- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3112: trackster: load block data incrementally, huge...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b9b9fe0612b9 changeset: 3112:b9b9fe0612b9 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Nov 19 18:55:35 2009 -0500 description: trackster: load block data incrementally, huge performance gains from drawing smaller tiles diffstat: lib/galaxy/visualization/tracks/data/interval_index.py | 4 +- static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 81 +++++++++---------- 4 files changed, 42 insertions(+), 47 deletions(-) diffs (233 lines): diff -r b70e23d80a75 -r b9b9fe0612b9 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Thu Nov 19 12:56:24 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Thu Nov 19 18:55:35 2009 -0500 @@ -18,11 +18,10 @@ index = Indexes( self.converted_dataset.file_name ) results = [] - uid = 0 for start, end, offset in index.find(chrom, start, end): source.seek(offset) feature = source.readline().split() - payload = { 'uid': uid, 'start': start, 'end': end, 'name': feature[3] } + payload = { 'uid': offset, 'start': start, 'end': end, 'name': feature[3] } try: payload['strand'] = feature[5] except IndexError: @@ -44,6 +43,5 @@ pass results.append(payload) - uid += 1 return results diff -r b70e23d80a75 -r b9b9fe0612b9 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Thu Nov 19 12:56:24 2009 -0500 +++ b/static/scripts/packed/galaxy.base.js Thu Nov 19 18:55:35 2009 -0500 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ens ure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}; \ No newline at end of file +$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo(" body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b}; \ No newline at end of file diff -r b70e23d80a75 -r b9b9fe0612b9 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu Nov 19 12:56:24 2009 -0500 +++ b/static/scripts/packed/trackster.js Thu Nov 19 18:55:35 2009 -0500 @@ -1,1 +1,1 @@ -var DENSITY=1000,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 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Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){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){ 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LabelTrack=function(a){Track.call(this,null,a);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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.dataset_id=b;this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low: 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e]=g;$(document).trigger("redraw")})},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache[l]){this.get_data(d,a);return}var g=this.cache[l];c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143"};$.extend(Featur 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y=0;for(var z=0,A=this.values.length;z<A;z++){var f=this.values[z];if(f.start<=c&&f.end>=C){var e=Math.floor(Math.max(0,(f.start-C)*n)),h=Math.ceil(Math.min(u,(f.end-C)*n)),d=this.slots[f.name]*this.vertical_gap;var a,G,b=null,o=null;if(f.thick_start&&f.thick_end){b=Math.floor(Math.max(0,(f.thick_start-C)*n));o=Math.ceil(Math.min(u,(f.thick_end-C)*n))}if(!this.showing_labels){v.fillRect(e,d+5,h-e,1)}else{if(v.fillText){v.fillText(f.name,e-1,d+8)}var E=f.blocks;if(E){if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND}else{if(f.strand=="-"){v.fillStyle=LEFT_STRAND}}v.fillRect(e,d,h-e,10);v.fillStyle=this.base_color}for(var x=0,F=E.length;x<F;x++){var m=E[x],l=Math.floor(Math.max(0,(m[0]-C)*n)),D=Math.ceil(Math.min(u,(m[1]-C)*n));a=5;G=3;v.fillRect(l,d+G,D-l,a);if(b&&(l<o||D>b)){a=9;G=1;var r=Math.max(l,b),p=Math.min(D,o);v.fillRect(r,d+G,p-r,a)}}}else{a=9;G=1;v.fillRect(e,d+G,h-e,a);if(f.strand){if(f.strand=="+"){v.fillStyle=RIGHT_STRAND_INV}else{if(f.strand=="-") 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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,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.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}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#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));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:fun ction(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.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.zo om_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)}else{h=this.draw_tile(d,a,k,l);if(h){this.tile_cache.set(j,h)}}a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.contain er_div.addClass("line-track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="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");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({positi on:"relative",top:a.height_px+32+"px"});d.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;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=t rue}}}n.stroke();m.append(c);return c}});var FeatureTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NO NE)}else{if(b=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{track_type:b.track_type,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 c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},increment al_slots:function(a,b){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c] ]=true;this.get_data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left _offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}}); \ No newline at end of file diff -r b70e23d80a75 -r b9b9fe0612b9 static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Nov 19 12:56:24 2009 -0500 +++ b/static/scripts/trackster.js Thu Nov 19 18:55:35 2009 -0500 @@ -1,7 +1,7 @@ /* Trackster 2009, James Taylor, Kanwei Li */ -var DEBUG = true; +var DEBUG = false; var DENSITY = 1000, FEATURE_LEVELS = 100, @@ -109,7 +109,7 @@ // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); - this.zoom_res = Math.max(1,Math.ceil( Math.log( (this.high - this.low) / FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )); + this.zoom_res = Math.max(1,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )); // Overview $("#overview-box").css( { @@ -404,7 +404,7 @@ }); }, get_data: function( low, high ) { - console.log("getting: ", low, high); + // console.log("getting: ", low, high); var track = this, key = low + '_' + high; @@ -420,39 +420,24 @@ }); } }, - calc_slots: function( include_labels ) { + calc_slots: function() { // console.log("num vals: " + this.values.length); var end_ary = [], scale = this.content_div.width() / (this.view.high - this.view.low), - labels_scale = this.show_labels_scale, max_high = this.view.max_high, max_low = this.view.max_low; // console.log(scale, this.view.high, this.view.low); - if (include_labels) { - this.zi_slots = {}; - } - var dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); for (var i = 0, len = this.values.length; i < len; i++) { var f_start, f_end, feature = this.values[i]; - if (include_labels) { - f_start = Math.floor( (feature.start - max_low) * labels_scale ); - f_start -= dummy_canvas.measureText(feature.name).width; - f_end = Math.ceil( (feature.end - max_low) * labels_scale ); - } else { - f_start = Math.floor( (feature.start - max_low) * scale ); - f_end = Math.ceil( (feature.end - max_low) * scale ); - } + f_start = Math.floor( (feature.start - max_low) * scale ); + f_end = Math.ceil( (feature.end - max_low) * scale ); + // if (include_labels) { console.log(f_start, f_end); } - var j = 0; while (true) { if (end_ary[j] === undefined || end_ary[j] < f_start) { end_ary[j] = f_end; - if (include_labels) { - this.zi_slots[feature.uid] = j; - } else { - this.zo_slots[feature.uid] = j; - } + this.zo_slots[feature.uid] = j; break; } j++; @@ -464,20 +449,23 @@ incremental_slots: function( level, features ) { if (!this.inc_slots[level]) { this.inc_slots[level] = {}; - this.inc_slots[level].w_scale = 1000 / Math.pow(FEATURE_LEVELS, level); + this.inc_slots[level].w_scale = DENSITY / Math.pow(FEATURE_LEVELS, level+1); + // this.inc_slots[level].w_scale = 1000 / (this.view.high - this.view.low); + } var slots = this.inc_slots[level]; - if (slots[uid]) { - return slots[uid]; - } + // console.log(level, slots.w_scale, slots); var end_ary = [], undone = [], - max_high = this.view.max_high, + highest_slot = 0, // To measure how big to draw canvas + dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"), max_low = this.view.max_low; for (var i = 0, len = features.length; i < len; i++) { var feature = features[i]; + // console.log(feature.name, feature.uid, slots[feature.uid]); if (slots[feature.uid]) { + highest_slot = Math.max(highest_slot, slots[feature.uid]); end_ary[ slots[feature.uid] ] = Math.ceil( (feature.end - max_low) * slots.w_scale ); } else { undone.push(feature); @@ -488,6 +476,19 @@ f_start = Math.floor( (feature.start - max_low) * slots.w_scale ); f_start -= dummy_canvas.measureText(feature.name).width; f_end = Math.ceil( (feature.end - max_low) * slots.w_scale ); + // console.log(f_start, f_end, feature.name); + var j = 0; + while (true) { + if (end_ary[j] === undefined || end_ary[j] < f_start) { + end_ary[j] = f_end; + slots[feature.uid] = j; + highest_slot = Math.max(highest_slot, j); + break; + } + j++; + } + } + return highest_slot; }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { @@ -499,14 +500,10 @@ tile_span = DENSITY * resolution; // console.log("drawing " + tile_index); // Once we zoom in enough, show name labels - var data; + var data, slots, required_height; if (w_scale > this.show_labels_scale) { if (!this.showing_labels) { this.showing_labels = true; - if (!this.zi_slots) { - this.calc_slots(true); - } - this.slots = this.zi_slots; } for (var k in this.data_cache.obj_cache) { var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1]; @@ -520,20 +517,20 @@ this.get_data(tile_low, tile_high); return; } - + required_height = this.incremental_slots( this.view.zoom_res, data ) * this.vertical_gap + 15; + // console.log(required_height); + slots = this.inc_slots[this.view.zoom_res]; } else { if (this.showing_labels) { this.showing_labels = false; - this.slots = this.zo_slots; } + required_height = this.height_px; + slots = this.zo_slots; data = this.values; } - // console.log(this.slots); - - + // console.log(tile_low, tile_high, tile_length, w_scale); var width = Math.ceil( tile_span * w_scale ), - height = this.height_px, new_canvas = $("<canvas class='tile'></canvas>"); new_canvas.css({ @@ -542,7 +539,7 @@ left: ( tile_low - this.view.low ) * w_scale - this.left_offset }); new_canvas.get(0).width = width + this.left_offset; - new_canvas.get(0).height = height; + new_canvas.get(0).height = required_height; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); ctx.fillStyle = this.base_color; @@ -555,7 +552,7 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = this.slots[feature.uid] * this.vertical_gap; + y_center = slots[feature.uid] * this.vertical_gap; var thickness, y_start, thick_start = null, thick_end = null; if (feature.thick_start && feature.thick_end) { @@ -569,7 +566,7 @@ // Showing labels, blocks, details if (ctx.fillText && feature.start > tile_low) { ctx.fillText(feature.name, f_start - 1 + this.left_offset, y_center + 8); - // ctx.fillText(commatize(feature.start), f_start - 1, y_center + 8); + // ctx.fillText(commatize(feature.start), f_start - 1 + this.left_offset, y_center + 8); } var blocks = feature.blocks; if (blocks) {

