October 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 3 new changesets
by Bitbucket 14 Oct '11

14 Oct '11

3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f27db62ff0fe/ changeset: f27db62ff0fe user: jmchilton date: 2011-10-11 16:42:05 summary: Small refactoring to the code used by job runners and job wrapper to access the job runner url and compute the job runner name. Should not change functionality at all, just tighten some abstractions and reduce code duplication. affected #: 5 files (-1 bytes) --- a/lib/galaxy/jobs/__init__.py Tue Oct 11 10:09:32 2011 -0400 +++ b/lib/galaxy/jobs/__init__.py Tue Oct 11 09:42:05 2011 -0500 @@ -331,6 +331,9 @@ # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) + def get_job_runner( self ): + return self.tool.job_runner + def get_job( self ): return self.sa_session.query( model.Job ).get( self.job_id ) @@ -1102,22 +1105,22 @@ self.job_runners[name] = runner( self.app ) log.debug( 'Loaded job runner: %s' % display_name ) + def __get_runner_name( self, job_wrapper ): + if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper): + runnner_name = "tasks" + else: + runner_name = ( job_wrapper.get_job_runner().split(":", 1) )[0] + return runner_name + def put( self, job_wrapper ): try: - if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None: - if isinstance(job_wrapper, TaskWrapper): - #DBTODO Refactor - runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0] - log.debug( "dispatching task %s, of job %d, to %s runner" %( job_wrapper.task_id, job_wrapper.job_id, runner_name ) ) - self.job_runners[runner_name].put( job_wrapper ) - else: - runner_name = "tasks" - log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) - self.job_runners[runner_name].put( job_wrapper ) + runner_name = self.__get_runner_name( job_wrapper ) + if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and isinstance(job_wrapper, TaskWrapper): + #DBTODO Refactor + log.debug( "dispatching task %s, of job %d, to %s runner" %( job_wrapper.task_id, job_wrapper.job_id, runner_name ) ) else: - runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0] log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) ) - self.job_runners[runner_name].put( job_wrapper ) + self.job_runners[runner_name].put( job_wrapper ) except KeyError: log.error( 'put(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' ) --- a/lib/galaxy/jobs/runners/drmaa.py Tue Oct 11 10:09:32 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Tue Oct 11 09:42:05 2011 -0500 @@ -128,7 +128,7 @@ log.exception("failure running job %s" % job_wrapper.get_id_tag()) return - runner_url = job_wrapper.tool.job_runner + runner_url = job_wrapper.get_job_runner() # This is silly, why would we queue a job with no command line? if not command_line: @@ -336,7 +336,7 @@ drm_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id) drm_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id) drm_job_state.job_id = str( job.job_runner_external_id ) - drm_job_state.runner_url = job_wrapper.tool.job_runner + drm_job_state.runner_url = job_wrapper.get_job_runner() job_wrapper.command_line = job.command_line drm_job_state.job_wrapper = job_wrapper if job.state == model.Job.states.RUNNING: --- a/lib/galaxy/jobs/runners/lwr.py Tue Oct 11 10:09:32 2011 -0400 +++ b/lib/galaxy/jobs/runners/lwr.py Tue Oct 11 09:42:05 2011 -0500 @@ -236,7 +236,7 @@ return lwr_url def get_client_from_wrapper(self, job_wrapper): - return self.get_client( job_wrapper.tool.job_runner, job_wrapper.job_id ) + return self.get_client( job_wrapper.get_job_runner(), job_wrapper.job_id ) def get_client(self, job_runner, job_id): lwr_url = self.determine_lwr_url( job_runner ) @@ -245,7 +245,7 @@ def run_job( self, job_wrapper ): stderr = stdout = command_line = '' - runner_url = job_wrapper.tool.job_runner + runner_url = job_wrapper.get_job_runner() try: job_wrapper.prepare() --- a/lib/galaxy/jobs/runners/pbs.py Tue Oct 11 10:09:32 2011 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Tue Oct 11 09:42:05 2011 -0500 @@ -204,7 +204,7 @@ log.exception("failure running job %d" % job_wrapper.job_id) return - runner_url = job_wrapper.tool.job_runner + runner_url = job_wrapper.get_job_runner() # This is silly, why would we queue a job with no command line? if not command_line: @@ -581,7 +581,7 @@ pbs_job_state.efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job.id) pbs_job_state.job_id = str( job.job_runner_external_id ) - pbs_job_state.runner_url = job_wrapper.tool.job_runner + pbs_job_state.runner_url = job_wrapper.get_job_runner() job_wrapper.command_line = job.command_line