- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3216: trackster: support BAM visualization with samt...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7d3667e8e415 changeset: 3216:7d3667e8e415 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Jan 07 15:45:15 2010 -0500 description: trackster: support BAM visualization with samtools, automatically enable tracks for any datatype with "get_track_type" defined diffstat: datatypes_conf.xml.sample | 4 +- eggs.ini | 2 + lib/galaxy/datatypes/binary.py | 4 +- lib/galaxy/datatypes/coverage.py | 2 - lib/galaxy/datatypes/interval.py | 7 +- lib/galaxy/datatypes/registry.py | 8 ++- lib/galaxy/web/controllers/tracks.py | 38 ++++++-------- static/scripts/packed/galaxy.panels.js | 2 +- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 88 +++++++++++++++++++++++++++++---- templates/tracks/browser.mako | 2 +- templates/tracks/new_browser.mako | 4 +- 12 files changed, 117 insertions(+), 46 deletions(-) diffs (439 lines): diff -r 427d93bf3d39 -r 7d3667e8e415 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Thu Jan 07 14:52:51 2010 -0500 +++ b/datatypes_conf.xml.sample Thu Jan 07 15:45:15 2010 -0500 @@ -3,7 +3,9 @@ <registration converters_path="lib/galaxy/datatypes/converters"> <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/> <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/> - <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + </datatype> <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"> <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> <converter file="interval_to_coverage.xml" target_datatype="coverage"/> diff -r 427d93bf3d39 -r 7d3667e8e415 eggs.ini --- a/eggs.ini Thu Jan 07 14:52:51 2010 -0500 +++ b/eggs.ini Thu Jan 07 15:45:15 2010 -0500 @@ -19,6 +19,7 @@ pbs_python = 2.9.4 psycopg2 = 2.0.6 pycrypto = 2.0.1 +pysam = 0.1.1 pysqlite = 2.5.6 python_lzo = 1.08 threadframe = 0.2 @@ -74,6 +75,7 @@ pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2 pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz +pysam = http://bitbucket.org/kanwei/kanwei-pysam/get/e3c601a062fd.gz pysqlite = http://pypi.python.org/packages/source/p/pysqlite/pysqlite-2.5.6.tar.gz python_lzo = http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar… http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/binary.py Thu Jan 07 15:45:15 2010 -0500 @@ -132,7 +132,9 @@ return dataset.peek except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) - + def get_track_type( self ): + return "ReadTrack", "bai" + class Binseq( Binary ): """Class describing a zip archive of binary sequence files""" file_ext = "binseq.zip" diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/coverage.py --- a/lib/galaxy/datatypes/coverage.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/coverage.py Thu Jan 07 15:45:15 2010 -0500 @@ -63,6 +63,4 @@ resolution = max( resolution, 1 ) return resolution - def get_track_type( self ): - return "LineTrack" diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/interval.py Thu Jan 07 15:45:15 2010 -0500 @@ -325,8 +325,6 @@ def get_track_resolution( self, dataset, start, end): return None - def get_track_type( self ): - return "FeatureTrack" class Bed( Interval ): """Tab delimited data in BED format""" @@ -484,6 +482,9 @@ else: return False return True except: return False + + def get_track_type( self ): + return "FeatureTrack", "interval_index" class _RemoteCallMixin: def _get_remote_call_url( self, redirect_url, site_name, dataset, type, app, base_url ): @@ -904,7 +905,7 @@ resolution = max( resolution, 1 ) return resolution def get_track_type( self ): - return "LineTrack" + return "LineTrack", "array_tree" class CustomTrack ( Tabular ): """UCSC CustomTrack""" diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/registry.py Thu Jan 07 15:45:15 2010 -0500 @@ -18,6 +18,7 @@ self.datatype_converters = odict() self.datatype_indexers = odict() self.converters = [] + self.available_tracks = [] self.set_external_metadata_tool = None self.indexers = [] self.sniff_order = [] @@ -54,6 +55,8 @@ # Use default mime type as per datatype spec mimetype = self.datatypes_by_extension[extension].get_mime() self.mimetypes_by_extension[extension] = mimetype + if hasattr( getattr( module, datatype_class ), "get_track_type" ): + self.available_tracks.append( extension ) if display_in_upload: self.upload_file_formats.append( extension ) for converter in elem.findall( 'converter' ): @@ -206,7 +209,10 @@ if not included: self.sniff_order.append(datatype) append_to_sniff_order() - + + def get_available_tracks(self): + return self.available_tracks + def get_mimetype_by_extension(self, ext ): """Returns a mimetype based on an extension""" try: diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Thu Jan 07 15:45:15 2010 -0500 @@ -23,35 +23,26 @@ from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider from galaxy.visualization.tracks.data.interval_index import IntervalIndexDataProvider +from galaxy.visualization.tracks.data.bam import BamDataProvider # Message strings returned to browser messages = Bunch( PENDING = "pending", NO_DATA = "no data", NO_CHROMOSOME = "no chromosome", + NO_CONVERTER = "no converter", DATA = "data", ERROR = "error" ) -# Dataset type required for each track type. This needs to be more flexible, -# there might be multiple types of indexes that suffice for a given track type. -track_type_to_dataset_type = { - "line": "array_tree", - "feature": "interval_index" -} - # Mapping from dataset type to a class that can fetch data from a file of that # type. This also needs to be more flexible. dataset_type_to_data_provider = { "array_tree": ArrayTreeDataProvider, - "interval_index": IntervalIndexDataProvider + "interval_index": IntervalIndexDataProvider, + "bai": BamDataProvider } -# FIXME: hardcoding this for now, but it should be derived from the available -# converters -browsable_types = ( "wig", "bed" ) - - class TracksController( BaseController ): """ Controller for track browser interface. Handles building a new browser from @@ -107,11 +98,12 @@ # Find all datasets in the current history that are of that dbkey # and can be displayed datasets = {} + available_tracks = trans.app.datatypes_registry.get_available_tracks() for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): - if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types: + if dataset.metadata.dbkey == dbkey and dataset.extension in available_tracks: datasets[dataset.id] = (dataset.extension, dataset.name) # Render the template - return trans.fill_template( "tracks/new_browser.mako", converters=browsable_types, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) + return trans.fill_template( "tracks/new_browser.mako", available_tracks=available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) @web.expose def browser(self, trans, id, chrom=""): @@ -127,8 +119,10 @@ for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id'] dataset = hda_query.get( dataset_id ) + track_type, indexer = dataset.datatype.get_track_type() tracks.append( { - "type": dataset.datatype.get_track_type(), + "type": track_type, + "indexer": indexer, "name": dataset.name, "dataset_id": dataset.id } ) @@ -184,14 +178,14 @@ return manifest @web.json - def data( self, trans, dataset_id, track_type, chrom, low, high, **kwargs ): + def data( self, trans, dataset_id, indexer, chrom, low, high, **kwargs ): """ Called by the browser to request a block of data """ # Load the requested dataset dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) # No dataset for that id - if not dataset: + if not dataset or not chrom: return messages.NO_DATA # Dataset is in error state, can't display if dataset.state == trans.app.model.Job.states.ERROR: @@ -200,12 +194,11 @@ if dataset.state != trans.app.model.Job.states.OK: return messages.PENDING # Determine what to return based on the type of track being drawn. - converted_dataset_type = track_type_to_dataset_type[track_type] + converted_dataset_type = indexer converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type ) - # If at this point we still don't have an `array_tree_dataset`, there - # is no way we can display this data as an array tree if not converted_dataset: - return messages.ERROR + # No converter + return messages.NO_CONVERTER # Need to check states again for the converted version if converted_dataset.state == model.Dataset.states.ERROR: return messages.ERROR @@ -228,6 +221,7 @@ converted dataset (possibly new) is returned, if it cannot be converted, None is returned. """ + log.debug("Inside dataset as type") # Already of correct type if dataset.extension == type: return dataset diff -r 427d93bf3d39 -r 7d3667e8e415 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Thu Jan 07 14:52:51 2010 -0500 +++ b/static/scripts/packed/galaxy.panels.js Thu Jan 07 15:45:15 2010 -0500 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var 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img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.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}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=2;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;thi s.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_off set){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass ("line-track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="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.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",t op:a.height_px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},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;$.getJSON(data_url,{track_type:this.track_type,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke( );m.append(c);return c}});var FeatureTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b== "pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{track_type:b.track_type,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:functi on(a,b){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get _data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}va r I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",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=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_ img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.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}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;thi s.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_off set){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("line -track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="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.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_ px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},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;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);retu rn c}});var FeatureTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addCla ss("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,b){if(!this.inc_slots[a]){this.inc _slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_sl ots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.st rand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureT rack.prototype,{draw_tile:function(w,A,n,o){if(!this.values){return}var B=A*DENSITY*w,f=(A+1)*DENSITY*w,r=DENSITY*w;var E,q,k;k=this.height_px;q=this.zo_slots;E=this.values;var u=Math.ceil(r*o),s=$("<canvas class='tile'></canvas>");var b=$("<canvas></canvas>").get(0).getContext("2d");s.css({position:"absolute",top:0,left:(B-this.view.low)*o-this.left_offset});s.get(0).width=u+this.left_offset;s.get(0).height=k;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font=this.default_font;v.textAlign="right";var t=v.measureText("A").width;var x=0;for(var y=0,z=E.length;y<z;y++){var m=E[y];if(m.start<=f&&m.end>=B){var h=Math.floor(Math.max(0,(m.start-B)*o)),l=Math.ceil(Math.min(u,(m.end-B)*o)),g=q[m.uid]*this.vertical_gap;var a,F,e=null,p=null;if(o>t){for(var C=0,d=m.name.length;C<d;C++){var D=Math.floor(Math.max(0,(m.start+C-B)*o));v.fillText(m.name[C],D+this.left_offset,g+8)}}else{v.fillRect(h+this.left_offset,g+4,l-h,3)}}}n.append(s);return s}}); \ No newline at end of file diff -r 427d93bf3d39 -r 7d3667e8e415 static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Jan 07 14:52:51 2010 -0500 +++ b/static/scripts/trackster.js Thu Jan 07 15:45:15 2010 -0500 @@ -81,7 +81,7 @@ this.max_high = max_high; this.center = (this.max_high - this.max_low) / 2; this.span = this.max_high - this.max_low; - this.zoom_factor = 2; + this.zoom_factor = 3; this.zoom_level = 0; }; $.extend( View.prototype, { @@ -241,12 +241,12 @@ } }); -var LineTrack = function ( name, dataset_id, height ) { +var LineTrack = function ( name, dataset_id, indexer, height ) { this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); - this.track_type = "line"; + this.indexer = indexer; this.height_px = (height ? height : 100); this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; @@ -258,7 +258,7 @@ init: function() { var track = this; track.content_div.text(DATA_LOADING); - $.getJSON( data_url, { stats: true, track_type: track.track_type, + $.getJSON( data_url, { stats: true, indexer: track.indexer, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { @@ -300,7 +300,7 @@ if (!track.data_queue[key]) { track.data_queue[key] = true; - $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, + $.getJSON( data_url, { indexer: this.indexer, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id, resolution: this.view.resolution }, function ( data ) { track.cache.set(key, data); @@ -360,12 +360,12 @@ } }); -var FeatureTrack = function ( name, dataset_id, height ) { +var FeatureTrack = function ( name, dataset_id, indexer, height ) { this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); - this.track_type = "feature"; + this.indexer = indexer; this.height_px = (height ? height : 100); this.container_div.addClass( "feature-track" ); this.dataset_id = dataset_id; @@ -384,7 +384,7 @@ init: function() { var track = this; track.content_div.text(DATA_LOADING); - $.getJSON( data_url, { track_type: track.track_type, low: track.view.max_low, + $.getJSON( data_url, { indexer: track.indexer, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { if (data == "error") { @@ -414,7 +414,7 @@ if (!track.data_queue[key]) { track.data_queue[key] = true; - $.getJSON( data_url, { track_type: track.track_type, chrom: track.view.chrom, + $.getJSON( data_url, { indexer: track.indexer, chrom: track.view.chrom, low: low, high: high, dataset_id: track.dataset_id, include_blocks: true }, function ( data ) { track.data_cache.set(key, data); @@ -454,8 +454,6 @@ if (!this.inc_slots[level]) { this.inc_slots[level] = {}; this.inc_slots[level].w_scale = DENSITY / Math.pow(FEATURE_LEVELS, level+1); - // this.inc_slots[level].w_scale = 1000 / (this.view.high - this.view.low); - } var slots = this.inc_slots[level]; // console.log(level, slots.w_scale, slots); @@ -629,3 +627,71 @@ return new_canvas; } }); + +var ReadTrack = function ( name, dataset_id, indexer, height ) { + this.tile_cache = new Cache(CACHED_TILES_FEATURE); + Track.call( this, name, $("#viewport") ); + TiledTrack.call( this ); + FeatureTrack.call( this, name, dataset_id, indexer, height ); + this.default_font = "9px Monaco, Lucida Console, monospace"; + +}; +$.extend( ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { + draw_tile: function( resolution, tile_index, parent_element, w_scale ) { + if (!this.values) { + return; + } + var tile_low = tile_index * DENSITY * resolution, + tile_high = ( tile_index + 1 ) * DENSITY * resolution, + tile_span = DENSITY * resolution; + // console.log("drawing " + tile_index); + // Once we zoom in enough, show name labels + var data, slots, required_height; + required_height = this.height_px; + slots = this.zo_slots; + data = this.values; + + // console.log(tile_low, tile_high, tile_length, w_scale); + var width = Math.ceil( tile_span * w_scale ), + new_canvas = $("<canvas class='tile'></canvas>"); + + var dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); + + new_canvas.css({ + position: "absolute", + top: 0, + left: ( tile_low - this.view.low ) * w_scale - this.left_offset + }); + new_canvas.get(0).width = width + this.left_offset; + new_canvas.get(0).height = required_height; + // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); + var ctx = new_canvas.get(0).getContext("2d"); + ctx.fillStyle = this.base_color; + ctx.font = this.default_font; + ctx.textAlign = "right"; + var px_per_char = ctx.measureText("A").width; + + var j = 0; + for (var i = 0, len = data.length; i < len; i++) { + var feature = data[i]; + 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, (feature.end - tile_low) * w_scale) ), + y_center = slots[feature.uid] * this.vertical_gap; + + var thickness, y_start, thick_start = null, thick_end = null; + if (w_scale > px_per_char) { + for (var c = 0, str_len = feature.name.length; c < str_len; c++) { + var c_start = Math.floor( Math.max(0, (feature.start + c - tile_low) * w_scale) ); + ctx.fillText(feature.name[c], c_start + this.left_offset, y_center + 8); + } + } else { + ctx.fillRect(f_start + this.left_offset, y_center + 4, f_end - f_start, 3); + } + } + } + + parent_element.append( new_canvas ); + return new_canvas; + } +}); diff -r 427d93bf3d39 -r 7d3667e8e415 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu Jan 07 14:52:51 2010 -0500 +++ b/templates/tracks/browser.mako Thu Jan 07 15:45:15 2010 -0500 @@ -20,7 +20,7 @@ view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) ); %for track in tracks: - view.add_track( new ${track["type"]}( "${track['name']}", ${track['dataset_id']} ) ); + view.add_track( new ${track["type"]}( "${track['name']}", ${track['dataset_id']}, "${track['indexer']}" ) ); %endfor $(document).bind( "redraw", function( e ) { diff -r 427d93bf3d39 -r 7d3667e8e415 templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Thu Jan 07 14:52:51 2010 -0500 +++ b/templates/tracks/new_browser.mako Thu Jan 07 15:45:15 2010 -0500 @@ -11,7 +11,7 @@ </script> </%def> -% if not converters: +% if not available_tracks: <div class="errormessagelarge"> There are no available converters needed for visualization. Please verify that your tool_conf.xml file contains converters for datatypes (see tool_conf.xml.sample) for examples. @@ -46,7 +46,7 @@ <div style="clear: both;"></div> </div> <div class="form-row"> - <label for="dataset_ids">Datasets to include: </label> + <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label> %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): <div> <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" />