1 0

[hg] galaxy 3113: Eliminate the ability to delete/undelete/purge...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5c46679d0755 changeset: 3113:5c46679d0755 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Nov 20 08:46:49 2009 -0500 description: Eliminate the ability to delete/undelete/purge users until the grid helper can access config settings. diffstat: lib/galaxy/web/controllers/admin.py | 10 +++++----- 1 files changed, 5 insertions(+), 5 deletions(-) diffs (23 lines): diff -r b9b9fe0612b9 -r 5c46679d0755 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Thu Nov 19 18:55:35 2009 -0500 +++ b/lib/galaxy/web/controllers/admin.py Fri Nov 20 08:46:49 2009 -0500 @@ -91,14 +91,14 @@ grids.GridAction( "Create new user", dict( controller='admin', action='users', operation='create' ) ) ] operations = [ - grids.GridOperation( "Manage Roles & Groups", condition=( lambda item: not item.deleted ), allow_multiple=False ) + grids.GridOperation( "Manage Roles & Groups", condition=( lambda item: not item.deleted ), allow_multiple=False ), + grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False ) ] #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if # the setting is False - operations.append( grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False ) ) - operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) + #operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) + #operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) + #operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ),

1 0

[hg] galaxy 3109: revert to sqlite default in universe.sample
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c507bad7e373 changeset: 3109:c507bad7e373 user: Kanwei Li <kanwei(a)gmail.com> date: Wed Nov 18 13:45:53 2009 -0500 description: revert to sqlite default in universe.sample diffstat: lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py | 6 +- lib/galaxy/visualization/tracks/data/array_tree.py | 30 +- lib/galaxy/visualization/tracks/data/interval_index.py | 26 +- static/scripts/trackster.js | 116 +++++++++-- universe_wsgi.ini.sample | 12 +- 5 files changed, 131 insertions(+), 59 deletions(-) diffs (352 lines): diff -r bcb3c0eeb72f -r c507bad7e373 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Wed Nov 18 13:37:41 2009 -0500 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Wed Nov 18 13:45:53 2009 -0500 @@ -8,7 +8,7 @@ from bx.arrays.array_tree import * from bx.arrays.wiggle import IntervalReader -BLOCK_SIZE = 1000 +BLOCK_SIZE = 100 def main(): @@ -20,8 +20,8 @@ # Fill array from wiggle d = array_tree_dict_from_wiggle_reader( reader, {}, block_size = BLOCK_SIZE ) - for value in d.itervalues(): - value.root.build_summary() + for array_tree in d.itervalues(): + array_tree.root.build_summary() f = open( out_fname, "w" ) FileArrayTreeDict.dict_to_file( d, f ) diff -r bcb3c0eeb72f -r c507bad7e373 lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Wed Nov 18 13:37:41 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Wed Nov 18 13:45:53 2009 -0500 @@ -12,9 +12,6 @@ # Maybe this should be included in the datatype itself, so users can add their # own types to the browser as long as they return the right format of data? -# FIXME: Assuming block size is always 1000 for the moment -BLOCK_SIZE = 1000 - class ArrayTreeDataProvider( object ): def __init__( self, dataset, original_dataset ): self.dataset = dataset @@ -32,32 +29,33 @@ return { 'max': float( max(root_summary.maxs) ), 'min': float( min(root_summary.mins) ) } def get_data( self, chrom, start, end, **kwargs ): - start = int( start ) - end = int( end ) - resolution = max(1, ceil(float(kwargs['resolution']))) - - level = int( floor( log( resolution, BLOCK_SIZE ) ) ) - level = max( level, 0 ) - stepsize = BLOCK_SIZE ** level - step1 = stepsize * BLOCK_SIZE - - # Open the file f = open( self.dataset.file_name ) d = FileArrayTreeDict( f ) + # Get the right chromosome try: chrom_array_tree = d[chrom] except KeyError: return None + + block_size = chrom_array_tree.block_size + start = int( start ) + end = int( end ) + resolution = max(1, ceil(float(kwargs['resolution']))) + + level = int( floor( log( resolution, block_size ) ) ) + level = max( level, 0 ) + stepsize = block_size ** level + step1 = stepsize * block_size + # Is the requested level valid? assert 0 <= level <= chrom_array_tree.levels - # Calculate the actual start/range/step of the block we're getting results = [] - for block_start in range( start, end, stepsize * BLOCK_SIZE ): + for block_start in range( start, end, stepsize * block_size ): # print block_start # Return either data point or a summary depending on the level - indexes = range( block_start, block_start + stepsize * BLOCK_SIZE, stepsize ) + indexes = range( block_start, block_start + stepsize * block_size, stepsize ) if level > 0: s = chrom_array_tree.get_summary( block_start, level ) if s is not None: diff -r bcb3c0eeb72f -r c507bad7e373 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Wed Nov 18 13:37:41 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Wed Nov 18 13:45:53 2009 -0500 @@ -27,19 +27,21 @@ payload['strand'] = feature[5] except IndexError: pass - try: - block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] - block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] - blocks = zip(block_sizes, block_starts) - payload['blocks'] = [ (start + block[1], start + block[1] + block[0]) for block in blocks] - except IndexError: - pass + + if 'include_blocks' in kwargs: + try: + block_sizes = [ int(n) for n in feature[10].split(',') if n != ''] + block_starts = [ int(n) for n in feature[11].split(',') if n != '' ] + blocks = zip(block_sizes, block_starts) + payload['blocks'] = [ (start + block[1], start + block[1] + block[0]) for block in blocks] + except IndexError: + pass - try: - payload['thick_start'] = int(feature[6]) - payload['thick_end'] = int(feature[7]) - except IndexError: - pass + try: + payload['thick_start'] = int(feature[6]) + payload['thick_end'] = int(feature[7]) + except IndexError: + pass results.append(payload) uid += 1 diff -r bcb3c0eeb72f -r c507bad7e373 static/scripts/trackster.js --- a/static/scripts/trackster.js Wed Nov 18 13:37:41 2009 -0500 +++ b/static/scripts/trackster.js Wed Nov 18 13:45:53 2009 -0500 @@ -1,9 +1,10 @@ /* Trackster 2009, James Taylor, Kanwei Li */ -var DEBUG = false; +var DEBUG = true; var DENSITY = 1000, + FEATURE_LEVELS = 100, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", @@ -108,6 +109,7 @@ // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); + this.zoom_res = Math.max(1,Math.ceil( Math.log( (this.high - this.low) / FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) )); // Overview $("#overview-box").css( { @@ -171,7 +173,7 @@ resolution = this.view.resolution; - if (DEBUG) { $("#debug").text(resolution); } + if (DEBUG) { $("#debug").text(resolution + " " + this.view.zoom_res); } var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -279,7 +281,7 @@ max_label.css({ position: "relative", top: "35px" }); max_label.prependTo(track.container_div) - min_label.css({ position: "relative", top: track.height_px + 32 + "px", }); + min_label.css({ position: "relative", top: track.height_px + 32 + "px" }); min_label.prependTo(track.container_div); track.draw(); @@ -297,7 +299,7 @@ $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id, resolution: this.view.resolution }, function ( data ) { - track.cache[key] = data; + track.cache.set(key, data); delete track.data_queue[key]; track.draw(); }); @@ -313,12 +315,12 @@ canvas = $("<canvas class='tile'></canvas>"), key = resolution + "_" + tile_index; - if (!this.cache[key]) { + if (!this.cache.get(key)) { this.get_data( resolution, tile_index ); return; } - var data = this.cache[key]; + var data = this.cache.get(key); canvas.css( { position: "absolute", top: 0, @@ -368,7 +370,11 @@ this.showing_labels = false; this.vertical_gap = 10; this.base_color = "#2C3143"; + this.default_font = "9px Monaco, Lucida Console, monospace"; this.left_offset = 200; + this.inc_slots = {}; + this.data_queue = {}; + this.data_cache = new Cache(20); }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { @@ -397,6 +403,23 @@ } }); }, + get_data: function( low, high ) { + console.log("getting: ", low, high); + var track = this, + key = low + '_' + high; + + if (!track.data_queue[key]) { + track.data_queue[key] = true; + $.getJSON( data_url, { track_type: track.track_type, chrom: track.view.chrom, + low: low, high: high, dataset_id: track.dataset_id, + include_blocks: true }, function ( data ) { + track.data_cache.set(key, data); + // console.log("datacache", track.data_cache.get(key)); + delete track.data_queue[key]; + track.draw(); + }); + } + }, calc_slots: function( include_labels ) { // console.log("num vals: " + this.values.length); var end_ary = [], @@ -438,27 +461,76 @@ this.height_px = end_ary.length * this.vertical_gap + 15; this.content_div.css( "height", this.height_px + "px" ); }, + incremental_slots: function( level, features ) { + if (!this.inc_slots[level]) { + this.inc_slots[level] = {}; + this.inc_slots[level].w_scale = 1000 / Math.pow(FEATURE_LEVELS, level); + } + var slots = this.inc_slots[level]; + if (slots[uid]) { + return slots[uid]; + } + var end_ary = [], + undone = [], + max_high = this.view.max_high, + max_low = this.view.max_low; + + for (var i = 0, len = features.length; i < len; i++) { + var feature = features[i]; + if (slots[feature.uid]) { + end_ary[ slots[feature.uid] ] = Math.ceil( (feature.end - max_low) * slots.w_scale ); + } else { + undone.push(feature); + } + } + for (var i = 0, len = undone.length; i < len; i++) { + var feature = undone[i]; + f_start = Math.floor( (feature.start - max_low) * slots.w_scale ); + f_start -= dummy_canvas.measureText(feature.name).width; + f_end = Math.ceil( (feature.end - max_low) * slots.w_scale ); + + }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { - if (!this.values) { // Still loading - return null; + if (!this.values) { + return; } + var tile_low = tile_index * DENSITY * resolution, + tile_high = ( tile_index + 1 ) * DENSITY * resolution, + tile_span = DENSITY * resolution; // console.log("drawing " + tile_index); // Once we zoom in enough, show name labels - if (w_scale > this.show_labels_scale && !this.showing_labels) { - this.showing_labels = true; - if (!this.zi_slots) { - this.calc_slots(true); + var data; + if (w_scale > this.show_labels_scale) { + if (!this.showing_labels) { + this.showing_labels = true; + if (!this.zi_slots) { + this.calc_slots(true); + } + this.slots = this.zi_slots; } - this.slots = this.zi_slots; - } else if (w_scale <= this.show_labels_scale && this.showing_labels) { - this.showing_labels = false; - this.slots = this.zo_slots; + for (var k in this.data_cache.obj_cache) { + var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1]; + if (k_low <= tile_low && k_high >= tile_high) { + data = this.data_cache.get(k); + break; + } + } + if (!data) { + this.data_queue[ [tile_low, tile_high] ] = true; + this.get_data(tile_low, tile_high); + return; + } + + } else { + if (this.showing_labels) { + this.showing_labels = false; + this.slots = this.zo_slots; + } + data = this.values; } // console.log(this.slots); - var tile_low = tile_index * DENSITY * resolution, - tile_high = ( tile_index + 1 ) * DENSITY * resolution, - tile_span = DENSITY * resolution; + // console.log(tile_low, tile_high, tile_length, w_scale); var width = Math.ceil( tile_span * w_scale ), height = this.height_px, @@ -474,12 +546,12 @@ // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); ctx.fillStyle = this.base_color; - ctx.font = "10px monospace"; + ctx.font = this.default_font; ctx.textAlign = "right"; var j = 0; - for (var i = 0, len = this.values.length; i < len; i++) { - var feature = this.values[i]; + for (var i = 0, len = data.length; i < len; i++) { + var feature = data[i]; if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), diff -r bcb3c0eeb72f -r c507bad7e373 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Wed Nov 18 13:37:41 2009 -0500 +++ b/universe_wsgi.ini.sample Wed Nov 18 13:45:53 2009 -0500 @@ -31,15 +31,15 @@ paste.app_factory = galaxy.web.buildapp:app_factory # By default, Galaxy uses a SQLite database found here -#database_file = database/universe.sqlite +database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database # instead. PostgreSQL and MySQL are supported. -database_connection = postgres:///galaxy -database_engine_option_echo = true -database_engine_option_echo_pool = true -database_engine_option_pool_size = 10 -database_engine_option_max_overflow = 20 +#database_connection = postgres:///galaxy +#database_engine_option_echo = true +#database_engine_option_echo_pool = true +#database_engine_option_pool_size = 10 +#database_engine_option_max_overflow = 20 # If using MySQL, see: # http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-2…

