- galaxy-commits - lists.galaxyproject.org

[hg] galaxy 3735: Enable users not logged in to view a shared/ac...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c75c0f9b0bf7 changeset: 3735:c75c0f9b0bf7 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon May 03 16:32:35 2010 -0400 description: Enable users not logged in to view a shared/accessible/published visualization. diffstat: lib/galaxy/web/base/controller.py | 3 ++- lib/galaxy/web/controllers/tracks.py | 21 ++++++++++++++------- lib/galaxy/web/framework/__init__.py | 5 +++++ templates/tracks/browser.mako | 2 +- templates/visualization/display.mako | 2 +- 5 files changed, 23 insertions(+), 10 deletions(-) diffs (105 lines): diff -r 5ebac527fa31 -r c75c0f9b0bf7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon May 03 15:33:34 2010 -0400 +++ b/lib/galaxy/web/base/controller.py Mon May 03 16:32:35 2010 -0400 @@ -208,7 +208,8 @@ if dbkey is None: dbkey = dataset.dbkey # Hack for backward compat ## TODO: chrom needs to be able to be set; right now it's empty. - config = { "title": visualization.title, "vis_id": id, "tracks": tracks, "chrom": "", "dbkey": dbkey } + config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), + "tracks": tracks, "chrom": "", "dbkey": dbkey } return config diff -r 5ebac527fa31 -r c75c0f9b0bf7 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Mon May 03 15:33:34 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon May 03 16:32:35 2010 -0400 @@ -72,7 +72,7 @@ .filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) \ .filter( model.Dataset.state != "error") -class TracksController( BaseController ): +class TracksController( BaseController, UsesVisualization ): """ Controller for track browser interface. Handles building a new browser from datasets in the current history, and display of the resulting browser. @@ -158,8 +158,7 @@ return trans.fill_template( 'tracks/browser.mako', config=config ) @web.json - @web.require_login() - def chroms(self, trans, dbkey=None ): + def chroms(self, trans, vis_id=None ): """ Returns a naturally sorted list of chroms/contigs for the given dbkey """ @@ -171,18 +170,26 @@ def split_by_number(s): return [ check_int(c) for c in re.split('([0-9]+)', s) ] - - chroms = self._chroms( trans, dbkey ) + + # Get visualization and config. + visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True ) + visualization.config = self.get_visualization_config( trans, visualization ) + if visualization is None: + raise web.httpexceptions.HTTPNotFound() + + # Get chroms data. + chroms = self._chroms( trans, visualization ) to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()] to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) )) return to_sort - def _chroms( self, trans, dbkey ): + def _chroms( self, trans, visualization ): """ Called by the browser to get a list of valid chromosomes and lengths """ # If there is any dataset in the history of extension `len`, this will use it - user = trans.get_user() + user = visualization.user + dbkey = visualization.config['dbkey'] if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) if dbkey in user_keys: diff -r 5ebac527fa31 -r c75c0f9b0bf7 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon May 03 15:33:34 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Mon May 03 16:32:35 2010 -0400 @@ -675,6 +675,11 @@ """ Returns the db_file dataset associated/needed by `dataset`, or `None`. """ + + # If no history, return None. + if self.history is None: + return None + datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=self.history.id, extension="len" ) for ds in datasets: diff -r 5ebac527fa31 -r c75c0f9b0bf7 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Mon May 03 15:33:34 2010 -0400 +++ b/templates/tracks/browser.mako Mon May 03 16:32:35 2010 -0400 @@ -272,7 +272,7 @@ $.ajax({ url: "${h.url_for( action='chroms' )}", - data: { dbkey: view.dbkey }, + data: { vis_id: view.vis_id }, dataType: "json", success: function ( data ) { view.chrom_data = data; diff -r 5ebac527fa31 -r c75c0f9b0bf7 templates/visualization/display.mako --- a/templates/visualization/display.mako Mon May 03 15:33:34 2010 -0400 +++ b/templates/visualization/display.mako Mon May 03 16:32:35 2010 -0400 @@ -124,7 +124,7 @@ $.ajax({ ## JG: added controller name url: "${h.url_for( controller='/tracks', action='chroms' )}", - data: { dbkey: view.dbkey }, + data: { vis_id: view.vis_id }, dataType: "json", success: function ( data ) { view.chrom_data = data;

1 0

[hg] galaxy 3733: Pack scripts.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8bdbd5fc8721 changeset: 3733:8bdbd5fc8721 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon May 03 14:03:01 2010 -0400 description: Pack scripts. diffstat: static/scripts/packed/trackster.js | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (8 lines): diff -r 2cf1ad5edaa6 -r 8bdbd5fc8721 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Mon May 03 14:02:08 2010 -0400 +++ b/static/scripts/packed/trackster.js Mon May 03 14:03:01 2010 -0400 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,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 Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_hi! gh=0;this.center=(this.max_high-this.max_low)/2;this.zoom_factor=3;thi s.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.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();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},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)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.hi! gh-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:funct ion(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NO! CONVERTER)}else{if(d.data&&d.data.length===0||d.data===null){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");a.enabled=true;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=$("<div style='position: relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;! var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b}) ;k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.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,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("! #track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval"). val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px"});d.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;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,q,c,e){if(this.vert! ical_range===undefined){return}var r=q*DENSITY*o,a=DENSITY*o,b=$("<canvas class='tile'></canvas>"),u=o+"_"+q;if(this.data_cache.get(u)===undefined){this.get_data(o,q);return}var t=this.data_cache.get(u);if(t===null){return}b.css({position:"absolute",top:0,left:(r-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,s=this.total_frequency,d=this.height_px;n.beginPath();if(t.length>1){var f=Math.ceil((t[1][0]-t[0][0])*e)}else{var f=10}for(var p=0;p<t.length;p++){var j=t[p][0]-r;var h=t[p][1];if(this.prefs.mode=="Intensity"){if(h===null){continue}j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(j,0,f,this.height_px)}else{if(h===null){k=false;continue}else{j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/m*d);if(k){n.lineTo(j,h)}else{n.moveTo(j,h);k=true}}}}n.stroke();c! .append(b);return b},gen_options:function(n){var a=$("<div></div>").ad dClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_val! ue||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_! color=b.block_color}if(b.label_color!==undefined){this.prefs.label_col or=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h! =Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else! {n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,a k){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}! else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5! ][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}} else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);i! f(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label>").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").appen! d(b).append(c);return a.append(k).append(l).append(g).append(h).append (d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file +var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/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="/static/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="/static/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 Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.m! ax_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;th is.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.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();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},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)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=! a/b.width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redr aw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d==="no converter"){a.container_div.addClass("error");a.cont! ent_div.text(DATA_NOCONVERTER)}else{if(d.data&&d.data.length===0||d.data===null){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");a.enabled=true;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=$("<div style='position: relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c! ){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_of fset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.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,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.ma! x_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#t rack_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px"});d.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;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o! ,q,c,e){if(this.vertical_range===undefined){return}var r=q*DENSITY*o,a=DENSITY*o,b=$("<canvas class='tile'></canvas>"),u=o+"_"+q;if(this.data_cache.get(u)===undefined){this.get_data(o,q);return}var t=this.data_cache.get(u);if(t===null){return}b.css({position:"absolute",top:0,left:(r-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,s=this.total_frequency,d=this.height_px;n.beginPath();if(t.length>1){var f=Math.ceil((t[1][0]-t[0][0])*e)}else{var f=10}for(var p=0;p<t.length;p++){var j=t[p][0]-r;var h=t[p][1];if(this.prefs.mode=="Intensity"){if(h===null){continue}j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(j,0,f,this.height_px)}else{if(h===null){k=false;continue}else{j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/m*d);if(k){n.lineTo(j,h)}else{n.moveTo(j,h);k=! true}}}}n.stroke();c.append(b);return b},gen_options:function(n){var a =$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!! ==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefine! d){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){ this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[! a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_! offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_t ile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q! [1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak! ,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillR ect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillR! ect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label>").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$(! "<div></div>").append(b).append(c);return a.append(k).append(l).append (g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file