pbs_job_state.job_wrapper = job_wrapper if job.state == model.Job.states.RUNNING: --- a/lib/galaxy/jobs/runners/sge.py Tue Oct 11 10:09:32 2011 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Tue Oct 11 09:42:05 2011 -0500 @@ -164,7 +164,7 @@ log.exception("failure running job %d" % job_wrapper.job_id) return - runner_url = job_wrapper.tool.job_runner + runner_url = job_wrapper.get_job_runner() # This is silly, why would we queue a job with no command line? if not command_line: @@ -377,7 +377,7 @@ sge_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id) sge_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id) sge_job_state.job_id = str( job.job_runner_external_id ) - sge_job_state.runner_url = job_wrapper.tool.job_runner + sge_job_state.runner_url = job_wrapper.get_job_runner() job_wrapper.command_line = job.command_line sge_job_state.job_wrapper = job_wrapper if job.state == model.Job.states.RUNNING: http://bitbucket.org/galaxy/galaxy-central/changeset/2530cda12a54/ changeset: 2530cda12a54 user: jmchilton date: 2011-10-12 15:30:14 summary: Merged galaxy-central. affected #: 8 files (-1 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Tue Oct 11 09:42:05 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Oct 12 08:30:14 2011 -0500 @@ -205,7 +205,10 @@ # Score (filter data) if length >= 5 and filter_cols and filter_cols[0] == "Score": - payload.append( float(feature[4]) ) + try: + payload.append( float( feature[4] ) ) + except: + payload.append( feature[4] ) rval.append( payload ) @@ -804,7 +807,7 @@ # Return full feature. payload = [ feature.start, feature.end, - feature.name(), + feature.name(), feature.strand, # No notion of thick start, end in GFF, so make everything # thick. @@ -828,9 +831,16 @@ # Add filter data to payload. for col in filter_cols: if col == "Score": - payload.append( feature.score ) + try: + payload.append( float( feature.score ) ) + except: + payload.append( feature.score ) elif col in feature.attributes: - payload.append( feature.attributes[col] ) + try: + payload.append( float( feature.attributes[col] ) ) + except: + # Feature is not a float. + payload.append( feature.attributes[col] ) else: # Dummy value. payload.append( "na" ) --- a/lib/galaxy/web/controllers/dataset.py Tue Oct 11 09:42:05 2011 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Wed Oct 12 08:30:14 2011 -0500 @@ -1134,7 +1134,10 @@ if history in target_histories: refresh_frames = ['history'] trans.sa_session.flush() - hist_names_str = ", ".join( [ hist.name for hist in target_histories ] ) + hist_names_str = ", ".join( ['<a href="%s" target="_top">%s</a>' % + ( url_for( controller="history", action="switch_to_history", \ + hist_id=trans.security.encode_id( hist.id ) ), hist.name ) \ + for hist in target_histories ] ) num_source = len( source_dataset_ids ) - invalid_datasets num_target = len(target_histories) done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) --- a/static/june_2007_style/blue/trackster.css Tue Oct 11 09:42:05 2011 -0500 +++ b/static/june_2007_style/blue/trackster.css Wed Oct 12 08:30:14 2011 -0500 @@ -24,7 +24,7 @@ .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{overflow:hidden;text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} +.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;} @@ -62,3 +62,4 @@ .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;} .intro{padding:1em;} .intro > .action-button{background-color:#CCC;padding:1em;} +.feature-popup{background-color:#DDD;position:absolute;z-index:1000} --- a/static/june_2007_style/trackster.css.tmpl Tue Oct 11 09:42:05 2011 -0500 +++ b/static/june_2007_style/trackster.css.tmpl Wed Oct 12 08:30:14 2011 -0500 @@ -156,7 +156,6 @@ } .track-content { - overflow: hidden; text-align: center; border-top: 1px solid #eee; border-bottom: 2px solid #eee; @@ -335,4 +334,8 @@ background-color: #CCC; padding: 1em; } - +.feature-popup{ + background-color: #DDD; + position: absolute; + z-index: 1000 +} --- a/static/scripts/packed/trackster.js Tue Oct 11 09:42:05 2011 -0500 +++ b/static/scripts/packed/trackster.js Wed Oct 12 08:30:14 2011 -0500 @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. 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focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(ak,aj,ai,an,am,ah){b.call(this,ak,aj,ai,an);this.message=am;this.feature_mapper=ah;var al=this;$(this.canvas).mousemove(function(ap){var ao=al.feature_mapper.get_feature_data(ap.offsetX,ap.offsetY)})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aM.