1 0

[hg] galaxy 3111: Fixed a bug in cloud store update. Also, added...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b70e23d80a75 changeset: 3111:b70e23d80a75 user: Enis Afgan <afgane(a)gmail.com> date: Thu Nov 19 12:56:24 2009 -0500 description: Fixed a bug in cloud store update. Also, added method comments to EC2 cloud provider implementation class. diffstat: lib/galaxy/cloud/providers/ec2.py | 90 ++++++++++++++++++++--------- lib/galaxy/cloud/providers/eucalyptus.py | 32 +++++----- templates/cloud/list_images.mako | 2 + 3 files changed, 81 insertions(+), 43 deletions(-) diffs (316 lines): diff -r 53de6aea6445 -r b70e23d80a75 lib/galaxy/cloud/providers/ec2.py --- a/lib/galaxy/cloud/providers/ec2.py Wed Nov 18 16:18:09 2009 -0500 +++ b/lib/galaxy/cloud/providers/ec2.py Thu Nov 19 12:56:24 2009 -0500 @@ -94,13 +94,16 @@ log.info( "EC2 cloud manager stopped" ) def put( self, uci_wrapper ): - # Get rid of UCI from state description + """ + Add uci_wrapper object to the end of the request queue to be handled by + this cloud provider. + """ state = uci_wrapper.get_uci_state() uci_wrapper.change_state( state.split('U')[0] ) # remove 'UCI' from end of state description (i.e., mark as accepted and ready for processing) self.queue.put( uci_wrapper ) def run_next( self ): - """Run the next job, waiting until one is available if necessary""" + """Process next request, waiting until one is available if necessary.""" cnt = 0 while 1: @@ -125,7 +128,7 @@ def get_connection( self, uci_wrapper ): """ - Establishes EC2 cloud connection using user's credentials associated with given UCI + Establishes cloud connection using user's credentials associated with given UCI """ log.debug( 'Establishing %s cloud connection.' % self.type ) provider = uci_wrapper.get_provider() @@ -152,7 +155,10 @@ def check_key_pair( self, uci_wrapper, conn ): """ - Generate key pair using user's credentials + Check if a key pair associated with this UCI exists on cloud provider. + If yes, return key pair name; otherwise, generate a key pair with the cloud + provider and, again, return key pair name. + Key pair name for given UCI is generated from UCI's name and suffix '_kp' """ kp = None kp_name = uci_wrapper.get_name().replace(' ','_') + "_kp" @@ -200,6 +206,7 @@ return None def create_key_pair( self, conn, kp_name ): + """ Initiate creation of key pair under kp_name by current cloud provider. """ try: return conn.create_key_pair( kp_name ) except boto.exception.EC2ResponseError, e: @@ -226,8 +233,8 @@ def create_uci( self, uci_wrapper ): """ - Creates User Configured Instance (UCI). Essentially, creates storage volume on cloud provider - and registers relevant information in Galaxy database. + Create User Configured Instance (UCI) - i.e., create storage volume on cloud provider + and register relevant information in local Galaxy database. """ conn = self.get_connection( uci_wrapper ) if uci_wrapper.get_uci_availability_zone()=='': @@ -279,8 +286,11 @@ def delete_uci( self, uci_wrapper ): """ - Deletes UCI. NOTE that this implies deletion of any and all data associated + Delete UCI - i.e., delete all storage volumes associated with this UCI. + NOTE that this implies deletion of any and all data associated with this UCI from the cloud. All data will be deleted. + Information in local Galaxy database is marked as deleted but not actually removed + from the database. """ conn = self.get_connection( uci_wrapper ) vl = [] # volume list @@ -318,7 +328,8 @@ def snapshot_uci( self, uci_wrapper ): """ - Creates snapshot of all storage volumes associated with this UCI. + Initiate creation of a snapshot by cloud provider for all storage volumes + associated with this UCI. """ if uci_wrapper.get_uci_state() != uci_states.ERROR: conn = self.get_connection( uci_wrapper ) @@ -362,7 +373,7 @@ def start_uci( self, uci_wrapper ): """ - Starts instance(s) of given UCI on the cloud. + Start instance(s) of given UCI on the cloud. """ if uci_wrapper.get_uci_state() != uci_states.ERROR: conn = self.get_connection( uci_wrapper ) @@ -461,7 +472,7 @@ def stop_uci( self, uci_wrapper): """ - Stops all of cloud instances associated with given UCI. + Stop all of cloud instances associated with given UCI. """ conn = self.get_connection( uci_wrapper ) @@ -543,11 +554,15 @@ def update( self ): """ - Runs a global status update on all instances that are in 'running', 'pending', or 'shutting-down' state. - Also, runs update on all storage volumes that are in 'in-use', 'creating', or 'None' state. + Run status update on all instances that are in 'running', 'pending', or 'shutting-down' state. + Run status update on all storage volumes whose status is 'in-use', 'creating', or 'None'. + Run status update on all snapshots whose status is 'pending' or 'delete' + Run status update on any zombie UCIs, i.e., UCI's that is in 'submitted' state for an + extended period of time. + Reason behind this method is to sync state of local DB and real-world resources """ - log.debug( "Running general status update for EC2 UCIs..." ) + log.debug( "Running general status update for %s UCIs..." % self.type ) # Update instances instances = self.sa_session.query( model.CloudInstance ) \ .filter( or_( model.CloudInstance.table.c.state==instance_states.RUNNING, @@ -610,7 +625,11 @@ self.process_zombie( z_inst ) def update_instance( self, inst ): - + """ + Update information in local database for given instance as it is obtained from cloud provider. + Along with updating information about given instance, information about the UCI controlling + this instance is also updated. + """ # Get credentials associated wit this instance uci_id = inst.uci_id uci = self.sa_session.query( model.UCI ).get( uci_id ) @@ -683,6 +702,11 @@ return None def update_store( self, store ): + """ + Update information in local database for given storage volume as it is obtained from cloud provider. + Along with updating information about given storage volume, information about the UCI controlling + this storage volume is also updated. + """ # Get credentials associated wit this store uci_id = store.uci_id uci = self.sa_session.query( model.UCI ).get( uci_id ) @@ -705,6 +729,7 @@ # Update store status in local DB with info from cloud provider if len(vl) > 0: try: + log.debug( "Storage volume '%s' current status: '%s'" % (store.volume_id, vl[0].status ) ) if store.status != vl[0].status: # In case something failed during creation of UCI but actual storage volume