1 0

[hg] galaxy 3215: Template for async history selection grid.
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/427d93bf3d39 changeset: 3215:427d93bf3d39 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jan 07 14:52:51 2010 -0500 description: Template for async history selection grid. diffstat: templates/page/select_histories_grid_async.mako | 8 ++++++++ 1 files changed, 8 insertions(+), 0 deletions(-) diffs (13 lines): diff -r d4ee51cd8bc9 -r 427d93bf3d39 templates/page/select_histories_grid_async.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/page/select_histories_grid_async.mako Thu Jan 07 14:52:51 2010 -0500 @@ -0,0 +1,8 @@ +<%namespace file="../grid_base.mako" import="*" /> + +## Always show item checkboxes so that users can select histories. +${render_grid_table_body_contents(show_item_checkboxes=True)} +***** +${num_pages} +***** +${render_grid_message()} \ No newline at end of file

1 0

[hg] galaxy 3214: Fixed compatibility issues between pages and n...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d4ee51cd8bc9 changeset: 3214:d4ee51cd8bc9 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jan 07 14:52:07 2010 -0500 description: Fixed compatibility issues between pages and new tagging functionality. diffstat: lib/galaxy/web/controllers/page.py | 3 +- templates/grid_base.mako | 34 +++++++++++++++++---------- templates/grid_base_async.mako | 2 +- templates/page/display.mako | 2 +- templates/page/history_annotation_table.mako | 9 ++++--- templates/page/select_histories_grid.mako | 2 +- 6 files changed, 31 insertions(+), 21 deletions(-) diffs (174 lines): diff -r 5b99d58c6f54 -r d4ee51cd8bc9 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Thu Jan 07 13:41:44 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Thu Jan 07 14:52:07 2010 -0500 @@ -112,7 +112,8 @@ # Grid definition. title = "Saved Histories" - template = "/page/select_histories_grid.mako" + template = "/page/select_histories_grid.mako" + async_template = "/page/select_histories_grid_async.mako" model_class = model.History default_filter = { "deleted" : "False" , "shared" : "All" } default_sort_key = "-update_time" diff -r 5b99d58c6f54 -r d4ee51cd8bc9 templates/grid_base.mako --- a/templates/grid_base.mako Thu Jan 07 13:41:44 2010 -0500 +++ b/templates/grid_base.mako Thu Jan 07 14:52:07 2010 -0500 @@ -775,13 +775,17 @@ </%def> ## Render grid. -<%def name="render_grid_table()"> +<%def name="render_grid_table(show_item_checkboxes=False)"> <% # Set flag to indicate whether grid has operations that operate on multiple items. multiple_item_ops_exist = False for operation in grid.operations: if operation.allow_multiple: multiple_item_ops_exist = True + + # Show checkboxes if flag is set or if multiple item ops exist. + if show_item_checkboxes or multiple_item_ops_exist: + show_item_checkboxes = True %> <form action="${url()}" method="post" onsubmit="return false;"> @@ -789,7 +793,9 @@ <table id='grid-table' class="grid"> <thead id="grid-table-header"> <tr> - <th></th> + %if show_item_checkboxes: + <th></th> + %endif %for column in grid.columns: %if column.visible: <% @@ -825,17 +831,17 @@ </tr> </thead> <tbody id="grid-table-body"> - ${render_grid_table_body_contents(multiple_item_ops_exist)} + ${render_grid_table_body_contents(show_item_checkboxes)} </tbody> <tfoot> - ${render_grid_table_footer_contents(multiple_item_ops_exist)} + ${render_grid_table_footer_contents(show_item_checkboxes)} </tfoot> </table> </form> </%def> ## Render grid table body contents. -<%def name="render_grid_table_body_contents(multiple_item_ops_exist=False)"> +<%def name="render_grid_table_body_contents(show_item_checkboxes=False)"> <% num_rows_rendered = 0 %> %if query.count() == 0: ## No results. @@ -849,11 +855,11 @@ %endif > ## Item selection column - <td style="width: 1.5em;"> - %if multiple_item_ops_exist: - <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - %endif - </td> + %if show_item_checkboxes: + <td style="width: 1.5em;"> + <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> + </td> + %endif ## Data columns %for column in grid.columns: %if column.visible: @@ -925,7 +931,7 @@ </%def> ## Render grid table footer contents. -<%def name="render_grid_table_footer_contents(multiple_item_ops_exist=False)"> +<%def name="render_grid_table_footer_contents(show_item_checkboxes=False)"> ## Row for navigating among pages. <% # Mapping between item class and plural term for item. @@ -941,9 +947,11 @@ elif grid.model_class == Group: items_plural = "groups" %> + %if show_item_checkboxes: + <td></td> + %endif %if grid.use_paging and num_pages > 1: <tr id="page-links-row"> - <td></td> <td colspan="100"> <span id='page-link-container'> ## Page links. @@ -965,7 +973,7 @@ </tr> %endif ## Grid operations for multiple items. - %if multiple_item_ops_exist: + %if show_item_checkboxes: <tr> <td></td> <td colspan="100"> diff -r 5b99d58c6f54 -r d4ee51cd8bc9 templates/grid_base_async.mako --- a/templates/grid_base_async.mako Thu Jan 07 13:41:44 2010 -0500 +++ b/templates/grid_base_async.mako Thu Jan 07 14:52:07 2010 -0500 @@ -8,7 +8,7 @@ multiple_item_ops_exist = True %> -${render_grid_table_body_contents(multiple_item_ops_exist=multiple_item_ops_exist)} +${render_grid_table_body_contents(show_item_checkboxes=multiple_item_ops_exist)} ***** ${num_pages} ***** diff -r 5b99d58c6f54 -r d4ee51cd8bc9 templates/page/display.mako --- a/templates/page/display.mako Thu Jan 07 13:41:44 2010 -0500 +++ b/templates/page/display.mako Thu Jan 07 14:52:07 2010 -0500 @@ -194,7 +194,7 @@ %> </%def> -<%namespace file="../tagging_common.mako" import="render_tagging_element, render_community_tagging_element" /> +<%namespace file="../tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> <%def name="center_panel()"> diff -r 5b99d58c6f54 -r d4ee51cd8bc9 templates/page/history_annotation_table.mako --- a/templates/page/history_annotation_table.mako Thu Jan 07 13:41:44 2010 -0500 +++ b/templates/page/history_annotation_table.mako Thu Jan 07 14:52:07 2010 -0500 @@ -1,4 +1,4 @@ -<%namespace file="../tagging_common.mako" import="render_individual_tagging_element_html" /> +<%namespace file="../tagging_common.mako" import="render_tagging_element_html" /> <%namespace file="../root/history_common.mako" import="render_dataset" /> <table> @@ -14,9 +14,10 @@ ${_('This is a deleted history.')} </div> %endif - %if trans.get_user() is not None: - Tags: ${render_individual_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )} - %endif + ## Tags come for free with community tagging, so not sure if this is necessary. + ##%if trans.get_user() is not None: + ## Tags: ${render_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )} + ##%endif </td> </tr> <tr> diff -r 5b99d58c6f54 -r d4ee51cd8bc9 templates/page/select_histories_grid.mako --- a/templates/page/select_histories_grid.mako Thu Jan 07 13:41:44 2010 -0500 +++ b/templates/page/select_histories_grid.mako Thu Jan 07 14:52:07 2010 -0500 @@ -4,7 +4,7 @@ ${javascripts()} ${stylesheets()} ${render_grid_header(False)} -${render_grid_table()} +${render_grid_table(show_item_checkboxes=True)} ## Initialize the grid. <script type="text/javascript">

