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commit/galaxy-central: jgoecks: Trackster: (a) handle corner case when feature starts at tile boundary and (b) remove poor tile index usage. Pack script.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7369eda82e2c/ changeset: 7369eda82e2c user: jgoecks date: 2013-03-01 22:18:23 summary: Trackster: (a) handle corner case when feature starts at tile boundary and (b) remove poor tile index usage. Pack script. affected #: 2 files diff -r 5f20704ea90836a5fa54f63c78ceaa536010c4e8 -r 7369eda82e2cf7e10338232569ed9185bc3b526b static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=ref_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file diff -r 5f20704ea90836a5fa54f63c78ceaa536010c4e8 -r 7369eda82e2cf7e10338232569ed9185bc3b526b static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -6,6 +6,7 @@ * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first * region overlaps the start (but not the end) of the second region. + * NOTE: Coordinates are assumed to be in BED format: half open (start is closed, end is open). */ var BEFORE = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005, AFTER = 1006; var compute_overlap = function(first_region, second_region) { @@ -14,7 +15,7 @@ second_start = second_region[0], second_end = second_region[1], overlap; if (first_start < second_start) { - if (first_end < second_start) { + if (first_end <= second_start) { overlap = BEFORE; } else if (first_end <= second_end) { @@ -763,7 +764,7 @@ } var seq_start = feature_start + base_offset, // -0.5 to offset sequence between bases. - s_start = Math.floor( Math.max(0, (seq_start - tile_low - 0.5) * w_scale) ), + s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) ); // Make sure that read is drawn even if it too small to be rendered officially; in this case, @@ -858,7 +859,7 @@ var insert_x_coord = s_start - gap; if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { - var seq = ref_seq.slice(seq_offset, seq_offset + cig_len); + var seq = read_seq.slice(seq_offset, seq_offset + cig_len); // Insertion point is between the sequence start and the previous base: (-gap) moves // back from sequence start to insertion point. if (this.prefs.show_insertions) { @@ -869,7 +870,7 @@ // Draw sequence. // X center is offset + start - <half_sequence_length> var x_center = s_start - (s_end - s_start)/2; - if ( (mode === "Pack" || this.mode === "Auto") && ref_seq !== undefined && w_scale > char_width_px) { + if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Draw sequence container. ctx.fillStyle = "yellow"; ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); @@ -905,7 +906,7 @@ } } else { - if ( (mode === "Pack" || this.mode === "Auto") && ref_seq !== undefined && w_scale > char_width_px) { + if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Show insertions with a single number at the insertion point. draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } ); } @@ -955,7 +956,7 @@ feature_end = feature[2], feature_name = feature[3], // -0.5 to put element between bases. - f_start = Math.floor( Math.max(0, (feature_start - tile_low - 0.5) * w_scale) ), + f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ), y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, label_color = this.prefs.label_color; @@ -997,12 +998,10 @@ // Read is single. this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]); } - if (mode === "Pack" && feature_start > tile_low && feature_name !== ".") { + if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") { // Draw label. ctx.fillStyle = this.prefs.label_color; - // FIXME: eliminate tile_index - var tile_index = 1; - if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { + if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8); } else { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Be conservative when displaying custom datatypes in the tool shed.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f20704ea908/ changeset: 5f20704ea908 user: greg date: 2013-03-01 22:13:29 summary: Be conservative when displaying custom datatypes in the tool shed. affected #: 1 file diff -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a -r 5f20704ea90836a5fa54f63c78ceaa536010c4e8 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -967,9 +967,9 @@ num_datatype_dicts = len( datatype_dicts ) for index, datatype_dict in enumerate( datatype_dicts ): # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} - extension = datatype_dict[ 'extension' ] - dtype = datatype_dict[ 'dtype' ] - mimetype = datatype_dict[ 'mimetype' ] + extension = datatype_dict.get( 'extension', '' ) + dtype = datatype_dict.get( 'dtype', '' ) + mimetype = datatype_dict.get( 'mimetype', '' ) display_in_upload = datatype_dict.get( 'display_in_upload', False ) datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) if index < num_datatype_dicts - 1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Implement more granular grids for valid Galaxy utilities in the tool shed - custom datatypes, tools, tool dependencies and repository dependencies are now accessible.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c7c8316a1d13/ changeset: c7c8316a1d13 user: greg date: 2013-03-01 22:08:25 summary: Implement more granular grids for valid Galaxy utilities in the tool shed - custom datatypes, tools, tool dependencies and repository dependencies are now accessible. affected #: 2 files diff -r 513adadb31a2a4b014b3f03c5af2817919ea1760 -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -646,13 +646,15 @@ class RepositoryNameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.repository.name ) + repository = repository_metadata.repository + return escape_html( repository.name ) class RepositoryOwnerColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.user.username ) + repository = repository_metadata.repository + return escape_html( repository.user.username ) class ChangesetRevisionColumn( grids.TextColumn ): @@ -763,18 +765,53 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ): - - title = "Repository dependencies available in this Tool Shed" + + + class RequiredRepositoryColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + rd_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + rd_dict = metadata.get( 'repository_dependencies', {} ) + if rd_dict: + rd_tups = rd_dict[ 'repository_dependencies' ] + # "repository_dependencies": [["http://localhost:9009", "bwa059", "test", "a07baa797d53"]] + # Sort rd_tups by by required repository name. + sorted_rd_tups = sorted( rd_tups, key=lambda rd_tup: rd_tup[ 1 ] ) + num_tups = len( sorted_rd_tups ) + for index, rd_tup in enumerate( sorted_rd_tups ): + name = rd_tup[ 1 ] + owner = rd_tup[ 2 ] + required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + if required_repository: + required_repository_id = trans.security.encode_id( required_repository.id ) + rd_str += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id + rd_str += '<b>name:</b> %s | <b>owner:</b> %s | <b>revision:</b> %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) + if required_repository: + rd_str += '</a>' + if index < num_tups - 1: + rd_str += '<br/>' + return rd_str + + title = "Repository dependency definitions in this tool shed" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), + model_class=model.Repository, + link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", model_class=model.User, attach_popup=False, - key="User.username" ) + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + RequiredRepositoryColumn( "Repository dependency", + attach_popup=False ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, @@ -790,9 +827,190 @@ .order_by( model.Repository.name ) +class ToolDependenciesGrid( RepositoryMetadataGrid ): + + + class ToolDependencyColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + td_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tds_dict = metadata.get( 'tool_dependencies', {} ) + if tds_dict: + # Example: {"bwa/0.5.9": {"name": "bwa", "type": "package", "version": "0.5.9"}} + sorted_keys = sorted( [ k for k in tds_dict.keys() ] ) + num_keys = len( sorted_keys ) + # Handle environment settings first. + if 'set_environment' in sorted_keys: + # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}] + env_dicts = tds_dict[ 'set_environment' ] + num_env_dicts = len( env_dicts ) + td_str += '<b>environment:</b> ' + for index, env_dict in enumerate( env_dicts ): + td_str += '%s' % escape_html( env_dict[ 'name' ] ) + if index < num_env_dicts - 1: + td_str += ', ' + td_str += '<br/>' + for index, key in enumerate( sorted_keys ): + if key == 'set_environment': + continue + td_dict = tds_dict[ key ] + # Example: {"name": "bwa", "type": "package", "version": "0.5.9"} + name = td_dict[ 'name' ] + type = td_dict[ 'type' ] + version = td_dict[ 'version' ] + td_str += '<b>%s</b> version <b>%s</b>' % ( escape_html( name ), escape_html( version ) ) + if index < num_keys - 1: + td_str += '<br/>' + return td_str + + title = "Tool dependency definitions in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + ToolDependencyColumn( "Tool dependency", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + +class ToolsGrid( RepositoryMetadataGrid ): + + + class ToolsColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + tool_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tool_dicts = metadata.get( 'tools', [] ) + if tool_dicts: + num_tool_dicts = len( tool_dicts ) + for index, tool_dict in enumerate( tool_dicts ): + tool_id = tool_dict[ 'id' ] + name = tool_dict[ 'name' ] + version = tool_dict[ 'version' ] + tool_str += '<b>%s</b> | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) + if index < num_tool_dicts - 1: + tool_str += '<br/>' + return tool_str + + title = "Valid tools in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + ToolsColumn( "Tool id | name | version", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + +class DatatypesGrid( RepositoryMetadataGrid ): + + + class DatatypesColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + datatype_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + datatype_dicts = metadata.get( 'datatypes', [] ) + if datatype_dicts: + num_datatype_dicts = len( datatype_dicts ) + for index, datatype_dict in enumerate( datatype_dicts ): + # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} + extension = datatype_dict[ 'extension' ] + dtype = datatype_dict[ 'dtype' ] + mimetype = datatype_dict[ 'mimetype' ] + display_in_upload = datatype_dict.get( 'display_in_upload', False ) + datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) + if index < num_datatype_dicts - 1: + datatype_str += '<br/>' + return datatype_str + + title = "Custom datatypes in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + DatatypesColumn( "Datatype extension | Type | Mimetype", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + class RepositoryController( BaseUIController, common_util.ItemRatings ): category_grid = CategoryGrid() + datatypes_grid = DatatypesGrid() deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid() email_alerts_repository_grid = EmailAlertsRepositoryGrid() install_matched_repository_grid = InstallMatchedRepositoryGrid() @@ -800,9 +1018,12 @@ my_writable_repositories_grid = MyWritableRepositoriesGrid() repositories_by_user_grid = RepositoriesByUserGrid() repositories_i_own_grid = RepositoriesIOwnGrid() + repository_dependencies_grid = RepositoryDependenciesGrid() repository_grid = RepositoryGrid() # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. repository_metadata_grid = RepositoryMetadataGrid() + tool_dependencies_grid = ToolDependenciesGrid() + tools_grid = ToolsGrid() valid_category_grid = ValidCategoryGrid() valid_repository_grid = ValidRepositoryGrid() @@ -824,7 +1045,7 @@ pass return self.browse_repositories( trans, **kwd ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation in [ "repositories_by_category", "repositories_by_user" ]: # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -836,6 +1057,16 @@ return self.category_grid( trans, **kwd ) @web.expose + def browse_datatypes( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + return self.datatypes_grid( trans, **kwd ) + + @web.expose def browse_invalid_tools( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -881,7 +1112,7 @@ # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search # link. We have to take this approach because the "-" character is illegal in HTTP requests. if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', @@ -1000,6 +1231,40 @@ status=status ) @web.expose + def browse_repository_dependencies( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "browse_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + **kwd ) ) + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + return self.repository_dependencies_grid( trans, **kwd ) + + @web.expose + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + return self.tools_grid( trans, **kwd ) + + @web.expose + def browse_tool_dependencies( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "browse_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + **kwd ) ) + return self.tool_dependencies_grid( trans, **kwd ) + + @web.expose def browse_valid_categories( self, trans, **kwd ): # The request came from Galaxy, so restrict category links to display only valid repository changeset revisions. galaxy_url = kwd.get( 'galaxy_url', None ) @@ -1022,7 +1287,7 @@ pass return self.browse_valid_repositories( trans, **kwd ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation in [ "valid_repositories_by_category", "valid_repositories_by_user" ]: # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -2420,7 +2685,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "receive email alerts": if trans.user: if kwd[ 'id' ]: diff -r 513adadb31a2a4b014b3f03c5af2817919ea1760 -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -67,6 +67,22 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Valid Galaxy Utilities + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_tools' )}">Tools</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_datatypes' )}">Custom datatypes</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repository_dependencies' )}">Repository dependency definitions</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_tool_dependencies' )}">Tool dependency definitions</a> + </div> %endif <div class="toolSectionPad"></div><div class="toolSectionTitle"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Improved documentation for automated repository installation and testing. Handle cases where a repository is missing test data. Limit the list of repositories to test to those that have tools. Update the parse_tool_panel_config method to return a flag specifying whether test data was found for the specified tool panel entry.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/513adadb31a2/ changeset: 513adadb31a2 user: inithello date: 2013-03-01 21:13:20 summary: Improved documentation for automated repository installation and testing. Handle cases where a repository is missing test data. Limit the list of repositories to test to those that have tools. Update the parse_tool_panel_config method to return a flag specifying whether test data was found for the specified tool panel entry. affected #: 3 files diff -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a -r 513adadb31a2a4b014b3f03c5af2817919ea1760 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -321,10 +321,10 @@ if testing_migrated_tools or testing_installed_tools: shed_tools_dict = {} if testing_migrated_tools: - shed_tools_dict = parse_tool_panel_config( migrated_tool_panel_config, shed_tools_dict ) + has_test_data, shed_tools_dict = parse_tool_panel_config( migrated_tool_panel_config, shed_tools_dict ) elif testing_installed_tools: for shed_tool_config in installed_tool_panel_configs: - shed_tools_dict = parse_tool_panel_config( shed_tool_config, shed_tools_dict ) + has_test_data, shed_tools_dict = parse_tool_panel_config( shed_tool_config, shed_tools_dict ) # Persist the shed_tools_dict to the galaxy_tool_shed_test_file. shed_tools_file = open( galaxy_tool_shed_test_file, 'w' ) shed_tools_file.write( to_json_string( shed_tools_dict ) ) diff -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a -r 513adadb31a2a4b014b3f03c5af2817919ea1760 test/base/util.py --- a/test/base/util.py +++ b/test/base/util.py @@ -1,4 +1,6 @@ -import os, sys +import os, sys, logging + +log = logging.getLogger(__name__) cwd = os.getcwd() if cwd not in sys.path: @@ -27,6 +29,8 @@ # Locate the test-data directory. installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision ) for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )): + if '.hg' in dirs: + dirs.remove( '.hg' ) if 'test-data' in dirs: return os.path.join( root, 'test-data' ), repository_name, changeset_revision return None, repository_name, changeset_revision @@ -40,6 +44,7 @@ last_tested_repository_name = None last_tested_changeset_revision = None tool_path = None + has_test_data = False tree = parse_xml( config ) root = tree.getroot() tool_path = root.get('tool_path') @@ -53,6 +58,8 @@ last_tested_changeset_revision, tool_path ) if galaxy_test_file_dir: + if not has_test_data: + has_test_data = True if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) @@ -70,11 +77,13 @@ last_tested_changeset_revision, tool_path ) if galaxy_test_file_dir: + if not has_test_data: + has_test_data = True if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) guid = section_elem.get( 'guid' ) shed_tools_dict[ guid ] = galaxy_test_file_dir last_galaxy_test_file_dir = galaxy_test_file_dir - return shed_tools_dict + return has_test_data, shed_tools_dict diff -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a -r 513adadb31a2a4b014b3f03c5af2817919ea1760 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -5,6 +5,7 @@ # will execute this script with the appropriate parameters. import os, sys, shutil, tempfile, re, string, urllib, platform +from time import strftime # Assume we are run from the galaxy root directory, add lib to the python path cwd = os.getcwd() @@ -114,6 +115,27 @@ else: galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] +def execute_uninstall_method( repository_dict ): + # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them + # and try to re-run the tests after uninstalling the repository. + tests_to_delete = [] + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) + tests_to_delete.append( key ) + for key in tests_to_delete: + del test_toolbox.