + track_config['dataset_id'], + track_config['prefs'], + track_config['filters'], + track_config['tool'], + (track_config.is_child ? parent_track : undefined)); + parent_obj = view; + if (track_config.is_child) { + parent_obj = parent_track; + } + else { + // New parent track is this track. + parent_track = track; + } + parent_obj.add_track(track); + } + + // + // Keyboard navigation. Scroll ~7% of height when scrolling up/down. + // + $(document).keydown(function(e) { + // Key codes: left == 37, up == 38, right == 39, down == 40 + switch(e.which) { + case 37: + view.move_fraction(0.25); + break + case 38: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTo('-=' + change + 'px'); + break; + case 39: + view.move_fraction(-0.25); + break; + case 40: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTo('+=' + change + 'px'); + break; + } + }); }); </script> 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 Bitbucket 10 Mar '11

10 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d69e36d1d2f6/ changeset: r5210:d69e36d1d2f6 user: kanwei date: 2011-03-10 22:09:03 summary: Make workflow run_complete.mako modern affected #: 1 file (621 bytes) --- a/templates/workflow/run_complete.mako Thu Mar 10 15:48:00 2011 -0500 +++ b/templates/workflow/run_complete.mako Thu Mar 10 16:09:03 2011 -0500 @@ -1,38 +1,20 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<%inherit file="/base.mako"/> -<head> -<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> -<script> -if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' ) }"; -} -</script> -</head> - -<body> - <div class="donemessage"> - <p> - Successfully ran workflow "${workflow.name}", the following datasets have - been added to the queue. - %if new_history: - These datasets will appear in a new history: - <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}"> - '${h.to_unicode(new_history.name)}'. - </a> - %endif - </p> - <div style="padding-left: 10px;"> - %for step_outputs in outputs.itervalues(): - %for data in step_outputs.itervalues(): - %if not new_history or data.history == new_history: - <p><b>${data.hid}</b>: ${data.name}</p> - %endif - %endfor +<div class="donemessagelarge"> + Successfully ran workflow "${workflow.name}". The following datasets have been added to the queue: + %if new_history: + These datasets will appear in a new history: + <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}"> + '${h.to_unicode(new_history.name)}'. + </a> + %endif + <div style="padding-left: 10px;"> + %for step_outputs in outputs.itervalues(): + %for data in step_outputs.itervalues(): + %if not new_history or data.history == new_history: + <p><strong>${data.hid}</strong>: ${data.name}</p> + %endif %endfor - </div> + %endfor </div> -</body> - -</html> +</div> \ No newline at end of file http://bitbucket.org/galaxy/galaxy-central/changeset/394e58a5e63c/ changeset: r5211:394e58a5e63c user: kanwei date: 2011-03-10 22:11:49 summary: merge affected #: 0 files (0 bytes) --- a/tool-data/shared/ucsc/manual_builds.txt Thu Mar 10 16:09:03 2011 -0500 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu Mar 10 16:11:49 2011 -0500 @@ -696,3 +696,5 @@ Spur_v2.6 Purple Sea Urchin (Strongylocentrotus purpuratus) v2.6 Ptrichocarpa_156 Poplar (Populus trichocarpa) Hydra_JCVI Hydra magnipapillata str. 105 +Araly1 Arabidopsis lyrata +Zea_mays_B73_RefGen_v2 Maize (Zea mays) chr1=301354135,chr2=237068928,chr3=232140222,chr4=241473566,chr5=217872898,chr6=169174371,chr7=176764813,chr8=175793772,chr9=156750718,chr10=150189513,chr11=7140224 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: kellyv: Added two more builds to the manual builds list
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0c5d60534ea8/ changeset: r5209:0c5d60534ea8 user: kellyv date: 2011-03-10 22:08:39 summary: Added two more builds to the manual builds list affected #: 1 file (233 bytes) --- a/tool-data/shared/ucsc/manual_builds.txt Thu Mar 10 15:48:00 2011 -0500 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu Mar 10 16:08:39 2011 -0500 @@ -696,3 +696,5 @@ Spur_v2.6 Purple Sea Urchin (Strongylocentrotus purpuratus) v2.6 Ptrichocarpa_156 Poplar (Populus trichocarpa) Hydra_JCVI Hydra magnipapillata str. 105 +Araly1 Arabidopsis lyrata +Zea_mays_B73_RefGen_v2 Maize (Zea mays) chr1=301354135,chr2=237068928,chr3=232140222,chr4=241473566,chr5=217872898,chr6=169174371,chr7=176764813,chr8=175793772,chr9=156750718,chr10=150189513,chr11=7140224 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: greg: Add a checkbox to the Create Group page that if checked will create a new Role with the same name. This provides a similar feature the the existing checkbox on the Create Role page.
