From 4ea8dd779bb40d338ba2a85ea081342f632b64b0 Mon Sep 17 00:00:00 2001 From: Kanwei Li Date: Wed, 1 Sep 2010 18:20:42 -0400 Subject: [PATCH] trackster: Changing display mode from "Auto" now fetches additional detail data and displays features. Displays error messages in canvas elements if present. Limit number of features displayed in one tile due to above feature. Fix bugs in visualization creation from form --- .../tracks/data/interval_index.py | 10 +++- lib/galaxy/web/controllers/tracks.py | 3 +- lib/galaxy/web/controllers/visualization.py | 51 +++++++------------ static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 25 ++++++--- templates/tracks/browser.mako | 1 + 6 files changed, 48 insertions(+), 44 deletions(-) diff --git a/lib/galaxy/visualization/tracks/data/interval_index.py b/lib/galaxy/visualization/tracks/data/interval_index.py index a974c6ff382..3bca5ca1019 100644 --- a/lib/galaxy/visualization/tracks/data/interval_index.py +++ b/lib/galaxy/visualization/tracks/data/interval_index.py @@ -9,6 +9,8 @@ import pkg_resources; pkg_resources.require( "bx-python" ) from bx.interval_index_file import Indexes from galaxy.datatypes.interval import Bed, Gff +MAX_VALS = 500 # only display first MAX_VALS features + class IntervalIndexDataProvider( object ): def __init__( self, converted_dataset, original_dataset ): self.original_dataset = original_dataset @@ -20,8 +22,14 @@ class IntervalIndexDataProvider( object ): source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) results = [] + count = 0 + message = None for start, end, offset in index.find(chrom, start, end): + if count >= MAX_VALS: + message = "Only the first %s features are being displayed." % MAX_VALS + break + count += 1 source.seek(offset) feature = source.readline().split() payload = [ offset, start, end ] @@ -53,4 +61,4 @@ class IntervalIndexDataProvider( object ): results.append(payload) - return results + return { 'data': results, 'message': message } diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py index 770acb02e45..95d2b926539 100644 --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -291,7 +291,8 @@ class TracksController( BaseController, UsesVisualization ): # Have to choose between indexer and data provider indexer = dataset_type_to_data_provider[data_sources['index']]( dataset.get_converted_dataset(trans, data_sources['index']), dataset ) summary = indexer.get_summary( chrom, low, high, **kwargs ) - if summary is not None: + if summary is not None and kwargs.get("mode", "Auto") == "Auto": + # Only check for summary if it's Auto mode (which is the default) if summary == "no_detail": kwargs["no_detail"] = True # meh extra_info = "no_detail" diff --git a/lib/galaxy/web/controllers/visualization.py b/lib/galaxy/web/controllers/visualization.py index 0f589309ce9..e5f75b485a6 100644 --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -228,7 +228,7 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi # Get session and visualization. session = trans.sa_session - visualization = trans.sa_session.query( model.Visualization ).get( trans.security.decode_id( id ) ) + visualization = self.get_visualization( trans, id, check_ownership=True ) # Do operation on visualization. if 'make_accessible_via_link' in kwargs: @@ -261,7 +261,7 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi def share( self, trans, id=None, email="", use_panels=False ): """ Handle sharing a visualization with a particular user. """ msg = mtype = None - visualization = trans.sa_session.query( model.Visualization ).get( trans.security.decode_id( id ) ) + visualization = self.get_visualization( trans, id, check_ownership=True ) if email: other = trans.sa_session.query( model.User ) \ .filter( and_( model.User.table.c.email==email, @@ -330,7 +330,7 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi @web.require_login( "get item name and link" ) def get_name_and_link_async( self, trans, id=None ): """ Returns visualization's name and link. """ - visualization = self.get_visualization( trans, id ) + visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) if self.create_item_slug( trans.sa_session, visualization ): trans.sa_session.flush() @@ -342,7 +342,7 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi """ Returns item content in HTML format. """ # Get visualization, making sure it's accessible. - visualization = self.get_visualization( trans, id, False, True ) + visualization = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) if visualization is None: raise web.httpexceptions.HTTPNotFound() @@ -373,25 +373,26 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi visualization = model.Visualization() visualization.title = visualization_title visualization.slug = visualization_slug + visualization.dbkey = visualization_dbkey + visualization.type = 'trackster' # HACK: set visualization type to trackster since it's the only viz visualization_annotation = sanitize_html( visualization_annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans, visualization, visualization_annotation ) visualization.user = user + # And the first (empty) visualization revision visualization_revision = model.VisualizationRevision() visualization_revision.title = visualization_title + visualization_revision.config = {} + visualization_revision.dbkey = visualization_dbkey visualization_revision.visualization = visualization - # HACK: set visualization type to trackster; when we have multiple visualization types, we'll need to get type from the user. - visualization.type = 'trackster' visualization.latest_revision = visualization_revision - # Visualization config is dbkey for now. - visualization.latest_revision.config = { 'dbkey' : visualization_dbkey } - visualization_revision.content = "" + # Persist session = trans.sa_session - session.add( visualization ) + session.add(visualization) + session.add(visualization_revision) session.flush() - # Display the management visualization - ## trans.set_message( "Visualization '%s' created" % visualization.title ) + return trans.response.send_redirect( web.url_for( action='list' ) ) return trans.show_form( @@ -414,12 +415,9 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi """ Edit a visualization's attributes. """ - encoded_id = id - id = trans.security.decode_id( id ) + visualization = self.get_visualization( trans, id, check_ownership=True ) session = trans.sa_session - visualization = session.query( model.Visualization ).get( id ) - user = trans.user - assert visualization.user == user + visualization_title_err = visualization_slug_err = visualization_annotation_err = "" if trans.request.method == "POST": if not visualization_title: @@ -428,7 +426,7 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi visualization_slug_err = "Visualization id is required" elif not VALID_SLUG_RE.match( visualization_slug ): visualization_slug_err = "Visualization identifier must consist of only lowercase letters, numbers, and the '-' character" - elif visualization_slug != visualization.slug and trans.sa_session.query( model.Visualization ).filter_by( user=user, slug=visualization_slug, deleted=False ).first(): + elif visualization_slug != visualization.slug and trans.sa_session.query( model.Visualization ).filter_by( user=visualization.user, slug=visualization_slug, deleted=False ).first(): visualization_slug_err = "Visualization id must be unique" else: visualization.title = visualization_title @@ -449,7 +447,7 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi if not visualization_annotation: visualization_annotation = "" return trans.show_form( - web.FormBuilder( web.url_for( id=encoded_id ), "Edit visualization attributes", submit_text="Submit" ) + web.FormBuilder( web.url_for( id=id ), "Edit visualization attributes", submit_text="Submit" ) .add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err ) .add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err, help="""A unique identifier that will be used for @@ -460,18 +458,5 @@ class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVi .add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err, help="A description of the visualization; annotation is shown alongside published visualizations."), template="visualization/create.mako" ) - - # @web.expose - # @web.require_login() - # def list( self, trans, *args, **kwargs ): - # return self.list_grid( trans, *args, **kwargs ) - - #@web.expose - #@web.require_admin - #def index( self, trans, *args, **kwargs ): - # # Build grid - # grid = self.list( trans, *args, **kwargs ) - # # Render grid wrapped in panels - # return trans.fill_template( "visualization/index.mako", grid=grid ) - + \ No newline at end of file diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js index ccb0759f993..92ee7e0ad19 100644 --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1 +1 @@ -var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. 