__dict__[ key ] + # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. + test_install_repositories.generate_uninstall_method( repository_dict ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed + # repository and delete it from disk. + result = run_tests( test_config ) + success = result.wasSuccessful() + return success + def get_api_url( base, parts=[], params=None, key=None ): if 'api' in parts and parts.index( 'api' ) != 0: parts.pop( parts.index( 'api' ) ) @@ -187,7 +209,7 @@ return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) def register_test_success( url, metadata_id ): - params = dict( tools_functionally_correct='true', do_not_test='false' ) + params = dict( tools_functionally_correct='true', do_not_test='true' ) return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) def run_tests( test_config ): @@ -209,6 +231,11 @@ galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', default_galaxy_test_host ) galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( default_galaxy_test_port_max ) ) + # Initialize some variables for the summary that will be printed to stdout. + repositories_tested = 0 + repositories_passed = 0 + repositories_failed = 0 + tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales @@ -373,132 +400,189 @@ log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) ) repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' ) log.info( "Retrieved %d repositories to install..." % len( repositories_to_install ) ) + repositories_tested = len( repositories_to_install ) + # This loop will iterate through the list of repositories returned by the above method, skipping any that are marked + # as deleted. For each repository, it will generate a test method that will use Twill to install that repository into the + # embedded Galaxy application that was started up, selecting to install repository and tool dependencies if they are + # defined. If the installation completes successfully, it will then generate a test case for each functional test + # defined for each tool in the repository, and execute the generated test cases. When this completes, it will record + # the result of the tests, and if any failed, the traceback and captured output of the tool that was run. + # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with + # the next repository's functional tests. for repository_to_install_dict in repositories_to_install: """ Each repository_to_install_dict looks something like: - {'repository_id': '175812cd7caaf439', - 'url': '/api/repository_revisions/175812cd7caaf439', - 'malicious': False, - 'downloadable': True, - 'changeset_revision': '2388033730f3', - 'id': '175812cd7caaf439'} + { + "changeset_revision": "13fa22a258b5", + "downloadable": true, + "id": "529fd61ab1c6cc36", + "malicious": false, + "repository_id": "529fd61ab1c6cc36", + "url": "/api/repository_revisions/529fd61ab1c6cc36" + } """ repository_id = repository_to_install_dict.get( 'repository_id', None ) changeset_revision = repository_to_install_dict.get( 'changeset_revision', None ) metadata_revision_id = repository_to_install_dict.get( 'id', None ) + # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_to_install_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the + # module that will generate the install methods. repository_info_dict = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict ) - # If a repository is deleted or malicious, we don't need to test it. - if repository_info_dict[ 'deleted' ] or repository_info_dict[ 'deprecated' ]: - log.info( "Skipping revision %s of repository id %s since it is either deleted or deprecated..." % ( str( changeset_revision ), str( repository_id ) ) ) + # We are testing deprecated repositories, because it is possible that a deprecated repository contains valid + # and functionally correct tools that someone has previously installed. Deleted repositories have never been installed, + # and therefore do not need to be checked. If they are undeleted, this script will then test them the next time it runs. + if repository_info_dict[ 'deleted' ]: + log.info( "Skipping revision %s of repository id %s since the repository is deleted..." % ( str( changeset_revision ), str( repository_id ) ) ) continue log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) + # Add repository details to the basic repository dict. repository_dict = dict( repository_info_dict.items() + repository_to_install_dict.items() ) """ - Each repository_dict looks something like: - {'repository_id': '175812cd7caaf439', - 'url': '/api/repository_revisions/175812cd7caaf439', - 'malicious': False, - 'downloadable': True, - 'changeset_revision': '2388033730f3', - 'id': '175812cd7caaf439'} + After the addition of the repository details, each repository_dict should now contain something like: + { + "changeset_revision": "13fa22a258b5", + "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", + "deleted": false, + "deprecated": false, + "description": "Convert column case.", + "downloadable": true, + "id": "529fd61ab1c6cc36", + "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", + "malicious": false, + "name": "change_case", + "owner": "test", + "private": false, + "repository_id": "529fd61ab1c6cc36", + "times_downloaded": 0, + "tool_shed_url": "http://toolshed.local:10001", + "url": "/api/repository_revisions/529fd61ab1c6cc36", + "user_id": "529fd61ab1c6cc36" + } """ - # Generate the method that will install this repository into the running Galaxy instance. + # Use the repository information dict to generate an install method that will install the repository into the embedded + # Galaxy application, with tool dependencies and repository dependencies, if any. test_install_repositories.generate_install_method( repository_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host # Configure nose to run the install method as a test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) - # Run the configured install method as a test. This method uses the Galaxy web interface to install the specified + # Run the configured install method as a test. This method uses the embedded Galaxy application's web interface to install the specified # repository, with tool and repository dependencies also selected for installation. result = run_tests( test_config ) success = result.wasSuccessful() - # If the installation succeeds, set up and run functional tests for this repository. This is equivalent to + # If the installation succeeds, configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed if success: log.debug( 'Installation of %s succeeded, running all defined functional tests.' % repository_dict[ 'name' ] ) - # Parse the tool panel config to get the test-data path for this repository. - if not os.path.exists( galaxy_shed_tools_dict ): - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) - shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # Write this to a file, so the functional test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - # Set up the environment so that test.functional.test_toolbox can find the Galaxy server we configured in this framework. - os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict - os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host - os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port - # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. - test_toolbox.toolbox = app.toolbox - # Generate the test methods for this installed repository. We need to pass in True here, or it will look - # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. - test_toolbox.build_tests( testing_shed_tools=True ) - # Set up nose to run the generated functional tests. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the configured tests. - result = run_tests( test_config ) - success = result.wasSuccessful() - repository_dict[ 'test_environment' ] = get_test_environment() - repository_dict[ 'functional_tests_passed' ] = success - test_errors = [] - if success: - register_test_success( galaxy_tool_shed_url, metadata_revision_id ) - log.debug( 'Repository %s installed and passed functional tests.' % repository_dict[ 'name' ] ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository + # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, + # and the tools_functionally_correct flag to False, as well as updating tool_test_errors. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) + has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + if not has_test_data: + log.error( 'Test data is missing for this repository. Updating repository and skipping functional tests.' ) + repository_status[ 'test_environment' ] = get_test_environment() + test_id = 'Find functional test data for %s' % repository_dict[ 'name' ] + test_errors = dict( test_id=test_id, + stdout='No test data found for changeset revision %s of repository %s owned by %s.' % \ + ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ], repository_dict[ 'owner' ] ) ) + repository_status[ 'test_errors' ] = [ test_errors ] + # Record the status of this repository in the tool shed. + register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_status ) + # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # repository using Twill. + execute_uninstall_method( repository_dict ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox + repositories_failed += 1 else: - # If the functional tests fail, log the output and submit it to the tool shed whence the repository was installed. - for failure in result.failures: - test_status = dict( test=str( failure[0] ) ) - log_output = failure[1].replace( '\\n', '\n' ) - log_output = re.sub( r'control \d+:.+', r'', log_output ) - log_output = re.sub( r'\n+', r'\n', log_output ) - appending_to = 'output' - tmp_output = {} - output = {} - for line in log_output.split( '\n' ): - if line.startswith( 'Traceback' ): - appending_to = 'traceback' - elif '>> end captured' in line: - continue - elif 'request returned None from get_history' in line: - continue - elif '>> begin captured logging <<' in line: - appending_to = 'logging' - continue - elif '>> begin captured stdout <<' in line: - appending_to = 'stdout' - continue - elif '>> begin captured stderr <<' in line: - appending_to = 'stderr' - continue - if appending_to not in tmp_output: - tmp_output[ appending_to ] = [] - tmp_output[ appending_to ].append( line ) - for output_type in [ 'stderr', 'stdout', 'traceback' ]: - if output_type in tmp_output: - test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] ) - test_errors.append( test_status ) - if test_errors: - repository_status[ 'test_environment' ] = get_test_environment() - repository_status[ 'test_errors' ] = test_errors - register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_status ) - log.debug( 'Repository %s installed, but did not pass functional tests.' % repository_dict[ 'name' ] ) - # Delete the completed tool functional tests from the test_toolbox.__dict__, otherwise nose will find them and try to re-run the - # tests after uninstalling the repository. - tests_to_delete = [] - for key in test_toolbox.__dict__: - if key.startswith( 'TestForTool_' ): - tests_to_delete.append( key ) - for key in tests_to_delete: - del test_toolbox.__dict__[ key ] - # Generate an uninstall method for this repository, so that the next repository has a clean environment for testing. - test_install_repositories.generate_uninstall_method( repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed - # repository and delete it from disk. - result = run_tests( test_config ) - success = result.wasSuccessful() + # If the repository does have a test-data directory, we write the generated shed_tools_dict to a file, so the functional + # test framework can find it. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) + log.info( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, str( shed_tools_dict ) ) ) + # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file, so that test.base.twilltestcase.setUp + # will find and parse it properly. + os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict + os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host + os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. + test_toolbox.toolbox = app.toolbox + # Generate the test methods for this installed repository. We need to pass in True here, or it will look + # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. + test_toolbox.build_tests( testing_shed_tools=True ) + # Set up nose to run the generated functional tests. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the configured tests. + result = run_tests( test_config ) + success = result.wasSuccessful() + # Record some information about the environment in which this test was run, in case a failure is specific to a certain processor + # architecture or operating system. + repository_dict[ 'test_environment' ] = get_test_environment() + repository_dict[ 'functional_tests_passed' ] = success + test_errors = [] + if success: + # This repository's tools passed all functional tests. Update the repository_metadata table in the tool shed's database + # to reflect that. Call the register_test_success method, which executes a PUT request to the repository_revisions API + # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and + # updates the time_last_tested field to today's date. + repositories_passed += 1 + register_test_success( galaxy_tool_shed_url, metadata_revision_id ) + log.debug( 'Revision %s of repository %s installed and passed functional tests.' % \ + ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ] ) ) + else: + # If the functional tests fail, log the output and update the failed changeset revision's metadata record in the tool shed via the API. + for failure in result.failures: + # Record the twill test identifier, so the repository owner can discover which test is failing. + test_status = dict( test_id=str( failure[0] ) ) + log_output = failure[1].replace( '\\n', '\n' ) + # Remove debug output that the reviewer or owner doesn't need. + log_output = re.sub( r'control \d+:.+', r'', log_output ) + log_output = re.sub( r'\n+', r'\n', log_output ) + appending_to = 'output' + tmp_output = {} + output = {} + # Iterate through the functional test output and extract only the important data. Captured logging is not recorded. + for line in log_output.split( '\n' ): + if line.startswith( 'Traceback' ): + appending_to = 'traceback' + elif '>> end captured' in line or '>> end tool' in line: + continue + elif 'request returned None from get_history' in line: + continue + elif '>> begin captured logging <<' in line: + appending_to = 'logging' + continue + elif '>> begin captured stdout <<' in line: + appending_to = 'stdout' + continue + elif '>> begin captured stderr <<' in line or '>> begin tool stderr <<' in line: + appending_to = 'stderr' + continue + if appending_to not in tmp_output: + tmp_output[ appending_to ] = [] + tmp_output[ appending_to ].append( line ) + for output_type in [ 'stderr', 'stdout', 'traceback' ]: + if output_type in tmp_output: + test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] ) + test_errors.append( test_status ) + if test_errors: + # Only update test_errors for this repository if it's not empty. + repository_status[ 'test_environment' ] = get_test_environment() + repository_status[ 'test_errors' ] = test_errors + # Call the register_test_failure method, which executes a PUT request to the repository_revisions API controller with the failure + # status of the test, and updates tool_test_errors with the relevant log data. + # This also sets the do_not_test and tools_functionally correct flags, and updates the time_last_tested field to today's date. + repositories_failed += 1 + register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_status ) + log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ + ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ] ) ) + # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # repository using Twill. + execute_uninstall_method( repository_dict ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox else: log.debug( 'Repository %s failed to install correctly.' % repository_dict[ 'name' ] ) except: @@ -528,10 +612,25 @@ pass else: log.debug( 'GALAXY_INSTALL_TEST_NO_CLEANUP set, not cleaning up.' ) + + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - repository installation and testing script completed." % now + print "# Repository revisions tested: %d" % repositories_tested + if repositories_tested > 0: + print "# Repository revisions passed: %d" % repositories_passed + print "# Repository revisions failed: %d" % repositories_failed + print "####################################################################################" + if success: return 0 else: return 1 if __name__ == "__main__": - sys.exit( main() ) + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - running repository installation and testing script." % now + print "####################################################################################" + return_code = main() + sys.exit( return_code ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: fix server_env saved output dir name; clean up prev. debugging statements