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8c04153e4cf6/ changeset: r5208:8c04153e4cf6 user: greg date: 2011-03-10 21:48:00 summary: Add a checkbox to the Create Group page that if checked will create a new Role with the same name. This provides a similar feature the the existing checkbox on the Create Role page. However, the behavior is now changed such that new associations are created when the checkbox is checked whereas before, only the Group or Role objects with the same name were created, but not associated with anything. This code was very old, so I did some cleanup / improvements as well. Functional tests enhanced to reflect changes. affected #: 6 files (3.9 KB) --- a/lib/galaxy/web/base/controller.py Thu Mar 10 15:20:40 2011 -0500 +++ b/lib/galaxy/web/base/controller.py Thu Mar 10 15:48:00 2011 -0500 @@ -1185,16 +1185,24 @@ webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + name = util.restore_text( params.get( 'name', '' ) ) + description = util.restore_text( params.get( 'description', '' ) ) + in_users = util.listify( params.get( 'in_users', [] ) ) + out_users = util.listify( params.get( 'out_users', [] ) ) + in_groups = util.listify( params.get( 'in_groups', [] ) ) + out_groups = util.listify( params.get( 'out_groups', [] ) ) + create_group_for_role = params.get( 'create_group_for_role', '' ) + create_group_for_role_checked = CheckboxField.is_checked( create_group_for_role ) + ok = True if params.get( 'create_role_button', False ): - name = util.restore_text( params.name ) - description = util.restore_text( params.description ) - in_users = util.listify( params.get( 'in_users', [] ) ) - in_groups = util.listify( params.get( 'in_groups', [] ) ) - create_group_for_role = params.get( 'create_group_for_role', 'no' ) if not name or not description: - message = "Enter a valid name and a description" + message = "Enter a valid name and a description." + status = 'error' + ok = False elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==name ).first(): - message = "A role with that name already exists" + message = "Role names must be unique and a role with that name already exists, so choose another name." + status = 'error' + ok = False else: # Create the role role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.ADMIN ) @@ -1207,41 +1215,44 @@ for group in [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in in_groups ]: gra = trans.app.model.GroupRoleAssociation( group, role ) trans.sa_session.add( gra ) - if create_group_for_role == 'yes': + if create_group_for_role_checked: # Create the group group = trans.app.model.Group( name=name ) trans.sa_session.add( group ) - message = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ - ( group.name, role.name, len( in_users ), len( in_groups ) ) + # Associate the group with the role + gra = trans.model.GroupRoleAssociation( group, role ) + trans.sa_session.add( gra ) + num_in_groups = len( in_groups ) + 1 else: - message = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) + num_in_groups = len( in_groups ) trans.sa_session.flush() + message = "Role '%s' has been created with %d associated users and %d associated groups. " \ + % ( role.name, len( in_users ), num_in_groups ) + if create_group_for_role_checked: + message += 'One of the groups associated with this role is the newly created group with the same name.' trans.response.send_redirect( web.url_for( controller='admin', action='roles', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - trans.response.send_redirect( web.url_for( controller='admin', - action='create_role', - webapp=webapp, - message=util.sanitize_text( message ), - status='error' ) ) - out_users = [] - for user in trans.sa_session.query( trans.app.model.User ) \ - .filter( trans.app.model.User.table.c.deleted==False ) \ - .order_by( trans.app.model.User.table.c.email ): - out_users.append( ( user.id, user.email ) ) - out_groups = [] - for group in trans.sa_session.query( trans.app.model.Group ) \ - .filter( trans.app.model.Group.table.c.deleted==False ) \ - .order_by( trans.app.model.Group.table.c.name ): - out_groups.append( ( group.id, group.name ) ) + if ok: + for user in