February 2010 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3422: Make anchor ID/name editable in pages.
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/94741c94de0a changeset: 3422:94741c94de0a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 22 08:12:03 2010 -0500 description: Make anchor ID/name editable in pages. diffstat: templates/page/editor.mako | 3 ++- 1 files changed, 2 insertions(+), 1 deletions(-) diffs (13 lines): diff -r 831bbcccc4b2 -r 94741c94de0a templates/page/editor.mako --- a/templates/page/editor.mako Mon Feb 22 07:43:12 2010 -0500 +++ b/templates/page/editor.mako Mon Feb 22 08:12:03 2010 -0500 @@ -138,7 +138,8 @@ // Set input elt class, value. var attribute_input = $(".wym_href"); attribute_input.addClass("wym_id").removeClass("wym_href"); - attribute_input.val( attribute_input.attr('id') ); + if (selected) + attribute_input.val( $(selected).attr('id') ); // Remove link. $(this).remove();

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[hg] galaxy 3421: Pack script.
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/831bbcccc4b2 changeset: 3421:831bbcccc4b2 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 22 07:43:12 2010 -0500 description: Pack script. diffstat: static/scripts/packed/galaxy.panels.js | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (8 lines): diff -r 47aa31eb9cb6 -r 831bbcccc4b2 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Mon Feb 22 07:42:07 2010 -0500 +++ b/static/scripts/packed/galaxy.panels.js Mon Feb 22 07:43:12 2010 -0500 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragen! d",function(i){$("#DD-helper").hide()}).bind("drag",function(i){x=i.offsetX;x=Math.min(400,Math.max(100,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(i){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false;var g=false;var c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=fals! e};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=t rue}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(f,c,e,d){if(f){$(".dialog-box").find(".title").html(f);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(e){$.each(e,function(b,g){a.a! ppend($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,g){a.append($("<button/>").text(b).click(g));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img src='../images/yui/rel_interstitial_loading.gif')' />")}$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;' src='../images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button")! .bind("click",function(){hide_modal()})}$(function(){$(".tab").each(fu nction(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file +function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(i){$("#DD-helper").show()}).bind("dragen! d",function(i){$("#DD-helper").hide()}).bind("drag",function(i){x=i.offsetX;x=Math.min(400,Math.max(100,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(i){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false;var g=false;var c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=fals! e};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=t rue}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(k){$("#DD-helper").show()}).bind("dragend",function(k){$("#DD-helper").hide()}).bind("drag",function(k){x=k.offsetX;w=$(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(k){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(g,c,e,d,f){if(g){$(".dialog-box").find(".title").html(g);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(e){$.each(e,function(b,h){a! .append($("<button/>").text(b).click(h));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,h){a.append($("<button/>").text(b).click(h));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img src='../images/yui/rel_interstitial_loading.gif')' />")}$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}if(f){f()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;' src='../images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#cl! ose_button").bind("click",function(){hide_modal()})}$(function(){$(".t ab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file