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2454aa4b6e7c/ changeset: 2454aa4b6e7c user: carlfeberhard date: 2013-03-01 18:49:08 summary: fix server_env saved output dir name; clean up prev. debugging statements affected #: 3 files diff -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -45,8 +45,6 @@ self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) else: self.tool_shed_registry = None - log.debug( 'self.config.tool_sheds_config: %s, self.tool_shed_registry: %s', - self.config.tool_sheds_config, self.tool_shed_registry ) # Initialize database / check for appropriate schema version. # If this # is a new installation, we'll restrict the tool migration messaging. from galaxy.model.migrate.check import create_or_verify_database diff -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -42,7 +42,6 @@ import nose.loader import nose.plugins.manager -import pprint log = logging.getLogger( "functional_tests.py" ) default_galaxy_test_host = "localhost" @@ -227,7 +226,6 @@ kwargs[ 'object_store' ] = 'distributed' kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample' # Build the Universe Application - print 'app.kwargs:\n%s' %( pprint.pformat( kwargs ) ) app = UniverseApplication( job_queue_workers = 5, id_secret = 'changethisinproductiontoo', template_path = "templates", diff -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a test/casperjs/server_env.py --- a/test/casperjs/server_env.py +++ b/test/casperjs/server_env.py @@ -29,6 +29,9 @@ @classmethod def instance( cls, config=None ): + """Returns the singleton of TestEnvironment, instantiating it first if it + does not yet exist. + """ # singleton pattern if( ( not cls._instance ) or ( config ) ): @@ -36,25 +39,26 @@ cls._instance = cls( config ) return cls._instance - @classmethod - def get_server_url( cls ): - return cls.instance().url - def __init__( self, env_config_dict=None ): self.config = env_config_dict or {} - self.protocol = self._get_setting_from_config_or_env( 'protocol', self.ENV_PROTOCOL, self.DEFAULT_PROTOCOL ) - self.host = self._get_setting_from_config_or_env( 'host', self.ENV_HOST, self.DEFAULT_HOST ) - self.port = self._get_setting_from_config_or_env( 'port', self.ENV_PORT, self.DEFAULT_PORT ) + self.protocol = self._get_setting_from_config_or_env( + 'protocol', self.ENV_PROTOCOL, self.DEFAULT_PROTOCOL ) + self.host = self._get_setting_from_config_or_env( + 'host', self.ENV_HOST, self.DEFAULT_HOST ) + self.port = self._get_setting_from_config_or_env( + 'port', self.ENV_PORT, self.DEFAULT_PORT ) - self.history_id = self._get_setting_from_config_or_env( 'history_id', self.ENV_HISTORY_ID, default=None ) - self.file_dir = self._get_setting_from_config_or_env( 'file_dir', self.ENV_FILE_DIR, default=None ) + self.history_id = self._get_setting_from_config_or_env( + 'history_id', self.ENV_HISTORY_ID, default=None ) + self.file_dir = self._get_setting_from_config_or_env( + 'file_dir', self.ENV_FILE_DIR, default=None ) self.tool_shed_test_file = self._get_setting_from_config_or_env( 'tool_shed_test_file', self.ENV_TOOL_SHED_TEST_FILE, default=None ) self.shed_tools_dict = self._get_shed_tools_dict() - self.keepOutdir = self._get_setting_from_config_or_env( + self.saved_output_dir = self._get_setting_from_config_or_env( 'saved_output_dir', self.ENV_SAVED_FILES_DIR, default=None ) self._init_saved_files_dir() @@ -62,6 +66,7 @@ """Try to get a setting from (in order): TestEnvironment.config, the os env, or some default (if not False). """ + #TODO: if falsy value needed, use None - not ideal config = self.config.get( config_name, None ) env = os.environ.get( env_name, None ) if( ( not ( config or env ) ) @@ -94,6 +99,8 @@ @property def url( self ): + """Builds and returns the url of the test server. + """ url = '%s://%s' %( self.protocol, self.host ) if self.port and self.port != 80: url += ':%s' %( str( self.port ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add RepositoryMetadata attributes that enable improved query abilities for tool shed repository revisions that contain Galaxy utilities.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/153f7f450f4b/ changeset: 153f7f450f4b user: greg date: 2013-03-01 17:13:15 summary: Add RepositoryMetadata attributes that enable improved query abilities for tool shed repository revisions that contain Galaxy utilities. affected #: 6 files diff -r 21c69586390abeefde4a52560321b826473ad041 -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -33,6 +33,7 @@ class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): return category.name @@ -43,6 +44,7 @@ class RepositoriesColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): if category.repositories: viewable_repositories = 0 @@ -82,6 +84,7 @@ class RepositoriesColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): if category.repositories: viewable_repositories = 0 @@ -123,6 +126,7 @@ class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): return escape_html( repository.name ) @@ -468,6 +472,7 @@ class CategoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): rval = '<ul>' if repository.categories: @@ -481,6 +486,7 @@ class RepositoryCategoryColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): """Modify query to filter by category.""" if column_filter == "All": @@ -501,6 +507,7 @@ elif len( select_field.options ) == 1: return select_field.options[ 0 ][ 0 ] return '' + title = "Valid repositories" columns = [ RepositoryGrid.NameColumn( "Name", @@ -633,19 +640,171 @@ attach_popup=False ) +class RepositoryMetadataGrid( grids.Grid ): + + + class RepositoryNameColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + return escape_html( repository_metadata.repository.name ) + + + class RepositoryOwnerColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + return escape_html( repository_metadata.user.username ) + + + class ChangesetRevisionColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + return escape_html( repository_metadata.changeset_revision ) + + + class MaliciousColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.malicious: + return 'yes' + return '' + + + class DownloadableColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.downloadable: + return 'yes' + return '' + + + class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.tools_functionally_correct: + return 'yes' + return '' + + + class DoNotTestColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.do_not_test: + return 'yes' + return '' + + + class TimeLastTestedColumn( grids.DateTimeColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.time_last_tested + + + class HasRepositoryDependenciesColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.has_repository_dependencies: + return 'yes' + return '' + + + class IncludesDatatypesColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.includes_datatypes: + return 'yes' + return '' + + + class IncludesToolsColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.includes_tools: + return 'yes' + return '' + + + class IncludesToolDependenciesColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.includes_tool_dependencies: + return 'yes' + return '' + + + class IncludesWorkflowsColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.includes_workflows: + return 'yes' + return '' + + title = "Repository metadata" + model_class = model.RepositoryMetadata + template='/webapps/tool_shed/repository/grid.mako' + default_sort_key = "Repository.name" + columns = [ + RepositoryNameColumn( "Repository name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=False ), + RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, description", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [] + standard_filters = [] + default_filter = dict( malicious="False" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + +class RepositoryDependenciesGrid( RepositoryMetadataGrid ): + + title = "Repository dependencies available in this Tool Shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=False ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, description", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.has_repository_dependencies == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + class RepositoryController( BaseUIController, common_util.ItemRatings ): + category_grid = CategoryGrid() + deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid() + email_alerts_repository_grid = EmailAlertsRepositoryGrid() install_matched_repository_grid = InstallMatchedRepositoryGrid() matched_repository_grid = MatchedRepositoryGrid() + my_writable_repositories_grid = MyWritableRepositoriesGrid() + repositories_by_user_grid = RepositoriesByUserGrid() + repositories_i_own_grid = RepositoriesIOwnGrid() + repository_grid = RepositoryGrid() + # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. + repository_metadata_grid = RepositoryMetadataGrid() + valid_category_grid = ValidCategoryGrid() valid_repository_grid = ValidRepositoryGrid() - repository_grid = RepositoryGrid() - email_alerts_repository_grid = EmailAlertsRepositoryGrid() - category_grid = CategoryGrid() - valid_category_grid = ValidCategoryGrid() - my_writable_repositories_grid = MyWritableRepositoriesGrid() - repositories_i_own_grid = RepositoriesIOwnGrid() - deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid() - repositories_by_user_grid = RepositoriesByUserGrid() @web.expose def browse_categories( self, trans, **kwd ): @@ -3036,7 +3195,11 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: repository_metadata_id = trans.security.encode_id( repository_metadata.id ) - tool_test_errors = json.from_json_string( repository_metadata.tool_test_errors ) + # TODO: Fix this when the install and test framework is completed. + # if repository_metadata.tool_test_errors: + # tool_test_errors = json.from_json_string( repository_metadata.tool_test_errors ) + # else: + # tool_test_errors = None metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: @@ -3070,7 +3233,7 @@ else: repository_metadata_id = None metadata = None - tool_test_errors = None + #tool_test_errors = None is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, @@ -3094,7 +3257,7 @@ tool=tool, tool_metadata_dict=tool_metadata_dict, tool_lineage=tool_lineage, - tool_test_errors=tool_test_errors, + #tool_test_errors=tool_test_errors, changeset_revision=changeset_revision, revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, diff -r 21c69586390abeefde4a52560321b826473ad041 -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -191,11 +191,14 @@ fp.close() class RepositoryMetadata( object, APIItem ): - api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable' ) + api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'has_repository_dependencies', 'includes_datatypes', + 'includes_tools', 'includes_tool_dependencies', 'includes_workflows' ) api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', - 'do_not_test', 'time_last_tested', 'tool_test_errors' ) + 'do_not_test', 'time_last_tested', 'tool_test_errors', 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', + 'includes_tool_dependencies', 'includes_workflows' ) def __init__( self, id=None, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, - tools_functionally_correct=False, do_not_test=False, time_last_tested=None, tool_test_errors=None ): + tools_functionally_correct=False, do_not_test=False, time_last_tested=None, tool_test_errors=None, has_repository_dependencies=False, + includes_datatypes=False, includes_tools=False, includes_tool_dependencies=False, includes_workflows=False ): self.id = id self.repository_id = repository_id self.changeset_revision = changeset_revision @@ -207,6 +210,11 @@ self.do_not_test = do_not_test self.time_last_tested = time_last_tested self.tool_test_errors = tool_test_errors + self.has_repository_dependencies = has_repository_dependencies + self.includes_datatypes = includes_datatypes + self.includes_tools = includes_tools + self.includes_tool_dependencies = includes_tool_dependencies + self.includes_workflows = includes_workflows def as_dict( self, value_mapper=None ): return self.get_api_value( view='element', value_mapper=value_mapper ) def get_api_value( self, view='collection', value_mapper=None ): @@ -227,8 +235,8 @@ return rval class RepositoryReview( object, APIItem ): - api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating' ) - api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating' ) + api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' ) + api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'user_id', 'rating', 'deleted' ) approved_states = Bunch( NO='no', YES='yes' ) def __init__( self, repository_id=None, changeset_revision=None, user_id=None, rating=None, deleted=False ): self.repository_id = repository_id diff -r 21c69586390abeefde4a52560321b826473ad041 -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -134,7 +134,12 @@ Column( "tools_functionally_correct", Boolean, default=False, index=True ), Column( "do_not_test", Boolean, default=False, index=True ), Column( "time_last_tested", DateTime, default=None, nullable=True ), - Column( "tool_test_errors", JSONType, nullable=True ) ) + Column( "tool_test_errors", JSONType, nullable=True ), + Column( "has_repository_dependencies", Boolean, default=False, index=True ), + Column( "includes_datatypes", Boolean, default=False, index=True ), + Column( "includes_tools", Boolean, default=False, index=True ), + Column( "includes_tool_dependencies", Boolean, default=False, index=True ), + Column( "includes_workflows", Boolean, default=False, index=True ) ) RepositoryReview.table = Table( "repository_review", metadata, Column( "id", Integer, primary_key=True ), diff -r 21c69586390abeefde4a52560321b826473ad041 -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py @@ -0,0 +1,115 @@ +""" +Migration script to add the includes_datatypes, has_repository_dependencies, includes_tools, includes_tool_dependencies and includes_workflows +columns to the repository_metadata table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + # Initialize. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + # Create and initialize tools_functionally_correct, do_not_test, time_last_tested, and tool_test_errors columns in repository_metadata table. + RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) + + # Create tools_functionally_correct column + c = Column( "includes_datatypes", Boolean, default=False, index=True ) + try: + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.includes_datatypes + db_session.execute( "UPDATE repository_metadata SET includes_datatypes=%s" % default_false ) + except Exception, e: + print "Adding includes_datatypes column to the repository_metadata table failed: %s" % str( e ) + + # Create includes_datatypes column + c = Column( "has_repository_dependencies", Boolean, default=False, index=True ) + try: + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.has_repository_dependencies + db_session.execute( "UPDATE repository_metadata SET has_repository_dependencies=%s" % default_false ) + except Exception, e: + print "Adding has_repository_dependencies column to the repository_metadata table failed: %s" % str( e ) + + # Create includes_tools column + c = Column( "includes_tools", Boolean, default=False, index=True ) + try: + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.includes_tools + db_session.execute( "UPDATE repository_metadata SET includes_tools=%s" % default_false ) + except Exception, e: + print "Adding includes_tools column to the repository_metadata table failed: %s" % str( e ) + + # Create includes_tool_dependencies column + c = Column( "includes_tool_dependencies", Boolean, default=False, index=True ) + try: + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.includes_tool_dependencies + db_session.execute( "UPDATE repository_metadata SET includes_tool_dependencies=%s" % default_false ) + except Exception, e: + print "Adding includes_tool_dependencies column to the repository_metadata table failed: %s" % str( e ) + + # Create includes_workflows column + c = Column( "includes_workflows", Boolean, default=False, index=True ) + try: + c.create( RepositoryMetadata_table ) + assert c is RepositoryMetadata_table.c.includes_workflows + db_session.execute( "UPDATE repository_metadata SET includes_workflows=%s" % default_false ) + except Exception, e: + print "Adding includes_workflows column to the repository_metadata table failed: %s" % str( e ) + +def