trans.sa_session.query( trans.app.model.User ) \ + .filter( trans.app.model.User.table.c.deleted==False ) \ + .order_by( trans.app.model.User.table.c.email ): + out_users.append( ( user.id, user.email ) ) + for group in trans.sa_session.query( trans.app.model.Group ) \ + .filter( trans.app.model.Group.table.c.deleted==False ) \ + .order_by( trans.app.model.Group.table.c.name ): + out_groups.append( ( group.id, group.name ) ) return trans.fill_template( '/admin/dataset_security/role/role_create.mako', - in_users=[], + webapp=webapp, + name=name, + description=description, + in_users=in_users, out_users=out_users, - in_groups=[], + in_groups=in_groups, out_groups=out_groups, - webapp=webapp, + create_group_for_role_checked=create_group_for_role_checked, message=message, status=status ) @web.expose @@ -1617,14 +1628,23 @@ webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + name = util.restore_text( params.get( 'name', '' ) ) + in_users = util.listify( params.get( 'in_users', [] ) ) + out_users = util.listify( params.get( 'out_users', [] ) ) + in_roles = util.listify( params.get( 'in_roles', [] ) ) + out_roles = util.listify( params.get( 'out_roles', [] ) ) + create_role_for_group = params.get( 'create_role_for_group', '' ) + create_role_for_group_checked = CheckboxField.is_checked( create_role_for_group ) + ok = True if params.get( 'create_group_button', False ): - name = util.restore_text( params.name ) - in_users = util.listify( params.get( 'in_users', [] ) ) - in_roles = util.listify( params.get( 'in_roles', [] ) ) if not name: - message = "Enter a valid name" + message = "Enter a valid name." + status = 'error' + ok = False elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first(): - message = "A group with that name already exists" + message = "Group names must be unique and a group with that name already exists, so choose another name." + status = 'error' + ok = False else: # Create the group group = trans.app.model.Group( name=name ) @@ -1634,39 +1654,49 @@ for user in [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users ]: uga = trans.app.model.UserGroupAssociation( user, group ) trans.sa_session.add( uga ) - trans.sa_session.flush() # Create the GroupRoleAssociations for role in [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in in_roles ]: gra = trans.app.model.GroupRoleAssociation( group, role ) trans.sa_session.add( gra ) - trans.sa_session.flush() - message = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_users ), len( in_roles ) ) + if create_role_for_group_checked: + # Create the role + role = trans.app.model.Role( name=name, description='Role for group %s' % name ) + trans.sa_session.add( role ) + # Associate the role with the group + gra = trans.model.GroupRoleAssociation( group, role ) + trans.sa_session.add( gra ) + num_in_roles = len( in_roles ) + 1 + else: + num_in_roles = len( in_roles ) + trans.sa_session.flush() + message = "Group '%s' has been created with %d associated users and %d associated roles. " \ + % ( group.name, len( in_users ), num_in_roles ) + if create_role_for_group_checked: + message += 'One of the roles associated with this group is the newly created role with the same name.' trans.response.send_redirect( web.url_for( controller='admin', action='groups', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - trans.response.send_redirect( web.url_for( controller='admin', - action='create_group', - webapp=webapp, - message=util.sanitize_text( message ), - status='error' ) ) - out_users = [] - for user in trans.sa_session.query( trans.app.model.User ) \ - .filter( trans.app.model.User.table.c.deleted==False ) \ - .order_by( trans.app.model.User.table.c.email ): - out_users.append( ( user.id, user.email ) ) - out_roles = [] - for role in trans.sa_session.query( trans.app.model.Role ) \ - .filter( trans.app.model.Role.table.c.deleted==False ) \ - .order_by( trans.app.model.Role.table.c.name ): - out_roles.append( ( role.id, role.name ) ) + + + if ok: + for user in trans.sa_session.query( trans.app.model.User ) \ + .filter( trans.app.model.User.table.c.deleted==False ) \ + .order_by( trans.app.model.User.table.c.email ): + out_users.append( ( user.id, user.email ) ) + for role in trans.sa_session.query( trans.app.model.Role ) \ + .filter( trans.app.model.Role.table.c.deleted==False ) \ + .order_by( trans.app.model.Role.table.c.name ): + out_roles.append( ( role.id, role.name ) ) return trans.fill_template( '/admin/dataset_security/group/group_create.mako', - in_users=[], + webapp=webapp, + name=name, + in_users=in_users, out_users=out_users, - in_roles=[], + in_roles=in_roles, out_roles=out_roles, - webapp=webapp, + create_role_for_group_checked=create_role_for_group_checked, message=message, status=status ) @web.expose --- a/lib/galaxy/web/controllers/library_common.py Thu Mar 10 15:20:40 2011 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Thu Mar 10 15:48:00 2011 -0500 @@ -1986,13 +1986,7 @@ # We've been called from a menu option for a library dataset search result set move_ldda_ids = util.listify( item_id ) if move_ldda_ids: - # Checkboxes cause 2 copies of each id to be included in the request move_ldda_ids = map( trans.security.decode_id, move_ldda_ids ) - unique_ldda_ids = [] - for ldda_id in move_ldda_ids: - if ldda_id not in unique_ldda_ids: - unique_ldda_ids.append( ldda_id ) - move_ldda_ids = unique_ldda_ids elif item_type == 'folder': move_folder_id = item_id move_folder = trans.sa_session.query( trans.model.LibraryFolder ).get( trans.security.decode_id( move_folder_id ) ) --- a/templates/admin/dataset_security/group/group_create.mako Thu Mar 10 15:20:40 2011 -0500 +++ b/templates/admin/dataset_security/group/group_create.mako Thu Mar 10 15:48:00 2011 -0500 @@ -42,7 +42,12 @@ }); }); </script> - + +<% + from galaxy.web.form_builder import CheckboxField + create_role_for_group_checkbox = CheckboxField( 'create_role_for_group' ) +%> + %if message: ${render_msg( message, status )} %endif @@ -54,7 +59,7 @@ <div class="form-row"><input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label> - <input name="name" type="textfield" value="" size=40"/> + <input name="name" type="textfield" value="${name}" size=40"/></div><div class="form-row"><div style="float: left; margin-right: 10px;"> @@ -81,6 +86,12 @@ </div></div><div class="form-row"> + %if create_role_for_group_checked: + <% create_role_for_group_checkbox.checked = True %> + %endif + ${create_role_for_group_checkbox.get_html()} Create a new role of the same name for this group + </div> + <div class="form-row"><input type="submit" name="create_group_button" value="Save"/></div></form> --- a/templates/admin/dataset_security/role/role_create.mako Thu Mar 10 15:20:40 2011 -0500 +++ b/templates/admin/dataset_security/role/role_create.mako Thu Mar 10 15:48:00 2011 -0500 @@ -19,30 +19,35 @@ </%def><script type="text/javascript"> -$().ready(function() { - $('#groups_add_button').click(function() { - return !$('#out_groups option:selected').remove().appendTo('#in_groups'); - }); - $('#groups_remove_button').click(function() { - return !$('#in_groups option:selected').remove().appendTo('#out_groups'); - }); - $('#users_add_button').click(function() { - return !$('#out_users option:selected').remove().appendTo('#in_users'); - }); - $('#users_remove_button').click(function() { - return !$('#in_users option:selected').remove().appendTo('#out_users'); - }); - $('form#associate_role_group_user').submit(function() { - $('#in_groups option').each(function(i) { - $(this).attr("selected", "selected"); + $().ready(function() { + $('#groups_add_button').click(function() { + return !$('#out_groups option:selected').remove().appendTo('#in_groups'); }); - $('#in_users option').each(function(i) { - $(this).attr("selected", "selected"); + $('#groups_remove_button').click(function() { + return !$('#in_groups option:selected').remove().appendTo('#out_groups'); + }); + $('#users_add_button').click(function() { + return !$('#out_users option:selected').remove().appendTo('#in_users'); + }); + $('#users_remove_button').click(function() { + return !