1 0

[hg] galaxy 3213: Full model & controller (but not yet view/UI) ...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5b99d58c6f54 changeset: 3213:5b99d58c6f54 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Jan 07 13:41:44 2010 -0500 description: Full model & controller (but not yet view/UI) support for community tags and workflows tags. Specific enhancements include: (1) added columns to associate users with tags; (2) added tables to support workflow tagging; (3) augmented data model to support community tags; (4) refactored tag handler to use both individual and community tags; and (5) added individual and community tag columns for grids. Also fixed a couple bugs in grid framework. diffstat: lib/galaxy/model/__init__.py | 11 +- lib/galaxy/model/mapping.py | 51 ++- lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py | 171 ++++++++++ lib/galaxy/tags/tag_handler.py | 19 +- lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/controllers/history.py | 4 +- lib/galaxy/web/controllers/page.py | 4 +- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 2 +- lib/galaxy/web/controllers/tag.py | 105 ++--- lib/galaxy/web/framework/__init__.py | 7 +- lib/galaxy/web/framework/helpers/grids.py | 62 ++- templates/dataset/edit_attributes.mako | 4 +- templates/grid_base.mako | 28 +- templates/grid_base_async.mako | 10 +- templates/history/view.mako | 8 +- templates/page/display.mako | 4 +- templates/page/history_annotation_table.mako | 4 +- templates/root/history.mako | 4 +- templates/tagging_common.mako | 56 +- 20 files changed, 388 insertions(+), 170 deletions(-) diffs (1151 lines): diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/model/__init__.py Thu Jan 07 13:41:44 2010 -0500 @@ -1424,8 +1424,9 @@ return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name ) class ItemTagAssociation ( object ): - def __init__( self, id=None, item_id=None, tag_id=None, user_tname=None, value=None ): + def __init__( self, id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None ): self.id = id + self.user = user self.item_id = item_id self.tag_id = tag_id self.user_tname = user_tname @@ -1437,7 +1438,7 @@ class HistoryTagAssociation ( ItemTagAssociation ): pass - + class DatasetTagAssociation ( ItemTagAssociation ): pass @@ -1447,6 +1448,12 @@ class PageTagAssociation ( ItemTagAssociation ): pass +class WorkflowTagAssociation ( ItemTagAssociation ): + pass + +class StoredWorkflowTagAssociation ( ItemTagAssociation ): + pass + class UserPreference ( object ): def __init__( self, name=None, value=None ): self.name = name diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/model/mapping.py Thu Jan 07 13:41:44 2010 -0500 @@ -710,6 +710,7 @@ Column( "id", Integer, primary_key=True ), Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), Column( "value", TrimmedString(255), index=True), Column( "user_value", TrimmedString(255), index=True) ) @@ -718,6 +719,7 @@ Column( "id", Integer, primary_key=True ), Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), Column( "value", TrimmedString(255), index=True), Column( "user_value", TrimmedString(255), index=True) ) @@ -726,14 +728,34 @@ Column( "id", Integer, primary_key=True ), Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), Column( "value", TrimmedString(255), index=True), Column( "user_value", TrimmedString(255), index=True) ) + +WorkflowTagAssociation.table = Table( "workflow_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "user_tname", Unicode(255), index=True), + Column( "value", Unicode(255), index=True), + Column( "user_value", Unicode(255), index=True) ) + +StoredWorkflowTagAssociation.table = Table( "stored_workflow_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "user_tname", Unicode(255), index=True), + Column( "value", Unicode(255), index=True), + Column( "user_value", Unicode(255), index=True) ) PageTagAssociation.table = Table( "page_tag_association", metadata, Column( "id", Integer, primary_key=True ), Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), Column( "value", TrimmedString(255), index=True), Column( "user_value", TrimmedString(255), index=True) ) @@ -1127,7 +1149,9 @@ properties=dict( steps=relation( WorkflowStep, backref='workflow', order_by=asc(WorkflowStep.table.c.order_index), cascade="all, delete-orphan", - lazy=False ) ) ) + lazy=False ), + tags=relation(WorkflowTagAssociation, order_by=WorkflowTagAssociation.table.c.id, backref="workflows") + ) ) assign_mapper( context, WorkflowStep, WorkflowStep.table ) @@ -1181,7 +1205,8 @@ primaryjoin=( StoredWorkflow.table.c.id == Workflow.table.c.stored_workflow_id ) ), latest_workflow=relation( Workflow, post_update=True, primaryjoin=( StoredWorkflow.table.c.latest_workflow_id == Workflow.table.c.id ), - lazy=False ) + lazy=False ), + tags=relation(StoredWorkflowTagAssociation, order_by=StoredWorkflowTagAssociation.table.c.id, backref="stored_workflows") ) ) assign_mapper( context, StoredWorkflowUserShareAssociation, StoredWorkflowUserShareAssociation.table, @@ -1225,24 +1250,28 @@ ) ) assign_mapper( context, HistoryTagAssociation, HistoryTagAssociation.table, - properties=dict( tag=relation(Tag, backref="tagged_histories") ), - primary_key=[HistoryTagAssociation.table.c.history_id, HistoryTagAssociation.table.c.tag_id] + properties=dict( tag=relation(Tag, backref="tagged_histories"), user=relation( User ) ) ) assign_mapper( context, DatasetTagAssociation, DatasetTagAssociation.table, - properties=dict( tag=relation(Tag, backref="tagged_datasets") ), - primary_key=[DatasetTagAssociation.table.c.dataset_id, DatasetTagAssociation.table.c.tag_id] + properties=dict( tag=relation(Tag, backref="tagged_datasets"), user=relation( User ) ) ) assign_mapper( context, HistoryDatasetAssociationTagAssociation, HistoryDatasetAssociationTagAssociation.table, - properties=dict( tag=relation(Tag, backref="tagged_history_dataset_associations") ), - primary_key=[HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id, HistoryDatasetAssociationTagAssociation.table.c.tag_id] + properties=dict( tag=relation(Tag, backref="tagged_history_dataset_associations"), user=relation( User ) ) ) assign_mapper( context, PageTagAssociation, PageTagAssociation.table, - properties=dict( tag=relation(Tag, backref="tagged_pages") ), - primary_key=[PageTagAssociation.table.c.page_id, PageTagAssociation.table.c.tag_id] - ) + properties=dict( tag=relation(Tag, backref="tagged_pages"), user=relation( User ) ) + ) + +assign_mapper( context, WorkflowTagAssociation, WorkflowTagAssociation.table, + properties=dict( tag=relation(Tag, backref="tagged_workflows"), user=relation( User ) ) + ) + +assign_mapper( context, StoredWorkflowTagAssociation, StoredWorkflowTagAssociation.table, + properties=dict( tag=relation(Tag, backref="tagged_stored_workflows"), user=relation( User ) ) + ) assign_mapper( context, UserPreference, UserPreference.table, properties = {} diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py Thu Jan 07 13:41:44 2010 -0500 @@ -0,0 +1,171 @@ +""" +Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and \ +(b) add table for doing individual and community tagging of workflows. + +SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will generate error messages when run against \ +SQLite; however, script does execute successfully against SQLite. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +StoredWorkflowTagAssociation_table = Table( "stored_workflow_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "user_tname", Unicode(255), index=True), + Column( "value", Unicode(255), index=True), + Column( "user_value", Unicode(255), index=True) ) + +WorkflowTagAssociation_table = Table( "workflow_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "user_tname", Unicode(255), index=True), + Column( "value", Unicode(255), index=True), + Column( "user_value", Unicode(255), index=True) ) + +def upgrade(): + print __doc__ + metadata.reflect() + + # Create user_id column in history_tag_association table. + HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) + c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) + try: + c.create( HistoryTagAssociation_table ) + assert c is HistoryTagAssociation_table.c.user_id + except Exception, e: + # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. + print str(e) + log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) + + # Create user_id index for history_tag_association table. + try: + i = Index( "ix_history_tag_association_user_id", HistoryTagAssociation_table.c.user_id ) + i.create() + except: + # Mysql doesn't have a named index, but alter should work + HistoryTagAssociation_table.c.user_id.alter( unique=False ) + + # Populate column so that user_id is the id of the user who owns the history (and, up to now, was the only person able to tag the history). + if c is HistoryTagAssociation_table.c.user_id: + db_session.execute( + "UPDATE history_tag_association SET user_id=( SELECT user_id FROM history WHERE history_tag_association.history_id = history.id )" + ) + + # Create user_id column in history_dataset_association_tag_association table. + HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) + c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) + try: + c.create( HistoryDatasetAssociationTagAssociation_table ) + assert c is HistoryDatasetAssociationTagAssociation_table.c.user_id + except Exception, e: + # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. + print str(e) + log.debug( "Adding user_id column to history_dataset_association_tag_association table failed: %s" % str( e ) ) + + # Create user_id index for history_dataset_association_tag_association table. + try: + i = Index( "ix_history_dataset_association_tag_association_user_id", HistoryDatasetAssociationTagAssociation_table.c.user_id ) + i.create() + except: + # Mysql doesn't have a named index, but alter should work + HistoryDatasetAssociationTagAssociation_table.c.user_id.alter( unique=False ) + + # Populate column so that user_id is the id of the user who owns the history_dataset_association (and, up to now, was the only person able to tag the page). + if c is HistoryDatasetAssociationTagAssociation_table.c.user_id: + db_session.execute( + "UPDATE history_dataset_association_tag_association SET user_id=( SELECT history.user_id FROM history, history_dataset_association WHERE history_dataset_association.history_id = history.id AND history_dataset_association.id = history_dataset_association_tag_association.history_dataset_association_id)" + ) + + # Create user_id column in page_tag_association table. + PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) + c = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ) + try: + c.create( PageTagAssociation_table ) + assert c is PageTagAssociation_table.c.user_id + except Exception, e: + # SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so catch exception if it arises. + print str(e) + log.debug( "Adding user_id column to history_tag_association table failed: %s" % str( e ) ) + + # Create user_id index