downgrade(): + metadata.reflect() + # Drop tool_test_errors, time_last_tested, do_not_test, and tools_functionally_correct columns from repository_metadata table. + RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True ) + + # Drop the includes_workflows column. + try: + RepositoryMetadata_table.c.includes_workflows.drop() + except Exception, e: + print "Dropping column includes_workflows from the repository_metadata table failed: %s" % str( e ) + + # Drop the includes_tool_dependencies column. + try: + RepositoryMetadata_table.c.includes_tool_dependencies.drop() + except Exception, e: + print "Dropping column includes_tool_dependencies from the repository_metadata table failed: %s" % str( e ) + + # Drop the includes_tools column. + try: + RepositoryMetadata_table.c.includes_tools.drop() + except Exception, e: + print "Dropping column includes_tools from the repository_metadata table failed: %s" % str( e ) + + # Drop the has_repository_dependencies column. + try: + RepositoryMetadata_table.c.has_repository_dependencies.drop() + except Exception, e: + print "Dropping column has_repository_dependencies from the repository_metadata table failed: %s" % str( e ) + + # Drop the includes_datatypes column. + try: + RepositoryMetadata_table.c.includes_datatypes.drop() + except Exception, e: + print "Dropping column includes_datatypes from the repository_metadata table failed: %s" % str( e ) diff -r 21c69586390abeefde4a52560321b826473ad041 -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -900,16 +900,42 @@ shutil.copy( full_source_path, os.path.join( dest_path, copied_file ) ) def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): """Create or update a repository_metadatqa record in the tool shed.""" - downloadable = is_downloadable( metadata_dict ) + has_repository_dependencies = False + includes_datatypes = False + includes_tools = False + includes_tool_dependencies = False + includes_workflows = False + if metadata_dict: + if 'repository_dependencies' in metadata_dict: + has_repository_dependencies = True + if 'datatypes' in metadata_dict: + includes_datatypes = True + if 'tools' in metadata_dict: + includes_tools = True + if 'tool_dependencies' in metadata_dict: + includes_tool_dependencies = True + if 'workflows' in metadata_dict: + includes_workflows = True + downloadable = has_repository_dependencies or includes_datatypes or includes_tools or includes_tool_dependencies or includes_workflows repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: repository_metadata.metadata = metadata_dict repository_metadata.downloadable = downloadable + repository_metadata.has_repository_dependencies = has_repository_dependencies + repository_metadata.includes_datatypes = includes_datatypes + repository_metadata.includes_tools = includes_tools + repository_metadata.includes_tool_dependencies = includes_tool_dependencies + repository_metadata.includes_workflows = includes_workflows else: repository_metadata = trans.model.RepositoryMetadata( repository_id=repository.id, changeset_revision=changeset_revision, metadata=metadata_dict, - downloadable=downloadable ) + downloadable=downloadable, + has_repository_dependencies=has_repository_dependencies, + includes_datatypes=includes_datatypes, + includes_tools=includes_tools, + includes_tool_dependencies=includes_tool_dependencies, + includes_workflows=includes_workflows ) # Always set the default values for the following columns. When resetting all metadata on a repository, this will reset the values. repository_metadata.tools_functionally_correct = False repository_metadata.do_not_test = False diff -r 21c69586390abeefde4a52560321b826473ad041 -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee templates/webapps/tool_shed/repository/view_tool_metadata.mako --- a/templates/webapps/tool_shed/repository/view_tool_metadata.mako +++ b/templates/webapps/tool_shed/repository/view_tool_metadata.mako @@ -22,6 +22,8 @@ can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) can_upload = can_push can_view_change_log = trans.webapp.name == 'tool_shed' and not is_new + # TODO: fix the following when the install and test buildbot is functional. + #can_view_tool_test_errors = tool_test_errors is not None if can_push: browse_label = 'Browse or delete repository tip files' @@ -265,11 +267,26 @@ ${tool.force_history_refresh | h} <div style="clear: both"></div></div> - <div class="form-row"> - <label>Parallelism:</label> - ${tool.parallelism | h} - <div style="clear: both"></div> - </div> + <% parallelism_info = tool.parallelism %> + %if parallelism_info: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Parallelism</td></tr> + </table> + </div> + <div class="form-row"> + <label>Method:</label> + ${parallelism_info.method | h} + <div style="clear: both"></div> + </div> + %for key, val in parallelism_info.attributes.items(): + <div class="form-row"> + <label>${key}:</label> + ${val | h} + <div style="clear: both"></div> + </div> + %endfor + %endif %endif <div class="form-row"><table width="100%"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix the level 16 database migration script for the tool shed.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/21c69586390a/ changeset: 21c69586390a user: greg date: 2013-03-01 16:52:13 summary: Fix the level 16 database migration script for the tool shed. affected #: 1 file diff -r 12dc58f5831ef32aff9c69761a251476f567ef69 -r 21c69586390abeefde4a52560321b826473ad041 lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py --- a/lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py @@ -65,7 +65,6 @@ log.debug( "Adding time_last_tested column to the repository_metadata table failed: %s" % str( e ) ) c = Column( "tool_test_errors", JSONType, nullable=True ) try: - pass # Create tool_test_errors column c.create( RepositoryMetadata_table ) assert c is RepositoryMetadata_table.c.tool_test_errors Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for starting up Galaxy after community webapp was renamed to be tool_shed.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/12dc58f5831e/ changeset: 12dc58f5831e user: greg date: 2013-03-01 16:16:20 summary: Fix for starting up Galaxy after community webapp was renamed to be tool_shed. affected #: 1 file diff -r 5f774e034512d06c497febcf042d3dbc44d91cf8 -r 12dc58f5831ef32aff9c69761a251476f567ef69 lib/tool_shed/galaxy_install/__init__.py --- a/lib/tool_shed/galaxy_install/__init__.py +++ b/lib/tool_shed/galaxy_install/__init__.py @@ -28,9 +28,9 @@ ElementInclude.include( root ) tool_path = root.get( 'tool_path', None ) if tool_path: - tool_shed = tool_shed.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) + ts = tool_shed.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) relative_path = os.path.join( tool_path, - tool_shed, + ts, 'repos', tool_shed_repository.owner, tool_shed_repository.name, @@ -45,13 +45,13 @@ .order_by( self.model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - installed_repository_dict = galaxy.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = tool_shed.util.shed_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) if installed_repository_dict: self.installed_repository_dicts.append( installed_repository_dict ) def load_proprietary_converters_and_display_applications( self, deactivate=False ): for installed_repository_dict in self.installed_repository_dicts: if installed_repository_dict[ 'converter_path' ]: - galaxy.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + tool_shed.util.shed_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - galaxy.util.shed_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + tool_shed.util.shed_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the method for displaying tool functional test errors for a repository in the tool shed to the repository controller in preparation for the upcoming install and test framework.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f774e034512/ changeset: 5f774e034512 user: greg date: 2013-03-01 15:14:38 summary: Add the method for displaying tool functional test errors for a repository in the tool shed to the repository controller in preparation for the upcoming install and test framework. affected #: 1 file diff -r 15eafd606d97f9700b5ec9bfc92bb8c50badd365 -r 5f774e034512d06c497febcf042d3dbc44d91cf8 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1137,6 +1137,9 @@ @web.expose @web.require_login( "deprecate repository" ) def deprecate( self, trans, **kwd ): + """Mark a repository in the tool shed as deprecated or not deprecated.""" + # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset revisions that may be associated with the + # repository. Revisions are not marked as not downlaodable because those that have installed the repository must be allowed to get updates. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1195,6 +1198,43 @@ status='error' ) ) @web.expose + def display_tool_functional_test_errors( self, trans, repository_id, repository_metadata_id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = suc.get_repository_by_id( trans.app, repository_id ) + if repository: + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + changeset_revision = repository_metadata.changeset_revision + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + return trans.fill_template( '/webapps/tool_shed/repository/display_tool_functional_test_errors.mako', + repository=repository, + repository_metadata=repository_metadata, + message=message, + status=status ) + else: + message = 'Missing metadata for revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b>.' % \ + ( str( changeset_revision ), str( repository.name ), str( repository.user.username ) ) + else: + message = 'Invalid repository_metadata_id <b>%s</b> received for displaying functional test errors for repository <b>%s</b>.' % \ + ( str( repository_metadata_id ), str( repository.name ) ) + else: + message = 'Invalid repository_id received for displaying functional test errors.<b>%s</b>.' % str( repository_id ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + message=message, + status='error' ) ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + operation='view_or_manage_repository', + id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) + + @web.expose def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): # Download an archive of the repository files compressed as zip, gz or bz2. params = util.Params( kwd ) @@ -2995,6 +3035,8 @@ revision_label = suc.get_revision_label( trans, repository, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ) + tool_test_errors = json.from_json_string( repository_metadata.tool_test_errors ) metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: @@ -3026,7 +3068,9 @@ if guid: tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) else: + repository_metadata_id = None metadata = None + tool_test_errors = None is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, @@ -3045,10 +3089,12 @@ review_id = None return trans.fill_template( "/webapps/tool_shed/repository/view_tool_metadata.mako", repository=repository, + repository_metadata_id=repository_metadata_id, metadata=metadata, tool=tool, tool_metadata_dict=tool_metadata_dict, tool_lineage=tool_lineage, + tool_test_errors=tool_test_errors, changeset_revision=changeset_revision, revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cede7e36e826/ changeset: cede7e36e826 user: jmchilton date: 2013-03-01 06:56:56 summary: Update LWR client to pass along tool id and version, required if LWR server is configured to point to a toolbox. The LWR server uses this information to match the job up with a tool and uses the tool to validate inputs. For more information see: https://lwr.readthedocs.org/en/latest/#setting-up-a-public-lwr-server https://bitbucket.org/jmchilton/lwr/src/tip/test/validator_test.py Updates the LWR client to revision 8a249f4254eb6aa1eed8669f738c5a9764caccdb of the LWR. https://bitbucket.org/jmchilton/lwr/commits/8a249f4254eb6aa1eed8669f738c5a9… affected #: 2 files diff -r d1ab12313b6acfbfd51a38195d9c5e75716e7752 -r cede7e36e8261b2cd11f04db67dc92292412b74c lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -69,7 +69,8 @@ output_files = self.get_output_files(job_wrapper) input_files = job_wrapper.get_input_fnames() working_directory = job_wrapper.working_directory - file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory) + tool = job_wrapper.tool + file_stager = FileStager(client, tool, command_line, job_wrapper.extra_filenames, input_files, output_files, working_directory) rebuilt_command_line = file_stager.get_rewritten_command_line() job_id = file_stager.job_id client.launch( rebuilt_command_line ) @@ -228,4 +229,4 @@ elif job.get_state() == model.Job.states.QUEUED: # LWR doesn't queue currently, so this indicates galaxy was shutoff while # job was being staged. Not sure how to recover from that. - job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) \ No newline at end of file + job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) diff -r d1ab12313b6acfbfd51a38195d9c5e75716e7752 -r cede7e36e8261b2cd11f04db67dc92292412b74c lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -132,7 +132,7 @@ """ - def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory): + def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): """ """ self.client = client @@ -140,7 +140,9 @@ self.config_files = config_files self.input_files = input_files self.output_files = output_files - self.tool_dir = os.path.abspath(tool_dir) + self.tool_id = tool.id + self.tool_version = tool.version + self.tool_dir = os.path.abspath(tool.tool_dir) self.working_directory = working_directory # Setup job inputs, these will need to be rewritten before @@ -161,7 +163,7 @@ self.__upload_rewritten_config_files() def __handle_setup(self): - job_config = self.client.setup() + job_config = self.client.setup(self.tool_id, self.tool_version) self.new_working_directory = job_config['working_directory'] self.new_outputs_directory = job_config['outputs_directory'] @@ -480,11 +482,16 @@ self.__raw_execute("clean", {"job_id": self.job_id}) @parseJson() - def setup(self): + def setup(self, tool_id=None, tool_version=None): """ Setup remote LWR server to run this job. """ - return self.__raw_execute("setup", {"job_id": self.job_id}) + setup_args = {"job_id": self.job_id} + if tool_id: + setup_args["tool_id"] = tool_id + if tool_version: + setup_args["tool_version"] = tool_version + return self.__raw_execute("setup", setup_args) def _read(path): https://bitbucket.org/galaxy/galaxy-central/commits/15eafd606d97/ changeset: 15eafd606d97 user: natefoo date: 2013-03-01 14:23:58 summary: Merged in jmchilton/galaxy-central-lwr (pull request #132) Updates required to target LWR servers configured to point to a toolbox. affected #: 2 files diff -r 3110de3062acd1eea7f57b717b434a44b0429447 -r 15eafd606d97f9700b5ec9bfc92bb8c50badd365 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -69,7 +69,8 @@ output_files = self.get_output_files(job_wrapper) input_files = job_wrapper.get_input_fnames() working_directory = job_wrapper.working_directory - file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory) + tool = job_wrapper.tool + file_stager = FileStager(client, tool, command_line, job_wrapper.extra_filenames, input_files, output_files, working_directory) rebuilt_command_line = file_stager.get_rewritten_command_line() job_id = file_stager.job_id client.launch( rebuilt_command_line ) @@ -228,4 +229,4 @@ elif job.get_state() == model.Job.states.QUEUED: # LWR doesn't queue currently, so this indicates galaxy was shutoff while # job was being staged. Not sure how to recover from that. - job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) \ No newline at end of file + job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." ) diff -r 3110de3062acd1eea7f57b717b434a44b0429447 -r 15eafd606d97f9700b5ec9bfc92bb8c50badd365 lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -132,7 +132,7 @@ """ - def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory): + def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory): """ """ self.client = client @@ -140,7 +140,9 @@ self.config_files = config_files self.input_files = input_files self.output_files = output_files - self.tool_dir = os.path.abspath(tool_dir) + self.tool_id = tool.id + self.tool_version = tool.version + self.tool_dir = os.path.abspath(tool.tool_dir) self.working_directory = working_directory # Setup job inputs, these will need to be rewritten before @@ -161,7 +163,7 @@ self.__upload_rewritten_config_files() def __handle_setup(self): - job_config = self.client.setup() + job_config = self.client.setup(self.tool_id, self.tool_version) self.new_working_directory = job_config['working_directory'] self.new_outputs_directory = job_config['outputs_directory'] @@ -480,11 +482,16 @@ self.__raw_execute("clean", {"job_id": self.job_id}) @parseJson() - def setup(self): + def setup(self, tool_id=None, tool_version=None): """ Setup remote LWR server to run this job. """ - return self.__raw_execute("setup", {"job_id": self.job_id}) + setup_args = {"job_id": self.job_id} + if tool_id: + setup_args["tool_id"] = tool_id + if tool_version: + setup_args["tool_version"] = tool_version + return self.__raw_execute("setup", setup_args) def _read(path): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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