$('#in_users option:selected').remove().appendTo('#out_users'); + }); + $('form#associate_role_group_user').submit(function() { + $('#in_groups option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_users option').each(function(i) { + $(this).attr("selected", "selected"); + }); }); }); -}); </script> +<% + from galaxy.web.form_builder import CheckboxField + create_group_for_role_checkbox = CheckboxField( 'create_group_for_role' ) +%> + %if message: ${render_msg( message, status )} %endif @@ -54,11 +59,11 @@ <div class="form-row"><input name="webapp" type="hidden" value="${webapp}" size=40"/><label>Name:</label> - <input name="name" type="textfield" value="" size=40"/> + <input name="name" type="textfield" value="${name}" size=40"/></div><div class="form-row"><label>Description:</label> - <input name="description" type="textfield" value="" size=40"/> + <input name="description" type="textfield" value="${description}" size=40"/></div><div class="form-row"><div style="float: left; margin-right: 10px;"> @@ -85,7 +90,10 @@ </div></div><div class="form-row"> - <input type="checkbox" name="create_group_for_role" value="yes" />Create a new group of the same name for this role + %if create_group_for_role_checked: + <% create_group_for_role_checkbox.checked = True %> + %endif + ${create_group_for_role_checkbox.get_html()} Create a new group of the same name for this role </div><div class="form-row"><input type="submit" name="create_role_button" value="Save"/> --- a/test/base/twilltestcase.py Thu Mar 10 15:20:40 2011 -0500 +++ b/test/base/twilltestcase.py Thu Mar 10 15:48:00 2011 -0500 @@ -1229,25 +1229,22 @@ description="This is Role One", in_user_ids=[], in_group_ids=[], - create_group_for_role='no', - private_role='' ): + create_group_for_role='', + private_role='', + strings_displayed=[] ): """Create a new role""" - url = "%s/admin/roles?operation=create&create_role_button=Save&name=%s&description=%s" % ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) + url = "%s/admin/roles?operation=create&create_role_button=Save&name=%s&description=%s" % \ + ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) if in_user_ids: url += "&in_users=%s" % ','.join( in_user_ids ) if in_group_ids: url += "&in_groups=%s" % ','.join( in_group_ids ) if create_group_for_role == 'yes': - url += '&create_group_for_role=yes' + url += '&create_group_for_role=yes&create_group_for_role=yes' self.home() self.visit_url( url ) - if create_group_for_role == 'yes': - check_str = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ - ( name, name, len( in_user_ids ), len( in_group_ids ) ) - else: - check_str = "Role '%s' has been created with %d associated users and %d associated groups" % \ - ( name, len( in_user_ids ), len( in_group_ids ) ) - self.check_page_for_string( check_str ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) if private_role: # Make sure no private roles are displayed try: @@ -1304,17 +1301,19 @@ self.home() # Tests associated with groups - def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[] ): + def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[], create_role_for_group='', strings_displayed=[] ): """Create a new group""" url = "%s/admin/groups?operation=create&create_group_button=Save&name=%s" % ( self.url, name.replace( ' ', '+' ) ) if in_user_ids: url += "&in_users=%s" % ','.join( in_user_ids ) if in_role_ids: url += "&in_roles=%s" % ','.join( in_role_ids ) + if create_role_for_group == 'yes': + url += '&create_role_for_group=yes&create_role_for_group=yes' self.home() self.visit_url( url ) - check_str = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_user_ids ), len( in_role_ids ) ) - self.check_page_for_string( check_str ) + for check_str in strings_displayed: + self.check_page_for_string( check_str ) self.home() self.visit_url( "%s/admin/groups" % self.url ) self.check_page_for_string( name ) --- a/test/functional/test_admin_features.py Thu Mar 10 15:20:40 2011 -0500 +++ b/test/functional/test_admin_features.py Thu Mar 10 15:48:00 2011 -0500 @@ -126,21 +126,26 @@ # Logged in as admin_user name = 'Role One' description = "This is Role Ones description" - user_ids=[ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ] + in_user_ids = [ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ] + in_group_ids = [] + # Add 1 to the number of associated groups since we are creating