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[hg] galaxy 3420: Added functionality for creating links on page...
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/47aa31eb9cb6 changeset: 3420:47aa31eb9cb6 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Feb 22 07:42:07 2010 -0500 description: Added functionality for creating links on pages: (1) existing links are editable and (2) can create in-page, named anchors. diffstat: static/scripts/galaxy.panels.js | 5 ++- templates/page/editor.mako | 64 ++++++++++++++++++++++++++++++++-------- 2 files changed, 54 insertions(+), 15 deletions(-) diffs (119 lines): diff -r 1e23f73647bb -r 47aa31eb9cb6 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Fri Feb 19 17:54:44 2010 -0500 +++ b/static/scripts/galaxy.panels.js Mon Feb 22 07:42:07 2010 -0500 @@ -165,7 +165,7 @@ } ); }; -function show_modal( title, body, buttons, extra_buttons ) { +function show_modal( title, body, buttons, extra_buttons, init_fn ) { if ( title ) { $( ".dialog-box" ).find( ".title" ).html( title ); $( ".dialog-box" ).find( ".unified-panel-header" ).show(); @@ -200,6 +200,9 @@ $("#overlay").show(); $(".dialog-box-container").fadeIn() } + if ( init_fn ) { + init_fn(); + } }; function show_in_overlay( options ) { diff -r 1e23f73647bb -r 47aa31eb9cb6 templates/page/editor.mako --- a/templates/page/editor.mako Fri Feb 19 17:54:44 2010 -0500 +++ b/templates/page/editor.mako Mon Feb 22 07:42:07 2010 -0500 @@ -126,6 +126,25 @@ var sStamp = wym.uniqueStamp(); var selected = wym.selected(); + // Swap out URL attribute for id/name attribute in link creation to enable anchor creation in page. + function set_link_id() + { + // When "set link id" link clicked, update UI. + $('#set_link_id').click( function() + { + // Set label. + $("#link_attribute_label").text("ID/Name"); + + // Set input elt class, value. + var attribute_input = $(".wym_href"); + attribute_input.addClass("wym_id").removeClass("wym_href"); + attribute_input.val( attribute_input.attr('id') ); + + // Remove link. + $(this).remove(); + }); + } + // LINK DIALOG if ( dialogType == WYMeditor.DIALOG_LINK ) { if(selected) { @@ -134,28 +153,45 @@ jQuery(wym._options.titleSelector).val(jQuery(selected).attr(WYMeditor.TITLE)); jQuery(wym._options.altSelector).val(jQuery(selected).attr(WYMeditor.ALT)); } + // Get current URL, title. + var curURL, curTitle; + if (selected) + { + curURL = $(selected).attr("href"); + if (curURL == undefined) + curURL = ""; + curTitle = $(selected).attr("title"); + if (curTitle == undefined) + curTitle = ""; + } show_modal( - "Link", - "<div><div><label>URL</label><br><input type='text' class='wym_href' value='' size='40' /></div>" - + "<div><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div><div>", + "Create Link", + "<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='" + curURL + "' size='40' /></div>" + + "<div><label>Title</label><br><input type='text' class='wym_title' value='" + curTitle + "' size='40' /></div><div>", { "Make link": function() { var sUrl = jQuery(wym._options.hrefSelector).val(); - if(sUrl.length > 0) { - - wym._exec(WYMeditor.CREATE_LINK, sStamp); - - jQuery("a[href=" + sStamp + "]", wym._doc.body) - .attr(WYMeditor.HREF, sUrl) - .attr(WYMeditor.TITLE, jQuery(wym._options.titleSelector).val()); - + sUrl = ( sUrl ? sUrl : "" ); + var sName = $(".wym_id").val(); + sName = ( sName ? sName : "" ); + if ( (sUrl.length > 0) || (sName.length > 0) ) { + // Create link. + wym._exec(WYMeditor.CREATE_LINK, sStamp); + + var link = jQuery("a[href=" + sStamp + "]", wym._doc.body); + link.attr(WYMeditor.HREF, sUrl); + link.attr(WYMeditor.TITLE, jQuery(wym._options.titleSelector).val()); + if (sName.length > 0) + link.attr("id", sName); } hide_modal(); }, - "Cancel:": function() { + "Cancel": function() { hide_modal(); } - } + }, + {}, + set_link_id ); return; } @@ -668,7 +704,7 @@ ##"Embed Page": function() { ## editor.dialog(Galaxy.DIALOG_EMBED_PAGE); ##} - }); + }); }); </script> </%def>