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new R(aI,aE,aj,aw.data,aw.message,aJ)}});var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),M=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,H=9,E=20,U=H+2,A=100,J=12000,S=200,D=5,w=10,L=5000,x=100,p="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var I=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(I.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new O(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no 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ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new X(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var P=function(ai,ah){M.AlphaGenerator.call(this,ah);this.filter=ai};P.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(G.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:L);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(F)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var N=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(N.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:E-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});N.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new I(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);N.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,N.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new M.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);N.call(this,ak,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};q(e.prototype,r.prototype,N.prototype,{postdraw_actions:function(ax,ah,ay,aw){N.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aL=am[0],ai=am[1],ay=ai-aL,aC=Math.ceil(ay*ar),aP=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aO=aw.data;if(this.view.high-this.view.low>J){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aL,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new M.SummaryTreePainter(aw,aL,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,U);aM.draw(aD,aC,an);return new l(aB,aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aK=0,aN=au.length;aK<aN;aK++){av=au[aK];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new P(this.filters_manager.alpha_filter):null);var aM=new (this.painter)(aq,aL,ai,this.prefs,az,aA,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aJ=null;aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aJ=aM.draw(aD,aC,an,ax);aJ.translation=-al}return new Q(aB,aI,aE,aj,aw.data,az,aw.message,aJ)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=M.VariantPainter};q(V.prototype,r.prototype,N.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,N.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,N.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=L;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var g=function(z){this.default_alpha=(z?z:1)};g.prototype.gen_alpha=function(z){return this.default_alpha};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(C,E,z,B,D,A){n.call(this,C,E,z,B,D);this.alpha_generator=(A?A:new g())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,f=1,t=3,e=3,a=9,l=2,h="#ccc";var s=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(L,E,T,G,N,ae,ai,ak,z){var Q=T[0],ag=T[1],Y=T[2],O=T[3],Z=Math.floor(Math.max(0,(ag-N)*ai)),M=Math.ceil(Math.min(z,Math.max(0,(Y-N)*ai))),X=Z,aj=M,W=(E==="Dense"?0:(0+G))*ak,K,ac,P=null,al=null,C=this.prefs.block_color,ab=this.prefs.label_color;L.globalAlpha=this.alpha_generator.gen_alpha(T);if(E=="Dense"){G=1}if(E==="no_detail"){L.fillStyle=C;L.fillRect(Z,W+5,M-Z,f)}else{var J=T[4],V=T[5],aa=T[6],D=T[7];if(V&&aa){P=Math.floor(Math.max(0,(V-N)*ai));al=Math.ceil(Math.min(z,Math.max(0,(aa-N)*ai)))}var ah,R;if(E==="Squish"||E==="Dense"){ah=1;R=e}else{ah=5;R=a}if(!D){if(T.strand){if(T.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(T.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=C}L.fillRect(Z,W,M-Z,R)}else{var I,S;if(E==="Squish"||E==="Dense"){L.fillStyle=h;I=W+Math.floor(e/2)+1;S=1}else{if(J){var I=W;var S=R;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=h;I+=(e/2)+1;S=1}}L.fillRect(Z,I,M-Z,S);for(var af=0,B=D.length;af<B;af++){var F=D[af],A=Math.floor(Math.max(0,(F[0]-N)*ai)),U=Math.ceil(Math.min(z,Math.max((F[1]-N)*ai)));if(A>U){continue}L.fillStyle=C;L.fillRect(A,W+(R-ah)/2+1,U-A,ah);if(P!==undefined&&aa>V&&!