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galaxy-dist commit 04c59f0a5202: New config option to prevent Galaxy from retrying set_meta internally if it fails externally, and accompanying code to allow users to retry set_meta upon failure.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1283437371 14400 # Node ID 04c59f0a5202a89731f76b33525a4e753e0cfa42 # Parent a37dacb261540967fb21a2f5fe928464346a897a New config option to prevent Galaxy from retrying set_meta internally if it fails externally, and accompanying code to allow users to retry set_meta upon failure. --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -92,7 +92,9 @@ </div></form> %if data.missing_meta(): - <div class="errormessagesmall">${_('Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.')}</div> + <div class="form-row"> + <div class="errormessagesmall">${_('Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values.')}</div> + </div> %endif </div></div> --- a/templates/mobile/history/detail.mako +++ b/templates/mobile/history/detail.mako @@ -55,8 +55,11 @@ <div>Metadata is being Auto-Detected.</div> %elif data_state == "empty": <div>No data: <i>${data.display_info()}</i></div> - %elif data_state == "ok": + %elif data_state in [ "ok", "failed_metadata" ]: <div> + %if data_state == "failed_metadata": + Warning: setting metadata failed, + %endif ${data.blurb}, format: <span class="${data.ext}">${data.ext}</span>, database: <span class="${data.dbkey}">${data.dbkey}</span> --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -492,9 +492,12 @@ class JobWrapper( object ): #either use the metadata from originating output dataset, or call set_meta on the copies #it would be quicker to just copy the metadata from the originating output dataset, #but somewhat trickier (need to recurse up the copied_from tree), for now we'll call set_meta() - if not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ): - # Only set metadata values if they are missing... + if not self.app.config.set_metadata_externally or \ + ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) \ + and self.app.config.retry_metadata_internally ): dataset.set_meta( overwrite = False ) + elif not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and not context['stderr']: + dataset._state = model.Dataset.states.FAILED_METADATA else: #load metadata from file #we need to no longer allow metadata to be edited while the job is still running, --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -402,7 +402,8 @@ class Dataset( object ): EMPTY = 'empty', ERROR = 'error', DISCARDED = 'discarded', - SETTING_METADATA = 'setting_metadata' ) + SETTING_METADATA = 'setting_metadata', + FAILED_METADATA = 'failed_metadata' ) permitted_actions = get_permitted_actions( filter='DATASET' ) file_path = "/tmp/" engine = None --- a/static/june_2007_style/blue/history.css +++ b/static/june_2007_style/blue/history.css @@ -7,6 +7,8 @@ div.historyItem .historyItemTitle{font-w div.historyItem div.historyItem{margin-right:-11px;} div.historyItem-ok{border-color:#66AA66;background:#CCFFCC;} div.historyItem-ok .state-icon{display:none;} +div.historyItem-failed_metadata{border-color:#66AA66;background:#CCFFCC;} +div.historyItem-failed_metadata .state-icon{display:none;} div.historyItem-error{border-color:#AA6666;background:#FFCCCC;} div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px -0px;} div.historyItem-empty{border-color:#AA6666;background:#FFCCCC;} --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1708,6 +1708,11 @@ class SetMetadataTool( Tool ): external_metadata = galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper( job ) if external_metadata.external_metadata_set_successfully( dataset, app.model.context ): dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset, app.model.context ).filename_out ) + else: + dataset._state = model.Dataset.states.FAILED_METADATA + self.sa_session.add( dataset ) + self.sa_session.flush() + return # If setting external metadata has failed, how can we inform the user? # For now, we'll leave the default metadata and set the state back to its original. dataset.datatype.after_setting_metadata( dataset ) --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -19,7 +19,7 @@ <script type="text/javascript"> -<% TERMINAL_STATES = ["ok", "error", "empty", "deleted", "discarded"] %> +<% TERMINAL_STATES = ["ok", "error", "empty", "deleted", "discarded", "failed_metadata"] %> TERMINAL_STATES = ${ h.to_json_string(TERMINAL_STATES) }; $(function() { --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -335,6 +335,9 @@ class RootController( BaseController, Us if params.annotation: annotation = sanitize_html( params.annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans, data, annotation ) + # If setting metadata previously failed and all required elements have now been set, clear the failed state. + if data._state == trans.model.Dataset.states.FAILED_METADATA and not data.missing_meta(): + data._state = None trans.sa_session.flush() return trans.show_ok_message( "Attributes updated%s" % message, refresh_frames=['history'] ) else: --- a/static/june_2007_style/history.css.tmpl +++ b/static/june_2007_style/history.css.tmpl @@ -46,13 +46,15 @@ div.historyItem div.historyItem { } ## Change background/border color depending on state -div.historyItem-ok { +div.historyItem-ok, +div.historyItem-failed_metadata { border-color: $history_ok_border; background: $history_ok_bg; .state-icon { display: none; } } + div.historyItem-error { border-color: $history_error_border; background: $history_error_bg; --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -100,7 +100,12 @@ <div>${_('Metadata is being Auto-Detected.')