for page_tag_association table. + try: + i = Index( "ix_page_tag_association_user_id", PageTagAssociation_table.c.user_id ) + i.create() + except: + # Mysql doesn't have a named index, but alter should work + PageTagAssociation_table.c.user_id.alter( unique=False ) + + # Populate column so that user_id is the id of the user who owns the page (and, up to now, was the only person able to tag the page). + if c is PageTagAssociation_table.c.user_id: + db_session.execute( + "UPDATE page_tag_association SET user_id=( SELECT user_id FROM page WHERE page_tag_association.page_id = page.id )" + ) + + # Create stored_workflow_tag_association table. + try: + StoredWorkflowTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating stored_workflow_tag_association table failed: %s" % str( e ) ) + + # Create workflow_tag_association table. + try: + WorkflowTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating workflow_tag_association table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # Drop user_id column from history_tag_association table. + HistoryTagAssociation_table = Table( "history_tag_association", metadata, autoload=True ) + try: + HistoryTagAssociation_table.c.user_id.drop() + except Exception, e: + print str(e) + log.debug( "Dropping column user_id from history_tag_association table failed: %s" % str( e ) ) + + + # Drop user_id column from history_dataset_association_tag_association table. + HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, autoload=True ) + try: + HistoryDatasetAssociationTagAssociation_table.c.user_id.drop() + except Exception, e: + print str(e) + log.debug( "Dropping column user_id from history_dataset_association_tag_association table failed: %s" % str( e ) ) + + # Drop user_id column from page_tag_association table. + PageTagAssociation_table = Table( "page_tag_association", metadata, autoload=True ) + try: + PageTagAssociation_table.c.user_id.drop() + except Exception, e: + print str(e) + log.debug( "Dropping column user_id from page_tag_association table failed: %s" % str( e ) ) + + # Drop stored_workflow_tag_association table. + try: + StoredWorkflowTagAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping stored_workflow_tag_association table failed: %s" % str( e ) ) + + # Drop workflow_tag_association table. + try: + WorkflowTagAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping workflow_tag_association table failed: %s" % str( e ) ) \ No newline at end of file diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/tags/tag_handler.py Thu Jan 07 13:41:44 2010 -0500 @@ -73,10 +73,10 @@ return community_tags - def remove_item_tag( self, trans, item, tag_name ): + def remove_item_tag( self, trans, user, item, tag_name ): """Remove a tag from an item.""" # Get item tag association. - item_tag_assoc = self._get_item_tag_assoc(item, tag_name) + item_tag_assoc = self._get_item_tag_assoc(user, item, tag_name) # Remove association. if item_tag_assoc: @@ -87,7 +87,7 @@ return False - def delete_item_tags( self, trans, item ): + def delete_item_tags( self, trans, user, item ): """Delete tags from an item.""" # Delete item-tag associations. for tag in item.tags: @@ -96,7 +96,7 @@ # Delete tags from item. del item.tags[:] - def item_has_tag(self, item, tag): + def item_has_tag(self, user, item, tag): """Returns true if item is has a given tag.""" # Get tag name. if isinstance(tag, basestring): @@ -105,13 +105,13 @@ tag_name = tag.name # Check for an item-tag association to see if item has a given tag. - item_tag_assoc = self._get_item_tag_assoc(item, tag_name) + item_tag_assoc = self._get_item_tag_assoc(user, item, tag_name) if item_tag_assoc: return True return False - def apply_item_tags(self, db_session, item, tags_str): + def apply_item_tags(self, db_session, user, item, tags_str): """Apply tags to an item.""" # Parse tags. parsed_tags = self.parse_tags(tags_str) @@ -122,7 +122,7 @@ lc_name = name.lower() # Get or create item-tag association. - item_tag_assoc = self._get_item_tag_assoc(item, lc_name) + item_tag_assoc = self._get_item_tag_assoc(user, item, lc_name) if not item_tag_assoc: # # Create item-tag association. @@ -141,6 +141,7 @@ # Add tag to association. item.tags.append(item_tag_assoc) item_tag_assoc.tag = tag + item_tag_assoc.user = user # Apply attributes to item-tag association. Strip whitespace from user name and tag. lc_value = None @@ -211,12 +212,12 @@ return tag - def _get_item_tag_assoc(self, item, tag_name): + def _get_item_tag_assoc(self, user, item, tag_name): """Return ItemTagAssociation object for an item and a tag string; returns None if there is no such tag.""" scrubbed_tag_name = self._scrub_tag_name(tag_name) for item_tag_assoc in item.tags: - if item_tag_assoc.tag.name == scrubbed_tag_name: + if ( item_tag_assoc.user == user ) and ( item_tag_assoc.tag.name == scrubbed_tag_name ): return item_tag_assoc return None diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Thu Jan 07 13:41:44 2010 -0500 @@ -87,7 +87,7 @@ link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced" ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), + grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Thu Jan 07 13:41:44 2010 -0500 @@ -59,7 +59,7 @@ return accepted_filters class SharingColumn( grids.GridColumn ): - def filter( self, db_session, query, column_filter ): + def filter( self, db_session, user, query, column_filter ): """ Modify query to filter histories by sharing status. """ if column_filter == "All": pass @@ -95,7 +95,7 @@ link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), + grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Thu Jan 07 13:41:44 2010 -0500 @@ -84,7 +84,7 @@ return accepted_filters class SharingColumn( grids.GridColumn ): - def filter( self, db_session, query, column_filter ): + def filter( self, db_session, user, query, column_filter ): """ Modify query to filter histories by sharing status. """ if column_filter == "All": pass @@ -121,7 +121,7 @@ num_rows_per_page = 10 columns = [ NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/controllers/requests.py Thu Jan 07 13:41:44 2010 -0500 @@ -40,7 +40,7 @@ elif request.state() == request.states.COMPLETE: return '<div class="count-box state-color-ok">%s</div>' % request.state() return request.state() - def filter( self, db_session, query, column_filter ): + def filter( self, db_session, user, query, column_filter ): """ Modify query to filter request by state. """ if column_filter == "All": return query diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Jan 07 13:41:44 2010 -0500 @@ -45,7 +45,7 @@ elif request.state() == request.states.COMPLETE: return '<div class="count-box state-color-ok">%s</div>' % request.state() return request.state() - def filter( self, db_session, query, column_filter ): + def filter( self, db_session, user, query, column_filter ): """ Modify query to filter request by state. """ if column_filter == "All": return query diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/controllers/tag.py Thu Jan 07 13:41:44 2010 -0500 @@ -19,63 +19,59 @@ @web.expose @web.require_login( "Add tag to an item." ) - def add_tag_async( self, trans, id=None, item_class=None, new_tag=None, context=None ): + def add_tag_async( self, trans, item_id=None, item_class=None, new_tag=None, context=None ): """ Add tag to an item. """ - - # Check that user owns item. - item = self._get_item(trans, item_class, trans.security.decode_id( id ) ) - self._do_security_check( trans, item ) - + # Apply tag. - self.tag_handler.apply_item_tags( trans.sa_session, item, new_tag.encode('utf-8') ) + item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) + user = trans.get_user() + self.tag_handler.apply_item_tags( trans.sa_session, user, item, new_tag.encode('utf-8') ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=new_tag) - trans.log_action( unicode( "tag"), context, params ) + trans.log_action( user, unicode( "tag"), context, params ) @web.expose @web.require_login( "Remove tag from an item." ) - def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None, context=None ): + def remove_tag_async( self, trans, item_id=None, item_class=None, tag_name=None, context=None ): """ Remove tag from an item. """ - # Check that user owns item. - item = self._get_item(trans, item_class, trans.security.decode_id(id)) - self._do_security_check(trans, item) - # Remove tag. - self.tag_handler.remove_item_tag( trans, item, tag_name.encode('utf-8') ) + item = self._get_item( trans, item_class, trans.security.decode_id( item_id) ) + user = trans.get_user() + self.tag_handler.remove_item_tag( trans, user, item, tag_name.encode('utf-8') ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=tag_name) - trans.log_action( unicode( "untag"), context, params ) + trans.log_action( user, unicode( "untag"), context, params ) # Retag an item. All previous tags are deleted and new tags are applied. - @web.expose + #(a)web.expose @web.require_login( "Apply a new set of tags to an item; previous tags are deleted." ) - def retag_async( self, trans, id=None, item_class=None, new_tags=None ): - """ Apply a new set of tags to an item; previous tags are deleted. """ - item = self._get_item(trans, item_class, trans.security.decode_id(id)) + def retag_async( self, trans, item_id=None, item_class=None, new_tags=None ): + """ Apply a new set of tags to an item; previous tags are deleted. """ - self._do_security_check(trans, item) - + # Apply tags. + item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) + user = trans.get_user() tag_handler.delete_item_tags( trans, item ) - self.tag_handler.apply_item_tags( trans.sa_session, item, new_tags.encode('utf-8') ) + self.tag_handler.apply_item_tags( trans.sa_session, user, item, new_tags.encode('utf-8') ) trans.sa_session.flush() @web.expose @web.require_login( "get autocomplete data for an item's tags" ) - def tag_autocomplete_data( self, trans, q=None, limit=None, timestamp=None, id=None, item_class=None ): + def tag_autocomplete_data( self, trans, q=None, limit=None, timestamp=None, item_id=None, item_class=None ): """ Get autocomplete data for an item's tags. """ # # Get item, do security check, and get autocomplete data. # item = None - if id is not None: - item = self._get_item(trans, item_class, trans.security.decode_id(id)) - self._do_security_check(trans, item) + if item_id is not None: + item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) + user = trans.get_user() # Get item class. TODO: we should have a mapper that goes from class_name to class object. if item_class == 'History': @@ -87,11 +83,11 @@ q = q.encode('utf-8') if q.find(":") == -1: - return self._get_tag_autocomplete_names(trans, q, limit, timestamp, item, item_class) + return self._get_tag_autocomplete_names(trans, q, limit, timestamp, user, item, item_class) else: - return self._get_tag_autocomplete_values(trans, q, limit, timestamp, item, item_class) + return self._get_tag_autocomplete_values(trans, q, limit, timestamp, user, item, item_class) - def _get_tag_autocomplete_names( self, trans, q, limit, timestamp, item=None, item_class=None ): + def _get_tag_autocomplete_names( self, trans, q, limit, timestamp, user=None, item=None, item_class=None ): """Returns autocomplete data for tag names ordered from most frequently used to least frequently used.""" # @@ -109,8 +105,10 @@ # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.tag_id, func.count('*') ] from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag.table) - where_clause = and_(self._get_column_for_filtering_item_by_user_id(item_class)==trans.get_user().id, - Tag.table.c.name.like(q + "%")) + where_clause = and_( + Tag.table.c.name.like(q + "%"), + item_tag_assoc_class.table.c.user_id == user.id + ) order_by = [ func.count("*").desc() ] group_by = item_tag_assoc_class.table.c.tag_id @@ -125,7 +123,7 @@ tag = self.tag_handler.get_tag_by_id(trans.sa_session, row[0]) # Exclude tags that are already applied to the item. - if ( item is not None ) and ( self.tag_handler.item_has_tag(item, tag) ): + if ( item is not None ) and ( self.tag_handler.item_has_tag( trans.get_user(), item, tag ) ): continue # Add tag to autocomplete data. Use the most frequent name that user # has employed for the tag. @@ -135,7 +133,7 @@ return ac_data - def _get_tag_autocomplete_values(self, trans, q, limit, timestamp, item=None, item_class=None): + def _get_tag_autocomplete_values(self, trans, q, limit, timestamp, user=None, item=None, item_class=None): """Returns autocomplete data for tag values ordered from most frequently used to least frequently used.""" @@ -158,9 +156,9 @@ # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.value, func.count('*') ] from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag.table) - where_clause = and_(self._get_column_for_filtering_item_by_user_id(item_class)==trans.get_user().id, - Tag.table.c.id==tag.id, - item_tag_assoc_class.table.c.value.like(tag_value + "%")) + where_clause = and_( item_tag_assoc_class.table.c.user_id == user.id, + Tag.table.c.id==tag.id, + item_tag_assoc_class.table.c.value.like(tag_value + "%") ) order_by = [ func.count("*").desc(), item_tag_assoc_class.table.c.value ] group_by = item_tag_assoc_class.table.c.value @@ -182,8 +180,8 @@ # Build select stmt. cols_to_select = [ item_tag_assoc_class.table.c.user_tname, func.count('*') ] - where_clause = and_(self._get_column_for_filtering_item_by_user_id(item_class)==user.id , - item_tag_assoc_class.table.c.tag_id==tag.id) + where_clause = and_( item_tag_assoc_class.table.c.user_id == user.id, + item_tag_assoc_class.table.c.tag_id == tag.id ) group_by = item_tag_assoc_class.table.c.user_tname order_by = [ func.count("*").desc() ] @@ -198,35 +196,8 @@ return user_tag_names - def _get_column_for_filtering_item_by_user_id(self, item_class): - """ Returns the column to use when filtering by user id. """ - if item_class is HistoryDatasetAssociation: - # Use the user_id associated with the HDA's history. - return History.table.c.user_id - else: - # Generically, just use the user_id column of the tagged item's table. - return item_class.table.c.user_id - - def _get_item(self, trans, item_class_name, id): + def _get_item( self, trans, item_class_name, id ): """ Get an item based on type and id. """ item_class = self.tag_handler.item_tag_assoc_info[item_class_name].item_class item = trans.sa_session.query(item_class).filter("id=" + str(id))[0] - return item; - - def _do_security_check(self, trans, item): - """ Do security check on an item. """ - if isinstance(item, History): - history = item; - # Check that the history exists, and is either owned by the current - # user (if logged in) or the current history - assert history is not None - if history.user is None: - assert history == trans.get_history() - else: - assert history.user == trans.user - elif isinstance(item, HistoryDatasetAssociation): - # TODO. - pass - elif isinstance(item, Page): - # TODO. - pass + return item diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/framework/__init__.py Thu Jan 07 13:41:44 2010 -0500 @@ -171,14 +171,17 @@ to allow migration toward a more SQLAlchemy 0.4 style of use. """ return self.app.model.context.current - def log_action( self, action, context, params): + def log_action( self, user=None, action=None, context=None, params=None): """ Application-level logging of user actions. """ if self.app.config.log_actions: action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) try: - action.user = self.user + if user: + action.user = user + else: + action.user = self.user except: action.user = None try: diff -r 3aa8c1020261 -r 5b99d58c6f54 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Thu Jan 07 11:13:38 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Thu Jan 07 13:41:44 2010 -0500 @@ -129,7 +129,7 @@ if column_filter == '': continue # Update query. - query = column.filter( trans.sa_session, query, column_filter ) + query = column.filter( trans.sa_session, trans.get_user(), query, column_filter ) # Upate current filter dict. cur_filter_dict[ column.key ] = column_filter # Carry filter along to newly generated urls; make sure filter is a string so @@ -208,7 +208,7 @@ params = cur_filter_dict.copy() params['sort'] = sort_key params['async'] = ( 'async' in kwargs ) - trans.log_action( unicode( "grid.view"), context, params ) + trans.log_action( trans.get_user(), unicode( "grid.view"), context, params ) # Render grid. def url( *args, **kwargs ): @@ -308,7 +308,7 @@ if self.link and self.link( item ): return self.link( item ) return None - def filter( self, db_session, query, column_filter ): + def filter( self, db_session, user, query, column_filter ): """ Modify query to reflect the column filter. """ if column_filter == "All": pass @@ -328,14 +328,14 @@ # Generic column that employs freetext and, hence, supports freetext, case-independent filtering. class TextColumn( GridColumn ): - def filter( self, db_session, query, column_filter ): + def filter( self, db_session, user, query, column_filter ): """ Modify query to filter using free text, case independence. """ if column_filter == "All": pass elif column_filter: - query = query.filter( self.get_filter( column_filter ) ) + query = query.filter( self.get_filter( user, column_filter ) ) return query - def get_filter( self, column_filter ): + def get_filter( self, user, column_filter ): """ Returns a SQLAlchemy criterion derived from column_filter. """ model_class_key_field = getattr( self.model_class, self.key ) @@ -347,30 +347,26 @@ clause_list.append( func.lower( model_class_key_field ).like( "%" + filter.lower() + "%" ) ) return and_( *clause_list ) -# Generic column that supports tagging. -class TagsColumn( TextColumn ): +# Column that supports community tags. +class CommunityTagsColumn( TextColumn ): def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) self.model_tag_association_class = model_tag_association_class # Tags cannot be sorted. self.sortable = False # Column-specific attributes. - self.tag_elt_id_gen = 0 self.grid_name = grid_name def get_value( self, trans, grid, item ): - self.tag_elt_id_gen += 1 - elt_id="tagging-elt" + str( self.tag_elt_id_gen ) - div_elt = "<div id=%s></div>" % elt_id - return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, elt_context=self.grid_name, - elt_id = elt_id, in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter" ) - def filter( self, db_session, query, column_filter ): + return trans.fill_template( "/tagging_common.mako", tag_type="community", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name, + in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter" ) + def filter( self, db_session, user, query, column_filter ): """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ if column_filter == "All": pass elif column_filter: - query = query.filter( self.get_filter( column_filter ) ) + query = query.filter( self.get_filter( user, column_filter ) ) return query - def get_filter( self, column_filter ): + def get_filter( self, user, column_filter ): # Parse filter to extract multiple tags. tag_handler = TagHandler() if isinstance( column_filter, list ): @@ -380,19 +376,41 @@ clause_list = [] for name, value in raw_tags.items(): if name: - # Search for tag names. + # Filter by all tags. clause_list.append( self.model_class.tags.any( func.lower( self.model_tag_association_class.user_tname ).like( "%" + name.lower() + "%" ) ) ) if value: - # Search for tag values. + # Filter by all values. clause_list.append( self.model_class.tags.any( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ) ) ) return and_( *clause_list ) +# Column that supports individual tags. +class IndividualTagsColumn( CommunityTagsColumn ): + def get_value( self, trans, grid, item ): + return trans.fill_template( "/tagging_common.mako", tag_type="individual", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name, + in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter" ) + def get_filter( self, user, column_filter ): + # Parse filter to extract multiple tags. + tag_handler = TagHandler() + if isinstance( column_filter, list ): + # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags. + column_filter = ",".join( column_filter ) + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + clause_list = [] + for name, value in raw_tags.items(): + if name: + # Filter by individual's tag names. + clause_list.append( self.model_class.tags.any( and_( func.lower( self.model_tag_association_class.user_tname ).like( "%" + name.lower() + "%" ), self.model_tag_association_class.user == user ) ) ) + if value: + # Filter by individual's tag values. + clause_list.append( self.model_class.tags.any( and_( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ), self.model_tag_association_class.user == user ) ) ) + return and_( *clause_list ) + # Column that performs multicolumn filtering. class MulticolFilterColumn( TextColumn ): def __init__( self, col_name, cols_to_filter, key, visible, filterable="default" ): GridColumn.__init__( self, col_name, key=key, visible=visible, filterable=filterable) self.cols_to_filter = cols_to_filter - def filter( self, db_session, query, column_filter ): + def filter( self, db_session, user, query, column_filter ): """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ if column_filter == "All": return query @@ -401,13 +419,13 @@ for filter in column_filter: part_clause_list = [] for column in self.cols_to_filter: - part_clause_list.append( column.get_filter( filter ) ) + part_clause_list.append( column.get_filter( user, filter ) ) clause_list.append( or_( *part_clause_list ) ) complete_filter = and_( *clause_list ) else: clause_list = [] for column in self.cols_to_filter: - clause_list.append( column.get_filter( column_filter ) ) + clause_list.append( column.get_filter( user, column_filter ) ) complete_filter = or_( *clause_list ) return query.filter( complete_filter ) diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/dataset/edit_attributes.mako Thu Jan 07 13:41:44 2010 -0500 @@ -55,7 +55,7 @@ <div style="clear: both"></div> </div> %if trans.get_user() is not None: - <%namespace file="../tagging_common.mako" import="render_tagging_element" /> + <%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /> <div class="form-row"> <label> Tags: @@ -66,7 +66,7 @@ border: none; } </style> - ${render_tagging_element(data, "edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="30")} + ${render_individual_tagging_element(user=trans.get_user(), tagged_item=data, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="30")} </div> <div style="clear: both"></div> </div> diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/grid_base.mako --- a/templates/grid_base.