1 0

[hg] galaxy 3732: Enable viewing of shared/accessible/published ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/2cf1ad5edaa6 changeset: 3732:2cf1ad5edaa6 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon May 03 14:02:08 2010 -0400 description: Enable viewing of shared/accessible/published visualizations. diffstat: lib/galaxy/web/base/controller.py | 38 ++++ lib/galaxy/web/controllers/visualization.py | 8 +- static/scripts/trackster.js | 8 +- templates/visualization/display.mako | 219 +++++++++++++++++++++++++++- 4 files changed, 263 insertions(+), 10 deletions(-) diffs (349 lines): diff -r 5f93447d642d -r 2cf1ad5edaa6 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon May 03 09:42:51 2010 -0400 +++ b/lib/galaxy/web/base/controller.py Mon May 03 14:02:08 2010 -0400 @@ -7,6 +7,7 @@ from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.workflow.modules import * +from galaxy.web.framework import simplejson from Cheetah.Template import Template @@ -164,6 +165,7 @@ class UsesVisualization( SharableItemSecurity ): """ Mixin for controllers that use Visualization objects. """ + def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a Visualization from the database by id, verifying ownership. """ # Load workflow from database @@ -173,6 +175,42 @@ error( "Visualization not found" ) else: return self.security_check( trans.get_user(), visualization, check_ownership, check_accessible ) + + def get_visualization_config( self, trans, visualization ): + """ Returns a visualization's configuration. Only works for trackster visualizations right now. """ + + config = None + if visualization.type == 'trackster': + # Trackster config; taken from tracks/browser + latest_revision = visualization.latest_revision + tracks = [] + + try: + dbkey = latest_revision.config['dbkey'] + except KeyError: + dbkey = None + + hda_query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) + for t in visualization.latest_revision.config['tracks']: + dataset_id = t['dataset_id'] + try: + prefs = t['prefs'] + except KeyError: + prefs = {} + dataset = hda_query.get( dataset_id ) + track_type, _ = dataset.datatype.get_track_type() + tracks.append( { + "track_type": track_type, + "name": dataset.name, + "dataset_id": dataset.id, + "prefs": simplejson.dumps(prefs), + } ) + if dbkey is None: dbkey = dataset.dbkey # Hack for backward compat + + ## TODO: chrom needs to be able to be set; right now it's empty. + config = { "title": visualization.title, "vis_id": id, "tracks": tracks, "chrom": "", "dbkey": dbkey } + + return config class UsesStoredWorkflow( SharableItemSecurity ): """ Mixin for controllers that use StoredWorkflow objects. """ diff -r 5f93447d642d -r 2cf1ad5edaa6 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py Mon May 03 09:42:51 2010 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Mon May 03 14:02:08 2010 -0400 @@ -256,9 +256,13 @@ visualization = trans.sa_session.query( model.Visualization ).filter_by( user=user, slug=slug, deleted=False ).first() if visualization is None: raise web.httpexceptions.HTTPNotFound() + # Security check raises error if user cannot access visualization. - self.security_check( trans.get_user(), visualization, False, True) - return trans.fill_template_mako( "visualization/display.mako", item=visualization, item_data=None, content_only=True ) + self.security_check( trans.get_user(), visualization, False, True) + + # Display. + visualization_config = self.get_visualization_config( trans, visualization ) + return trans.fill_template_mako( "visualization/display.mako", item=visualization, item_data=visualization_config, content_only=True ) @web.expose @web.json diff -r 5f93447d642d -r 2cf1ad5edaa6 static/scripts/trackster.js --- a/static/scripts/trackster.js Mon May 03 09:42:51 2010 -0400 +++ b/static/scripts/trackster.js Mon May 03 14:02:08 2010 -0400 @@ -17,22 +17,22 @@ RIGHT_STRAND, LEFT_STRAND; var right_img = new Image(); -right_img.src = "../images/visualization/strand_right.png"; +right_img.src = "/static/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.src = "/static/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.src = "/static/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.src = "/static/images/visualization/strand_left_inv.png"; left_img_inv.onload = function() { LEFT_STRAND_INV = CONTEXT.createPattern(left_img_inv, "repeat"); }; diff -r 5f93447d642d -r 2cf1ad5edaa6 templates/visualization/display.mako --- a/templates/visualization/display.mako Mon May 03 09:42:51 2010 -0400 +++ b/templates/visualization/display.mako Mon May 03 14:02:08 2010 -0400 @@ -2,18 +2,229 @@ <%def name="javascripts()"> ${parent.javascripts()} - ## Need visualization JS. + ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "trackster", "ui.core", "ui.sortable" )} + + ## HACK: set config as item_data. + <% config = item_data %> + + ## TODO: Copied from browser.mako -- probably should create JS file for visualization code and include visualization JS above. + <script type="text/javascript"> + + ## JG: add controller name. + var data_url = "${h.url_for( controller='/tracks', action='data' )}"; + var view; + + $(function() { + + %if config: + view = new View( "${config.get('chrom')}", "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); + %for track in config.get('tracks'): + view.add_track( + new ${track["track_type"]}( "${track['name'] | h}", ${track['dataset_id']}, ${track['prefs']} ) + ); + %endfor + init(); + %else: + continue_fn = function() { + view = new View( undefined, $("#new-title").val(), undefined, $("#new-dbkey").val() ); + init(); + hide_modal(); + }; + $.ajax({ + url: "${h.url_for( action='new_browser' )}", + data: {}, + error: function() { alert( "Couldn't create new browser" ) }, + success: function(form_html) { + show_modal("New Track Browser", form_html, { + "Cancel": function() { window.location = "/"; }, + "Continue": function() { $(document).trigger("convert_dbkeys"); continue_fn(); } + }); + $("#new-title").focus(); + replace_big_select_inputs(); + } + }); + %endif + + // Execute this when everything is ready + function init() { + $("ul#sortable-ul").sortable({ + update: function(event, ui) { + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + } + } + }); + + $(document).bind( "redraw", function( e ) { + view.redraw(); + }); + + $("#content").bind("mousewheel", function( e, delta ) { + if (delta > 0) { + view.zoom_in(e.pageX, $("#viewport-container")); + } else { + view.zoom_out(); + } + e.preventDefault(); + }); + + $("#content").bind("dblclick", function( e ) { + view.zoom_in(e.pageX, $("#viewport-container")); + }); + + // To let the overview box be draggable + $("#overview-box").bind("dragstart", function( e ) { + this.current_x = e.offsetX; + }).bind("drag", function( e ) { + var delta = e.offsetX - this.current_x; + this.current_x = e.offsetX; + + var delta_chrom = Math.round(delta / $(document).width() * view.span); + view.center += delta_chrom; + view.redraw(); + }); + + // To adjust the size of the viewport to fit the fixed-height footer + var refresh = function( e ) { + $("#viewport-container").height( $(window).height() - 120 ); + $("#nav-container").width( $("#center").width() ); + view.redraw(); + }; + $(window).bind( "resize", function(e) { refresh(e); } ); + $("#right-border").bind( "click", function(e) { refresh(e); } ); + $("#right-border").bind( "dragend", function(e) { refresh(e); } ); + $(window).trigger( "resize" ); + + $("#viewport-container").bind( "dragstart", function( e ) { + this.original_low = view.low; + this.current_height = e.clientY; + this.current_x = e.offsetX; + }).bind( "drag", function( e ) { + var container = $(this); + var delta = e.offsetX - this.current_x; + var new_scroll = container.scrollTop() - (e.clientY - this.current_height); + if ( new_scroll < container.get(0).scrollHeight - container.height() ) { + container.scrollTop(new_scroll); + } + this.current_height = e.clientY; + this.current_x = e.offsetX; + + var delta_chrom = Math.round(delta / $(document).width() * (view.high - view.low)); + view.center -= delta_chrom; + view.redraw(); + }); + + ## JG: Removed 'add-track' init code. + + ## JG: Removed 'save-button' init code + + view.add_label_track( new LabelTrack( $("#top-labeltrack" ) ) ); + view.add_label_track( new LabelTrack( $("#nav-labeltrack" ) ) ); + + $.ajax({ + ## JG: added controller name + url: "${h.url_for( controller='/tracks', action='chroms' )}", + data: { dbkey: view.dbkey }, + dataType: "json", + success: function ( data ) { + view.chrom_data = data; + var chrom_options = '<option value="">Select Chrom/Contig</option>'; + for (i in data) { + var chrom = data[i]['chrom'] + chrom_options += '<option value="' + chrom + '">' + chrom + '</option>'; + } + $("#chrom").html(chrom_options); + $("#chrom").bind( "change", function () { + view.chrom = $("#chrom").val(); + var found = $.grep(view.chrom_data, function(v, i) { + return v.chrom === view.chrom; + })[0]; + view.max_high = found.len; + view.reset(); + view.redraw(true); + + for (var track_id in view.tracks) { + var track = view.tracks[track_id]; + if (track.init) { + track.init(); + } + } + view.redraw(); + }); + }, + error: function() { + alert( "Could not load chroms for this dbkey:", view.dbkey ); + } + }); + + ## JG: Removed function sidebar_box() and sidebar init code. + + $(window).trigger("resize"); + }; + + }); + + </script> + </%def> <%def name="stylesheets()"> ${parent.stylesheets()} - ## Need visualization CSS. + + ${h.css( "history" )} + <link rel="stylesheet" type="text/css" href="${h.url_for('/static/trackster.css')}" /> + + <style type="text/css"> + ul#sortable-ul { + list-style: none; + padding: 0; + margin: 5px; + } + ul#sortable-ul li { + display: block; + margin: 5px 0; + background: #eee; + } + </style> </%def> <%def name="render_item_links( visualization )"> ## TODO </%def> -<%def name="render_item( visualization, visualization_data )"> - ## TODO +<%def name="render_item( visualization, config )"> + <br><br> + ## Copied from center_panel() in browser.mako -- probably need to create visualization_common.mako to render view. + <div id="content"> + <div id="top-labeltrack"></div> + <div id="viewport-container" style="overflow-x: hidden; overflow-y: auto;"> + <div id="viewport"></div> + </div> + </div> + <div id="nav-container" style="width:100%;"> + <div id="nav-labeltrack"></div> + <div id="nav"> + <div id="overview"> + <div id="overview-viewport"> + <div id="overview-box"></div> + </div> + </div> + <div id="nav-controls"> + <form action="#"> + <select id="chrom" name="chrom" style="width: 15em;"> + <option value="">Loading</option> + </select> + <input id="low" size="12" />:<input id="high" size="12" /> + <input type="hidden" name="id" value="${config.get('vis_id', '')}" /> + <a href="#" onclick="javascript:view.zoom_in();view.redraw();"> + <img src="${h.url_for('/static/images/fugue/magnifier-zoom.png')}" /> + </a> + <a href="#" onclick="javascript:view.zoom_out();view.redraw();"> + <img src="${h.url_for('/static/images/fugue/magnifier-zoom-out.png')}" /> + </a> + </form> + <div id="debug" style="float: right"></div> + </div> + </div> + </div> </%def> \ No newline at end of file