a new one with the same name as the role + num_gras = len( in_group_ids ) + 1 self.create_role( name=name, description=description, - in_user_ids=user_ids, - in_group_ids=[], + in_user_ids=in_user_ids, + in_group_ids=in_group_ids, create_group_for_role='yes', - private_role=admin_user.email ) + private_role=admin_user.email, + strings_displayed=[ "Role '%s' has been created with %d associated users and %d associated groups." % ( name, len( in_user_ids ), num_gras ), + "One of the groups associated with this role is the newly created group with the same name." ] ) # Get the role object for later tests global role_one role_one = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first() assert role_one is not None, 'Problem retrieving role named "Role One" from the database' # Make sure UserRoleAssociations are correct - if len( role_one.users ) != len( user_ids ): + if len( role_one.users ) != len( in_user_ids ): raise AssertionError( '%d UserRoleAssociations were created for role id %d when it was created ( should have been %d )' \ - % ( len( role_one.users ), role_one.id, len( user_ids ) ) ) + % ( len( role_one.users ), role_one.id, len( in_user_ids ) ) ) # Each of the following users should now have 2 role associations, their private role and role_one for user in [ admin_user, regular_user1, regular_user3 ]: refresh( user ) @@ -162,29 +167,36 @@ # Reset the role back to the original name and description self.rename_role( self.security.encode_id( role_one.id ), name=name, description=description ) def test_035_create_group( self ): - """Testing creating new group with 3 members and 1 associated role, then renaming it""" + """Testing creating new group with 3 members and 2 associated roles, then renaming it""" # Logged in as admin_user name = "Group One's Name" - user_ids=[ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ] - role_ids=[ str( role_one.id ) ] - self.create_group( name=name, in_user_ids=user_ids, in_role_ids=role_ids ) + in_user_ids = [ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ] + in_role_ids = [ str( role_one.id ) ] + # The number of GroupRoleAssociations should be 2, role_one and the newly created role named 'Group One's Name' + num_gras = len( in_role_ids ) + 1 + self.create_group( name=name, + in_user_ids=in_user_ids, + in_role_ids=in_role_ids, + create_role_for_group='yes', + strings_displayed=[ "Group '%s' has been created with %d associated users and %d associated roles." % ( name, len( in_user_ids ), num_gras ), + "One of the roles associated with this group is the newly created role with the same name." ] ) # Get the group object for later tests global group_one group_one = get_group_by_name( name ) assert group_one is not None, 'Problem retrieving group named "Group One" from the database' # Make sure UserGroupAssociations are correct - if len( group_one.users ) != len( user_ids ): + if len( group_one.users ) != len( in_user_ids ): raise AssertionError( '%d UserGroupAssociations were created for group id %d when it was created ( should have been %d )' \ - % ( len( group_one.users ), group_one.id, len( user_ids ) ) ) + % ( len( group_one.users ), group_one.id, len( in_user_ids ) ) ) # Each user should now have 1 group association, group_one for user in [ admin_user, regular_user1, regular_user3 ]: refresh( user ) if len( user.groups ) != 1: raise AssertionError( '%d UserGroupAssociations are associated with user %s ( should be 1 )' % ( len( user.groups ), user.email ) ) # Make sure GroupRoleAssociations are correct - if len( group_one.roles ) != len( role_ids ): + if len( group_one.roles ) != num_gras: raise AssertionError( '%d GroupRoleAssociations were created for group id %d when it was created ( should have been %d )' \ - % ( len( group_one.roles ), group_one.id, len( role_ids ) ) ) + % ( len( group_one.roles ), group_one.id, num_gras ) ) # Rename the group rename = "Group One's been Renamed" self.rename_group( self.security.encode_id( group_one.id ), name=rename, ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Allow composite datatype datasets to be populated in the Upload tool from files that were uploaded to the Galaxy FTP server.