was created and yet # UCI state remained as 'new', try to remedy this by updating UCI state here @@ -721,18 +746,19 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.inst.instance_id != vl[0].instance_id: - store.inst.instance_id = vl[0].instance_id - self.sa_session.add( store ) - self.sa_session.flush() - if store.attach_time != vl[0].attach_time: - store.attach_time = vl[0].attach_time - self.sa_session.add( store ) - self.sa_session.flush() - if store.device != vl[0].device: - store.device = vl[0].device - self.sa_session.add( store ) - self.sa_session.flush() + if store.inst != None: + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id + self.sa_session.add( store ) + self.sa_session.flush() + if store.attach_time != vl[0].attach_time: + store.attach_time = vl[0].attach_time + self.sa_session.add( store ) + self.sa_session.flush() + if store.device != vl[0].device: + store.device = vl[0].device + self.sa_session.add( store ) + self.sa_session.flush() except boto.exception.EC2ResponseError, e: err = "Updating status of volume(s) from cloud failed for UCI '"+ uci.name + "' during general status update: " + str( e ) log.error( err ) @@ -753,6 +779,11 @@ self.sa_session.flush() def update_snapshot( self, snapshot ): + """ + Update information in local database for given snapshot as it is obtained from cloud provider. + Along with updating information about given snapshot, information about the UCI controlling + this snapshot is also updated. + """ # Get credentials associated wit this store uci_id = snapshot.uci_id uci = self.sa_session.query( model.UCI ).get( uci_id ) @@ -799,6 +830,9 @@ self.sa_session.flush() def delete_snapshot( self, snapshot ): + """ + Initiate deletion of given snapshot from cloud provider. + """ if snapshot.status == snapshot_status.DELETE: # Get credentials associated wit this store uci_id = snapshot.uci_id @@ -845,7 +879,7 @@ def process_zombie( self, inst ): """ - Attempt at discovering if starting an instance was successful but local database was not updated + Attempt at discovering if starting a cloud instance was successful but local database was not updated accordingly or if something else failed and instance was never started. Currently, no automatic repairs are being attempted; instead, appropriate error messages are set. """ @@ -921,7 +955,7 @@ def get_connection_from_uci( self, uci ): """ - Establishes and returns connection to cloud provider. Information needed to do so is obtained + Establish and return connection to cloud provider. Information needed to do so is obtained directly from uci database object. """ log.debug( 'Establishing %s cloud connection' % self.type ) diff -r 53de6aea6445 -r b70e23d80a75 lib/galaxy/cloud/providers/eucalyptus.py --- a/lib/galaxy/cloud/providers/eucalyptus.py Wed Nov 18 16:18:09 2009 -0500 +++ b/lib/galaxy/cloud/providers/eucalyptus.py Thu Nov 19 12:56:24 2009 -0500 @@ -94,7 +94,7 @@ def put( self, uci_wrapper ): """ - Adds uci_wrapper object to the end of the request queue to be handled by + Add uci_wrapper object to the end of the request queue to be handled by this cloud provider. """ state = uci_wrapper.get_uci_state() @@ -536,7 +536,7 @@ Reason behind this method is to sync state of local DB and real-world resources """ - log.debug( "Running general status update for EPC UCIs..." ) + log.debug( "Running general status update for %s UCIs..." % self.type ) # Update instances instances = self.sa_session.query( model.CloudInstance ) \ .filter( or_( model.CloudInstance.table.c.state==instance_states.RUNNING, @@ -695,7 +695,8 @@ # Update store status in local DB with info from cloud provider if len(vl) > 0: try: - if store.status != vl[0].status and store.availability_zone != 'epc': + log.debug( "Storage volume '%s' current status: '%s'" % (store.volume_id, vl[0].status ) ) + if store.status != vl[0].status: # In case something failed during creation of UCI but actual storage volume was created and yet # UCI state remained as 'new', try to remedy this by updating UCI state here if ( store.status == None ) and ( store.volume_id != None ): @@ -718,10 +719,11 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.inst.instance_id != vl[0].instance_id: - store.inst.instance_id = vl[0].instance_id - self.sa_session.add( store ) - self.sa_session.flush() + if store.inst != None: + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id + self.sa_session.add( store ) + self.sa_session.flush() if store.attach_time != vl[0].attach_time: store.attach_time = vl[0].attach_time self.sa_session.add( store ) @@ -937,7 +939,7 @@ def get_connection_from_uci( self, uci ): """ - Establishes and returns connection to cloud provider. Information needed to do so is obtained + Establish and return connection to cloud provider. Information needed to do so is obtained directly from uci database object. """ log.debug( 'Establishing %s cloud connection' % self.type ) @@ -946,13 +948,13 @@ # Get connection try: region = RegionInfo( None, uci.credentials.provider.region_name, uci.credentials.provider.region_endpoint ) - log.debug( "[%s] Using following command to connect to cloud provider: " - "conn = EC2Connection( aws_access_key_id=%s, " - "aws_secret_access_key=%s, " - "port=%s, " - "is_secure=%s, " - "region=region, " - "path=%s )" % ( self.type, a_key, s_key, uci.credentials.provider.is_secure, uci.credentials.provider.port, uci.credentials.provider.path ) ) +# log.debug( "[%s] Using following command to connect to cloud provider: " +# "conn = EC2Connection( aws_access_key_id=%s, " +# "aws_secret_access_key=%s, " +# "port=%s, " +# "is_secure=%s, " +# "region=region, " +# "path=%s )" % ( self.type, a_key, s_key, uci.credentials.provider.is_secure, uci.credentials.provider.port, uci.credentials.provider.path ) ) conn = EC2Connection( aws_access_key_id=a_key, aws_secret_access_key=s_key, is_secure=uci.credentials.provider.is_secure, diff -r 53de6aea6445 -r b70e23d80a75 templates/cloud/list_images.mako --- a/templates/cloud/list_images.mako Wed Nov 18 16:18:09 2009 -0500 +++ b/templates/cloud/list_images.mako Thu Nov 19 12:56:24 2009 -0500 @@ -78,6 +78,8 @@ </tr> %endfor </table> + + <p /></p><a href="${h.url_for( controller='cloud', action='add_new_image' )}" target="galaxy_main">Add another machine image</a> %else: <h3>There are no registered machine images.</h3><br /> <a href="${h.url_for( controller='cloud', action='add_new_image' )}" target="galaxy_main">Add machine image now?</a>

