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. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init();this.reset()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("
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");this.container_div=$("
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").addClass("form-row");var e="track_"+k+"_minval",h=$("").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 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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=$("