}</div> %elif data_state == "empty": <div>${_('No data: ')}<i>${data.display_info()}</i></div> - %elif data_state == "ok": + %elif data_state in [ "ok", "failed_metadata" ]: + %if data_state == "failed_metadata": + <div class="warningmessagesmall" style="margin: 4px 0 4px 0"> + An error occurred setting the metadata for this dataset. You may be able to <a href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main">set it manually or retry auto-detection</a>. + </div> + %endif <div> ${data.blurb}, format: <span class="${data.ext}">${data.ext}</span>, --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -53,6 +53,7 @@ class Configuration( object ): self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) ) + self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -346,6 +346,13 @@ use_interactive = True # unresponsive when this operation occurs internally. #set_metadata_externally = False +# Although it is fairly reliable, setting metadata can occasionally fail. In +# these instances, you can choose to retry setting it internally or leave it in +# a failed state (since retrying internally may cause the Galaxy process to be +# unresponsive). If this option is set to False, the user will be given the +# option to retry externally, or set metadata manually (when possible). +#retry_metadata_internally = True + # Number of concurrent jobs to run (local job runner) #local_job_queue_workers = 5

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galaxy-dist commit fa1d4be02764: Add 'NullToolOutputActionOption' to tool output dataset actions. This action option is used implicitly when no ToolOutputActionOption's have been defined. This will allow e.g. setting a metadata value to a static value on a per ToolOutput basis.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1283439625 14400 # Node ID fa1d4be027649ad4d745c62a053e024fe2db35e9 # Parent 04c59f0a5202a89731f76b33525a4e753e0cfa42 Add 'NullToolOutputActionOption' to tool output dataset actions. This action option is used implicitly when no ToolOutputActionOption's have been defined. This will allow e.g. setting a metadata value to a static value on a per ToolOutput basis. Example which sets the strand assignment of an interval dataset to column 10: <outputs> <data format="interval" name="output1"> <actions> <action type="metadata" name="strandCol" default="10"/> </actions> </data> </outputs> --- a/lib/galaxy/tools/parameters/output.py +++ b/lib/galaxy/tools/parameters/output.py @@ -104,7 +104,6 @@ class ToolOutputAction( object ): self.parent = parent self.default = elem.get( 'default', None ) option_elem = elem.find( 'option' ) - assert option_elem is not None, "Required 'option' element missing from ToolOutputAction" self.option = ToolOutputActionOption.from_elem( self, option_elem ) def apply_action( self, output_dataset, other_values ): raise TypeError( "Not implemented" ) @@ -117,20 +116,29 @@ class ToolOutputActionOption( object ): @classmethod def from_elem( cls, parent, elem ): """Loads the proper action by the type attribute of elem""" - option_type = elem.get( 'type', None ) + if elem is None: + option_type = NullToolOutputActionOption.tag # no ToolOutputActionOption's have been defined, use implicit NullToolOutputActionOption + else: + option_type = elem.get( 'type', None ) assert option_type is not None, "Required 'type' attribute missing from ToolOutputActionOption" return option_types[ option_type ]( parent, elem ) def __init__( self, parent, elem ): self.parent = parent self.filters = [] - for filter_elem in elem.findall( 'filter' ): - self.filters.append( ToolOutputActionOptionFilter.from_elem( self, filter_elem ) ) + if elem is not None: + for filter_elem in elem.findall( 'filter' ): + self.filters.append( ToolOutputActionOptionFilter.from_elem( self, filter_elem ) ) def get_value( self, other_values ): raise TypeError( "Not implemented" ) @property def tool( self ): return self.parent.tool +class NullToolOutputActionOption( ToolOutputActionOption ): + tag = "null_option" + def get_value( self, other_values ): + return None + class FromFileToolOutputActionOption( ToolOutputActionOption ): tag = "from_file" def __init__( self, parent, elem ): @@ -454,7 +462,7 @@ for action_type in [ MetadataToolOutputA action_types[ action_type.tag ] = action_type option_types = {} -for option_type in [ FromFileToolOutputActionOption, FromParamToolOutputActionOption, FromDataTableOutputActionOption ]: +for option_type in [ NullToolOutputActionOption, FromFileToolOutputActionOption, FromParamToolOutputActionOption, FromDataTableOutputActionOption ]: option_types[ option_type.tag ] = option_type filter_types = {}

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galaxy-dist commit a37dacb26154: Fix for tools/filters/wig_to_bigwig.xml when coordinates extend beyond chromosome boundaries and -clip was specified.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1283383585 14400 # Node ID a37dacb261540967fb21a2f5fe928464346a897a # Parent 77753eec8e43449075a8f5599860e6c5a3d7c9b3 Fix for tools/filters/wig_to_bigwig.xml when coordinates extend beyond chromosome boundaries and -clip was specified. --- a/tools/filters/wig_to_bigwig.xml +++ b/tools/filters/wig_to_bigwig.xml @@ -1,6 +1,6 @@ <tool id="wig_to_bigWig" name="Wig to bigWig" version="1.0.0"><description>converter</description> - <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 -blockSize=$blockSize -itemsPerSlot=$itemsPerSlot $clip $unc</command> + <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 -blockSize=$blockSize -itemsPerSlot=$itemsPerSlot $clip $unc 2>&1 || echo "Error running wigToBigWig." >&2</command><requirements><requirement type="binary">wigToBigWig</requirement></requirements>

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galaxy-dist commit 833cfa90b337: Add setup of tool-data/shared/jars to the buildbot setup script.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1283441846 14400 # Node ID 833cfa90b33735f4f30f10d0d7e39cbf1a64d6d9 # Parent fa1d4be027649ad4d745c62a053e024fe2db35e9 Add setup of tool-data/shared/jars to the buildbot setup script. --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -20,6 +20,8 @@ case "$OSTYPE" in [ ! -d "$HYPHY" ] && unset HYPHY ;; solaris2.10) + # For the psu-production builder which is Solaris, but jobs run on a + # Linux cluster HYPHY="/galaxy/software/linux2.6-x86_64/hyphy" ;; esac @@ -73,6 +75,8 @@ database/import database/pbs " +JARS="/galaxy/software/jars" + for link in $LINKS; do echo "Linking $link" rm -f tool-data/`basename $link` @@ -85,6 +89,12 @@ if [ -d "$HYPHY" ]; then ln -sf $HYPHY tool-data/HYPHY fi +if [ -d "$JARS" ]; then + echo "Linking $JARS" + rm -f tool-data/shared/jars + ln -sf $JARS tool-data/shared/jars +fi + for sample in $SAMPLES; do file=`echo $sample | sed -e 's/\.sample$//'` echo "Copying $sample to $file"