1 0

[hg] galaxy 3731: forms default value bug fixed
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5f93447d642d changeset: 3731:5f93447d642d user: rc date: Mon May 03 09:42:51 2010 -0400 description: forms default value bug fixed diffstat: lib/galaxy/web/controllers/forms.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r e12587356892 -r 5f93447d642d lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon May 03 09:34:13 2010 -0400 +++ b/lib/galaxy/web/controllers/forms.py Mon May 03 09:42:51 2010 -0400 @@ -565,7 +565,7 @@ # helptext self.helptext.value = field['helptext'] # default value - self.default.value = field.get('default', TextField('field_default_'+str(index), 40, '')) + self.default.value = field.get('default', '') # type self.fieldtype = SelectField('field_type_'+str(self.index), refresh_on_change=True,

1 0

[hg] galaxy 3730: lims:
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e12587356892 changeset: 3730:e12587356892 user: rc date: Mon May 03 09:34:13 2010 -0400 description: lims: request page now shows a msg if the request has library selected forms default value bug fixed diffstat: lib/galaxy/model/__init__.py | 6 ++++++ lib/galaxy/web/controllers/forms.py | 4 ++-- templates/admin/requests/show_request.mako | 6 ++++++ 3 files changed, 14 insertions(+), 2 deletions(-) diffs (53 lines): diff -r a367a7cd53bb -r e12587356892 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Sun May 02 15:34:41 2010 -0400 +++ b/lib/galaxy/model/__init__.py Mon May 03 09:34:13 2010 -0400 @@ -1448,6 +1448,12 @@ return self.state() == self.states.NEW def complete(self): return self.state() == self.states.COMPLETE + def sequence_run_ready(self): + samples = [] + for s in self.samples: + if not s.library: + samples.append(s.name) + return samples class RequestEvent( object ): diff -r a367a7cd53bb -r e12587356892 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Sun May 02 15:34:41 2010 -0400 +++ b/lib/galaxy/web/controllers/forms.py Mon May 03 09:34:13 2010 -0400 @@ -469,7 +469,7 @@ 'required': row[3], 'type': row[4], 'selectlist': options, - 'default': row[7]}) + 'default': row[6]}) except: return trans.response.send_redirect( web.url_for( controller='forms', action='new', @@ -565,7 +565,7 @@ # helptext self.helptext.value = field['helptext'] # default value - self.default.value = field['default'] + self.default.value = field.get('default', TextField('field_default_'+str(index), 40, '')) # type self.fieldtype = SelectField('field_type_'+str(self.index), refresh_on_change=True, diff -r a367a7cd53bb -r e12587356892 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Sun May 02 15:34:41 2010 -0400 +++ b/templates/admin/requests/show_request.mako Mon May 03 09:34:13 2010 -0400 @@ -108,6 +108,12 @@ document.onkeypress = stopRKey </script> +%if request.submitted(): + <% samples_not_ready = request.sequence_run_ready() %> + %if samples_not_ready: + ${render_msg( "Select a target library and folder for all the samples before starting the sequence run", "warning" )} + %endif +%endif %if request.rejected(): ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}

1 0

[hg] galaxy 3729: Bug fixes for history import: (a) import can n...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a367a7cd53bb changeset: 3729:a367a7cd53bb user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun May 02 15:34:41 2010 -0400 description: Bug fixes for history import: (a) import can now be used by users who have access via sharing and (b) import changes the current history to the imported history. Functional tests updated to reflect new functionality and error messages. diffstat: lib/galaxy/web/controllers/history.py | 9 +++------ test/functional/test_history_functions.py | 9 +++++++-- 2 files changed, 10 insertions(+), 8 deletions(-) diffs (56 lines): diff -r 3ac0dfcdf44e -r a367a7cd53bb lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Apr 30 18:26:49 2010 -0400 +++ b/lib/galaxy/web/controllers/history.py Sun May 02 15:34:41 2010 -0400 @@ -513,7 +513,6 @@ """Import another user's history via a shared URL""" msg = "" user = trans.get_user() - user_history = trans.get_history() # Set referer message if 'referer' in kwd: referer = kwd['referer'] @@ -527,11 +526,9 @@ # Do import. if not id: return trans.show_error_message( "You must specify a history you want to import.<br>You can %s." % referer_message, use_panels=True ) - import_history = self.get_history( trans, id, check_ownership=False ) + import_history = self.get_history( trans, id, check_ownership=False, check_accessible=True ) if not import_history: return trans.show_error_message( "The specified history does not exist.<br>You can %s." % referer_message, use_panels=True ) - if not import_history.importable: - return trans.show_error_message( "The owner of this history has disabled imports via this link.<br>You can %s." % referer_message, use_panels=True ) if user: if import_history.user_id == user.id: return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) @@ -548,8 +545,8 @@ new_history.add_galaxy_session( galaxy_session, association=association ) trans.sa_session.add( new_history ) trans.sa_session.flush() - if not user_history.datasets: - trans.set_history( new_history ) + # Set imported history to be user's current history. + trans.set_history( new_history ) return trans.show_ok_message( message="""History "%s" has been imported. <br>You can <a href="%s">start using this history</a> or %s.""" % ( new_history.name, web.url_for( '/' ), referer_message ), use_panels=True ) diff -r 3ac0dfcdf44e -r a367a7cd53bb test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Fri Apr 30 18:26:49 2010 -0400 +++ b/test/functional/test_history_functions.py Sun May 02 15:34:41 2010 -0400 @@ -196,10 +196,15 @@ self.disable_access_via_link( self.security.encode_id( history3.id ), check_str='Anyone can view and import this history', check_str_after_submit='Make History Accessible via Link' ) - # Try importing history3 after disabling access via link. + # Try importing history3 after disabling access via link. To do this, need to login as regular user 2, who cannot access + # history via sharing or via link. + self.logout() + self.login( email=regular_user2.email ) self.import_history_via_url( self.security.encode_id( history3.id ), admin_user.email, - check_str_after_submit='The owner of this history has disabled imports via this link.' ) + check_str_after_submit='History is not accessible to current user' ) + self.logout() + self.login( email=admin_user.email ) # Test sharing history3 with an invalid user self.share_current_history( 'jack(a)jill.com', check_str_after_submit='jack(a)jill.com is not a valid Galaxy user.' )