1 0

[hg] galaxy 3110: Only fix OS X platform name on 2.5, the only v...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/53de6aea6445 changeset: 3110:53de6aea6445 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 18 16:18:09 2009 -0500 description: Only fix OS X platform name on 2.5, the only version on which it's broken diffstat: lib/galaxy/__init__.py | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (15 lines): diff -r c507bad7e373 -r 53de6aea6445 lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py Wed Nov 18 13:45:53 2009 -0500 +++ b/lib/galaxy/__init__.py Wed Nov 18 16:18:09 2009 -0500 @@ -12,8 +12,9 @@ import os, sys from distutils.sysconfig import get_config_vars -if ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ - ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ): +if sys.version_info[:2] == ( 2, 5 ) and \ + ( ( os.uname()[-1] in ( 'i386', 'ppc' ) and sys.platform == 'darwin' and os.path.abspath( sys.prefix ).startswith( '/System' ) ) or \ + ( sys.platform == 'darwin' and get_config_vars().get('UNIVERSALSDK', '').strip() ) ): # Has to be before anything imports pkg_resources def _get_platform_monkeypatch(): plat = distutils.util._get_platform()

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[hg] galaxy 3108: merge
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bcb3c0eeb72f changeset: 3108:bcb3c0eeb72f user: Enis Afgan <afgane(a)gmail.com> date: Wed Nov 18 13:37:41 2009 -0500 description: merge diffstat: lib/galaxy/web/framework/helpers/grids.py | 3 +++ static/images/mag_glass.png | templates/grid_base.mako | 35 +++++++++++++++++++++++++++++++++++ templates/grid_common.mako | 13 ++++++++----- 4 files changed, 46 insertions(+), 5 deletions(-) diffs (97 lines): diff -r 5fbda2fdb3ca -r bcb3c0eeb72f lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 13:36:37 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 13:37:41 2009 -0500 @@ -120,6 +120,9 @@ column_filter = from_json_string_recurse( column_filter ) if len( column_filter ) == 1: column_filter = column_filter[0] + # If filter criterion is empty, do nothing. + if column_filter == '': + continue # Update query. query = column.filter( trans.sa_session, query, column_filter ) # Upate current filter dict. diff -r 5fbda2fdb3ca -r bcb3c0eeb72f static/images/mag_glass.png Binary file static/images/mag_glass.png has changed diff -r 5fbda2fdb3ca -r bcb3c0eeb72f templates/grid_base.mako --- a/templates/grid_base.mako Wed Nov 18 13:36:37 2009 -0500 +++ b/templates/grid_base.mako Wed Nov 18 13:37:41 2009 -0500 @@ -62,6 +62,21 @@ t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); } + + // Initialize submit image elements. + $('.submit-image').each( function() + { + // On mousedown, add class to simulate click. + $(this).mousedown( function() { + $(this).addClass('gray-background'); + }); + + // On mouseup, add class to simulate click. + $(this).mouseup( function() { + $(this).removeClass('gray-background'); + }); + + }); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -168,6 +183,26 @@ text-align: center; display: inline-block; } + .submit-image { + vertical-align: text-bottom; + margin: 0; + padding: 0; + } + .no-padding-or-margin { + margin: 0; + padding: 0; + } + .gray-background { + background-color: #DDDDDD; + } + .text-filter-val { + border: solid 1px #AAAAAA; + padding: 1px 3px 1px 3px; + margin-right: 5px; + -moz-border-radius: .5em; + -webkit-border-radius: .5em; + font-style: italic; + } </style> </%def> diff -r 5fbda2fdb3ca -r bcb3c0eeb72f templates/grid_common.mako --- a/templates/grid_common.mako Wed Nov 18 13:36:37 2009 -0500 +++ b/templates/grid_common.mako Wed Nov 18 13:37:41 2009 -0500 @@ -32,10 +32,11 @@ <% column_filter = cur_filter_dict[column.key] %> %if isinstance( column_filter, basestring ): %if column_filter != "All": - <span style="font-style: italic">${cur_filter_dict[column.key]}</span> - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - | + <span class='text-filter-val'> + ${cur_filter_dict[column.key]} + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + </span> %endif %elif isinstance( column_filter, list ): %for i, filter in enumerate( column_filter ): @@ -53,7 +54,9 @@ %endif %endif - <span><input id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/></span> + <span> + <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/> + <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/></span> </form> %else: %for i, filter in enumerate( column.get_accepted_filters() ):