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/grid_base.mako Thu Jan 07 13:41:44 2010 -0500 @@ -776,6 +776,14 @@ ## Render grid. <%def name="render_grid_table()"> + <% + # Set flag to indicate whether grid has operations that operate on multiple items. + multiple_item_ops_exist = False + for operation in grid.operations: + if operation.allow_multiple: + multiple_item_ops_exist = True + %> + <form action="${url()}" method="post" onsubmit="return false;"> <div class='loading-elt-overlay'></div> <table id='grid-table' class="grid"> @@ -817,17 +825,17 @@ </tr> </thead> <tbody id="grid-table-body"> - ${render_grid_table_body_contents()} + ${render_grid_table_body_contents(multiple_item_ops_exist)} </tbody> <tfoot> - ${render_grid_table_footer_contents()} + ${render_grid_table_footer_contents(multiple_item_ops_exist)} </tfoot> </table> </form> </%def> ## Render grid table body contents. -<%def name="render_grid_table_body_contents()"> +<%def name="render_grid_table_body_contents(multiple_item_ops_exist=False)"> <% num_rows_rendered = 0 %> %if query.count() == 0: ## No results. @@ -842,7 +850,7 @@ > ## Item selection column <td style="width: 1.5em;"> - %if grid.operations: + %if multiple_item_ops_exist: <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> %endif </td> @@ -917,7 +925,7 @@ </%def> ## Render grid table footer contents. -<%def name="render_grid_table_footer_contents()"> +<%def name="render_grid_table_footer_contents(multiple_item_ops_exist=False)"> ## Row for navigating among pages. <% # Mapping between item class and plural term for item. @@ -956,14 +964,8 @@ </td> </tr> %endif - ## Grid operations. - <% - num_allow_multiple_ops = 0 - for operation in grid.operations: - if operation.allow_multiple: - num_allow_multiple_ops += 1 - %> - %if num_allow_multiple_ops: + ## Grid operations for multiple items. + %if multiple_item_ops_exist: <tr> <td></td> <td colspan="100"> diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/grid_base_async.mako --- a/templates/grid_base_async.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/grid_base_async.mako Thu Jan 07 13:41:44 2010 -0500 @@ -1,6 +1,14 @@ <%namespace file="./grid_base.mako" import="*" /> -${render_grid_table_body_contents()} +<% + # Set flag to indicate whether grid has operations that operate on multiple items. + multiple_item_ops_exist = False + for operation in grid.operations: + if operation.allow_multiple: + multiple_item_ops_exist = True +%> + +${render_grid_table_body_contents(multiple_item_ops_exist=multiple_item_ops_exist)} ***** ${num_pages} ***** diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/history/view.mako --- a/templates/history/view.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/history/view.mako Thu Jan 07 13:41:44 2010 -0500 @@ -1,7 +1,7 @@ <%inherit file="/base_panels.mako"/> <%namespace file="/display_common.mako" import="get_history_link" /> <%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="../tagging_common.mako" import="render_tagging_element, render_community_tagging_element" /> +<%namespace file="../tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> <%def name="javascripts()"> ${parent.javascripts()} @@ -404,11 +404,11 @@ none %endif </div> - ## User tags. + ## Individual tags. <p> <div> - ##Yours: - ##${render_tagging_element( tagged_item=history, elt_context='view.mako', use_toggle_link=False )} + Yours: + ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='view.mako', use_toggle_link=False )} </div> </div> diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/page/display.mako --- a/templates/page/display.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/page/display.mako Thu Jan 07 13:41:44 2010 -0500 @@ -238,8 +238,8 @@ ## User tags. <p> <div> - ##Yours: - ##${render_tagging_element( tagged_item=page, elt_context='display.mako', use_toggle_link=False )} + Yours: + ${render_individual_tagging_element( tagged_item=page, elt_context='display.mako', use_toggle_link=False )} </div> </div> </div> diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/page/history_annotation_table.mako --- a/templates/page/history_annotation_table.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/page/history_annotation_table.mako Thu Jan 07 13:41:44 2010 -0500 @@ -1,4 +1,4 @@ -<%namespace file="../tagging_common.mako" import="render_tagging_element_html" /> +<%namespace file="../tagging_common.mako" import="render_individual_tagging_element_html" /> <%namespace file="../root/history_common.mako" import="render_dataset" /> <table> @@ -15,7 +15,7 @@ </div> %endif %if trans.get_user() is not None: - Tags: ${render_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )} + Tags: ${render_individual_tagging_element_html( tags=history.tags, editable=False, use_toggle_link=False )} %endif </td> </tr> diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/root/history.mako --- a/templates/root/history.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/root/history.mako Thu Jan 07 13:41:44 2010 -0500 @@ -318,7 +318,7 @@ <p></p> %endif -<%namespace file="../tagging_common.mako" import="render_tagging_element" /> +<%namespace file="../tagging_common.mako" import="render_individual_tagging_element" /> <%namespace file="history_common.mako" import="render_dataset" /> %if trans.get_user() is not None: @@ -327,7 +327,7 @@ margin-bottom: 0.5em; } </style> - ${render_tagging_element( tagged_item=history, elt_context='history.mako', get_toggle_link_text_fn='get_toggle_link_text' )} + ${render_individual_tagging_element( user=trans.get_user(), tagged_item=history, elt_context='history.mako', get_toggle_link_text_fn='get_toggle_link_text' )} %endif %if not datasets: diff -r 3aa8c1020261 -r 5b99d58c6f54 templates/tagging_common.mako --- a/templates/tagging_common.mako Thu Jan 07 11:13:38 2010 -0500 +++ b/templates/tagging_common.mako Thu Jan 07 13:41:44 2010 -0500 @@ -12,7 +12,11 @@ ## Render a tagging element if there is a tagged_item. %if tagged_item is not None: - ${render_tagging_element(tagged_item=tagged_item, elt_context=elt_context, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)} + %if tag_type == "individual": + ${render_individual_tagging_element(user=user, tagged_item=tagged_item, elt_context=elt_context, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)} + %elif tag_type == "community": + ${render_community_tagging_element(tagged_item=tagged_item, elt_context=elt_context, tag_click_fn=tag_click_fn)} + %endif %endif ## Render HTML for a list of tags. @@ -78,7 +82,7 @@ </%def> ## Render community tagging element. -<%def name="render_community_tagging_element(tagged_item=None, use_toggle_link=False, tag_click_fn='default_tag_click_fn')"> +<%def name="render_community_tagging_element(tagged_item=None, elt_context=None, use_toggle_link=False, tag_click_fn='default_tag_click_fn')"> ## Build HTML. <% elt_id = int ( floor ( random()*maxint ) ) @@ -93,36 +97,26 @@ </%def> -## Render the tags 'tags' as an autocomplete element. -<%def name="render_tagging_element(tagged_item=None, elt_context=None, use_toggle_link=True, in_form=False, input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable=True)"> +## Render individual tagging element. +<%def name="render_individual_tagging_element(user=None, tagged_item=None, elt_context=None, use_toggle_link=True, in_form=False, input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable=True)"> ## Useful attributes. - <% - tagged_item_id = str( trans.security.encode_id (tagged_item.id) ) + <% + # Useful ids. + tagged_item_id = str( trans.security.encode_id ( tagged_item.id ) ) elt_id = int ( floor ( random()*maxint ) ) + + # Get list of user's item tags. TODO: this could be moved to a database query for speed purposes. + item_tags = [ tag for tag in tagged_item.tags if ( tag.user == user ) ] %> ## Build HTML. - ${self.render_tagging_element_html(elt_id, tagged_item.tags, editable, use_toggle_link, input_size, in_form)} + ${self.render_tagging_element_html(elt_id, item_tags, editable, use_toggle_link, input_size, in_form)} ## Build script that augments tags using progressive javascript. <script type="text/javascript"> // // Set up autocomplete tagger. // - <% - ## Build string of tag name, values. - tag_names_and_values = dict() - for tag in tagged_item.tags: - tag_name = tag.user_tname - tag_value = "" - if tag.value is not None: - tag_value = tag.user_value - ## Tag names and values may be string or unicode object. - if isinstance( tag_name, str ): - tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') - else: ## isInstance( tag_name, unicode ): - tag_names_and_values[tag_name] = tag_value - %> // // Default function get text to display on the toggle link. @@ -167,6 +161,20 @@ // Default function to handle a tag click. var default_tag_click_fn = function(tag_name, tag_value) { }; + <% + ## Build dict of tag name, values. + tag_names_and_values = dict() + for tag in item_tags: + tag_name = tag.user_tname + tag_value = "" + if tag.value is not None: + tag_value = tag.user_value + ## Tag names and values may be string or unicode object. + if isinstance( tag_name, str ): + tag_names_and_values[unicode(tag_name, 'utf-8')] = unicode(tag_value, 'utf-8') + else: ## isInstance( tag_name, unicode ): + tag_names_and_values[tag_name] = tag_value + %> var options = { tags : ${h.to_json_string(tag_names_and_values)}, @@ -174,9 +182,9 @@ get_toggle_link_text_fn: ${get_toggle_link_text_fn}, tag_click_fn: ${tag_click_fn}, ## Use forward slash in controller to suppress route memory. - ajax_autocomplete_tag_url: "${h.url_for( controller='/tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - ajax_add_tag_url: "${h.url_for( controller='/tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", - ajax_delete_tag_url: "${h.url_for( controller='/tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", + ajax_autocomplete_tag_url: "${h.url_for( controller='/tag', action='tag_autocomplete_data', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + ajax_add_tag_url: "${h.url_for( controller='/tag', action='add_tag_async', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", + ajax_delete_tag_url: "${h.url_for( controller='/tag', action='remove_tag_async', item_id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", use_toggle_link: ${iff( use_toggle_link, 'true', 'false' )},