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[hg] galaxy 3419: trackster:
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1e23f73647bb changeset: 3419:1e23f73647bb user: Kanwei Li <kanwei(a)gmail.com> date: Fri Feb 19 17:54:44 2010 -0500 description: trackster: - Refactor - Focus on new browser text - Fixed linetrack bug when switching chroms diffstat: static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 152 +++++++++++++++++------------------- templates/tracks/browser.mako | 13 +- templates/tracks/new_browser.mako | 2 +- 4 files changed, 83 insertions(+), 86 deletions(-) diffs (313 lines): diff -r 879432079138 -r 1e23f73647bb static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Fri Feb 19 14:34:25 2010 -0500 +++ b/static/scripts/packed/trackster.js Fri Feb 19 17:54:44 2010 -0500 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/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="../images/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="../images/visualization/strand_left_inv.png";left_! img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}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},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tr! acks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a. track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.ma! x(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.con! tent_div=$("<div class='track-content'>");this.container_div=$("<div>< /div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_! element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height)}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.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.content_div.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 LineTrack=function(c,a,d,b){this.track_type="LineTrack";this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.ad! dClass("line-track");this.dataset_id=a;this.prefs={min_value:undefined ,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){this.data_queue={};this.data_cache=new Cache(CACHED_DATA);var a=this,b=a.view.tracks.indexOf(a);a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d.length===0||d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");if(a.prefs.min_value===undefined||a.prefs.max_value===undefined){a.prefs.min_value=d! .min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;if($("#linetrack_"+b+"_minval").length===0){var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)}a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(this.vertical_range===undefined){! return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canva s>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("! <input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_o! ffset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};thi s.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.adClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=th! is,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!=! =undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slo ts[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)*h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;while(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.v! iew.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></canvas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.bloc! ks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{ if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.length;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.ceil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);! return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.prefs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color! ;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A") .width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l.uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/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="../images/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="../images/visualization/strand_left_inv.png";left_! img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}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},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tr! acks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a. track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.ma! x(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.con! tent_div=$("<div class='track-content'>");this.container_div=$("<div>< /div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");a.content_div.text(DATA_LOADING);a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d.length===0||d=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");b(d);a.draw()}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.! high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(k);var l=this.content_div.width()/f;var h;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height())}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden! =true;this.container_div.addClass("label-track")};$.extend(LabelTrack. prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,d,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:fu! nction(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(d){if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=d.min;a.prefs.max_value=d.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var c=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);c.css({position:"relative",top:"25px"});c.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;! if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer: this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution,},function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(n,p,c,e){if(this.vertical_range===undefined){return}var q=p*DENSITY*n,a=DENSITY*n,b=$("<canvas class='tile'></canvas>"),s=n+"_"+p;if(!this.data_cache.get(s)){this.get_data(n,p);return}var r=this.data_cache.get(s);b.css({position:"absolute",top:0,left:(q-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var m=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,f=this.prefs.max_value,l=this.vertical_range,d=this.height_px;m.beginPath();for(var o=0;o<r.length-1;o++){var h=r[o][0]-q;var g=r[o][1];if(isNaN(g)){j=false}else{h=h*e;if(g<=k){g=k}else{if(g>=f){g=f}}g=Math.round(d-(g-k)/l*d);if(j){m.lineTo(h,g)}else{m.moveTo(h,g);j=true}}}m.stroke();c.append(b);return b},gen_options:function(j){var a=$("<div></div>").addClass("form-row");var e="track_"+j+"_! minval",g="track_"+j+"_maxval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),i=$("<input></input>").attr("id",e).val(b),d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(i).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,d,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px! =100;this.container_div.addClass("feature-track");this.dataset_id=a;th is.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black"};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;this.init_each({indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){a.values=b;a.calc_slots();a.slots=a.zo_slots})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},! function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var b=[],a=this.content_div.width()/(this.view.high-this.view.low),d=this.view.max_low;for(var e=0,f=this.values.length;e<f;e++){var g,h,k=this.values[e];g=Math.floor((k.start-d)*a);h=Math.ceil((k.end-d)*a);var c=0;while(true){if(b[c]===undefined||b[c]<g){b[c]=h;this.zo_slots[k.uid]=c;break}c++}}this.height_px=b.length*this.vertical_nodetail_px+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,f){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var h=this.inc_slots[a].w_scale,s=[],g=0,b=$("<canvas></canvas>").get(0).getContext("2d"),l=this.view.max_low;var c,e,u=[];for(var p=0,q=f.length;p<q;p++){var d=f[p];if(this.inc_slots[a][d.uid]!