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galaxy-dist commit 77753eec8e43: 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
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1283379642 14400 # Node ID 77753eec8e43449075a8f5599860e6c5a3d7c9b3 # Parent 4a621d4e127a76467d996fdf25b3a7e1ead4ddb9 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 --- 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.requ 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 } --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +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=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONT EXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.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()};$.extend(View.prototype,{init:function(){var c=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide().appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_o 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/>").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this. nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show();c.content_div.hide()}else{c.intro_div.hide();c.content_div.show()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.hig h-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport_container.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this. max_high){e=this.max_high}if(this.high!==0&&d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.update_location(this.low,this.high);if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width( )*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSO N(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var c=t his,b=c.view;if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var g=c.display_modes[0];c.mode=g;c.mode_div.text(g);var a=function(h){c.mode_div.text(h);c.mode=h;c.tile_cache.clear();c.draw()};var e={};for(var d in c.display_modes){var f=c.display_modes[d];e[f]=function(h){return function(){a(h)}}(f)}make_popupmenu(c.mode_div,e)}else{c.mode_div.hide()}}if(c.overview_check_div===undefined){c.overview_check_div=$("<div class='right-float' />").css("margin-top","-3px").appendTo(c.header_div);c.overview_check=$("<input type='checkbox' class='overview_check' />").appendTo(c.overview_check_div);c.overview_check.bind("click",function(){var h=this;b.overview_viewport.find("canvas").remove();c.set_overview();$(".overview_check").each(function(){if(this!==h){$(this).attr("checked",false)}})});c.overview_check_div.append($("<label />").text("Overview"))}};$.extend(TiledTrack.prototype,Track.pro totype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width, l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.height(a.default_overview_height);if(this.initial_canvas&&this.overview_check.is(":checked")){a.overview_viewport.append(this.initial_canvas);a.overview_viewport.height(this.initial_canvas.height());a.overview_box.height(this.initial_canvas.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height : 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var 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=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){consol e.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),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<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefin ed,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id"," linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"relative",top:"32px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+32+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.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=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get (0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this .prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").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.addCl ass("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=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){v ar t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(Y,l,o,al){var F=l*DENSITY*Y,ae=(l+1)*DENSITY*Y,E=ae-F;var af=(!this.initial_canvas?"initial":F+"_"+ae);var A=this.data_cache.g et(af);var d;if(A===undefined){this.data_queue[[F,ae]]=true;this.get_data(F,ae);return}var a=Math.ceil(E*al),M=$("<canvas class='tile'></canvas>"),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;ah<z;ah++){var U=Ma th.floor((S[ah][0]-F)*al);var T=S[ah][1];if(!T){continue}L=Math.floor(ad-(T/D)*ad);B.fillStyle="rgb("+L+","+L+","+L+")";B.fillRect(U+Q,0,b,this.summary_draw_height);if(this.prefs.show_counts&&B.measureText(T).width<b){if(L>h){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<z;ah++){var N=aj[ah],K=N[0],ai=N[1],V=N[2],G=N[3];if(ai<=ae&&V>=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;af<e;af++){var p=f[af],c=Math.floor(Math.max(0,(p[0]-F)*al)),O=Math.ceil(M ath.min(a,Math.max((p[1]-F)*al)));if(c>O){continue}v=5;ab=3;B.fillRect(c+Q,R+ab,O-c,v);if(H!==undefined&&!(c>an||O<H)){v=9;ab=1;var ac=Math.max(c,H),r=Math.min(O,an);B.fillRect(ac+Q,R+ab,r-ac,v)}}}else{v=9;ab=1;B.fillRect(X+Q,R+ab,C-X,v);if(N.strand){if(N.strand=="+"){B.fillStyle=RIGHT_STRAND_INV}else{if(N.strand=="-"){B.fillStyle=LEFT_STRAND_INV}}B.fillRect(X+Q,R,C-X,10);B.fillStyle=prefs.block_color}}}}}ag++}}o.append(M);return M},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr(" checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); +var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),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=CONT EXT.