1 0

[hg] galaxy 3212: Remove print debug
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3aa8c1020261 changeset: 3212:3aa8c1020261 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Jan 07 11:13:38 2010 -0500 description: Remove print debug diffstat: lib/galaxy/tools/__init__.py | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r 81e2fad33ec3 -r 3aa8c1020261 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Jan 07 10:01:34 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Thu Jan 07 11:13:38 2010 -0500 @@ -1550,7 +1550,6 @@ out.close() def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): - log.debug('after proc called') name, data = out_data.items()[0] data.set_size() #TODO: these should be already be set before the tool runs:

1 0

[hg] galaxy 3211: Genetic welcome page
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/81e2fad33ec3 changeset: 3211:81e2fad33ec3 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Jan 07 10:01:34 2010 -0500 description: Genetic welcome page diffstat: static/images/noodles.png | 0 static/welcome.html | 152 +++------------------------------------------ 2 files changed, 13 insertions(+), 139 deletions(-) diffs (165 lines): diff -r b49627ef17a0 -r 81e2fad33ec3 static/images/noodles.png Binary file static/images/noodles.png has changed diff -r b49627ef17a0 -r 81e2fad33ec3 static/welcome.html --- a/static/welcome.html Wed Jan 06 16:03:16 2010 -0500 +++ b/static/welcome.html Thu Jan 07 10:01:34 2010 -0500 @@ -2,146 +2,20 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> -<link rel="stylesheet" href="style/base.css" type="text/css" /> -<style type="text/css"> - - .quickie { - text-align: center; - background: black; - margin: 10px; - } - - .current-quickie { - width: 300px; - background: white; - margin: auto; - } - - .current-quickie img { - padding: 15px; - border: 1px solid #ccc; - margin: auto; - background-color: white; - } - - .previous { - width: 100%; - overflow: auto; - border: solid #ccc 1px; - } - .previous .quickie { - padding-top: 10px; - min-height: 90px; - min-width: 150px; - } - #screencasts { - max-width: 50em; - margin-left: auto; - margin-right: auto; - } - -</style> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> -<script type="text/javascript"> - -$(document).ready(function() { - $('.current-quickie').cycle({ - fx: 'fade', - pause: 1, - speed: 100 - }); -}); -</script> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <link rel="stylesheet" href="style/base.css" type="text/css" /> </head> <body> -<div class="document"> -<h3 align="center">Galaxy in 2010...</h3> -<div align="center" class="current-quickie"> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200" /> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200" /> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /> - <img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /> -</div> -<br> -<hr> - -<h3 align="center">Galaxy Quickies</h3> - -<div class="previous" id="previous"> - <table border="0" cellpadding="0" cellspacing="0" width="100%"> - <tr> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie1_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie2_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie3_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie4_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie5_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie6_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie7_small.png" border="0"> - </div> - </a> - </td> - </tr> - </table> -</div> - -<script type="text/javascript"> - // Scroll to last quickie in box - document.getElementById("previous").scrollLeft = 100000000; -</script> - -<br/> -<br/> -<br/> -<hr/> - -<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> - -This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. -<p><small>Galaxy build: <b>$Rev 1733:a4214de3752e$</b></small></p> -</div> -</div> + <div class="document"> + <div class="warningmessagelarge"> + <strong>Hello world! It's running...</strong> + <hr> + To customize this page edit <code>static/welcome.html</code> + </div> + <br/> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <hr/> + This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. + </div> </body> </html>