1 0

[hg] galaxy 3728: merge
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3ac0dfcdf44e changeset: 3728:3ac0dfcdf44e user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 30 18:26:49 2010 -0400 description: merge diffstat: lib/galaxy/web/framework/__init__.py | 4 +- lib/galaxy/webapps/community/controllers/admin.py | 385 +++++++-- lib/galaxy/webapps/community/controllers/common.py | 105 ++- lib/galaxy/webapps/community/controllers/tool.py | 293 +++++-- lib/galaxy/webapps/community/controllers/upload.py | 68 +- lib/galaxy/webapps/community/model/__init__.py | 7 +- lib/galaxy/webapps/community/model/mapping.py | 14 +- lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py | 3 +- lib/galaxy/webapps/community/security/__init__.py | 6 + templates/webapps/community/admin/index.mako | 43 +- templates/webapps/community/category/edit_category.mako | 44 + templates/webapps/community/category/rename_category.mako | 44 - templates/webapps/community/index.mako | 64 +- templates/webapps/community/tool/browse_tool.mako | 37 - templates/webapps/community/tool/edit_tool.mako | 3 +- templates/webapps/community/tool/view_tool.mako | 58 +- templates/webapps/community/upload/upload.mako | 3 + tools/samtools/sam_to_bam.py | 2 +- tools/sr_mapping/bowtie_wrapper.py | 4 +- tools/sr_mapping/bwa_wrapper_code.py | 9 +- 20 files changed, 883 insertions(+), 313 deletions(-) diffs (1884 lines): diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Apr 30 18:26:49 2010 -0400 @@ -66,7 +66,7 @@ decorator.exposed = True return decorator -def require_login( verb="perform this action", use_panels=False ): +def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ): def argcatcher( func ): def decorator( self, trans, *args, **kwargs ): if trans.get_user(): @@ -74,7 +74,7 @@ else: return trans.show_error_message( 'You must be <a target="_top" href="%s">logged in</a> to %s</div>.' - % ( url_for( controller='user', action='login' ), verb ), use_panels=use_panels ) + % ( url_for( controller='user', action='login', webapp=webapp ), verb ), use_panels=use_panels ) return decorator return argcatcher diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 18:26:49 2010 -0400 @@ -2,7 +2,7 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids -from common import get_categories, get_category +from common import get_categories, get_category, get_tools, get_event, get_tool, get_versions import logging log = logging.getLogger( __name__ ) @@ -18,13 +18,6 @@ if user.username: return user.username return 'not set' - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.purged: - return "purged" - elif user.deleted: - return "deleted" - return "" class GroupsColumn( grids.GridColumn ): def get_value( self, trans, grid, user ): if user.groups: @@ -45,6 +38,16 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.purged: + return "purged" + elif user.deleted: + return "deleted" + return "" + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) # Grid definition webapp = "community" @@ -69,6 +72,10 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + ToolsColumn( "Uploaded Tools", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -200,7 +207,7 @@ return None def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( model.Role.type != model.Role.types.PRIVATE ) class GroupListGrid( grids.Grid ): @@ -280,34 +287,31 @@ def build_initial_query( self, session ): return session.query( self.model_class ) -class CategoryListGrid( grids.Grid ): +class ManageCategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, category ): - if category.deleted: - return "deleted" - return "" # Grid definition webapp = "community" - title = "Categories" + title = "Manage Categories" model_class = model.Category template='/webapps/community/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Edit category", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Edit", id=item.id, webapp="community" ) ), model_class=model.Category, - attach_popup=True, + attach_popup=False, filterable="advanced" ), - DescriptionColumn( "Description", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -318,13 +322,9 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new category", - dict( controller='admin', action='categories', operation='create', webapp="community" ) ) + dict( controller='admin', action='manage_categories', operation='create', webapp="community" ) ) ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( webapp="community", action="rename_category" ) ), - grids.GridOperation( "Delete", + operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, url_args=dict( webapp="community", action="mark_category_deleted" ) ), @@ -349,16 +349,77 @@ def build_initial_query( self, session ): return session.query( self.model_class ) +class ToolsByCategoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + return len( category.tools ) + return 0 + + # Grid definition + webapp = "community" + title = "Tools by Category" + model_class = model.Category + template='/webapps/community/category/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), + model_class=model.Category, + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans ): + return None + def build_initial_query( self, session ): + return session.query( self.model_class ) + class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval = '%s%s<br/>' % ( rval, tca.category.name ) + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -389,7 +450,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.email + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -402,36 +463,39 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='admin', webapp="community" ) ), attach_popup=True, filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), CategoryColumn( "Category", - key="category", model_class=model.Category, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", + StateColumn( "Status", model_class=model.Event, - attach_popup=False, - filterable="advanced" ), + attach_popup=False ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", model_class=model.Tool, key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Upload tool", dict( controller='upload', action='upload', type='tool' ) ) - ] operations = [ grids.GridOperation( "Edit information", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ), - grids.GridOperation( "Manage categories", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( controller="common", action="manage_categories", cntrller="admin", webapp="community" ) ) + url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ) ] standard_filters = [ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -443,57 +507,128 @@ use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): + tool_id = kwd.get( 'tool_id', False ) + if tool_id: + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) return query.filter( self.model_class.deleted==False ) -class AdminCommunity( BaseController, Admin ): +class AdminController( BaseController, Admin ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() - category_list_grid = CategoryListGrid() + manage_category_list_grid = ManageCategoryListGrid() + tools_by_category_list_grid = ToolsByCategoryListGrid() tool_list_grid = ToolListGrid() @web.expose @web.require_admin - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) + # Render the list view + return self.tool_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_category( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return self.browse_category( trans, id=kwd['id'] ) + # Render the list view + return self.tools_by_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_user( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='admin', - **kwargs ) ) - elif operation == "view tool": - return trans.response.send_redirect( web.url_for( controller='common', - action='view_tool', - cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) # Render the list view - return self.tool_list_grid( trans, **kwargs ) + return self.tool_list_grid( trans, **kwd ) @web.expose @web.require_admin - def categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def manage_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "create": - return self.create_category( trans, **kwargs ) + return self.create_category( trans, **kwd ) if operation == "delete": - return self.mark_category_deleted( trans, **kwargs ) + return self.mark_category_deleted( trans, **kwd ) if operation == "undelete": - return self.undelete_category( trans, **kwargs ) + return self.undelete_category( trans, **kwd ) if operation == "purge": - return self.purge_category( trans, **kwargs ) - if operation == "rename": - return self.rename_category( trans, **kwargs ) + return self.purge_category( trans, **kwd ) + if operation == "edit": + return self.edit_category( trans, **kwd ) # Render the list view - return self.category_list_grid( trans, **kwargs ) - + return self.manage_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_state( self, trans, state=None, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if state is None: + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a status', + status='error' ) ) + event = get_event( trans, id ) + state = event.state + tool_id = get_tools_by_state( trans, state ) + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + tool_id=tool_id ) ) + @web.expose + @web.require_admin + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) @web.expose @web.require_admin def create_category( self, trans, **kwd ): @@ -515,7 +650,7 @@ message = "Category '%s' has been created" % category.name trans.sa_session.flush() trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -530,42 +665,76 @@ status=status ) @web.expose @web.require_admin - def rename_category( self, trans, **kwd ): + def set_tool_state( self, trans, state, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + redirect = params.get( 'no_redirect', True ) + id = params.get( 'id', None ) + if not id: + message = "No tool id received for setting status" + status = 'error' + else: + tool = get_tool( trans, id ) + if state == trans.app.model.Tool.states.APPROVED: + # If we're approving a tool, all previous versions must be set to archived + for version in get_versions( trans, tool ): + if version != tool and version.is_approved(): + self.set_tool_state( trans, trans.app.model.Tool.states.ARCHIVED, id=trans.app.security.encode_id( version.id ), redirect='False' ) + event = trans.model.Event( state ) + # Flush so we an get an id + trans.sa_session.add( event ) + trans.sa_session.flush() + tea = trans.model.ToolEventAssociation( tool, event ) + trans.sa_session.add( tea ) + trans.sa_session.flush() + message = "State of tool '%s' is now %s" % ( tool.name, state ) + if redirect: + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + webapp=webapp, + message=message, + status=status ) ) + @web.expose + @web.require_admin + def edit_category( self, trans, **kwd ): params = util.Params( kwd ) webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) id = params.get( 'id', None ) if not id: - message = "No category ids received for renaming" + message = "No category ids received for editing" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) category = get_category( trans, id ) - if params.get( 'rename_category_button', False ): + if params.get( 'edit_category_button', False ): old_name = category.name new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) - if not new_name: - message = 'Enter a valid name' - status = 'error' - elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): - message = 'A category with that name already exists' - status = 'error' + if old_name != new_name: + if not new_name: + message = 'Enter a valid name' + status = 'error' + elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): + message = 'A category with that name already exists' + status = 'error' else: category.name = new_name category.description = new_description trans.sa_session.add( category ) trans.sa_session.flush() - message = "Category '%s' has been renamed to '%s'" % ( old_name, new_name ) + message = "The information has been saved for category '%s'" % ( new_name ) return trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - return trans.fill_template( '/webapps/community/category/rename_category.mako', + return trans.fill_template( '/webapps/community/category/edit_category.mako', category=category, webapp=webapp, message=message, @@ -579,7 +748,7 @@ if not id: message = "No category ids received for deleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -592,7 +761,7 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -605,7 +774,7 @@ if not id: message = "No category ids received for undeleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -617,7 +786,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be undeleted." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -628,7 +797,7 @@ undeleted_categories += " %s" % category.name message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -644,7 +813,7 @@ if not id: message = "No category ids received for purging" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -655,7 +824,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be purged." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -665,7 +834,41 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) + +## ---- Utility methods ------------------------------------------------------- + +def get_tools_by_state( trans, state ): + tool_id = [] + if state == trans.model.Tool.states.NEW: + for tool in get_tools( trans ): + if tool.is_new(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ERROR: + for tool in get_tools( trans ): + if tool.is_error(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.DELETED: + for tool in get_tools( trans ): + if tool.is_deleted(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.WAITING: + for tool in get_tools( trans ): + if tool.is_waiting(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.APPROVED: + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.REJECTED: + for tool in get_tools( trans ): + if tool.is_rejected(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ARCHIVED: + for tool in get_tools( trans ): + if tool.is_archived(): + tool_id.append( tool.id ) + return tool_id diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 18:26:49 2010 -0400 @@ -8,7 +8,7 @@ import logging log = logging.getLogger( __name__ ) -class CommunityCommon( BaseController ): +class CommonController( BaseController ): @web.expose def edit_tool( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -81,9 +81,11 @@ tool = get_tool( trans, id ) categories = [ tca.category for tca in tool.categories ] tool_file_contents = tarfile.open( tool.file_name, 'r' ).getnames() + versions = get_versions( trans, tool ) return trans.fill_template( '/webapps/community/tool/view_tool.mako', tool=tool, tool_file_contents=tool_file_contents, + versions=versions, categories=categories, cntrller=cntrller, message=message, @@ -100,22 +102,78 @@ message='Select a tool to to upload a new version', status='error' ) ) tool = get_tool( trans, id ) - if params.save_button and ( params.file_data != '' or params.url != '' ): - # TODO: call the upload method in the upload controller. - message = 'Uploading new version not implemented' - status = 'error' + return trans.response.send_redirect( web.url_for( controller='upload', + action='upload', + message=message, + status=status, + replace_id=id ) ) + @web.expose + def browse_category( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_categories', + message='Select a category', + status='error' ) ) + category = get_category( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool in addition to the category. + if cntrller == 'tool': + tool_id = get_approved_tools( trans, category=category ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tca.tool.id for tca in category.tools ] + if not tool_id: + tool_id = 'None' return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_tools', - message='Not yet implemented, sorry...', - status='error' ) ) + tool_id=tool_id ) ) + @web.expose + def browse_tools_by_user( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a user', + status='error' ) ) + user = get_user( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool if the user is not viewing his own tools + if cntrller == 'tool': + tool_id = get_approved_tools( trans, user=user ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tool.id for tool in user.tools ] + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools_by_user', + tool_id=tool_id ) ) ## ---- Utility methods ------------------------------------------------------- +def get_versions( trans, tool ): + versions = [tool] + this_tool = tool + while tool.newer_version: + versions.insert( 0, tool.newer_version ) + tool = tool.newer_version + tool = this_tool + while tool.older_version: + versions.append( tool.older_version[0] ) + tool = tool.older_version[0] + return versions def get_categories( trans ): """Get all categories from the database""" return trans.sa_session.query( trans.model.Category ) \ .filter( trans.model.Category.table.c.deleted==False ) \ - .order_by( trans.model.Category.table.c.name ) + .order_by( trans.model.Category.table.c.name ).all() def get_unassociated_categories( trans, obj ): """Get all categories from the database that are not associated with obj""" # TODO: we currently assume we are setting a tool category, so this method may need @@ -142,4 +200,33 @@ obj.categories.append( trans.model.ToolCategoryAssociation( obj, category ) ) def get_tool( trans, id ): return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) ) - +def get_tools( trans ): + return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name ) +def get_approved_tools( trans, category=None, user=None ): + tool_id = [] + if category: + # Return only the approved tools in the category + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + tool_id.append( tool.id ) + elif user: + if trans.user == user: + # If the current user is browsing his own tools, then don't filter on state + tool_id = [ tool.id for tool in user.tools ] + else: + # The current user is viewing all tools uploaded by another user, so show only + # approved tools + for tool in user.active_tools: + if tool.is_approved(): + tool_id.append( tool.id ) + else: + # Return all approved tools + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + return tool_id +def get_event( trans, id ): + return trans.sa_session.query( trans.model.Event ).get( trans.security.decode_id( id ) ) +def get_user( trans, id ): + return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/tool.py --- a/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 18:26:49 2010 -0400 @@ -15,38 +15,111 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval += '%s<br/>\n' % tca.category.name + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' - def filter( self, trans, user, query, column_filter ): - # Category.name conflicts with Tool.name, so we have to make our own filter - def get_single_filter( filter ): - return func.lower( model.Category.name ).like( "%" + filter.lower() + "%" ) - if column_filter == 'All': - pass - elif isinstance( column_filter, list ): - clause_list = [] - for filter in column_filter: - clause_list.append( get_single_filter( filter ) ) - query = query.filter( or_( *clause_list ) ) - else: - query = query.filter( get_single_filter( column_filter ) ) - return query - def get_link( self, trans, grid, tool, filter_params ): + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + # Grid definition + title = "Tools" + model_class = model.Tool + template='/webapps/community/tool/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + model_class=model.Tool, + link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), + attach_popup=True, + filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Download tool", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="tool", action="download_tool", cntrller="tool", webapp="community" ) ) + ] + standard_filters = [ + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + default_filter = dict( name="All", deleted="False", username="All" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, session ): + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) + +class ToolsByUserListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description + class CategoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): if tool.categories: - filter_params['f-category'] = [] + rval = '' for tca in tool.categories: - filter_params['f-category'].append( tca.category.name ) - if len( filter_params['f-category'] ) == 1: - filter_params['f-category'] = filter_params['f-category'][0] - filter_params['advanced-search'] = 'True' - return filter_params - return None + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + return rval + return 'not set' class StateColumn( grids.GridColumn ): def get_value( self, trans, grid, tool ): state = tool.state() @@ -75,13 +148,9 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.username - def get_link( self, trans, grid, tool, filter_params ): - filter_params['f-username'] = tool.user.username - filter_params['advanced-search'] = 'True' - return filter_params + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition - title = "Tools" + title = "Tools By User" model_class = model.Tool template='/webapps/community/tool/grid.mako' default_sort_key = "name" @@ -92,21 +161,26 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), attach_popup=True, filterable="advanced" ), - CategoryColumn( "Categories", - key="category", + VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + StateColumn( "Status", + model_class=model.Event, + attach_popup=False ), UserColumn( "Uploaded By", key="username", model_class=model.User, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", - model_class=model.Event, - attach_popup=False, - filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -130,18 +204,44 @@ preserve_state = False use_paging = True def build_initial_query( self, session ): - return session.query( self.model_class ).outerjoin( model.ToolCategoryAssociation ).outerjoin( model.Category ) - def apply_default_filter( self, trans, query, **kwargs ): - return query.filter( self.model_class.deleted==False ) + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) -class ToolCategoryListGrid( grids.Grid ): +class CategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + viewable_tools = 0 + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + viewable_tools += 1 + return viewable_tools + return 0 + # Grid definition + webapp = "community" title = "Tool Categories" model_class = model.Category template='/webapps/community/category/grid.mako' @@ -157,7 +257,13 @@ key="description", model_class=model.Category, attach_popup=False, - filterable="advanced" ) + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -165,21 +271,23 @@ visible=False, filterable="standard" ) ) standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] - default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( self.model_class.deleted==False ) -class ToolBrowserController( BaseController ): - - tool_category_list_grid = ToolCategoryListGrid() +class ToolController( BaseController ): + tool_list_grid = ToolListGrid() + tools_by_user_list_grid = ToolsByUserListGrid() + category_list_grid = CategoryListGrid() @web.expose def index( self, trans, **kwd ): @@ -188,53 +296,84 @@ status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/community/index.mako', message=message, status=status ) @web.expose - def browse_tool_categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse category": - category_id = int( trans.app.security.decode_id( kwargs['id'] ) ) - category = trans.sa_session.query( model.Category ).get( category_id ) - del kwargs['id'] - del kwargs['operation'] - kwargs['f-category'] = category.name - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', - **kwargs ) ) - return self.tool_category_list_grid( trans, **kwargs ) + return self.browse_category( trans, id=kwd['id'] ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_category', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_category', + cntrller='tool', + **kwd ) ) + # Render the list view + return self.category_list_grid( trans, **kwd ) @web.expose - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() - if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tool', + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + @web.expose + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "view tool": return trans.response.send_redirect( web.url_for( controller='common', action='view_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "download tool": return trans.response.send_redirect( web.url_for( controller='tool', action='download_tool', - **kwargs ) ) + **kwd ) ) # Render the list view - return self.tool_list_grid( trans, **kwargs ) + return self.tool_list_grid( trans, **kwd ) @web.expose - def browse_tool( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/tool/browse_tool.mako', - tools=tools, - message=message, - status=status ) + def browse_tools_by_user( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', + cntrller='tool', + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='tool', + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) + # Render the list view + return self.tools_by_user_list_grid( trans, **kwd ) @web.expose def download_tool( self, trans, **kwd ): params = util.Params( kwd ) diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 18:26:49 2010 -0400 @@ -3,23 +3,36 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * from galaxy.webapps.community import datatypes -from common import get_categories, get_category +from common import get_categories, get_category, get_versions log = logging.getLogger( __name__ ) # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +class UploadError( Exception ): + pass + class UploadController( BaseController ): @web.expose + @web.require_login( 'upload', use_panels=True, webapp='community' ) def upload( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) category_ids = util.listify( params.get( 'category_id', '' ) ) + replace_id = params.get( 'replace_id', None ) + replace_version = None uploaded_file = None - if params.file_data == '' and params.url.strip() == '': + categories = get_categories( trans ) + if not get_categories( trans ): + return trans.response.send_redirect( web.url_for( controller='tool', + action='browse_tools', + cntrller='tool', + message='No categories have been configured in this instance of the Galaxy Community. An administrator needs to create some via the Administrator control panel before anything can be uploaded', + status='error' ) ) + elif params.file_data == '' and params.url.strip() == '': message = 'No files were entered on the upload form.' status = 'error' elif params.file_data == '': @@ -47,6 +60,29 @@ obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) if isinstance( obj, trans.app.model.Tool ): + existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).all() + if existing and replace_id is None: + raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) + elif existing: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + if replace_version.newer_version: + # If the user has picked an old version, switch to the newest version + replace_version = get_versions( trans, replace_version )[0] + if trans.user != replace_version.user: + raise UploadError( 'You are not the owner of this tool and may not upload new versions of it.' ) + if replace_version.tool_id != meta.id: + raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Please check the tool XML file' % ( meta.id, replace_version.tool_id ) ) + for old_version in get_versions( trans, replace_version ): + if old_version.version == meta.version: + raise UploadError( 'The new version (%s) matches an old version. Please check your version in the tool XML file' % meta.version ) + if old_version.is_new(): + raise UploadError( 'There is an existing version of this tool which is unsubmitted. Please either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ) ) ) + if old_version.is_waiting(): + raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' ) + # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed if category_ids: for category_id in category_ids: category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) @@ -58,6 +94,9 @@ tea = trans.app.model.ToolEventAssociation( obj, event ) trans.sa_session.add_all( ( event, tea ) ) trans.sa_session.flush() + if replace_version and replace_id: + replace_version.newer_version_id = obj.id + trans.sa_session.flush() try: os.link( uploaded_file.name, obj.file_name ) except OSError: @@ -69,13 +108,29 @@ id=trans.app.security.encode_id( obj.id ), message='Uploaded %s' % meta.message, status='done' ) ) - except datatypes.DatatypeVerificationError, e: + except ( datatypes.DatatypeVerificationError, UploadError ), e: message = str( e ) status = 'error' - except sqlalchemy.exc.IntegrityError: - message = 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' - status = 'error' uploaded_file.close() + elif replace_id is not None: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + old_version = None + for old_version in get_versions( trans, replace_version ): + if old_version.is_new(): + message = 'There is an existing version of this tool which is unsubmitted. Please either submit or delete it before uploading a new version.' + break + if old_version.is_waiting(): + message = 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' + break + else: + old_version = None + if old_version is not None: + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ), + message=message, + status='error' ) ) selected_upload_type = params.get( 'type', 'tool' ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/upload/upload.mako', @@ -83,5 +138,6 @@ status=status, selected_upload_type=selected_upload_type, upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list(), + replace_id=replace_id, selected_categories=selected_categories, categories=get_categories( trans ) ) diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 18:26:49 2010 -0400 @@ -92,7 +92,8 @@ DELETED = 'deleted', WAITING = 'waiting for approval', APPROVED = 'approved', - REJECTED = 'rejected' ) + REJECTED = 'rejected', + ARCHIVED = 'archived' ) def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, category=None, version=None, user_id=None, external_filename=None ): self.guid = guid self.tool_id = tool_id @@ -153,10 +154,14 @@ return self.state() == self.states.ERROR def is_deleted( self ): return self.state() == self.states.DELETED + def is_waiting( self ): + return self.state() == self.states.WAITING def is_approved( self ): return self.state() == self.states.APPROVED def is_rejected( self ): return self.state() == self.states.REJECTED + def is_archived( self ): + return self.state() == self.states.ARCHIVED @property def extension( self ): # if instantiated via a query, this unmapped property won't exist diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 18:26:49 2010 -0400 @@ -103,9 +103,10 @@ Tool.table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), @@ -164,8 +165,8 @@ # With the tables defined we can define the mappers and setup the # relationships between the model objects. assign_mapper( context, User, User.table, - properties=dict( tools=relation( Tool, order_by=desc( Tool.table.c.update_time ) ), - active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=desc( Tool.table.c.update_time ) ), + properties=dict( tools=relation( Tool, primaryjoin=( Tool.table.c.user_id == User.table.c.id ), order_by=( Tool.table.c.name ) ), + active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=( Tool.table.c.name ) ), galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ) ) ) assign_mapper( context, Group, Group.table, @@ -215,7 +216,11 @@ properties = dict( categories=relation( ToolCategoryAssociation ), events=relation( ToolEventAssociation ), - user=relation( User.mapper ) + user=relation( User.mapper ), + older_version=relation( + Tool, + primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), + backref=backref( "newer_version", primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), remote_side=[Tool.table.c.id] ) ) ) ) assign_mapper( context, Event, Event.table, @@ -238,7 +243,6 @@ ) ) - def guess_dialect_for_url( url ): return (url.split(':', 1))[0] diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 18:26:49 2010 -0400 @@ -80,9 +80,10 @@ Tool_table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/security/__init__.py --- a/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 18:26:49 2010 -0400 @@ -167,6 +167,12 @@ # We currently assume the current user can edit the item if they are the owner (i.e., they # uploaded the item), and the item is in a NEW state. return user and user==item.user and item.is_new() + def can_upload_new_version( self, user, item, versions ): + state_ok = True + for version in versions: + if version.is_new() or version.is_approved(): + state_ok = False + return user and user==item.user and state_ok def get_permitted_actions( filter=None ): '''Utility method to return a subset of RBACAgent's permitted actions''' diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/admin/index.mako Fri Apr 30 18:26:49 2010 -0400 @@ -54,7 +54,6 @@ </style> </%def> - <%def name="init()"> <% self.has_left_panel=True @@ -71,32 +70,34 @@ <div class="toolMenu"> <div class="toolSectionList"> <div class="toolSectionTitle"> + <span>Tools</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_state', state=trans.model.Tool.states.WAITING, webapp='community' )}">Tools awaiting approval</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_category' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}">Browse all tools</a></div> + </div> + </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + <span>Categories</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a></div> + </div> + </div> + <div class="toolSectionTitle"> <span>Security</span> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp='community' )}" target="galaxy_main">Manage users</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp='community' )}" target="galaxy_main">Manage groups</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp='community' )}" target="galaxy_main">Manage roles</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a></div> </div> </div> - <div class="toolSectionTitle"> - <span>Tools</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - <span>Community</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='categories', webapp='community' )}" target="galaxy_main">Manage categories</a></div> - </div> - </div> </div> </div> </div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/category/edit_category.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/edit_category.mako Fri Apr 30 18:26:49 2010 -0400 @@ -0,0 +1,44 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Change category name and description</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='edit_category' )}" method="post" > + <div class="form-row"> + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${category.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input name="description" type="textfield" value="${category.description}" size=40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="rename" value="submitted"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="edit_category_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/category/rename_category.mako --- a/templates/webapps/community/category/rename_category.mako Fri Apr 30 18:26:06 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change category name and description</div> - <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='rename_category' )}" method="post" > - <div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${category.name}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${category.description}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="rename_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/index.mako Fri Apr 30 18:26:49 2010 -0400 @@ -1,6 +1,57 @@ <%inherit file="/webapps/community/base_panels.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ## TODO: Clean up these styles and move into panel_layout.css (they are + ## used here and in the editor). + <style type="text/css"> + #left { + background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; + } + div.toolMenu { + margin: 5px; + margin-left: 10px; + margin-right: 10px; + } + div.toolSectionPad { + margin: 0; + padding: 0; + height: 5px; + font-size: 0px; + } + div.toolSectionDetailsInner { + margin-left: 5px; + margin-right: 5px; + } + div.toolSectionTitle { + padding-bottom: 0px; + font-weight: bold; + } + div.toolMenuGroupHeader { + font-weight: bold; + padding-top: 0.5em; + padding-bottom: 0.5em; + color: #333; + font-style: italic; + border-bottom: dotted #333 1px; + margin-bottom: 0.5em; + } + div.toolTitle { + padding-top: 5px; + padding-bottom: 5px; + margin-left: 16px; + margin-right: 10px; + display: list-item; + list-style: square outside; + } + a:link, a:visited, a:active + { + color: #303030; + } + </style> +</%def> + <%def name="init()"> <% self.has_left_panel=True @@ -29,17 +80,20 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tool_categories' )}" target="galaxy_main">Browse tools by category</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tools' )}" target="galaxy_main">Browse all tools</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_categories' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools' )}">Browse all tools</a></div> + %if trans.user: + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> + %endif </div> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> <div class="toolTitle"> %if trans.user: - <a href="${h.url_for( controller='upload', action='upload', type='tool' )}" target="galaxy_main">Upload a tool</a> + <a target="galaxy_main" href="${h.url_for( controller='upload', action='upload', type='tool' )}">Upload a tool</a> %else: - Login to upload + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to upload</a> %endif </div> </div> @@ -54,7 +108,7 @@ if trans.app.config.require_login and not trans.user: center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='tool', action='browse_tool_categories', message=message, status=status ) + center_url = h.url_for( controller='tool', action='browse_categories', message=message, status=status ) %> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/tool/browse_tool.mako --- a/templates/webapps/community/tool/browse_tool.mako Fri Apr 30 18:26:06 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<%namespace file="/message.mako" import="render_msg" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="title()">Browse Tool</%def> - -<h2>Galaxy Tool</h2> - -%if message: - ${render_msg( message, status )} -%endif - -%if not tools: - There are no tools -%else: - <table class="grid"> - <thead> - <tr> - <th>Name</th> - <th>Description</th> - </tr> - </thead> - <tbody> - <tr class="formRow id="toolRow"> - <td><a href="${h.url_for( controller='tool', action='browse', id=trans.security.encode_id( tool.id ) )}">${tool.name}</a></td> - <td>${tool.description}</td> - </tr> - </tbody> - </table> -%endif diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 18:26:49 2010 -0400 @@ -58,7 +58,6 @@ <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="tool-${tool.id}-popup"> <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> </div> @@ -123,7 +122,7 @@ <div class="toolParamHelp" style="clear: both;"> Tools must be approved before they are made available to others in the community. After you have submitted your tool to be published, you will no longer be able to modify it, so make sure the information above is - correct and has been saved before submitting for approval. + correct and and save any changes before submitting for approval. </div> </div> </form> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 18:26:49 2010 -0400 @@ -6,6 +6,12 @@ if cntrller in [ 'tool' ]: can_edit = trans.app.security_agent.can_edit_item( trans.user, tool ) + can_upload_new_version = trans.app.security_agent.can_upload_new_version( trans.user, tool, versions ) + + visible_versions = [] + for version in versions: + if version.is_approved() or version.is_archived() or version.user == trans.user: + visible_versions.append( version ) %> <%! @@ -49,6 +55,30 @@ <h2>View Tool: ${tool.name} <em>${tool.description}</em></h2> +%if tool.is_approved(): + <b><i>This is the latest approved version of this tool</i></b> +%elif tool.is_deleted(): + <font color="red"><b><i>This is a deleted version of this tool</i></b></font> +%elif tool.is_archived(): + <font color="red"><b><i>This is an archived version of this tool</i></b></font> +%elif tool.is_new(): + <font color="red"><b><i>This is an unsubmitted version of this tool</i></b></font> +%elif tool.is_waiting(): + <font color="red"><b><i>This version of this tool is awaiting administrative approval</i></b></font> +%elif tool.is_rejected(): + <font color="red"><b><i>This version of this tool has been rejected by an administrator</i></b></font> +%endif +<p/> + +%if cntrller=='admin' and tool.is_waiting(): + <p> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.APPROVED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Approve</span></a></li> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.REJECTED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Reject</span></a></li> + </ul> + </p> +%endif + %if message: ${render_msg( message, status )} %endif @@ -59,7 +89,8 @@ <div popupmenu="tool-${tool.id}-popup"> %if cntrller=='admin' or can_edit: <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> + %endif + %if cntrller=='admin' or can_upload_new_version: <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> %endif <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> @@ -93,11 +124,30 @@ </div> <div class="form-row"> <label>Categories:</label> - %for category in categories: - ${category.name} - %endfor + %if categories: + %for category in categories: + ${category.name} + %endfor + %else: + none set + %endif <div style="clear: both"></div> </div> + %if len( visible_versions ) > 1: + <div class="form-row"> + <label>All Versions:</label> + <ul> + %for version in visible_versions: + %if version == tool: + <li><strong>${version.version} (this version)</strong></li> + %else: + <li><a href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( version.id ), cntrller=cntrller )}">${version.version}</a></li> + %endif + %endfor + </ul> + <div style="clear: both"></div> + </div> + %endif </div> </div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/upload/upload.mako --- a/templates/webapps/community/upload/upload.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/upload/upload.mako Fri Apr 30 18:26:49 2010 -0400 @@ -22,6 +22,9 @@ <div class="toolFormBody"> ## TODO: nginx <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload' )}" enctype="multipart/form-data" method="post"> + %if replace_id is not None: + <input type='hidden' name="replace_id" value="${replace_id}"/> + %endif <div class="form-row"> <label>Upload Type</label> <div class="form-row-input"> diff -r 8e00344d941a -r 3ac0dfcdf44e tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Fri Apr 30 18:26:06 2010 -0400 +++ b/tools/samtools/sam_to_bam.py Fri Apr 30 18:26:49 2010 -0400 @@ -94,7 +94,7 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( fai_index_file_path ).read().strip() ) == 0: + if os.path.getsize( fai_index_file_path ) == 0: raise Exception, 'Index file empty, there may be an error with your reference file or settings.' except Exception, e: #clean up temp files diff -r 8e00344d941a -r 3ac0dfcdf44e tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 18:26:06 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 18:26:49 2010 -0400 @@ -387,8 +387,8 @@ if returncode != 0: raise Exception, stderr # check that there are results in the output file - if len( open( options.output, 'rb' ).read().strip() ) == 0: - raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + if os.path.getsize( options.output ) == 0: + raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + '\nextra: ' + str(extra) except Exception, e: stop_err( 'Error aligning sequence. ' + str( e ) ) finally: diff -r 8e00344d941a -r 3ac0dfcdf44e tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 18:26:06 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 18:26:49 2010 -0400 @@ -2,11 +2,10 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value + refFile = param_dict[ 'genomeSource' ][ 'indices' ].value except: try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey + refFile = param_dict[ 'genomeSource' ][ 'ownFile' ].dbkey except: - out_data['output'].set_dbkey('?') - return - out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) + refFile = '?' + out_data[ 'output' ].set_dbkey( os.path.split( refFile )[1].split( '.' )[0] )