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=$("<div/>").addClass("top-labeltrack").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide().appendTo(c);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.nav_container=$("<div/>").addClass("nav-container").appendTo(c);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_o verview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(d){if(d.type==="focusout"||(d.keyCode||d.which)===13||(d.keyCode||d.which)===27){if((d.keyCode||d.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_i nput=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(d){if(d.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=d.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);a.intro_div.show();a.content_div.hide();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_d iv.bind("dblclick",function(d){a.zoom_in(d.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(d){this.current_x=d.offsetX}).bind("drag",function(d){var g=d.offsetX-this.current_x;this.current_x=d.offsetX;var f=Math.round(g/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-f)});this.viewport_container.bind("dragstart",function(d){this.original_low=a.low;this.current_height=d.clientY;this.current_x=d.offsetX;this.active=(d.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(g){if(!this.active){return}var d=$(this);var j=g.offsetX-this.current_x;var f=d.scrollTop()-(g.clientY-this.current_height);d.scrollTop(f);this.current_height=g.clientY;this.current_x=g.offsetX;var h=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(h)});this.top_labeltrack.bind("dragstart",function(d){this.drag_origin_x=d.clientX;this.drag_origin_pos=d.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_d iv=$("<div />").css({height:a.content_div.height()+30,top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var f=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,d=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,h=(a.high-a.low),g=a.viewport_container.width();a.update_location(Math.round(f/g*h)+a.low,Math.round(d/g*h)+a.low);this.drag_div.css({left:f+"px",width:(d-f)+"px"})}).bind("dragend",function(k){var f=Math.min(k.clientX,this.drag_origin_x),d=Math.max(k.clientX,this.drag_origin_x),h=(a.high-a.low),g=a.viewport_container.width(),j=a.low;a.low=Math.round(f/g*h)+j;a.high=Math.round(d/g*h)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack))},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this. nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(d,a,f){var c=this;var e=$.grep(c.chrom_data,function(h,j){return h.chrom===d})[0];if(e===undefined){return}if(d!==c.chrom){c.chrom=d;if(c.chrom===""){c.intro_div.show();c.content_div.hide()}else{c.intro_div.hide();c.content_div.show()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.hig h-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport_container.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this. max_high){e=this.max_high}if(this.high!==0&&d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.update_location(this.low,this.high);if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width( )*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSO N(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var c=t his,b=c.view;if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var g=c.display_modes[0];c.mode=g;c.mode_div.text(g);var a=function(h){c.mode_div.text(h);c.mode=h;c.tile_cache.clear();c.draw()};var e={};for(var d in c.display_modes){var f=c.display_modes[d];e[f]=function(h){return function(){a(h)}}(f)}make_popupmenu(c.mode_div,e)}else{c.mode_div.hide()}}if(c.overview_check_div===undefined){c.overview_check_div=$("<div class='right-float' />").css("margin-top","-3px").appendTo(c.header_div);c.overview_check=$("<input type='checkbox' class='overview_check' />").appendTo(c.overview_check_div);c.overview_check.bind("click",function(){var h=this;b.overview_viewport.find("canvas").remove();c.set_overview();$(".overview_check").each(function(){if(this!==h){$(this).attr("checked",false)}})});c.overview_check_div.append($("<label />").text("Overview"))}};$.extend(TiledTrack.prototype,Track.pro totype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width, l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.height(a.default_overview_height);if(this.initial_canvas&&this.overview_check.is(":checked")){a.overview_viewport.append(this.initial_canvas);a.overview_viewport.height(this.initial_canvas.height());a.overview_box.height(this.initial_canvas.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height : 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var 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=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){consol e.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),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<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefin ed,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id"," linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"relative",top:"32px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+32+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.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=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get (0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this .prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").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.addCl ass("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}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_da ta:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.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=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==unde fined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(Y,l,o,al){var F=l*DENSITY*Y,ae=(l+1)*DENSITY*Y,E=ae-F;var af=(!this.initial_canvas?"initial":F+"_"+ae);var A=this. data_cache.get(af);var d;if(A===undefined||(this.mode!