1 0

[hg] galaxy 3210: Fix linux hosts and all the interpreter paths ...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b49627ef17a0 changeset: 3210:b49627ef17a0 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Jan 06 16:03:16 2010 -0500 description: Fix linux hosts and all the interpreter paths for dist egg scrambling diffstat: dist-eggs.ini | 42 +++++++++++++++++++++--------------------- 1 files changed, 21 insertions(+), 21 deletions(-) diffs (56 lines): diff -r abfddb44a7ca -r b49627ef17a0 dist-eggs.ini --- a/dist-eggs.ini Wed Jan 06 11:56:55 2010 -0500 +++ b/dist-eggs.ini Wed Jan 06 16:03:16 2010 -0500 @@ -7,31 +7,31 @@ ; [hosts] -py2.4-linux-i686-ucs2 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs2/bin/python2.4 -py2.4-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.4 -py2.5-linux-i686-ucs2 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs2/bin/python2.5 -py2.5-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.5 -py2.6-linux-i686-ucs2 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs2/bin/python2.6 -py2.6-linux-i686-ucs4 = scofield.bx.psu.edu /depot/projects/pythons/linux-i686-ucs4/bin/python2.6 -py2.4-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.4 -py2.4-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.4 -py2.5-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.5 -py2.5-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.5 -py2.6-linux-x86_64-ucs2 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs2/bin/python2.6 -py2.6-linux-x86_64-ucs4 = herbie.bx.psu.edu /depot/projects/pythons/linux-x86_64-ucs4/bin/python2.6 +py2.4-linux-i686-ucs2 = basie.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.4 +py2.4-linux-i686-ucs4 = basie.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.4 +py2.5-linux-i686-ucs2 = basie.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.5 +py2.5-linux-i686-ucs4 = basie.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.5 +py2.6-linux-i686-ucs2 = basie.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs2/bin/python2.6 +py2.6-linux-i686-ucs4 = basie.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-i686-ucs4/bin/python2.6 +py2.4-linux-x86_64-ucs2 = scofield.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.4 +py2.4-linux-x86_64-ucs4 = scofield.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.4 +py2.5-linux-x86_64-ucs2 = scofield.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.5 +py2.5-linux-x86_64-ucs4 = scofield.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.5 +py2.6-linux-x86_64-ucs2 = scofield.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs2/bin/python2.6 +py2.6-linux-x86_64-ucs4 = scofield.bx.psu.edu /afs/bx.psu.edu/project/pythons/linux-x86_64-ucs4/bin/python2.6 py2.4-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.4 py2.5-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.5 py2.6-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.6 py2.5-macosx-10.5-i386-ucs2 = lion.bx.psu.edu /usr/bin/python2.5 -py2.4-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /depot/projects/pythons/solaris-2.10-i86pc-ucs2/bin/python2.4 -py2.5-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /depot/projects/pythons/solaris-2.10-i86pc-ucs2/bin/python2.5 -py2.6-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /depot/projects/pythons/solaris-2.10-i86pc-ucs2/bin/python2.6 -py2.4-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.4 -py2.5-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.5 -py2.6-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.6 -py2.4-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.4 -py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5 -py2.6-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.6 +py2.4-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc-ucs2/bin/python2.4 +py2.5-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc-ucs2/bin/python2.5 +py2.6-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc-ucs2/bin/python2.6 +py2.4-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.11-i86pc-ucs2/bin/python2.4 +py2.5-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.11-i86pc-ucs2/bin/python2.5 +py2.6-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.11-i86pc-ucs2/bin/python2.6 +py2.4-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u-ucs2/bin/python2.4 +py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5 +py2.6-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-sun4u-ucs2/bin/python2.6 [groups] py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4

1 0

[hg] galaxy 3209: Small fixes to solid2fastq
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/abfddb44a7ca changeset: 3209:abfddb44a7ca user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Wed Jan 06 11:56:55 2010 -0500 description: Small fixes to solid2fastq diffstat: tools/next_gen_conversion/solid2fastq.py | 1 - tools/next_gen_conversion/solid2fastq.xml | 18 +++++++++--------- 2 files changed, 9 insertions(+), 10 deletions(-) diffs (55 lines): diff -r 3863936b6f3e -r abfddb44a7ca tools/next_gen_conversion/solid2fastq.py --- a/tools/next_gen_conversion/solid2fastq.py Tue Jan 05 16:49:56 2010 -0500 +++ b/tools/next_gen_conversion/solid2fastq.py Wed Jan 06 11:56:55 2010 -0500 @@ -177,7 +177,6 @@ r_out = open ( options.rout, 'w' ) db = tempfile.NamedTemporaryFile() - print db.name try: con = sqlite3.connect(db.name) diff -r 3863936b6f3e -r abfddb44a7ca tools/next_gen_conversion/solid2fastq.xml --- a/tools/next_gen_conversion/solid2fastq.xml Tue Jan 05 16:49:56 2010 -0500 +++ b/tools/next_gen_conversion/solid2fastq.xml Wed Jan 06 11:56:55 2010 -0500 @@ -6,8 +6,8 @@ #end if# </command> <inputs> - <param name="input1" type="data" format="csfasta" label="Select Forward reads"/> - <param name="input2" type="data" format="qualsolid" label="Select Forward qualities"/> + <param name="input1" type="data" format="csfasta" label="Select reads"/> + <param name="input2" type="data" format="qualsolid" label="Select qualities"/> <conditional name="is_run"> <param name="paired" type="select" label="Is this a mate-pair run?"> <option value="no" selected="true">No</option> @@ -26,12 +26,12 @@ <option value="">No</option> </param> <param name="trim_first_base" type="select" label="Trim first base?"> - <option value="-f">Yes</option> - <option value="" selected="true">No</option> + <option value="-f">Yes (BWA)</option> + <option value="" selected="true">No (bowtie)</option> </param> <param name="double_encode" type="select" label="Double encode?"> - <option value="-d">Yes</option> - <option value="" selected="true">No</option> + <option value="-d">Yes (BWA)</option> + <option value="" selected="true">No (bowtie)</option> </param> </inputs> <outputs> @@ -93,9 +93,9 @@ **Mate pairs** -If your data is from a mate-paired run, you will have one additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3". -In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generated two output files: one for F3 reads and the other for R3 reads. -The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD runs (several hours). +If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3". +In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads. +The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours). ------

1 0

Dynamic Tool Configuration
by Goyder, Matthew 11 Jan '10

11 Jan '10

Hi Mailing List, When one defines the visual interface to a tool, we can specify HTML components like dropdown menus, text fields etc and we place those specifications into the XML file associated with the tool. Is there a straightforward way to incorporate any sort of dynamic behavior to the tool configuration visual interface? For example lets say for a certain parameter, options A, B and C are dependent on a selection of another parameter, for example, type 1, and options D, E and F are dependent on that parameter with a selection of type 2. If a user was to select type 1 I would like the dropdown menu to display only A, B and C, and D, E and F if type 2 was selected. This is pretty straight forward with a browser scripting language like javascript but its unclear how to plug it into the current schema. Do you have any suggestions on how to achieve this functionality? Thanks, Matt Goyder

3 2

request: "fixed" dataset inputs in workflows (long)
by Assaf Gordon 09 Jan '10

09 Jan '10

Hello, I'd like to request a feature that would tremendously help (my) users to use workflows and galaxy in general: The ability to specify fixed datasets as input to workflows. Here's a use case: I have a big workflow, with several input datasets (see attached image 1). The shown workflow is just an example, but it illustrates the point: The first dataset is the "real" input - a FASTQ file that will change every time I use the workflow. The other two input datasets are always the same (or more precisely: when the user will run the workflow, he/she should always choose the same datasets - two interval files, representing exons and UTRs, for example). A real world workflow can have many many more 'fixed' datasets, used at different steps of the workflow. If I have six FASTQ libraries and I need to run the same workflow on all of them - I need to select each time the proper input datasets. This is annoying and time consuming (minor problems), and very error prone (major problem). If I want to be well organized and use a different history for each FASTQ library - copying the input datasets between histories is also a bit frustrating. What I wish I had is a way to tell an input dataset in a workflow to always use a fixed dataset - selectable at the time I edit the workflow (see attached image 2 for a mock-up UI). When the use clicks on the "Select Dataset" button, he will be shown a the list of histories, then he will select a history, then he will be shown the list of datasets in that history, and the he will select the fixed dataset. When he runs the workflow, that specific input dataset will be 'locked' and will says something like: "Using dataset NAME from history NAME". I'd be glad to provide more details and use cases, if needed. Thanks for reading so far, -gordon

1 0