==undefined){g=Math.max(g,this.inc_slots[a][d.uid]);u.push(this.inc_slots[a][d.uid])}else{s.push(p)}}for(var p=0,q=s.length;p<q;p++){var d=f[s[p]];c=Math.floor((d.start-l)! *h);c-=b.measureText(d.name).width;e=Math.ceil((d.end-l)*h);var o=0;wh ile(true){var m=true;if(this.s_e_by_tile[a][o]!==undefined){for(var n=0,t=this.s_e_by_tile[a][o].length;n<t;n++){var r=this.s_e_by_tile[a][o][n];if(e>r[0]&&c<r[1]){m=false;break}}}if(m){if(this.s_e_by_tile[a][o]===undefined){this.s_e_by_tile[a][o]=[]}this.s_e_by_tile[a][o].push([c,e]);this.inc_slots[a][d.uid]=o;g=Math.max(g,o);break}o++}}return g},draw_tile:function(B,f,g,M){if(!this.values){return}var s=f*DENSITY*B,G=(f+1)*DENSITY*B,r=DENSITY*B;var K,L,m;if(M>this.show_labels_scale){if(!this.showing_details){this.showing_details=true}for(var H in this.data_cache.obj_cache){var C=H.split("_"),z=C[0],c=C[1];if(z<=s&&c>=G){K=this.data_cache.get(H);break}}if(!K){this.data_queue[[s,G]]=true;this.get_data(s,G);return}m=this.incremental_slots(this.view.zoom_res,K)*this.vertical_detail_px+15;L=this.inc_slots[this.view.zoom_res]}else{if(this.showing_details){this.showing_details=false}m=this.height_px;L=this.zo_slots;K=this.values}var a=Math.ceil(r*M),u=$("<canvas class='tile'></can! vas>"),D=this.prefs.label_color,e=this.prefs.block_color,x=this.left_offset,N=this.showing_details,O=(this.showing_details?this.vertical_detail_px:this.vertical_nodetail_px);u.css({position:"absolute",top:0,left:(s-this.view.low)*M-x});u.get(0).width=a+x;u.get(0).height=m;var p=u.get(0).getContext("2d");p.fillStyle=this.prefs.block_color;p.font=this.default_font;p.textAlign="right";var I=0;for(var J=0,o=K.length;J<o;J++){var v=K[J];if(v.start<=G&&v.end>=s){var A=Math.floor(Math.max(0,(v.start-s)*M)),q=Math.ceil(Math.min(a,(v.end-s)*M)),y=L[v.uid]*O;var n,E,t=null,P=null;if(v.thick_start&&v.thick_end){t=Math.floor(Math.max(0,(v.thick_start-s)*M));P=Math.ceil(Math.min(a,(v.thick_end-s)*M))}if(!N){p.fillRect(A+x,y+5,q-A,1)}else{if(v.start>s){p.fillStyle=D;p.fillText(v.name,A-1+x,y+8);p.fillStyle=e}var Q=v.blocks;if(Q){if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND}}p.fillRect(A+x,y,q-A,10);p.fillStyle=e}for(var H=0,d=Q.le! ngth;H<d;H++){var h=Q[H],b=Math.floor(Math.max(0,(h[0]-s)*M)),w=Math.c eil(Math.min(a,(h[1]-s)*M));if(b>w){continue}n=5;E=3;p.fillRect(b+x,y+E,w-b,n);if(t!==undefined&&!(b>P||w<t)){n=9;E=1;var F=Math.max(b,t),l=Math.min(w,P);p.fillRect(F+x,y+E,l-F,n)}}}else{n=9;E=1;p.fillRect(A+x,y+E,q-A,n);if(v.strand){if(v.strand=="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(v.strand=="-"){p.fillStyle=LEFT_STRAND_INV}}p.fillRect(A+x,y,q-A,10);p.fillStyle=prefs.block_color}}}I++}}g.append(u);return u},gen_options:function(g){var a=$("<div></div>").addClass("form-row");var d="track_"+g+"_block_color",c=$("<label></label>").attr("for",d).text("Block color:"),b=$("<input></input>").attr("id",d).attr("name",d).val(this.prefs.block_color),f="track_"+g+"_label_color",h=$("<label></label>").attr("for",f).text("Label color:"),e=$("<input></input>").attr("id",f).attr("name",f).val(this.prefs.label_color);return a.append(c).append(b).append(h).append(e)},update_options:function(c){var a=$("#track_"+c+"_block_color").val(),b=$("#track_"+c+"_label_color").val();if(a!==this.p! refs.block_color||b!==this.prefs.label_color){this.prefs.block_color=a;this.prefs.label_color=b;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,d,b){this.track_type="ReadTrack";this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,a,d,b)};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_tile:function(v,z,m,n){if(!this.values){return}var A=z*DENSITY*v,e=(z+1)*DENSITY*v,q=DENSITY*v;var D,p,h;h=this.height_px;p=this.zo_slots;D=this.values;var t=Math.ceil(q*n),r=$("<canvas class='tile'></canvas>");r.css({position:"absolute",top:0,left:(A-this.view.low)*n-this.left_offset});r.get(0).width=t+this.left_offset;r.get(0).height=h;var u=r.get(0).getContext("2d");u.fillStyle=this.prefs.block_color;u.font=this.default_font;u.textAlign="right";var s=u.measureText("A").width;var w=0;for(var x=0,y=D.length;x<y;x++){var l=D[x];if(l.start<=e&&l.end>=A){var g=Math.floor(! Math.max(0,(l.start-A)*n)),k=Math.ceil(Math.min(t,(l.end-A)*n)),f=p[l. uid]*this.vertical_detail_px;var a,E,d=null,o=null;if(n>s){for(var B=0,b=l.name.length;B<b;B++){var C=Math.floor(Math.max(0,(l.start+B-A)*n));u.fillText(l.name[B],C+this.left_offset,f+8)}}else{u.fillRect(g+this.left_offset,f+4,k-g,3)}}}m.append(r);return r}}); \ No newline at end of file diff -r 879432079138 -r 1e23f73647bb static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Feb 19 14:34:25 2010 -0500 +++ b/static/scripts/trackster.js Fri Feb 19 17:54:44 2010 -0500 @@ -198,6 +198,39 @@ this.content_div = $("<div class='track-content'>"); this.container_div = $("<div></div>").addClass('track').append( this.header_div ).append( this.content_div ); this.parent_element.append( this.container_div ); + }, + init_each: function(params, success_fn) { + var track = this; + track.data_queue = {}; + track.tile_cache.clear(); + track.data_cache.clear(); + track.content_div.css( "height", "30px" ); + track.content_div.text(DATA_LOADING); + track.container_div.removeClass("nodata error pending"); + + if (track.view.chrom) { + $.getJSON( data_url, params, function ( data ) { + if (!data || data == "error") { + track.container_div.addClass("error"); + track.content_div.text(DATA_ERROR); + } else if (data.length === 0 || data == "no data") { + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); + } else if (data == "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, 5000); + } else { + track.content_div.text(""); + track.content_div.css( "height", track.height_px + "px" ); + success_fn(data); + track.draw(); + } + }); + } else { + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); + } } }); @@ -233,9 +266,7 @@ if (this.left_offset) { left -= this.left_offset; } - cached.css( { - left: left - }); + cached.css({ left: left }); // Our responsibility to move the element to the new parent parent_element.append( cached ); this.max_height = Math.max( this.max_height, cached.height() ); @@ -252,7 +283,7 @@ if ( tile_element ) { track.tile_cache.set(key, tile_element); track.max_height = Math.max( track.max_height, tile_element.height() ); - track.content_div.css( "height", track.max_height ); + track.content_div.css( "height", track.max_height + "px"); } } }, 50); @@ -289,7 +320,6 @@ var LineTrack = function ( name, dataset_id, indexer, prefs ) { this.track_type = "LineTrack"; - this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -297,61 +327,42 @@ this.height_px = 100; this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; + this.data_cache = new Cache(CACHED_DATA); + this.tile_cache = new Cache(CACHED_TILES_LINE); this.prefs = { 'min_value': undefined, 'max_value': undefined }; if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; } if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; } }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { - this.data_queue = {}; - this.data_cache = new Cache(CACHED_DATA); // We need to cache some data because of - // asynchronous calls var track = this, track_id = track.view.tracks.indexOf(track); - track.content_div.text(DATA_LOADING); - track.container_div.removeClass("nodata error pending"); - $.getJSON( data_url, { stats: true, indexer: track.indexer, + track.vertical_range = undefined; + this.init_each({ stats: true, indexer: track.indexer, chrom: track.view.chrom, low: null, high: null, - dataset_id: track.dataset_id }, function ( data ) { - if (!data || data == "error") { - track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); - } else if (data.length === 0 || data == "no data") { - track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); - } else if (data == "pending") { - track.container_div.addClass("pending"); - track.content_div.text(DATA_PENDING); - setTimeout(function() { track.init(); }, 5000); - } else { - track.content_div.text(""); - track.content_div.css( "height", track.height_px + "px" ); - - if (track.prefs.min_value === undefined || track.prefs.max_value === undefined) { - track.prefs.min_value = data.min; - track.prefs.max_value = data.max; - - // Update the config - $('#track_' + track_id + '_minval').val(track.prefs.min_value); - $('#track_' + track_id + '_maxval').val(track.prefs.max_value); - } - track.vertical_range = track.prefs.max_value - track.prefs.min_value; - - // Draw y-axis labels if necessary - if ( $('#linetrack_' + track_id + '_minval').length === 0) { - var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); - var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); - - max_label.css({ position: "relative", top: "25px" }); - max_label.prependTo(track.container_div); - - min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); - min_label.prependTo(track.container_div); - } - - track.draw(); + dataset_id: track.dataset_id }, function(data) { + if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { + track.prefs.min_value = data.min; + track.prefs.max_value = data.max; + // Update the config + $('#track_' + track_id + '_minval').val(track.prefs.min_value); + $('#track_' + track_id + '_maxval').val(track.prefs.max_value); } + track.vertical_range = track.prefs.max_value - track.prefs.min_value; + + // Draw y-axis labels if necessary + $('#linetrack_' + track_id + '_minval').remove(); + $('#linetrack_' + track_id + '_maxval').remove(); + + var min_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value); + var max_label = $("<div></div>").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value); + + max_label.css({ position: "relative", top: "25px" }); + max_label.prependTo(track.container_div); + + min_label.css({ position: "relative", top: track.height_px + 55 + "px" }); + min_label.prependTo(track.container_div); }); }, get_data: function( resolution, position ) { @@ -362,9 +373,9 @@ if (!track.data_queue[key]) { track.data_queue[key] = true; - $.getJSON( data_url, { indexer: this.indexer, chrom: this.view.chrom, - low: low, high: high, dataset_id: this.dataset_id, - resolution: this.view.resolution }, function ( data ) { + $.getJSON( data_url, { "indexer": this.indexer, "chrom": this.view.chrom, + "low": low, "high": high, "dataset_id": this.dataset_id, + "resolution": this.view.resolution, }, function (data) { track.data_cache.set(key, data); delete track.data_queue[key]; track.draw(); @@ -392,7 +403,7 @@ top: 0, left: ( tile_low - this.view.low ) * w_scale }); - + canvas.get(0).width = Math.ceil( tile_length * w_scale ); canvas.get(0).height = this.height_px; var ctx = canvas.get(0).getContext("2d"), @@ -462,7 +473,6 @@ var FeatureTrack = function ( name, dataset_id, indexer, prefs ) { this.track_type = "FeatureTrack"; - this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -480,7 +490,9 @@ this.inc_slots = {}; this.data_queue = {}; this.s_e_by_tile = {}; + this.tile_cache = new Cache(CACHED_TILES_FEATURE); this.data_cache = new Cache(20); + this.prefs = { 'block_color': 'black', 'label_color': 'black' }; if (prefs.block_color !== undefined) { this.prefs.block_color = prefs.block_color; } if (prefs.label_color !== undefined) { this.prefs.label_color = prefs.label_color; } @@ -489,33 +501,15 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { var track = this; - track.content_div.text(DATA_LOADING); - track.container_div.removeClass("nodata error pending"); - $.getJSON( data_url, { indexer: track.indexer, low: track.view.max_low, - high: track.view.max_high, dataset_id: track.dataset_id, - chrom: track.view.chrom }, function ( data ) { - if (data == "error") { - track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); - } else if (data.length === 0 || data == "no data") { - track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); - } else if (data == "pending") { - track.container_div.adClass("pending"); - track.content_div.text(DATA_PENDING); - setTimeout(function() { track.init(); }, 5000); - } else { - track.content_div.text(""); - track.content_div.css( "height", track.height_px + "px" ); - track.values = data; - track.calc_slots(); - track.slots = track.zo_slots; - track.draw(); - } + this.init_each({ indexer: track.indexer, low: track.view.max_low, + high: track.view.max_high, dataset_id: track.dataset_id, + chrom: track.view.chrom }, function (data) { + track.values = data; + track.calc_slots(); + track.slots = track.zo_slots; }); }, get_data: function( low, high ) { - // console.log("getting: ", low, high); var track = this, key = low + '_' + high; @@ -523,7 +517,7 @@ track.data_queue[key] = true; $.getJSON( data_url, { indexer: track.indexer, chrom: track.view.chrom, low: low, high: high, dataset_id: track.dataset_id, - include_blocks: true }, function ( data ) { + include_blocks: true }, function (data) { track.data_cache.set(key, data); // console.log("datacache", track.data_cache.get(key)); delete track.data_queue[key]; diff -r 879432079138 -r 1e23f73647bb templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri Feb 19 14:34:25 2010 -0500 +++ b/templates/tracks/browser.mako Fri Feb 19 17:54:44 2010 -0500 @@ -107,8 +107,10 @@ error: function() { alert( "Couldn't create new browser" ) }, success: function(form_html) { show_modal("New Track Browser", form_html, { + "Cancel": function() { window.location = "/"; }, "Continue": continue_fn }); + $("#new-title").focus(); } }); %endif @@ -292,7 +294,7 @@ track.init(); } } - // view.redraw(); + view.redraw(); }); }); @@ -301,8 +303,9 @@ var track_id = track.track_id, label = $('<label for="track_' + track_id + 'title">' + track.name + '</label>'), title = $('<div class="historyItemTitle"></div>'), - del_icon = $('<a style="display:block; float:right" href="#" class="icon-button delete" />'), - edit_icon = $('<a style="display:block; float:right" href="#" class="icon-button edit" />'), + icon_div = $('<div class="historyItemButtons"></div>'); + del_icon = $('<a href="#" class="icon-button delete" />'), + edit_icon = $('<a href="#" class="icon-button edit" />'), body = $('<div class="historyItemBody"></div>'), checkbox = $('<input type="checkbox" checked="checked"></input>').attr("id", "track_" + track_id + "title"), li = $('<li class="sortable"></li>').attr("id", "track_" + track_id), @@ -318,8 +321,8 @@ view.remove_track(track); view.update_options(); }); - - title.append(label).append(del_icon).append(edit_icon); + icon_div.append(edit_icon).append(del_icon); + title.append(label).prepend(icon_div); if (track.gen_options) { editable.append(track.gen_options(track_id)).appendTo(body); } diff -r 879432079138 -r 1e23f73647bb templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Fri Feb 19 14:34:25 2010 -0500 +++ b/templates/tracks/new_browser.mako Fri Feb 19 17:54:44 2010 -0500 @@ -2,7 +2,7 @@ <div class="form-row"> <label for="title">Browser name:</label> <div class="form-row-input"> - <input type="text" name="title" id="new-title" value="Unnamed Browser"></input> + <input type="text" name="title" id="new-title" value="Unnamed"></input> </div> <div style="clear: both;"></div> </div>