=="Auto"&&A.dataset_type==="summary_tree")){this.data_queue[[F,ae]]=true;this.get_data(F,ae);return}var a=Math.ceil(E*al),M=$("<canvas class='tile'></canvas>"),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=25;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;ah<z;ah++){var U=Math.floor((S[ah][0]-F)*al);var T=S[ah][1];if(!T){continue}L=Math.floor(ad-(T/D)*ad);B.fillStyle="rgb("+L+","+L+","+L+")";B.fillRect(U+Q,0,b,this.summary_draw_height);if(this.prefs.show_counts&&B.measureText(T).width<b){if(L>h){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}if(A.message){M.css({border:"solid red","border-width":"2px 2px 2px 0px"});B.fillStyle="red";B.textAlign="left";B.fillText(A.message,100+Q,am)}var aj=A.data;var ag=0;for(var ah=0,z=aj.length;ah<z;ah++){var N=aj[ah],K=N[0],ai=N[1],V=N[2],G=N[3];if(ai<=ae&&V>=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"?1:(1+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.fillStyle=g;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;af<e;af++){var p=f[af],c=Math.floor(Math.max(0,(p[0]-F)*al)),O=Math.ceil(Math.min(a,Math.max((p[1]-F)*al)));if(c>O){continue}v=5;ab=3;B.fillRect(c+Q,R+ab,O-c,v);if(H!==undefined&&!(c>an||O<H)){v=9;ab=1;var ac=Math.max(c,H),r=Math.min(O,an);B.fillRect(ac+Q,R+ab,r-ac,v)}}}else{v=9;ab=1;B.fillRect(X+Q,R+ab,C-X,v);if(N.strand){if(N.strand=="+"){B.fillStyle=RIGHT_STRAND_INV}else{if(N.strand=="-"){B.fillStyle=LEFT_STRAND_INV}}B.fillRect(X+Q,R,C-X,10);B.fillStyle=g}}}}}ag++}}o.append(M);return M},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name ",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -951,9 +951,8 @@ var FeatureTrack = function ( name, view var track = this, key = "initial"; - this.init_each({ low: track.view.max_low, - high: track.view.max_high, dataset_id: track.dataset_id, - chrom: track.view.chrom, resolution: this.view.resolution }, function (result) { + this.init_each({ low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, + chrom: track.view.chrom, resolution: this.view.resolution, mode: track.mode }, function (result) { track.mode_div.show(); track.data_cache.set(key, result); track.draw(); @@ -1089,12 +1088,11 @@ var FeatureTrack = function ( name, view break; } }*/ - var k = (!this.initial_canvas ? "initial" : tile_low + '_' + tile_high); var result = this.data_cache.get(k); var cur_mode; - if (result === undefined) { + if (result === undefined || (this.mode !== "Auto" && result.dataset_type === "summary_tree")) { this.data_queue[ [tile_low, tile_high] ] = true; this.get_data(tile_low, tile_high); return; @@ -1112,7 +1110,7 @@ var FeatureTrack = function ( name, view if (result.dataset_type === "summary_tree") { required_height = this.summary_draw_height; } else if (mode === "Dense") { - required_height = 15; + required_height = 25; y_scale = 10; } else { // Calculate new slots incrementally for this new chunk of data and update height if necessary @@ -1169,6 +1167,16 @@ var FeatureTrack = function ( name, view return new_canvas; } + if (result.message) { + new_canvas.css({ + border: "solid red", + "border-width": "2px 2px 2px 0px" + }); + ctx.fillStyle = "red"; + ctx.textAlign = "left"; + ctx.fillText(result.message, 100 + left_offset, y_scale); + } + var data = result.data; var j = 0; for (var i = 0, len = data.length; i < len; i++) { @@ -1181,7 +1189,7 @@ var FeatureTrack = function ( name, view if (feature_start <= tile_high && feature_end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), - y_center = (mode === "Dense" ? 0 : slots[feature_uid] * y_scale); + y_center = (mode === "Dense" ? 1 : (1 + slots[feature_uid])) * y_scale; if (result.dataset_type === "bai") { ctx.fillStyle = block_color; @@ -1222,6 +1230,7 @@ var FeatureTrack = function ( name, view // console.log(feature_uid, feature_start, feature_end, f_start, f_end, y_center); if (no_detail) { + ctx.fillStyle = block_color; ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1); } else { // Showing labels, blocks, details @@ -1291,7 +1300,7 @@ var FeatureTrack = function ( name, view ctx.fillStyle = LEFT_STRAND_INV; } ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10); - ctx.fillStyle = prefs.block_color; + ctx.fillStyle = block_color; } } } --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -291,7 +291,8 @@ class TracksController( BaseController, # 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" --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -228,7 +228,7 @@ class VisualizationController( BaseContr # 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( BaseContr 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( BaseContr @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( BaseContr """ 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( BaseContr 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( BaseContr """ 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( BaseContr 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( BaseContr 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( BaseContr .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 ) - - #(a)web.expose - #(a)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 ) - - --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -41,6 +41,7 @@ <div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"><div style="float:left;" id="title"></div> + <a class="panel-header-button right-float" href="${h.url_for( controller='visualization', action='list' )}">Close</a><a id="save-button" class="panel-header-button right-float" href="javascript:void(0);">Save</a><a id="refresh-button" class="panel-header-button right-float" href="javascript:void(0);" onclick="view.update_options();return false;">Refresh</a></div>