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[hg] galaxy 3107: Fixed table migration bug encountered with Pos...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5fbda2fdb3ca changeset: 3107:5fbda2fdb3ca user: Enis Afgan <afgane(a)gmail.com> date: Wed Nov 18 13:36:37 2009 -0500 description: Fixed table migration bug encountered with PostgreSQL. diffstat: lib/galaxy/cloud/__init__.py | 12 ++++++++++-- lib/galaxy/cloud/providers/ec2.py | 8 ++++++-- lib/galaxy/cloud/providers/eucalyptus.py | 14 +++++++++----- lib/galaxy/model/__init__.py | 1 - lib/galaxy/model/mapping.py | 6 +++--- lib/galaxy/model/migrate/versions/0026_cloud_tables.py | 4 ++-- templates/cloud/view_instance.mako | 6 ++++-- universe_wsgi.ini.sample | 12 ++++++------ 8 files changed, 40 insertions(+), 23 deletions(-) diffs (258 lines): diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/__init__.py --- a/lib/galaxy/cloud/__init__.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/cloud/__init__.py Wed Nov 18 13:36:37 2009 -0500 @@ -45,6 +45,14 @@ ERROR = "error" ) +store_status = Bunch( + WAITING = "waiting", + IN_USE = "in-use", + CREATING = "creating", + DELETED = 'deleted', + ERROR = "error" +) + snapshot_status = Bunch( SUBMITTED = 'submitted', PENDING = 'pending', @@ -413,7 +421,7 @@ be given in following format: 'vol-78943248' """ vol = self.sa_session.query( model.CloudStore ).filter( model.CloudStore.table.c.volume_id == vol_id ).first() - vol.i_id = instance_id + vol.inst.instance_id = instance_id self.sa_session.add( vol ) self.sa_session.flush() @@ -559,7 +567,7 @@ def get_mi_id( self, instance_id=0 ): uci = self.sa_session.query( model.UCI ).get( self.uci_id ) self.sa_session.refresh( uci ) - return uci.instance[instance_id].mi_id + return uci.instance[instance_id].image.image_id def get_public_dns( self, instance_id=0 ): uci = self.sa_session.query( model.UCI ).get( self.uci_id ) diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/providers/ec2.py --- a/lib/galaxy/cloud/providers/ec2.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/cloud/providers/ec2.py Wed Nov 18 13:36:37 2009 -0500 @@ -49,6 +49,7 @@ ) store_status = Bunch( + WAITING = "waiting", IN_USE = "in-use", CREATING = "creating", DELETED = 'deleted', @@ -441,6 +442,8 @@ s = reservation.instances[0].state uci_wrapper.change_state( s, i_id, s ) uci_wrapper.set_security_group_name( self.security_group, i_id=i_id ) + vol_id = uci_wrapper.get_store_volume_id( store_id=0 ) # TODO: Once more that one vol/UCI is allowed, update this! + uci_wrapper.set_store_status( vol_id, store_status.WAITING ) log.debug( "Instance of UCI '%s' started, current state: '%s'" % ( uci_wrapper.get_name(), uci_wrapper.get_uci_state() ) ) except boto.exception.EC2ResponseError, e: err = "EC2 response error when retrieving instance information for UCI '" + uci_wrapper.get_name() + "': " + str( e ) @@ -560,6 +563,7 @@ stores = self.sa_session.query( model.CloudStore ) \ .filter( or_( model.CloudStore.table.c.status==store_status.IN_USE, model.CloudStore.table.c.status==store_status.CREATING, + model.CloudStore.table.c.status==store_status.WAITING, model.CloudStore.table.c.status==None ) ) \ .all() for store in stores: @@ -717,8 +721,8 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.i_id != vl[0].instance_id: - store.i_id = vl[0].instance_id + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id self.sa_session.add( store ) self.sa_session.flush() if store.attach_time != vl[0].attach_time: diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/cloud/providers/eucalyptus.py --- a/lib/galaxy/cloud/providers/eucalyptus.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/cloud/providers/eucalyptus.py Wed Nov 18 13:36:37 2009 -0500 @@ -49,6 +49,7 @@ ) store_status = Bunch( + WAITING = "waiting", IN_USE = "in-use", CREATING = "creating", DELETED = 'deleted', @@ -428,6 +429,8 @@ uci_wrapper.set_instance_id( i_index, i_id ) s = reservation.instances[0].state uci_wrapper.change_state( s, i_id, s ) + vol_id = uci_wrapper.get_store_volume_id( store_id=0 ) # TODO: Once more that one vol/UCI is allowed, update this! + uci_wrapper.set_store_status( vol_id, store_status.WAITING ) log.debug( "Instance of UCI '%s' started, current state: '%s'" % ( uci_wrapper.get_name(), uci_wrapper.get_uci_state() ) ) except boto.exception.EC2ResponseError, e: err = "EC2 response error when retrieving instance information for UCI '" + uci_wrapper.get_name() + "': " + str( e ) @@ -497,7 +500,7 @@ ## log.debug ( 'Error detaching volume; still going to try and stop instance %s.' % dbInstances.instance_id ) # store.attach_time = None # store.device = None -# store.i_id = None +# store.inst.instance_id = None # store.status = volStat # log.debug ( '***** volume status: %s' % volStat ) # @@ -549,6 +552,7 @@ stores = self.sa_session.query( model.CloudStore ) \ .filter( or_( model.CloudStore.table.c.status==store_status.IN_USE, model.CloudStore.table.c.status==store_status.CREATING, + model.CloudStore.table.c.status==store_status.WAITING, model.CloudStore.table.c.status==None ) ) \ .all() for store in stores: @@ -691,7 +695,7 @@ # Update store status in local DB with info from cloud provider if len(vl) > 0: try: - if store.status != vl[0].status: + if store.status != vl[0].status and store.availability_zone != 'epc': # In case something failed during creation of UCI but actual storage volume was created and yet # UCI state remained as 'new', try to remedy this by updating UCI state here if ( store.status == None ) and ( store.volume_id != None ): @@ -714,8 +718,8 @@ store.status = vl[0].status self.sa_session.add( store ) self.sa_session.flush() - if store.i_id != vl[0].instance_id: - store.i_id = vl[0].instance_id + if store.inst.instance_id != vl[0].instance_id: + store.inst.instance_id = vl[0].instance_id self.sa_session.add( store ) self.sa_session.flush() if store.attach_time != vl[0].attach_time: @@ -981,7 +985,7 @@ # try: # volumes = conn.get_all_volumes( vols ) # for i, v in enumerate( volumes ): -# uci.store[i].i_id = v.instance_id +# uci.store[i].inst.instance_id = v.instance_id # uci.store[i].status = v.status # uci.store[i].device = v.device # uci.store[i].flush() diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/model/__init__.py Wed Nov 18 13:36:37 2009 -0500 @@ -1077,7 +1077,6 @@ def __init__( self ): self.id = None self.volume_id = None - self.i_id = None self.user = None self.size = None self.availability_zone = None diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/model/mapping.py Wed Nov 18 13:36:37 2009 -0500 @@ -429,7 +429,7 @@ Column( "type", TEXT ), Column( "reservation_id", TEXT ), Column( "instance_id", TEXT ), - Column( "mi_id", TEXT, ForeignKey( "cloud_image.image_id" ), index=True ), + Column( "mi_id", Integer, ForeignKey( "cloud_image.id" ), index=True ), Column( "state", TEXT ), Column( "error", TEXT ), Column( "public_dns", TEXT ), @@ -447,7 +447,7 @@ Column( "volume_id", TEXT ), Column( "size", Integer, nullable=False ), Column( "availability_zone", TEXT ), - Column( "i_id", TEXT, ForeignKey( "cloud_instance.instance_id" ) ), + Column( "inst_id", Integer, ForeignKey( "cloud_instance.id" ) ), Column( "status", TEXT ), Column( "device", TEXT ), Column( "space_consumed", Integer ), @@ -1133,7 +1133,7 @@ assign_mapper( context, CloudStore, CloudStore.table, properties=dict( user=relation( User ), - i=relation( CloudInstance ), + inst=relation( CloudInstance ), snapshot=relation( CloudSnapshot, backref="store" ) ) ) diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca lib/galaxy/model/migrate/versions/0026_cloud_tables.py --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 13:36:37 2009 -0500 @@ -56,7 +56,7 @@ Column( "type", TEXT ), Column( "reservation_id", TEXT ), Column( "instance_id", TEXT ), - Column( "mi_id", TEXT, ForeignKey( "cloud_image.id" ), index=True ), + Column( "mi_id", Integer, ForeignKey( "cloud_image.id" ), index=True ), Column( "state", TEXT ), Column( "error", TEXT ), Column( "public_dns", TEXT ), @@ -74,7 +74,7 @@ Column( "volume_id", TEXT ), Column( "size", Integer, nullable=False ), Column( "availability_zone", TEXT ), - Column( "i_id", TEXT, ForeignKey( "cloud_instance.id" ) ), + Column( "inst_id", Integer, ForeignKey( "cloud_instance.id" ) ), Column( "status", TEXT ), Column( "device", TEXT ), Column( "space_consumed", Integer ), diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca templates/cloud/view_instance.mako --- a/templates/cloud/view_instance.mako Wed Nov 18 10:57:24 2009 -0500 +++ b/templates/cloud/view_instance.mako Wed Nov 18 13:36:37 2009 -0500 @@ -67,7 +67,7 @@ %endif <tr> <td> AMI: </td> - <td> ${liveInstance.mi_id} </td> + <td> ${liveInstance.image.image_id} </td> </tr> <tr> <td> State:</td> @@ -81,6 +81,7 @@ <td> Storage size:</td> <td> ${liveInstance.uci.total_size} </td> </tr> + %if liveInstance.public_dns != None and liveInstance.public_dns != '': <tr> <td> Public DNS:</td> <% @@ -88,7 +89,8 @@ %> <td> <a href="${lnk}" target="_blank">${liveInstance.public_dns}</a></td> </tr> - %if liveInstance.private_dns != None: + %endif + %if liveInstance.private_dns != None and liveInstance.private_dns != '': <tr> <td> Private DNS:</td> <td> ${liveInstance.private_dns}</td> diff -r f4c2bf76b2e2 -r 5fbda2fdb3ca universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Wed Nov 18 10:57:24 2009 -0500 +++ b/universe_wsgi.ini.sample Wed Nov 18 13:36:37 2009 -0500 @@ -31,15 +31,15 @@ paste.app_factory = galaxy.web.buildapp:app_factory # By default, Galaxy uses a SQLite database found here -database_file = database/universe.sqlite +#database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database # instead. PostgreSQL and MySQL are supported. -#database_connection = postgres:///galaxy -#database_engine_option_echo = true -#database_engine_option_echo_pool = true -#database_engine_option_pool_size = 10 -#database_engine_option_max_overflow = 20 +database_connection = postgres:///galaxy +database_engine_option_echo = true +database_engine_option_echo_pool = true +database_engine_option_pool_size = 10 +database_engine_option_max_overflow = 20 # If using MySQL, see: # http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-2…