(A>al||U<P)){var ad=Math.max(A,P),H=Math.min(U,al);L.fillRect(ad,W+1,H-ad,R);if(D.length==1&&E=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ad+14<H){ad+=2;H-=2}L.fillRect(ad,W+1,H-ad,R)}}}}if(E==="Pack"&&ag>N){L.fillStyle=ab;if(N===0&&Z-L.measureText(O).width<0){L.textAlign="left";L.fillText(O,M+l,W+8);aj+=L.measureText(O).width+l}else{L.textAlign="right";L.fillText(O,Z-l,W+8);X-=L.measureText(O).width+l}}}L.globalAlpha=1;return[X,aj]}});var b=function(C,E,z,B,D,A){p.call(this,C,E,z,B,D,A)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(D,F,z,C,E,A,B){p.call(this,D,F,z,C,E,A);this.ref_seq=B};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq,char_width_px=V.canvas.manager.char_width_px;var af=[];if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){S=Math.round(M/2)}if(!J){J=[[0,G.length]]}for(var N=0,Y=J.length;N<Y;N++){var K=J[N],C="MIDNSHP=X"[K[0]],O=K[1];if(C==="H"||C==="S"){P-=O}var H=U+P,ae=Math.floor(Math.max(0,(H-aa)*M)),I=Math.floor(Math.max(0,(H+O-aa)*M));if(ae===I){I+=1}switch(C){case"H":break;case"S":case"M":case"=":if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(S>0){V.fillStyle=this.prefs.block_color;V.fillRect(ae-S,F+1,I-ae,9);V.fillStyle=h;for(var ac=0,z=R.length;ac<z;ac++){if(this.prefs.show_differences&&ref_seq){var L=ref_seq[H-aa+ac];if(!L||L.toLowerCase()===R[ac].toLowerCase()){continue}}if(H+ac>=aa&&H+ac<=B){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad,F+9)}}}else{V.fillStyle=this.prefs.block_color;V.fillRect(ae,F+4,I-ae,e)}}W+=O;P+=O;break;case"N":V.fillStyle=h;V.fillRect(ae-S,F+5,I-ae,1);P+=O;break;case"D":V.fillStyle="red";V.fillRect(ae-S,F+4,I-ae,3);P+=O;break;case"P":break;case"I":var Z=ae-S;if(is_overlap([H,H+O],A)){var R=G.slice(W,W+O);if(this.prefs.show_insertions){var E=ae-(I-ae)/2;if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){V.fillStyle="yellow";V.fillRect(E-S,F-9,I-ae,9);af[af.length]={type:"triangle",data:[Z,F+4,5]};V.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):R=R.slice(aa-H);break;case (OVERLAP_END):R=R.slice(0,H-B);break;case (CONTAINED_BY):break;case (CONTAINS):R=R.slice(aa-H,H-B);break}for(var ac=0,z=R.length;ac<z;ac++){var ad=Math.floor(Math.max(0,(H+ac-aa)*M));V.fillText(R[ac],ad-(I-ae)/2,F)}}else{V.fillStyle="yellow";V.fillRect(E,F+(this.mode!=="Dense"?2:5),I-ae,(Q!=="Dense"?e:t))}}else{if((Q==="Pack"||this.mode==="Auto")&&G!==undefined&&M>char_width_px){af[af.length]={type:"text",data:[R.length,Z,F+9]}}else{}}}W+=O;break;case"X":W+=O;break}}V.fillStyle="yellow";var ab,D,ag;for(var X=0;X<af.length;X++){ab=af[X];D=ab.type;ag=ab.data;if(D==="text"){V.save();V.font="bold "+V.font;V.fillText(ag[0],ag[1],ag[2]);V.restore()}else{if(D=="triangle"){r(V,ag[0],ag[1],ag[2])}}}},draw_element:function(S,N,F,C,V,A,J,T,Q){var I=F[0],R=F[1],B=F[2],K=F[3],E=Math.floor(Math.max(0,(R-V)*J)),G=Math.ceil(Math.min(Q,Math.max(0,(B-V)*J))),D=(N==="Dense"?0:(0+C))*T,W=this.prefs.block_color,H=this.prefs.label_color,P=0;if((N==="Pack"||this.mode==="Auto")&&J>S.canvas.manager.char_width_px){var P=Math.round(J/2)}S.fillStyle=W;if(F[5] instanceof Array){var O=Math.floor(Math.max(0,(F[4][0]-V)*J)),M=Math.ceil(Math.min(Q,Math.max(0,(F[4][1]-V)*J))),L=Math.floor(Math.max(0,(F[5][0]-V)*J)),z=Math.ceil(Math.min(Q,Math.max(0,(F[5][1]-V)*J)));if(F[4][1]>=V&&F[4][0]<=A&&F[4][2]){this.draw_read(S,N,J,V,A,F[4][0],F[4][2],F[4][3],D)}if(F[5][1]>=V&&F[5][0]<=A&&F[5][2]){this.draw_read(S,N,J,V,A,F[5][0],F[5][2],F[5][3],D)}if(L>M){S.fillStyle=h;q(S,M-P,D+5,L-P,D+5)}}else{S.fillStyle=W;this.draw_read(S,N,J,V,A,R,F[4],F[5],D)}if(N==="Pack"&&R>V){S.fillStyle=this.prefs.label_color;var U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.AlphaGenerator=g;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file --- a/static/scripts/packed/trackster_ui.js Tue Oct 11 09:42:05 2011 -0500 +++ b/static/scripts/packed/trackster_ui.js Wed Oct 12 08:30:14 2011 -0500 @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name==m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file --- a/static/scripts/trackster.js Tue Oct 11 09:42:05 2011 -0500 +++ b/static/scripts/trackster.js Wed Oct 12 08:30:14 2011 -0500 @@ -309,10 +309,19 @@ CACHED_TILES_FEATURE = 10, CACHED_TILES_LINE = 5, CACHED_DATA = 5; - -function round_1000(num) { - return Math.round(num * 1000) / 1000; -}; + +/** + * Round a number to a given number of decimal places. + */ +function round(num, places) { + // Default rounding is to integer. + if (!places) { + places = 0; + } + + var val = Math.pow(10, places); + return Math.round(num * val) / val; +} /** * Generic cache that handles key/value pairs. @@ -799,8 +808,6 @@ this.vis_id = vis_id; this.dbkey = dbkey; this.title = title; - // Alias tracks to point at drawables. TODO: changes tracks to 'drawables' or something similar. - this.tracks = this.drawables; this.label_tracks = []; this.tracks_to_be_redrawn = []; this.max_low = 0; @@ -1097,10 +1104,10 @@ view.reset(); view.request_redraw(true); - for (var track_id = 0, len = view.tracks.length; track_id < len; track_id++) { - var track = view.tracks[track_id]; - if (track.init) { - track.init(); + for (var i = 0, len = view.drawables.length; i < len; i++) { + var drawable = view.drawables[i]; + if (drawable.init) { + drawable.init(); } } } @@ -1192,7 +1199,7 @@ var view = this, // Either redrawing a single track or all view's tracks. - track_list = (track ? [track] : view.tracks), + track_list = (track ? [track] : view.drawables), track_index; // Add/update tracks in track list to redraw list. @@ -1629,7 +1636,7 @@ // No element to filter on. return true; } - var val = parseFloat(element[this.index]); + var val = element[this.index]; return (isNaN(val) || (val >= this.low && val <= this.high)); }, /** @@ -2085,7 +2092,8 @@ /** * Tiles drawn by tracks. */ -var Tile = function(index, resolution, canvas, data) { +var Tile = function(track, index, resolution, canvas, data) { + this.track = track; this.index = index; this.low = index * DENSITY * resolution; this.high = (index + 1) * DENSITY * resolution; @@ -2096,26 +2104,114 @@ this.stale = false; }; -var SummaryTreeTile = function(index, resolution, canvas, data, max_val) { - Tile.call(this, index, resolution, canvas, data); +/** + * Perform pre-display actions. + */ +Tile.prototype.predisplay_actions = function() {}; + +var SummaryTreeTile = function(track, index, resolution, canvas, data, max_val) { + Tile.call(this, track, index, resolution, canvas, data); this.max_val = max_val; }; +extend(SummaryTreeTile.prototype, Tile.prototype); -var FeatureTrackTile = function(index, resolution, canvas, data, message, feature_mapper) { - Tile.call(this, index, resolution, canvas, data); +var FeatureTrackTile = function(track, index, resolution, canvas, data, mode, message, feature_mapper) { + Tile.call(this, track, index, resolution, canvas, data); + this.mode = mode; this.message = message; this.feature_mapper = feature_mapper; +}; +extend(FeatureTrackTile.prototype, Tile.prototype); + +/** + * Sets up support for popups. + */ +FeatureTrackTile.prototype.predisplay_actions = function() { + // + // Add support for popups. + // + var tile = this, + popups = {}; + + // Only show popups in Pack mode. + if (tile.mode !== "Pack") { return; } - // - // Set up display of feature data on mouseover. - // - var tile = this; $(this.canvas).mousemove(function (e) { - var feature_data = tile.feature_mapper.get_feature_data(e.offsetX, e.offsetY); - - // TODO: show popup with feature's information. + // Get feature data for position. + var + this_offset = $(this).offset(), + offsetX = e.pageX - this_offset.left, + offsetY = e.pageY - this_offset.top, + feature_data = tile.feature_mapper.get_feature_data(offsetX, offsetY), + feature_uid = (feature_data ? feature_data[0] : null); + // Hide visible popup if not over a feature or over a different feature. + $(this).siblings(".feature-popup").each(function() { + if ( !feature_uid || + $(this).attr("id") !== feature_uid.toString() ) { + $(this).remove(); + } + }); + + if (feature_data) { + // Get or create popup. + var popup = popups[feature_uid]; + if (!popup) { + // Create feature's popup element. + var + feature_uid = feature_data[0], + feature_dict = { + name: feature_data[3], + start: feature_data[1], + end: feature_data[2], + strand: feature_data[4] + }, + filters = tile.track.filters_manager.filters, + filter; + + // Add filter values to feature dict. + for (var i = 0; i < filters.length; i++) { + filter = filters[i]; + feature_dict[filter.name] = feature_data[filter.index]; + } + + // Build popup. + + var popup = $("<div/>").attr("id", feature_uid).addClass("feature-popup"), + key, value, + table = $("<table/>").appendTo(popup), row; + for (key in feature_dict) { + value = feature_dict[key]; + row = $("<tr/>").appendTo(table); + $("<th/>").appendTo(row).text(key); + $("<td/>").attr("align", "left").appendTo(row) + .text(typeof(value) == 'number' ? round(value, 2) : value); + } + popups[feature_uid] = popup; + } + + // Attach popup to canvas's parent. + popup.appendTo($(tile.canvas).parent()); + + // Offsets are within canvas, but popup must be positioned relative to parent element. + // parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not + // overlap popup. + var + popupX = offsetX + parseInt( tile.canvas.css("left") ) + 7, + popupY = offsetY + parseInt( tile.canvas.css("top") ) + 7; + popup.css("left", popupX + "px").css("top", popupY + "px") + } + else if (!e.isPropagationStopped()) { + // Propogate event to other tiles because overlapping tiles prevent mousemove from being + // called on tiles under this