1 0

[hg] galaxy 3418: Fix MySQL_python static egg on OS X
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/879432079138 changeset: 3418:879432079138 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Feb 19 14:34:25 2010 -0500 description: Fix MySQL_python static egg on OS X diffstat: eggs.ini | 2 +- scripts/scramble/scripts/MySQL_python.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (24 lines): diff -r 68eaeb1b1d69 -r 879432079138 eggs.ini --- a/eggs.ini Fri Feb 19 11:29:25 2010 -0500 +++ b/eggs.ini Fri Feb 19 14:34:25 2010 -0500 @@ -71,7 +71,7 @@ bx_python = http://bitbucket.org/james_taylor/bx-python/get/3b9d30e47619.bz2 Cheetah = http://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.2.2.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz -MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz +MySQL_python = http://downloads.sourceforge.net/project/mysql-python/mysql-python/1.2.2/My… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz pexpect = http://pypi.python.org/packages/source/p/pexpect/pexpect-2.4.tar.gz psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2 diff -r 68eaeb1b1d69 -r 879432079138 scripts/scramble/scripts/MySQL_python.py --- a/scripts/scramble/scripts/MySQL_python.py Fri Feb 19 11:29:25 2010 -0500 +++ b/scripts/scramble/scripts/MySQL_python.py Fri Feb 19 14:34:25 2010 -0500 @@ -80,7 +80,7 @@ CONFIGURE += "CXXFLAGS='-O -g -isysroot /Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc' " CONFIGURE += "LDFLAGS='-arch i386 -arch ppc' " CONFIGURE += "LD='gcc -mmacosx-version-min=10.4 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -nostartfiles -arch i386 -arch ppc' " - CONFIGURE += "./configure --prefix=%s/mysql --disable-dependency-tracking --without-server --without-uca --without-libwrap " %os.getcwd() + CONFIGURE += "./configure --prefix=%s/mysql --disable-dependency-tracking --disable-shared --without-server --without-uca --without-libwrap " %os.getcwd() CONFIGURE += "--without-extra-tools --without-openssl --without-yassl --without-docs --without-man --without-bench --enable-thread-safe-client" else: CONFIGURE = "CFLAGS='-fPIC' ./configure --prefix=%s/mysql --disable-shared --without-server --without-uca --without-libwrap " %os.getcwd()