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galaxy-dist commit 695a12fec1e2: Add a wig to bigWig converter tool.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1283375708 14400 # Node ID 695a12fec1e2195cf8ccdf80d6d5318a464c37e3 # Parent f205636ed466f490a081681e76b23196dbc80e7c Add a wig to bigWig converter tool. --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -88,6 +88,7 @@ <tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" /> + <tool file="filters/wig_to_bigwig.xml" /></section><section name="Extract Features" id="features"><tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> --- /dev/null +++ b/tools/filters/wig_to_bigwig.xml @@ -0,0 +1,54 @@ +<tool id="wig_to_bigWig" name="Wig to bigWig" version="1.0.0"> + <description>converter</description> + <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 -blockSize=$blockSize -itemsPerSlot=$itemsPerSlot $clip $unc</command> + <requirements> + <requirement type="binary">wigToBigWig</requirement> + </requirements> + <inputs> + <param format="wig" name="input1" type="data" label="Convert"> + <validator type="unspecified_build" /> + </param> + <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" /> + <param name="itemsPerSlot" size="4" type="integer" value="1024" label="Data points bundled at lowest level" help="Default is 1024 (itemsPerSlot)" /> + <param name="clip" type="boolean" truevalue="-clip" falsevalue="" checked="False" label="Clip chromosome positions" help="Issue warning messages rather than dying if wig file contains items off end of chromosome. (clip)"/> + <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/> + </inputs> + <outputs> + <data format="bigwig" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.wig" dbkey="hg17" /> + <param name="blockSize" value="256" /> + <param name="itemsPerSlot" value="1024" /> + <param name="clip" value="False" /> + <param name="unc" value="False" /> + <output name="out_file1" file="2.bigwig"/> + </test> + </tests> + <help> +**Syntax** + +This tool converts wiggle data into bigWig type. + +- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. + + - **BED format** with no declaration line and four columns of data:: + + chromA chromStartA chromEndA dataValueA + chromB chromStartB chromEndB dataValueB + + - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values:: + + variableStep chrom=chrN [span=windowSize] + chromStartA dataValueA + chromStartB dataValueB + + - **fixedStep** single column data; started by a declaration line and followed with data values:: + + fixedStep chrom=chrN start=position step=stepInterval [span=windowSize] + dataValue1 + dataValue2 + +</help> +</tool> Binary file test-data/2.bigwig has changed

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galaxy-dist commit 4a621d4e127a: More files for rgQC test outputs to satisfy the buildbot
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1283378497 14400 # Node ID 4a621d4e127a76467d996fdf25b3a7e1ead4ddb9 # Parent 695a12fec1e2195cf8ccdf80d6d5318a464c37e3 More files for rgQC test outputs to satisfy the buildbot Binary file test-data/rgtestouts/rgQC/tinywga_All_3x3-0.jpg has changed Binary file test-data/rgtestouts/rgQC/tinywga_All_Paged-8.jpg has changed --- /dev/null +++ b/test-data/rgtestouts/rgQC/QQtinywga_logphweunaff_cum.pdf @@ -0,0 +1,349 @@ +%PDF-1.4 +%��ρ�\r +1 0 obj +<< +/CreationDate (D:20100519151538) +/ModDate (D:20100519151538) +/Title (R Graphics Output) +/Producer (R 2.10.1) +/Creator (R) +>> +endobj +2 0 obj +<< +/Type /Catalog +/Pages 3 0 R +>> +endobj +5 0 obj +<< +/Type /Page +/Parent 3 0 R +/Contents 6 0 R +/Resources 4 0 R +>> +endobj +6 0 obj +<< +/Length 7 0 R +>> +stream +q +Q q 59.04 73.44 630.72 443.52 re W n +0.690 0.188 0.376 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galaxy-dist commit f205636ed466: Improved error checking for condition provided to tool 'gff_filter_by_feature_count.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1283373340 14400 # Node ID f205636ed466f490a081681e76b23196dbc80e7c # Parent 2ba0fe1297a8a31f99c412f05046ec7c2f749798 Improved error checking for condition provided to tool 'gff_filter_by_feature_count. --- a/tools/filters/gff/gff_filter_by_feature_count.py +++ b/tools/filters/gff/gff_filter_by_feature_count.py @@ -11,14 +11,25 @@ from galaxy.tools.util.gff_util import p assert sys.version_info[:2] >= ( 2, 4 ) +# Valid operators, ordered so that complex operators (e.g. '>=') are +# recognized before simple operators (e.g. '>') +ops = [ + '>=', + '<=', + '<', + '>', + '==', + '!=' +] + # Escape sequences for valid operators. mapped_ops = { - '__lt__': '<', - '__le__': '<=', - '__eq__': '==', - '__ne__': '!=', - '__gt__': '>', - '__ge__': '>=', + '__ge__': ops[0], + '__le__': ops[1], + '__lt__': ops[2], + '__gt__': ops[3], + '__eq__': ops[4], + '__ne__': ops[5], } @@ -34,7 +45,7 @@ def __main__(): condition = condition.replace( key, value ) # Error checking: condition should be of the form <operator><number> - for op in mapped_ops.itervalues(): + for op in ops: if op in condition: empty, number_str = condition.split( op ) try: @@ -44,6 +55,7 @@ def __main__(): if empty != "" or not number: print >> sys.stderr, "Invalid condition: %s, cannot filter." % condition return + break # Do filtering. kept_lines = 0

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galaxy-dist commit 12c032ebc303: Enhance wig datatype to only use first 100 data lines to determine column type metadata if dataset filesize exceeds max_optional_metadata_filesize configured in datatypes_conf.xml.