tile. + e.stopPropagation(); + $(this).siblings().each(function() { + $(this).trigger(e); + }); + } + }) + .mouseleave(function() { + $(this).siblings(".feature-popup").remove(); }); - }; /** @@ -2223,7 +2319,6 @@ track.container_div.addClass("error"); track.content_div.text(DATA_ERROR); if (result.message) { - var track_id = track.view.tracks.indexOf(track); var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").click(function() { show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); }); @@ -2492,7 +2587,7 @@ data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); // Need to undo offsets when placing image data. tgt_ctx.putImageData(data, -track.left_offset, (tile.data.dataset_type === "summary_tree" ? SUMMARY_TREE_TOP_PADDING : 0)); - new_tile = new Tile(-1, resolution, new_canvas); + new_tile = new Tile(track, -1, resolution, new_canvas); overview_tile.resolve(new_tile); }); @@ -2697,6 +2792,8 @@ // // Show tile element. // + + tile.predisplay_actions(); // Position tile element, recalculate left position at display time var range = this.view.high - this.view.low, @@ -2812,7 +2909,7 @@ var c_start = Math.round(c * w_scale); ctx.fillText(seq[c], c_start + track.left_offset, 10); } - return new Tile(tile_index, resolution, canvas, seq); + return new Tile(track, tile_index, resolution, canvas, seq); } this.content_div.css("height", "0px"); } @@ -2851,8 +2948,8 @@ track.set_name(track.prefs.name); track.vertical_range = track.prefs.max_value - track.prefs.min_value; // Update the y-axis - $('#linetrack_' + track.track_id + '_minval').text(track.prefs.min_value); - $('#linetrack_' + track.track_id + '_maxval').text(track.prefs.max_value); + $('#linetrack_' + track.dataset_id + '_minval').text(track.prefs.min_value); + $('#linetrack_' + track.dataset_id + '_maxval').text(track.prefs.max_value); track.tile_cache.clear(); track.request_draw(); } @@ -2899,8 +2996,7 @@ }).appendTo(track.container_div); }, predraw_init: function() { - var track = this, - track_id = track.view.tracks.indexOf(track); + var track = this; track.vertical_range = undefined; return $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: null, high: null, @@ -2911,8 +3007,8 @@ track.prefs.min_value = data.min; track.prefs.max_value = data.max; // Update the config - $('#track_' + track_id + '_minval').val(track.prefs.min_value); - $('#track_' + track_id + '_maxval').val(track.prefs.max_value); + $('#track_' + track.dataset_id + '_minval').val(track.prefs.min_value); + $('#track_' + track.dataset_id + '_maxval').val(track.prefs.max_value); } track.vertical_range = track.prefs.max_value - track.prefs.min_value; track.total_frequency = data.total_frequency; @@ -2920,8 +3016,8 @@ // Draw y-axis labels if necessary track.container_div.find(".yaxislabel").remove(); - var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(round_1000(track.prefs.min_value)); - var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(round_1000(track.prefs.max_value)); + var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_minval').text(round(track.prefs.min_value, 3)); + var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_maxval').text(round(track.prefs.max_value, 3)); max_label.css({ position: "absolute", top: "24px", left: "10px" }); max_label.prependTo(track.container_div); @@ -2955,7 +3051,7 @@ var painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode); painter.draw(ctx, width, height); - return new Tile(tile_index, resolution, canvas, result.data); + return new Tile(this.track, tile_index, resolution, canvas, result.data); } }); @@ -3288,7 +3384,7 @@ // Deal with left_offset by translating. ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING); painter.draw(ctx, width, required_height); - return new SummaryTreeTile(tile_index, resolution, canvas, result.data, result.max); + return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max); } // Start dealing with row-by-row tracks @@ -3347,7 +3443,7 @@ feature_mapper.translation = -left_offset; } - return new FeatureTrackTile(tile_index, resolution, canvas, result.data, result.message, feature_mapper); + return new FeatureTrackTile(track, tile_index, resolution, canvas, result.data, mode, result.message, feature_mapper); } }); @@ -3891,7 +3987,7 @@ */ FeaturePositionMapper.prototype.get_feature_data = function(x, y) { // Find slot using Y. - var slot = Math.floor(y/this.slot_height), + var slot = Math.floor( y/this.slot_height ), feature_dict; // May not be over a slot due to padding, margin, etc. --- a/static/scripts/trackster_ui.js Tue Oct 11 09:42:05 2011 -0500 +++ b/static/scripts/trackster_ui.js Wed Oct 12 08:30:14 