1 0

[hg] galaxy 3417: Fix bug so that, when a user submits edits to ...
by Greg Von Kuster 24 Feb '10

24 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/68eaeb1b1d69 changeset: 3417:68eaeb1b1d69 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Feb 19 11:29:25 2010 -0500 description: Fix bug so that, when a user submits edits to a page's attributes, he is redicted to his page list. diffstat: lib/galaxy/web/controllers/page.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (14 lines): diff -r d995557d383b -r 68eaeb1b1d69 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Fri Feb 19 10:01:33 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Fri Feb 19 11:29:25 2010 -0500 @@ -409,8 +409,8 @@ page.title = page_title page.slug = page_slug session.flush() - # Display the management page - return trans.response.send_redirect( web.url_for( action='index' ) ) + # Redirect to page list. + return trans.response.send_redirect( web.url_for( action='list' ) ) else: page_title = page.title page_slug = page.slug

1 0

Re: [galaxy-dev] Sqlite to MYSQL conversion in galaxy
by Roy Weckiewicz 23 Feb '10

23 Feb '10

Hi Nate, Sorry I had an empty database set the first time (which was giving me the revision error): Part of my problem has been trying to convert the db from sqlite to mysql -- the closest I got using scripts was 40 tables in the database: datasetdataset_permissionsdefault_history_permissions default_user_permissionseventform_definition_currentgalaxy_group galaxy_sessiongalaxy_session_to_historygalaxy_usergroup_role_association historyhistory_dataset_associationhistory_user_share_association implicitly_converted_dataset_associationjobjob_external_output_metadata job_parameterjob_to_input_datasetjob_to_output_datasetlibrarylibrary_dataset library_dataset_dataset_association library_dataset_dataset_association_permissionslibrary_dataset_permissions library_folderlibrary_folder_permissionslibrary_permissionsmetadata_file migrate_versionrolestored_workflowstored_workflow_menu_entry stored_workflow_user_share_connectionuser_group_association user_role_associationvalidation_errorworkflowworkflow_step workflow_step_connection When I try to run it linked to the above database I get the following error: galaxy.model.migrate.check DEBUG 2010-02-19 13:42:18,987 MySQL_python egg successfully loaded for mysql dialect Traceback (most recent call last): File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", line 102, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest ) ) Exception: Your database has version '22' but this code expects version '39'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. So when I try to run the manage_db.sh I get: 22 -> 23... Migration script to add columns for tracking whether pages are deleted and publicly accessible. Traceback (most recent call last): File "./scripts/manage_db.py", line 45, in <module> main( repository='lib/galaxy/model/migrate', url=db_url ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/sqlalchemy_migrate-0.5.4-py2.5.egg/migrate/versioning/script/py.py", line 101, in run func() File "lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py", line 20, in upgrade Page_table = Table( "page", metadata, autoload=True ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 108, in __call__ return type.__call__(self, name, metadata, *args, **kwargs) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/schema.py", line 236, in __init__ _bind_or_error(metadata).reflecttable(self, include_columns=include_columns) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1265, in reflecttable self.dialect.reflecttable(conn, table, include_columns) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1664, in reflecttable sql = self._show_create_table(connection, table, charset) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/eggs/py2.5-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/mysql.py", line 1835, in _show_create_table raise exc.NoSuchTableError(full_name) sqlalchemy.exc.NoSuchTableError: page I guess my problem all along is not having the full table schema for use in mySQL. Rgds, Roy Weckiewicz On Fri, Feb 19, 2010 at 1:33 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Roy Weckiewicz wrote: > >> Thanks again Nate, >> >> I just tried the one you sent me - it seems I just have a database >> revision issue: >> >> Traceback (most recent call last): >> File >> "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", >> line 61, in app_factory >> app = UniverseApplication( global_conf = global_conf, **kwargs ) >> File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", >> line 28, in __init__ >> create_or_verify_database( db_url, self.config.database_engine_options >> ) >> File >> "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", >> line 72, in create_or_verify_database >> raise Exception( "Your database is older than hg revision >> 1464:c7acaa1bb88f and will need to be updated manually" ) >> Exception: Your database is older than hg revision 1464:c7acaa1bb88f and >> will need to be updated manually >> > > Hi Roy, > > Is this the database you converted from sqlite? Does it include the > 'migrate_version' table? Could you paste the output of 'SHOW TABLES;'? > > Thanks, > > >> >> Rgds, >> >> >> Roy Weckiewicz >> >> >> On Fri, Feb 19, 2010 at 1:28 PM, Nate Coraor <nate(a)bx.psu.edu <mailto: >> nate(a)bx.psu.edu>> wrote: >> >> Roy Weckiewicz wrote: >> >> What's strange is that eventhough the file name on the egg is >> MySQL*fat-ucs2.egg the error still reports the file in question >> as MySQL*fat.egg -- I've tried renaming the egg to match the >> original file, but it didn't seem to make a difference. >> Furthermore, when I run.sh, the program will create a directory >> in home called .python-eggs/ containing the _MySQL.so file, >> among other things - Will I have to add a different URL to the >> eggs.ini to keep it from re-downloading the old file? >> >> >> Ah, sorry, that egg relies on some uncommitted patches. I've >> rebuilt it using a clean checkout, could you try this one instead?: >> >> >> http://www.bx.psu.edu/~nate/galaxy/MySQL_python-1.2.2_5.0.67_static-py2.5-m… >> >> Thanks, >> --nate >> >> >> >> >> -- >> Roy Weckiewicz >> Texas A&M University >> > > -- Roy Weckiewicz Texas A&M University