1 0

[hg] galaxy 3727: Cuffcompare wrapper handles all outputs gracef...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8e00344d941a changeset: 3727:8e00344d941a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 30 18:26:06 2010 -0400 description: Cuffcompare wrapper handles all outputs gracefully. Tests needed. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 30 +++++++++++++++++++-------- tools/ngs_rna/cuffcompare_wrapper.xml | 38 +++++++++++++++++++++++++++++++++- 2 files changed, 57 insertions(+), 11 deletions(-) diffs (130 lines): diff -r c642fbb301fc -r 8e00344d941a tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Fri Apr 30 13:09:29 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Fri Apr 30 18:26:06 2010 -0400 @@ -18,6 +18,11 @@ parser.add_option( '-A', '--transcripts-accuracy-output', dest='transcripts_accuracy_output_file', help='' ) parser.add_option( '-B', '--transcripts-combined-output', dest='transcripts_combined_output_file', help='' ) parser.add_option( '-C', '--transcripts-tracking-output', dest='transcripts_tracking_output_file', help='' ) + parser.add_option( '', '--input1-tmap-output', dest='input1_tmap_output_file', help='' ) + parser.add_option( '', '--input1-refmap-output', dest='input1_refmap_output_file', help='' ) + parser.add_option( '', '--input2-tmap-output', dest='input2_tmap_output_file', help='' ) + parser.add_option( '', '--input2-refmap-output', dest='input2_refmap_output_file', help='' ) + (options, args) = parser.parse_args() @@ -35,17 +40,22 @@ if options.ignore_nonoverlap: cmd += " -R " - # Output/debugging. - print cmd + # Add input files. - # Add input files. - cmd += " %s" % options.input1 + # Need to symlink inputs so that output files are written to temp directory. + print options.input1 + input1_file_name = tmp_output_dir + "/input1" + os.symlink( options.input1, input1_file_name ) + cmd += " %s" % input1_file_name two_inputs = ( options.input2 != None) if two_inputs: - cmd += " %s" % options.input2 + input2_file_name = tmp_output_dir + "/input2" + os.symlink( options.input2, input2_file_name ) + cmd += " %s" % input2_file_name + print cmd # Run command. - try: + try: tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name tmp_stderr = open( tmp_name, 'wb' ) proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stderr=tmp_stderr.fileno() ) @@ -79,16 +89,18 @@ try: try: shutil.copyfile( tmp_output_dir + "/cc_output", options.transcripts_accuracy_output_file ) + shutil.copyfile( tmp_output_dir + "/input1.tmap", options.input1_tmap_output_file ) + shutil.copyfile( tmp_output_dir + "/input1.refmap", options.input1_refmap_output_file ) if two_inputs: shutil.copyfile( tmp_output_dir + "/cc_output.combined.gtf", options.transcripts_combined_output_file ) shutil.copyfile( tmp_output_dir + "/cc_output.tracking", options.transcripts_tracking_output_file ) - - # TODO: also copy *.tmap, *.refmap to outputs? + shutil.copyfile( tmp_output_dir + "/input2.tmap", options.input2_tmap_output_file ) + shutil.copyfile( tmp_output_dir + "/input2.refmap", options.input2_refmap_output_file ) except Exception, e: stop_err( 'Error in cuffcompare:\n' + str( e ) ) finally: # Clean up temp dirs - if os.path.exists( tmp_output_dir ): + if not os.path.exists( tmp_output_dir ): shutil.rmtree( tmp_output_dir ) if __name__=="__main__": __main__() \ No newline at end of file diff -r c642fbb301fc -r 8e00344d941a tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Fri Apr 30 13:09:29 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Fri Apr 30 18:26:06 2010 -0400 @@ -3,9 +3,13 @@ <command interpreter="python"> cuffcompare_wrapper.py --transcripts-accuracy-output=$transcripts_accuracy + --input1-tmap-output=$input1_tmap + --input1-refmap-output=$input1_refmap #if $second_gtf.use_second_gtf == "Yes": --transcripts-combined-output=$transcripts_combined --transcripts-tracking-output=$transcripts_tracking + --input2-tmap-output=$input2_tmap + --input2-refmap-output=$input2_refmap #end if #if $annotation.use_ref_annotation == "Yes": -r $annotation.reference_annotation @@ -46,13 +50,43 @@ </inputs> <outputs> - <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> - <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"/> + <data format="tmap" name="input1_tmap" label="${tool.name} on ${on_string}: data ${input1.hid} tmap file"/> + <data format="refmap" name="input1_refmap" label="${tool.name} on ${on_string}: data ${input1.hid} refmap file"/> + <data format="tmap" name="input2_tmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} tmap file"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> + <data format="refmap" name="input2_refmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} refmap file"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> + <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> + <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> <data format="gtf" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"/> </outputs> <tests> +  <test> + <param name="input1" value="cuffcompare_in1.gtf" ftype="gtf"/> + <param name="use_second_gtf" value="Yes"/> + <param name="input2" value="cuffcompare_in2.gtf" ftype="gtf"/> + <param name="use_ref_annotation" value="Yes"/> + <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> + <param name="ignore_nonoverlapping_reference" value="Yes"/> + <output name="transcripts_combined" file="cuffcompare_out5.gtf"/> +  </test> </tests>