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan(a)bx.psu.edu> # Date 1283371068 14400 # Node ID 12c032ebc303060b838448ad8f6e0da96cacb631 # Parent eb75925d4b9705ab8722cab41c321bf15a4b2359 Enhance wig datatype to only use first 100 data lines to determine column type metadata if dataset filesize exceeds max_optional_metadata_filesize configured in datatypes_conf.xml. --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -25,14 +25,21 @@ class Tabular( data.Text ): def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip = None, **kwd ): + def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, **kwd ): """ Tries to determine the number of columns as well as those columns that contain numerical values in the dataset. A skip parameter is used because various tabular data types reuse this function, and their data type classes are responsible to determine how many invalid comment lines should be skipped. Using None for skip will cause skip - to be zero, but the first line will be processed as a header. + to be zero, but the first line will be processed as a header. A + max_data_lines parameter is used because various tabular data types + reuse this function, and their data type classes are responsible to + determine how many data lines should be processed to ensure that the + non-optional metadata parameters are properly set; if used, optional + metadata parameters will be set to None, unless the entire file has + already been read. Using None (default) for max_data_lines will + process all data lines. Items of interest: 1. We treat 'overwrite' as always True (we always want to set tabular metadata when called). @@ -97,7 +104,11 @@ class Tabular( data.Text ): first_line_column_types = [default_column_type] # default value is one column of type str if dataset.has_data(): #NOTE: if skip > num_check_lines, we won't detect any metadata, and will use default - for i, line in enumerate( file ( dataset.file_name ) ): + dataset_fh = open( dataset.file_name ) + i = 0 + while True: + line = dataset_fh.readline() + if not line: break line = line.rstrip( '\r\n' ) if i < skip or not line or line.startswith( '#' ): # We'll call blank lines comments @@ -127,6 +138,14 @@ class Tabular( data.Text ): # "column_types": ["int", "int", "str", "list"] first_line_column_types = column_types column_types = [ None for col in first_line_column_types ] + if max_data_lines is not None and data_lines >= max_data_lines: + if dataset_fh.tell() != dataset.get_size(): + data_lines = None #Clear optional data_lines metadata value + comment_lines = None #Clear optional comment_lines metadata value; additional comment lines could appear below this point + break + i += 1 + dataset_fh.close() + #we error on the larger number of columns #first we pad our column_types by using data from first line if len( first_line_column_types ) > len( column_types ): --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -1079,6 +1079,7 @@ class Wiggle( Tabular, _RemoteCallMixin def make_html_table( self, dataset ): return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) def set_meta( self, dataset, overwrite = True, **kwd ): + max_data_lines = None i = 0 for i, line in enumerate( file ( dataset.file_name ) ): line = line.rstrip('\r\n') @@ -1089,13 +1090,19 @@ class Wiggle( Tabular, _RemoteCallMixin break except: do_break = False - for str in data.col1_startswith: - if elems[0].lower().startswith(str): + for col_startswith in data.col1_startswith: + if elems[0].lower().startswith( col_startswith ): do_break = True break if do_break: break - Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) + if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: + #we'll arbitrarily only use the first 100 data lines in this wig file to calculate tabular attributes (column types) + #this should be sufficient, except when we have mixed wig track types (bed, variable, fixed), + # but those cases are not a single table that would have consistant column definitions + #optional metadata values set in Tabular class will be 'None' + max_data_lines = 100 + Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i, max_data_lines = max_data_lines ) def sniff( self, filename ): """ Determines wether the file is in wiggle format

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galaxy-dist commit 4ee5fca864a4: lims: find samples
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283367408 14400 # Node ID 4ee5fca864a44b2bf7e7efac7a97f564961df3f2 # Parent f41f4ace420a58e7316fbeddacd301ff6d5dfaf1 lims: find samples - the search settings are saved after the search - search now case insensitive and wildcard support added - masthead problem fixed when showing find samples page in user mode --- a/templates/requests/common/find.mako +++ b/templates/requests/common/find.mako @@ -54,47 +54,60 @@ <div class="toolFormBody"><form name="find_request" id="find_request" action="${h.url_for( controller='requests_common', action='find', cntrller=cntrller)}" method="post" ><div class="form-row"> - <label>Find in sequencing requests in state:</label> - <select name="request_state"> - <option value="In Progress" selected>In-Progress</option> - <option value="Complete">Complete</option> - <option value="Both">Both</option> - </select> + <label>Find sample(s) using:</label> + ${search_type.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Select a sample attribute to search through all the samples.<br/> + To search for a sample with a dataset name, select the dataset + option above. This will return all the sample(s) which has a + dataset with the given name associated with it. To search for + all samples created on a certain date select the 'date created' + option above. Enter date in 'YYYY-MM-DD' format. + </div></div><div class="form-row"> - <label>Find by sample:</label> - <select name="search_type"> - <option value="name" selected>name</option> - <option value="bar_code">barcode</option> - </select> + <label>Filter sequencing requests in state:</label> + ${request_states.get_html()} + <div class="toolParamHelp" style="clear: both;"> + This will filter the search results to show only those sample(s) <br/> + whose parent sequencing request is in the selected state. + </div></div><div class="form-row"> - <input type="text" name="search_string" size="40" value=""> - <input type="submit" name="go_button" value="Go"/> + ${search_box.get_html()} + <input type="submit" name="go_button" value="Find"/> + <div class="toolParamHelp" style="clear: both;"> + Wildcard search (%) can be used as placeholder for any sequence of characters or words.