4 5

new tool: calculate frequencies
by Assaf Gordon 22 Feb '10

22 Feb '10

Hi, Attached is a tool to calculate frequencies/distribution of values in a column (similar to "histogram" tool, but without plotting the chart). The tool allows finer control of the output, by setting min,max,bin-width or number-of-bins. This allows calculating distribution of multiple datasets, then comparing them or plotting them all together with the plotting tool. Also available for download here: http://cancan.cshl.edu/labmembers/gordon/files/calculate_frequncies.tar.bz2 comments are welcomed, -gordon

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GMOD Logo Program
by Dave Clements, GMOD Help Desk 22 Feb '10

22 Feb '10

Hello all, Need a logo that tells people what your web site, database or GMOD component is about? If your resource needs a logo then the GMOD Logo Program (http://gmod.org/wiki/GMOD_Logo_Program) can help. I am pleased to announce the first call for participation in the GMOD Logo Program. This program is for GMOD users and developers that would like have a custom designed logo for their web site, database or GMOD component. The program pairs GMOD community members with students in advanced design classes at colleges and universities. This spring we will be working with a class at Linn-Benton Community College. Participants will meet several times (remotely) over a 3 week period, with the end result being a new logo for your resource. Participation is limited to non-profits, and costs US$75. If you are interested, please see http://gmod.org/wiki/GMOD_Logo_Program for additional details and requirements, and an application form. The program is accepting applications until March 1. Thanks, Dave Clements GMOD Help Desk PS: This program was inspired by ZFIN's success with its logo (see http://zfin.org) ZFIN's excellent logo was created by working with a design class at the University of Oregon. -- Please keep responses on the list! http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_Logo_Program http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

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Exception when a tool has repeat, select and label options
by Assaf Gordon 19 Feb '10

19 Feb '10

Hello, First, thanks for fixing the boolean testing bug. We're having strange exception thrown in some of our tools, when a tool has a <repeat> section, a selection-box parameter and an output label. That might sound strange, but I've narrowed it down and it's (almost) definitely caused by the combination of those three. I know you don't use the "label" option in the public Galaxy, but we use it in many of our tools, and for some it simply doesn't work. Attached are three simple tools: tool_without_label: has a <repeat> parameter, a selection-box parameter, no 'label' in the <output>. works ok. tool_without_select: has a <repeat> parameter, a text parameter (instead of a selection box), and a label in the <output>. works ok. tool_with_label: has all three items: a <repeat>, a selection-box, and a label. Executing this tool throws an exception: ======================= URL: http://localhost:8080/tool_runner/index File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/gordon/temp/galaxy/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/home/gordon/temp/galaxy/lib/galaxy/web/controllers/tool_runner.py', line 53 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 792 in handle_input out_data = self.execute( trans, incoming=params ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 1064 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/actions/__init__.py', line 297 in execute for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 1067 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/parameters/__init__.py', line 80 in params_to_strings rval[ key ] = str( to_json_string( value ) ) File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/__init__.py', line 182 in dumps File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 312 in encode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 262 in _iterencode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 170 in _iterencode_list File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 265 in _iterencode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 235 in _iterencode_dict File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 273 in _iterencode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 279 in _iterencode_default File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 300 in default TypeError: <galaxy.tools.SelectToolParameterWrapper object at 0x49a8d10> is not JSON serializable ======================= Any help/fix would be greatly appreciated. thanks! -gordon

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