2011 -0500 @@ -113,9 +113,9 @@ // Set overview. var overview_track; - for (var i = 0; i < view.tracks.length; i++) { - if (view.tracks[i].name == overview_track_name) { - view.set_overview(view.tracks[i]); + for (var i = 0; i < view.drawables.length; i++) { + if (view.drawables[i].name == overview_track_name) { + view.set_overview(view.drawables[i]); break; } } http://bitbucket.org/galaxy/galaxy-central/changeset/261980e0dd3d/ changeset: 261980e0dd3d user: jmchilton date: 2011-10-12 19:51:09 summary: Re merged with galaxy central. affected #: 21 files (-1 bytes) --- a/datatypes_conf.xml.sample Wed Oct 12 08:30:14 2011 -0500 +++ b/datatypes_conf.xml.sample Wed Oct 12 12:51:09 2011 -0500 @@ -56,11 +56,22 @@ <converter file="fasta_to_2bit.xml" target_datatype="twobit"/><converter file="fasta_to_len.xml" target_datatype="len"/></datatype> - <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"/> - <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"/> - <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/> - <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/> - <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"> + <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/> + </datatype> + <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/><datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/><datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/><datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extract_dataset_parts.sh Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,8 @@ +#!/bin/sh + +cd `dirname $0` +for file in $1/split_info*.json +do + # echo processing $file + python ./scripts/extract_dataset_part.py $file +done --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,46 @@ +#!/usr/bin/env python + +import sys, os, gzip +from galaxy.datatypes.checkers import is_gzip + + +def main(): + """ + The format of the file is JSON: + { "sections" : [ + { "start" : "x", "end" : "y", "sequences" : "z" }, + ... + ]} + This works only for UNCOMPRESSED fastq files. The Python GzipFile does not provide seekable + offsets via tell(), so clients just have to split the slow way + """ + input_fname = sys.argv[1] + if is_gzip(input_fname): + print 'Conversion is only possible for uncompressed files' + sys.exit(1) + + out_file = open(sys.argv[2], 'w') + + current_line = 0 + sequences=1000000 + lines_per_chunk = 4*sequences + chunk_begin = 0 + + in_file = open(input_name) + + out_file.write('{"sections" : ['); + + for line in in_file: + current_line += 1 + if 0 == current_line % lines_per_chunk: + chunk_end = in_file.tell() + out_file.write('{"start":"%s","end":"%s","sequences":"%s"},' % (chunk_begin, chunk_end, sequences)) + chunk_begin = chunk_end + + chunk_end = in_file.tell() + out_file.write('{"start":"%s","end":"%s","sequences":"%s"}' % (chunk_begin, chunk_end, (current_line % lines_per_chunk) / 4)) + out_file.write(']}\n') + + +if __name__ == "__main__": + main() --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,13 @@ +<tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.0" hidden="true"> + <command interpreter="python">fastq_to_fqtoc.py $input1 $output1</command> + <inputs> + <page> + <param format="fastq" name="input1" type="data" label="Choose FASTQ file"/> + </page> + </inputs> + <outputs> + <data format="fqtoc" name="output1"/> + </outputs> + <help> + </help> +</tool> --- a/lib/galaxy/datatypes/data.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/datatypes/data.py Wed Oct 12 12:51:09 2011 -0500 @@ -351,6 +351,22 @@ @property def has_resolution(self): return False + + + + def merge( split_files, output_file): + """ + TODO: Do we need to merge gzip files using gzjoin? cat seems to work, + but might be brittle. Need to revisit this. + """ + if len(split_files) == 1: + cmd = 'mv -f %s %s' % ( split_files[0], output_file ) + else: + cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file ) + result = os.system(cmd) + if result != 0: + raise Exception('Result %s from %s' % (result, cmd)) + merge = staticmethod(merge) class Text( Data ): file_ext = 'txt' @@ -446,9 +462,83 @@ dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' + def split( input_files, subdir_generator_function, split_params): + """ + Split the input files by line. + """ + if split_params is None: + return + + if len(input_files) > 1: + raise Exception("Text file splitting does not support multiple files") + + lines_per_file = None + chunk_size = None + if split_params['split_mode'] == 'number_of_parts': + lines_per_file = [] + # Computing the length is expensive! + def _file_len(fname): + i = 0 + f = open(fname) + for