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").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.hidden=true;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$(""),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("
").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"relative",top:"32px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+32+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$(""),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("
").addClass("form-row");var e="track_"+k+"_minval",h=$("").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=2;this.summary_draw_height=20;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;wy[0]&&ePX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(Y,l,o,al){var F=l*DENSITY*Y,ae=(l+1)*DENSITY*Y,E=ae-F;var af=(!this.initial_canvas?"initial":F+"_"+ae);var A=this.data_cache.get(af);var d;if(A===undefined){this.data_queue[[F,ae]]=true;this.get_data(F,ae);return}var a=Math.ceil(E*al),M=$(""),aa=this.prefs.label_color,g=this.prefs.block_color,n=this.mode,W=(n==="Squish")||(n==="Dense")&&(n!=="Pack")||(n==="Auto"&&(A.extra_info==="no_detail")),Q=this.left_offset,ak,t,am;if(A.dataset_type==="summary_tree"){t=this.summary_draw_height}else{if(n==="Dense"){t=15;am=10}else{am=(W?this.vertical_nodetail_px:this.vertical_detail_px);t=this.incremental_slots(this.view.zoom_res,A.data,W,n)*am+15;ak=this.inc_slots[this.view.zoom_res]}}M.css({position:"absolute",top:0,left:(F-this.view.low)*al-Q});M.get(0).width=a+Q;M.get(0).height=t;o.parent().css("height",Math.max(this.height_px,t)+"px");var B=M.get(0).getContext("2d");B.fillStyle=g;B.font=this.default_font;B.textAlign="right";if(A.dataset_type=="summary_tree"){var L,I=55,ad=255-I,h=ad*2/3,S=A.data,D=A.max,m=A.avg,b=Math.ceil(A.delta*al);for(var ah=0,z=S.length;ahh){B.fillStyle="black"}else{B.fillStyle="#ddd"}B.textAlign="center";B.fillText(T,U+Q+(b/2),12)}}d="Summary";o.append(M);return M}var aj=A.data;var ag=0;for(var ah=0,z=aj.length;ah=F){var X=Math.floor(Math.max(0,(ai-F)*al)),C=Math.ceil(Math.min(a,Math.max(0,(V-F)*al))),R=(n==="Dense"?0:ak[K]*am);if(A.dataset_type==="bai"){B.fillStyle=g;if(N[4] instanceof Array){var u=Math.floor(Math.max(0,(N[4][0]-F)*al)),J=Math.ceil(Math.min(a,Math.max(0,(N[4][1]-F)*al))),s=Math.floor(Math.max(0,(N[5][0]-F)*al)),q=Math.ceil(Math.min(a,Math.max(0,(N[5][1]-F)*al)));if(N[4][1]>=F&&N[4][0]<=ae){this.rect_or_text(B,al,F,ae,N[4][0],N[4][2],u+Q,J-u,R)}if(N[5][1]>=F&&N[5][0]<=ae){this.rect_or_text(B,al,F,ae,N[5][0],N[5][2],s+Q,q-s,R)}if(s>J){B.fillStyle="#999";B.fillRect(J+Q,R+5,s-J,1)}}else{B.fillStyle=g;this.rect_or_text(B,al,F,ae,ai,G,X+Q,C-X,R)}if(n!=="Dense"&&!W&&ai>F){B.fillStyle=this.prefs.label_color;if(l===0&&X-B.measureText(G).width<0){B.textAlign="left";B.fillText(K,C+2+Q,R+8)}else{B.textAlign="right";B.fillText(K,X-2+Q,R+8)}B.fillStyle=g}}else{if(A.dataset_type==="interval_index"){if(W){B.fillRect(X+Q,R+5,C-X,1)}else{var w=N[4],P=N[5],Z=N[6],f=N[7];var v,ab,H=null,an=null;if(P&&Z){H=Math.floor(Math.max(0,(P-F)*al));an=Math.ceil(Math.min(a,Math.max(0,(Z-F)*al)))}if(n!=="Dense"&&G!==undefined&&ai>F){B.fillStyle=aa;if(l===0&&X-B.measureText(G).width<0){B.textAlign="left";B.fillText(G,C+2+Q,R+8)}else{B.textAlign="right";B.fillText(G,X-2+Q,R+8)}B.fillStyle=g}if(f){if(w){if(w=="+"){B.fillStyle=RIGHT_STRAND}else{if(w=="-"){B.fillStyle=LEFT_STRAND}}B.fillRect(X+Q,R,C-X,10);B.fillStyle=g}for(var af=0,e=f.length;afO){continue}v=5;ab=3;B.fillRect(c+Q,R+ab,O-c,v);if(H!==undefined&&!(c>an||O").addClass("form-row");var e="track_"+j+"_block_color",l=$("