1 0

[hg] galaxy 3726: Community: Add tool versioning and tighten up ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/42f3f5d78f9a changeset: 3726:42f3f5d78f9a user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Apr 30 16:11:17 2010 -0400 description: Community: Add tool versioning and tighten up the requirements in the upload/approval process diffstat: lib/galaxy/web/framework/__init__.py | 4 +- lib/galaxy/webapps/community/controllers/admin.py | 19 +- lib/galaxy/webapps/community/controllers/common.py | 28 ++- lib/galaxy/webapps/community/controllers/upload.py | 68 +++++++++- lib/galaxy/webapps/community/model/mapping.py | 9 +- lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py | 3 +- lib/galaxy/webapps/community/security/__init__.py | 6 + templates/webapps/community/tool/view_tool.mako | 49 ++++++- templates/webapps/community/upload/upload.mako | 3 + 9 files changed, 160 insertions(+), 29 deletions(-) diffs (410 lines): diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Apr 30 16:11:17 2010 -0400 @@ -66,7 +66,7 @@ decorator.exposed = True return decorator -def require_login( verb="perform this action", use_panels=False ): +def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ): def argcatcher( func ): def decorator( self, trans, *args, **kwargs ): if trans.get_user(): @@ -74,7 +74,7 @@ else: return trans.show_error_message( 'You must be <a target="_top" href="%s">logged in</a> to %s</div>.' - % ( url_for( controller='user', action='login' ), verb ), use_panels=use_panels ) + % ( url_for( controller='user', action='login', webapp=webapp ), verb ), use_panels=use_panels ) return decorator return argcatcher diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 16:11:17 2010 -0400 @@ -2,7 +2,7 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids -from common import get_categories, get_category, get_tools, get_event, get_tool +from common import get_categories, get_category, get_tools, get_event, get_tool, get_versions import logging log = logging.getLogger( __name__ ) @@ -670,12 +670,18 @@ webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + redirect = params.get( 'no_redirect', True ) id = params.get( 'id', None ) if not id: message = "No tool id received for setting status" status = 'error' else: tool = get_tool( trans, id ) + if state == trans.app.model.Tool.states.APPROVED: + # If we're approving a tool, all previous versions must be set to archived + for version in get_versions( trans, tool ): + if version != tool and version.is_approved(): + self.set_tool_state( trans, trans.app.model.Tool.states.ARCHIVED, id=trans.app.security.encode_id( version.id ), redirect='False' ) event = trans.model.Event( state ) # Flush so we an get an id trans.sa_session.add( event ) @@ -684,11 +690,12 @@ trans.sa_session.add( tea ) trans.sa_session.flush() message = "State of tool '%s' is now %s" % ( tool.name, state ) - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_tools', - webapp=webapp, - message=message, - status=status ) ) + if redirect: + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + webapp=webapp, + message=message, + status=status ) ) @web.expose @web.require_admin def edit_category( self, trans, **kwd ): diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 16:11:17 2010 -0400 @@ -81,9 +81,11 @@ tool = get_tool( trans, id ) categories = [ tca.category for tca in tool.categories ] tool_file_contents = tarfile.open( tool.file_name, 'r' ).getnames() + versions = get_versions( trans, tool ) return trans.fill_template( '/webapps/community/tool/view_tool.mako', tool=tool, tool_file_contents=tool_file_contents, + versions=versions, categories=categories, cntrller=cntrller, message=message, @@ -100,14 +102,11 @@ message='Select a tool to to upload a new version', status='error' ) ) tool = get_tool( trans, id ) - if params.save_button and ( params.file_data != '' or params.url != '' ): - # TODO: call the upload method in the upload controller. - message = 'Uploading new version not implemented' - status = 'error' - return trans.response.send_redirect( web.url_for( controller=cntrller, - action='browse_tools', - message='Not yet implemented, sorry...', - status='error' ) ) + return trans.response.send_redirect( web.url_for( controller='upload', + action='upload', + message=message, + status=status, + replace_id=id ) ) @web.expose def browse_category( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -159,11 +158,22 @@ ## ---- Utility methods ------------------------------------------------------- +def get_versions( trans, tool ): + versions = [tool] + this_tool = tool + while tool.newer_version: + versions.insert( 0, tool.newer_version ) + tool = tool.newer_version + tool = this_tool + while tool.older_version: + versions.append( tool.older_version[0] ) + tool = tool.older_version[0] + return versions def get_categories( trans ): """Get all categories from the database""" return trans.sa_session.query( trans.model.Category ) \ .filter( trans.model.Category.table.c.deleted==False ) \ - .order_by( trans.model.Category.table.c.name ) + .order_by( trans.model.Category.table.c.name ).all() def get_unassociated_categories( trans, obj ): """Get all categories from the database that are not associated with obj""" # TODO: we currently assume we are setting a tool category, so this method may need diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 16:11:17 2010 -0400 @@ -3,23 +3,36 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * from galaxy.webapps.community import datatypes -from common import get_categories, get_category +from common import get_categories, get_category, get_versions log = logging.getLogger( __name__ ) # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +class UploadError( Exception ): + pass + class UploadController( BaseController ): @web.expose + @web.require_login( 'upload', use_panels=True, webapp='community' ) def upload( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) category_ids = util.listify( params.get( 'category_id', '' ) ) + replace_id = params.get( 'replace_id', None ) + replace_version = None uploaded_file = None - if params.file_data == '' and params.url.strip() == '': + categories = get_categories( trans ) + if not get_categories( trans ): + return trans.response.send_redirect( web.url_for( controller='tool', + action='browse_tools', + cntrller='tool', + message='No categories have been configured in this instance of the Galaxy Community. An administrator needs to create some via the Administrator control panel before anything can be uploaded', + status='error' ) ) + elif params.file_data == '' and params.url.strip() == '': message = 'No files were entered on the upload form.' status = 'error' elif params.file_data == '': @@ -47,6 +60,29 @@ obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) if isinstance( obj, trans.app.model.Tool ): + existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).all() + if existing and replace_id is None: + raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) + elif existing: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + if replace_version.newer_version: + # If the user has picked an old version, switch to the newest version + replace_version = get_versions( trans, replace_version )[0] + if trans.user != replace_version.user: + raise UploadError( 'You are not the owner of this tool and may not upload new versions of it.' ) + if replace_version.tool_id != meta.id: + raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Please check the tool XML file' % ( meta.id, replace_version.tool_id ) ) + for old_version in get_versions( trans, replace_version ): + if old_version.version == meta.version: + raise UploadError( 'The new version (%s) matches an old version. Please check your version in the tool XML file' % meta.version ) + if old_version.is_new(): + raise UploadError( 'There is an existing version of this tool which is unsubmitted. Please either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ) ) ) + if old_version.is_waiting(): + raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' ) + # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed if category_ids: for category_id in category_ids: category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) @@ -58,6 +94,9 @@ tea = trans.app.model.ToolEventAssociation( obj, event ) trans.sa_session.add_all( ( event, tea ) ) trans.sa_session.flush() + if replace_version and replace_id: + replace_version.newer_version_id = obj.id + trans.sa_session.flush() try: os.link( uploaded_file.name, obj.file_name ) except OSError: @@ -69,13 +108,29 @@ id=trans.app.security.encode_id( obj.id ), message='Uploaded %s' % meta.message, status='done' ) ) - except datatypes.DatatypeVerificationError, e: + except ( datatypes.DatatypeVerificationError, UploadError ), e: message = str( e ) status = 'error' - except sqlalchemy.exc.IntegrityError: - message = 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' - status = 'error' uploaded_file.close() + elif replace_id is not None: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + old_version = None + for old_version in get_versions( trans, replace_version ): + if old_version.is_new(): + message = 'There is an existing version of this tool which is unsubmitted. Please either submit or delete it before uploading a new version.' + break + if old_version.is_waiting(): + message = 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' + break + else: + old_version = None + if old_version is not None: + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ), + message=message, + status='error' ) ) selected_upload_type = params.get( 'type', 'tool' ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/upload/upload.mako', @@ -83,5 +138,6 @@ status=status, selected_upload_type=selected_upload_type, upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list(), + replace_id=replace_id, selected_categories=selected_categories, categories=get_categories( trans ) ) diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 16:11:17 2010 -0400 @@ -103,9 +103,10 @@ Tool.table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), @@ -215,7 +216,11 @@ properties = dict( categories=relation( ToolCategoryAssociation ), events=relation( ToolEventAssociation ), - user=relation( User.mapper ) + user=relation( User.mapper ), + older_version=relation( + Tool, + primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), + backref=backref( "newer_version", primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), remote_side=[Tool.table.c.id] ) ) ) ) assign_mapper( context, Event, Event.table, diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 16:11:17 2010 -0400 @@ -80,9 +80,10 @@ Tool_table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/security/__init__.py --- a/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 16:11:17 2010 -0400 @@ -167,6 +167,12 @@ # We currently assume the current user can edit the item if they are the owner (i.e., they # uploaded the item), and the item is in a NEW state. return user and user==item.user and item.is_new() + def can_upload_new_version( self, user, item, versions ): + state_ok = True + for version in versions: + if version.is_new() or version.is_approved(): + state_ok = False + return user and user==item.user and state_ok def get_permitted_actions( filter=None ): '''Utility method to return a subset of RBACAgent's permitted actions''' diff -r e71a3d03a529 -r 42f3f5d78f9a templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 15:45:32 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 16:11:17 2010 -0400 @@ -6,6 +6,12 @@ if cntrller in [ 'tool' ]: can_edit = trans.app.security_agent.can_edit_item( trans.user, tool ) + can_upload_new_version = trans.app.security_agent.can_upload_new_version( trans.user, tool, versions ) + + visible_versions = [] + for version in versions: + if version.is_approved() or version.is_archived() or version.user == trans.user: + visible_versions.append( version ) %> <%! @@ -49,10 +55,26 @@ <h2>View Tool: ${tool.name} <em>${tool.description}</em></h2> +%if tool.is_approved(): + <b><i>This is the latest approved version of this tool</i></b> +%elif tool.is_deleted(): + <font color="red"><b><i>This is a deleted version of this tool</i></b></font> +%elif tool.is_archived(): + <font color="red"><b><i>This is an archived version of this tool</i></b></font> +%elif tool.is_new(): + <font color="red"><b><i>This is an unsubmitted version of this tool</i></b></font> +%elif tool.is_waiting(): + <font color="red"><b><i>This version of this tool is awaiting administrative approval</i></b></font> +%elif tool.is_rejected(): + <font color="red"><b><i>This version of this tool has been rejected by an administrator</i></b></font> +%endif +<p/> + %if cntrller=='admin' and tool.is_waiting(): <p> <ul class="manage-table-actions"> <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.APPROVED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Approve</span></a></li> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.REJECTED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Reject</span></a></li> </ul> </p> %endif @@ -67,6 +89,8 @@ <div popupmenu="tool-${tool.id}-popup"> %if cntrller=='admin' or can_edit: <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> + %endif + %if cntrller=='admin' or can_upload_new_version: <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> %endif <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> @@ -100,11 +124,30 @@ </div> <div class="form-row"> <label>Categories:</label> - %for category in categories: - ${category.name} - %endfor + %if categories: + %for category in categories: + ${category.name} + %endfor + %else: + none set + %endif <div style="clear: both"></div> </div> + %if len( visible_versions ) > 1: + <div class="form-row"> + <label>All Versions:</label> + <ul> + %for version in visible_versions: + %if version == tool: + <li><strong>${version.version} (this version)</strong></li> + %else: + <li><a href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( version.id ), cntrller=cntrller )}">${version.version}</a></li> + %endif + %endfor + </ul> + <div style="clear: both"></div> + </div> + %endif </div> </div> diff -r e71a3d03a529 -r 42f3f5d78f9a templates/webapps/community/upload/upload.mako --- a/templates/webapps/community/upload/upload.mako Fri Apr 30 15:45:32 2010 -0400 +++ b/templates/webapps/community/upload/upload.mako Fri Apr 30 16:11:17 2010 -0400 @@ -22,6 +22,9 @@ <div class="toolFormBody"> ## TODO: nginx <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload' )}" enctype="multipart/form-data" method="post"> + %if replace_id is not None: + <input type='hidden' name="replace_id" value="${replace_id}"/> + %endif <div class="form-row"> <label>Upload Type</label> <div class="form-row-input">

1 0

[hg] galaxy 3725: Fix dbkey setting for BWA.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e71a3d03a529 changeset: 3725:e71a3d03a529 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Apr 30 15:45:32 2010 -0400 description: Fix dbkey setting for BWA. diffstat: tools/sr_mapping/bwa_wrapper_code.py | 9 ++++----- 1 files changed, 4 insertions(+), 5 deletions(-) diffs (19 lines): diff -r 007f175c8b88 -r e71a3d03a529 tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 15:27:41 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 15:45:32 2010 -0400 @@ -2,11 +2,10 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value + refFile = param_dict[ 'genomeSource' ][ 'indices' ].value except: try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey + refFile = param_dict[ 'genomeSource' ][ 'ownFile' ].dbkey except: - out_data['output'].set_dbkey('?') - return - out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) + refFile = '?' + out_data[ 'output' ].set_dbkey( os.path.split( refFile )[1].split( '.' )[0] )

1 0