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/72d560d3e7fd/ changeset: r5207:72d560d3e7fd user: dan date: 2011-03-10 21:20:40 summary: Allow composite datatype datasets to be populated in the Upload tool from files that were uploaded to the Galaxy FTP server. affected #: 1 file (1.6 KB) --- a/lib/galaxy/tools/parameters/grouping.py Thu Mar 10 13:28:33 2011 -0500 +++ b/lib/galaxy/tools/parameters/grouping.py Thu Mar 10 15:20:40 2011 -0500 @@ -245,6 +245,7 @@ def get_one_filename( context ): data_file = context['file_data'] url_paste = context['url_paste'] + ftp_files = context['ftp_files'] name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) warnings = [] @@ -252,13 +253,34 @@ if context.get( 'space_to_tab', None ) not in [ "None", None, False ]: space_to_tab = True file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info ) - if file_bunch.path and url_paste: - if url_paste.strip(): + if file_bunch.path: + if url_paste is not None and url_paste.strip(): warnings.append( "All file contents specified in the paste box were ignored." ) - else: #we need to use url_paste + if ftp_files: + warnings.append( "All FTP uploaded file selections were ignored." ) + elif url_paste is not None and url_paste.strip(): #we need to use url_paste for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ): if file_bunch.path: break + if file_bunch.path and ftp_files is not None: + warnings.append( "All FTP uploaded file selections were ignored." ) + elif ftp_files is not None and trans.user is not None: # look for files uploaded via FTP + user_ftp_dir = os.path.join( trans.app.config.ftp_upload_dir, trans.user.email ) + for ( dirpath, dirnames, filenames ) in os.walk( user_ftp_dir ): + for filename in filenames: + for ftp_filename in ftp_files: + if ftp_filename == filename: + path = relpath( os.path.join( dirpath, filename ), user_ftp_dir ) + if not os.path.islink( os.path.join( dirpath, filename ) ): + ftp_data_file = { 'local_filename' : os.path.abspath( os.path.join( user_ftp_dir, path ) ), + 'filename' : os.path.basename( path ) } + file_bunch = get_data_file_filename( ftp_data_file, override_name = name, override_info = info ) + if file_bunch.path: + break + if file_bunch.path: + break + if file_bunch.path: + break file_bunch.space_to_tab = space_to_tab return file_bunch, warnings def get_filenames( context ): 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: kellyv: Modified script that adds manual builds to add build even if chrom length details not present; added a few new manual builds
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3d53f4f548c7/ changeset: r5206:3d53f4f548c7 user: kellyv date: 2011-03-10 19:28:33 summary: Modified script that adds manual builds to add build even if chrom length details not present; added a few new manual builds affected #: 2 files (656 bytes) 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: rc: Extending sample search to include search using form fields. Resolved #489
by Bitbucket 09 Mar '11

09 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b001ba3b7b3a/ changeset: r5205:b001ba3b7b3a user: rc date: 2011-03-09 21:33:04 summary: Extending sample search to include search using form fields. Resolved #489 affected #: 2 files (1.4 KB) --- a/lib/galaxy/web/controllers/requests_common.py Wed Mar 09 14:50:54 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Wed Mar 09 15:33:04 2011 -0500 @@ -748,6 +748,20 @@ trans.model.SampleDataset.table.c.sample_id==trans.model.Sample.table.c.id, func.lower( trans.model.SampleDataset.table.c.name ).like( "%" + search_string.lower() + "%" ) ) ) \ .order_by( trans.model.Sample.table.c.create_time.desc() ) + elif search_type == 'form value': + samples = [] + if search_string.find('=') != -1: + field_label, field_value = search_string.split('=') + all_samples = trans.sa_session.query( trans.model.Sample ) \ + .filter( trans.model.Sample.table.c.deleted==False ) \ + .order_by( trans.model.Sample.table.c.create_time.desc() ) + for sample in all_samples: + # find the field in the sample form with the given label + for field in sample.request.type.sample_form.fields: + if field_label == field['label']: + # check if the value is equal to the value in the search string + if sample.values.content[ field['name'] ] == field_value: + samples.append( sample ) if is_admin: for s in samples: if not s.request.deleted and s.request.state in request_states: @@ -770,7 +784,7 @@ display='checkboxes' ) # Build the search_type SelectField selected_value = kwd.get( 'search_type', 'sample name' ) - types = [ 'sample name', 'bar_code', 'dataset' ] + types = [ 'sample name', 'bar_code', 'dataset', 'form value' ] search_type = build_select_field( trans, types, 'self', 'search_type', selected_value=selected_value, refresh_on_change=False ) # Build the search_box TextField search_box = TextField( 'search_box', 50, kwd.get('search_box', '' ) ) --- a/templates/requests/common/find_samples.mako Wed Mar 09 14:50:54 2011 -0500 +++ b/templates/requests/common/find_samples.mako Wed Mar 09 15:33:04 2011 -0500 @@ -47,8 +47,15 @@ ${search_box.get_html()} <input type="submit" name="find_samples_button" value="Find"/><div class="toolParamHelp" style="clear: both;"> + <p> Wildcard search (%) can be used as placeholder for any sequence of characters or words.<br/> For example, to search for samples starting with 'mysample' use 'mysample%' as the search string. + </p> + <p> + When 'form value' search type is selected, then enter the search string in 'field label=value' format. + <br/>For example, when searching for all samples whose 'Volume' field is 1.3mL, then the search string + should be 'Volume=1.3mL' (without qoutes). + </p></div></div> %if results: 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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