<br/> + For example, to search for samples starting with 'mysample' use 'mysample%' as the search string. + </div></div> %if results: <div class="form-row"><label><i>${results}</i></label> + <div class="toolParamHelp" style="clear: both;"> + The search results are sorted by the date the samples where created. + </div></div> %endif <div class="form-row"> %if samples: %for s in samples: <div class="form-row"> - <a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}"><label>Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</label></a> + + Sample: ${s.name} | Barcode: ${s.bar_code}<br/> + State: ${s.current_state().name}<br/> + Datasets: <a href="${h.url_for(controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(s.id))}">${s.transferred_dataset_files()}/${len(s.datasets)}</a><br/> %if cntrller == 'requests_admin': <i>User: ${s.request.user.email}</i> %endif - <div class="toolParamHelp" style="clear: both;"> - Sample: ${s.name}<br/> - Barcode: ${s.bar_code}<br/> - State: ${s.current_state().name} - </div> + <div class="toolParamHelp" style="clear: both;"> + <a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}">Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</a> + </div> + </div><br/> %endfor %endif - </div></form></div> --- /dev/null +++ b/templates/requests/find_index.mako @@ -0,0 +1,16 @@ +<%inherit file="/webapps/galaxy/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view="requests" + self.message_box_visible=False +%> +</%def> + +<%def name="center_panel()"> + + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="requests_common", action="find" )}"></iframe> + +</%def> --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -135,6 +135,11 @@ class Requests( BaseController ): @web.require_login( "create/submit sequencing requests" ) def index( self, trans ): return trans.fill_template( "requests/index.mako" ) + + @web.expose + @web.require_login( "create/submit sequencing requests" ) + def find_index( self, trans ): + return trans.fill_template( "requests/find_index.mako" ) @web.expose @web.require_login( "create/submit sequencing requests" ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1256,6 +1256,25 @@ class RequestsCommon( BaseController, Us # # Find sequencing requests & samples # + def __find_widgets(self, trans, **kwd): + params = util.Params( kwd ) + request_states = SelectField('request_states', multiple=True, display="checkboxes") + sel_op = kwd.get('request_states', trans.app.model.Request.states.SUBMITTED) + for i, s in trans.app.model.Request.states.items(): + if s in sel_op: + request_states.add_option(s, s, True) + else: + request_states.add_option(s, s) + search_type = SelectField('search_type') + sel_op = kwd.get('search_type', 'sample name') + for s in ['sample name', 'barcode', 'dataset']: + if s in sel_op: + search_type.add_option(s, s, True) + else: + search_type.add_option(s, s) + search_box = TextField('search_box', 50, kwd.get('search_box', '')) + return request_states, search_type, search_box + @web.expose @web.require_admin def find( self, trans, **kwd ): @@ -1263,26 +1282,31 @@ class RequestsCommon( BaseController, Us cntrller = params.get( 'cntrller', 'requests' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - search_string = kwd.get( 'search_string', '' ) - search_type = params.get( 'search_type', '' ) - if params.get( 'request_state', 'In Progress' ) == 'Both': - request_states = ['In Progress', 'Complete'] - else: - request_states = [params.get( 'request_state', 'In Progress' )] - - samples_list = [] results = '' - if params.get('go_button', '') == 'Go': - if search_type == 'bar_code': + if params.get('go_button', '') == 'Find': + search_string = kwd.get( 'search_box', '' ) + search_type = params.get( 'search_type', '' ) + request_states = params.get( 'request_states', '' ) + samples = [] + if search_type == 'barcode': samples = trans.sa_session.query( trans.app.model.Sample ) \ .filter( and_( trans.app.model.Sample.table.c.deleted==False, trans.app.model.Sample.table.c.bar_code.like(search_string) ) )\ + .order_by( trans.app.model.Sample.table.c.create_time.desc())\ .all() - elif search_type == 'name': + elif search_type == 'sample name': samples = trans.sa_session.query( trans.app.model.Sample ) \ .filter( and_( trans.app.model.Sample.table.c.deleted==False, - trans.app.model.Sample.table.c.name.like(search_string) ) )\ + trans.app.model.Sample.table.c.name.ilike(search_string) ) )\ + .order_by( trans.app.model.Sample.table.c.create_time.desc())\ + .all() + elif search_type == 'dataset': + samples = trans.sa_session.query( trans.app.model.Sample ) \ + .filter( and_( trans.app.model.Sample.table.c.deleted==False, + trans.app.model.SampleDataset.table.c.sample_id==trans.app.model.Sample.table.c.id, + trans.app.model.SampleDataset.table.c.name.ilike(search_string) ) )\ + .order_by( trans.app.model.Sample.table.c.create_time.desc())\ .all() if cntrller == 'requests': for s in samples: @@ -1295,11 +1319,12 @@ class RequestsCommon( BaseController, Us if not s.request.deleted \ and s.request.state() in request_states: samples_list.append(s) - results = 'There are %i sequencing requests matching the search parameters.' % len(samples_list) + results = 'There are %i sample(s) matching the search parameters.' % len(samples_list) + request_states, search_type, search_box = self.__find_widgets(trans, **kwd) return trans.fill_template( '/requests/common/find.mako', - cntrller=cntrller, - samples=samples_list, - results=results ) + cntrller=cntrller, request_states=request_states, + samples=samples_list, search_type=search_type, + results=results, search_box=search_box ) --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -82,7 +82,7 @@ <% menu_options = [ [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ], - [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ], + [ 'Find Samples', h.url_for( controller='/requests', action='find_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] tab( "lab", "Lab", None, menu_options=menu_options )

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