1 0

[hg] galaxy 3105: Change a few foreign keys, this may change beh...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f4c2bf76b2e2 changeset: 3105:f4c2bf76b2e2 user: James Taylor <james(a)jamestaylor.org> date: Wed Nov 18 10:57:24 2009 -0500 description: Change a few foreign keys, this may change behavior of the cloud stuff, needs to be checked. diffstat: lib/galaxy/model/migrate/versions/0026_cloud_tables.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r 2beaa0783b69 -r f4c2bf76b2e2 lib/galaxy/model/migrate/versions/0026_cloud_tables.py --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:47:14 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:57:24 2009 -0500 @@ -56,7 +56,7 @@ Column( "type", TEXT ), Column( "reservation_id", TEXT ), Column( "instance_id", TEXT ), - Column( "mi_id", TEXT, ForeignKey( "cloud_image.image_id" ), index=True ), + Column( "mi_id", TEXT, ForeignKey( "cloud_image.id" ), index=True ), Column( "state", TEXT ), Column( "error", TEXT ), Column( "public_dns", TEXT ), @@ -74,7 +74,7 @@ Column( "volume_id", TEXT ), Column( "size", Integer, nullable=False ), Column( "availability_zone", TEXT ), - Column( "i_id", TEXT, ForeignKey( "cloud_instance.instance_id" ) ), + Column( "i_id", TEXT, ForeignKey( "cloud_instance.id" ) ), Column( "status", TEXT ), Column( "device", TEXT ), Column( "space_consumed", Integer ),

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[hg] galaxy 3106: Tweaks to grid filter UI: (1) added search ima...
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fb7dd12ea39c changeset: 3106:fb7dd12ea39c user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Wed Nov 18 11:51:09 2009 -0500 description: Tweaks to grid filter UI: (1) added search image/submit button for initiating search and (2) styled text filter criteria. diffstat: lib/galaxy/web/framework/helpers/grids.py | 3 +++ static/images/mag_glass.png | templates/grid_base.mako | 35 +++++++++++++++++++++++++++++++++++ templates/grid_common.mako | 13 ++++++++----- 4 files changed, 46 insertions(+), 5 deletions(-) diffs (97 lines): diff -r f4c2bf76b2e2 -r fb7dd12ea39c lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 10:57:24 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Nov 18 11:51:09 2009 -0500 @@ -120,6 +120,9 @@ column_filter = from_json_string_recurse( column_filter ) if len( column_filter ) == 1: column_filter = column_filter[0] + # If filter criterion is empty, do nothing. + if column_filter == '': + continue # Update query. query = column.filter( trans.sa_session, query, column_filter ) # Upate current filter dict. diff -r f4c2bf76b2e2 -r fb7dd12ea39c static/images/mag_glass.png Binary file static/images/mag_glass.png has changed diff -r f4c2bf76b2e2 -r fb7dd12ea39c templates/grid_base.mako --- a/templates/grid_base.mako Wed Nov 18 10:57:24 2009 -0500 +++ b/templates/grid_base.mako Wed Nov 18 11:51:09 2009 -0500 @@ -62,6 +62,21 @@ t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); } + + // Initialize submit image elements. + $('.submit-image').each( function() + { + // On mousedown, add class to simulate click. + $(this).mousedown( function() { + $(this).addClass('gray-background'); + }); + + // On mouseup, add class to simulate click. + $(this).mouseup( function() { + $(this).removeClass('gray-background'); + }); + + }); }); ## Can this be moved into base.mako? %if refresh_frames: @@ -168,6 +183,26 @@ text-align: center; display: inline-block; } + .submit-image { + vertical-align: text-bottom; + margin: 0; + padding: 0; + } + .no-padding-or-margin { + margin: 0; + padding: 0; + } + .gray-background { + background-color: #DDDDDD; + } + .text-filter-val { + border: solid 1px #AAAAAA; + padding: 1px 3px 1px 3px; + margin-right: 5px; + -moz-border-radius: .5em; + -webkit-border-radius: .5em; + font-style: italic; + } </style> </%def> diff -r f4c2bf76b2e2 -r fb7dd12ea39c templates/grid_common.mako --- a/templates/grid_common.mako Wed Nov 18 10:57:24 2009 -0500 +++ b/templates/grid_common.mako Wed Nov 18 11:51:09 2009 -0500 @@ -32,10 +32,11 @@ <% column_filter = cur_filter_dict[column.key] %> %if isinstance( column_filter, basestring ): %if column_filter != "All": - <span style="font-style: italic">${cur_filter_dict[column.key]}</span> - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - | + <span class='text-filter-val'> + ${cur_filter_dict[column.key]} + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + </span> %endif %elif isinstance( column_filter, list ): %for i, filter in enumerate( column_filter ): @@ -53,7 +54,9 @@ %endif %endif - <span><input id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/></span> + <span> + <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/> + <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/></span> </form> %else: %for i, filter in enumerate( column.get_accepted_filters() ):

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[hg] galaxy 3104: Another tweak to cloud table order
by Greg Von Kuster 23 Nov '09

23 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2beaa0783b69 changeset: 3104:2beaa0783b69 user: James Taylor <james(a)jamestaylor.org> date: Wed Nov 18 10:47:14 2009 -0500 description: Another tweak to cloud table order diffstat: lib/galaxy/model/migrate/versions/0026_cloud_tables.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (14 lines): diff -r cffcf1cae94c -r 2beaa0783b69 lib/galaxy/model/migrate/versions/0026_cloud_tables.py --- a/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:43:08 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0026_cloud_tables.py Wed Nov 18 10:47:14 2009 -0500 @@ -138,9 +138,9 @@ CloudImage_table.create() UCI_table.create() + CloudInstance_table.create() CloudStore_table.create() CloudSnapshot_table.create() - CloudInstance_table.create() def downgrade(): metadata.reflect()

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