i, l in enumerate(f): + pass + f.close() + return i + 1 + length = _file_len(input_files[0]) + parts = int(split_params['split_size']) + if length < parts: + parts = length + len_each, remainder = divmod(length, parts) + while length > 0: + chunk = len_each + if remainder > 0: + chunk += 1 + lines_per_file.append(chunk) + remainder=- 1 + length -= chunk + elif split_params['split_mode'] == 'to_size': + chunk_size = int(split_params['split_size']) + else: + raise Exception('Unsupported split mode %s' % split_params['split_mode']) + + f = open(input_files[0], 'rt') + try: + chunk_idx = 0 + file_done = False + part_file = None + while not file_done: + if lines_per_file is None: + this_chunk_size = chunk_size + elif chunk_idx < len(lines_per_file): + this_chunk_size = lines_per_file[chunk_idx] + chunk_idx += 1 + lines_remaining = this_chunk_size + part_file = None + while lines_remaining > 0: + a_line = f.readline() + if a_line == '': + file_done = True + break + if part_file is None: + part_dir = subdir_generator_function() + part_path = os.path.join(part_dir, os.path.basename(input_files[0])) + part_file = open(part_path, 'w') + part_file.write(a_line) + lines_remaining -= 1 + if part_file is not None: + part_file.close() + except Exception, e: + log.error('Unable to split files: %s' % str(e)) + f.close() + if part_file is not None: + part_file.close() + raise + f.close() + split = staticmethod(split) + class LineCount( Text ): - """ - Dataset contains a single line with a single integer that denotes the + """ + Dataset contains a single line with a single integer that denotes the line count for a related dataset. Used for custom builds. """ pass --- a/lib/galaxy/datatypes/sequence.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/datatypes/sequence.py Wed Oct 12 12:51:09 2011 -0500 @@ -2,10 +2,12 @@ Sequence classes """ +import gzip import data import logging import re import string +import os from cgi import escape from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes import metadata @@ -13,8 +15,52 @@ from galaxy import util from sniff import * +import pkg_resources +pkg_resources.require("simplejson") +import simplejson + log = logging.getLogger(__name__) +class SequenceSplitLocations( data.Text ): + """ + Class storing information about a sequence file composed of multiple gzip files concatenated as + one OR an uncompressed file. In the GZIP case, each sub-file's location is stored in start and end. + The format of the file is JSON: + { "sections" : [ + { "start" : "x", "end" : "y", "sequences" : "z" }, + ... + ]} + """ + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + try: + parsed_data = simplejson.load(open(dataset.file_name)) + # dataset.peek = simplejson.dumps(data, sort_keys=True, indent=4) + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = '%d sections' % len(parsed_data['sections']) + except Exception, e: + dataset.peek = 'Not FQTOC file' + dataset.blurb = 'Not FQTOC file' + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + file_ext = "fqtoc" + + def sniff( self, filename ): + if os.path.getsize(filename) < 50000: + try: + data = simplejson.load(open(filename)) + sections = data['sections'] + for section in sections: + if 'start' not in section or 'end' not in section or 'sequences' not in section: + return False + return True + except: + pass + return False + + class Sequence( data.Text ): """Class describing a sequence""" @@ -50,6 +96,239 @@ dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' + def get_sequences_per_file(total_sequences, split_params): + if split_params['split_mode'] == 'number_of_parts': + # legacy basic mode - split into a specified number of parts + parts = int(split_params['split_size']) + sequences_per_file = [total_sequences/parts for i in range(parts)] + for i in range(total_sequences % parts): + sequences_per_file[i] += 1 + elif split_params['split_mode'] == 'to_size': + # loop through the sections and calculate the number of sequences + chunk_size = long(split_params['split_size']) + + chunks = total_sequences / chunk_size + rem = total_sequences % chunk_size + sequences_per_file = [chunk_size for i in range(total_sequences / chunk_size)] + # TODO: Should we invest the time in a better way to handle small remainders? + if rem > 0: + sequences_per_file.append(rem) + else: + raise Exception('Unsupported split mode %s' % split_params['split_mode']) + return sequences_per_file + get_sequences_per_file = staticmethod(get_sequences_per_file) + + def do_slow_split( cls, input_datasets, subdir_generator_function, split_params): + # count the sequences so we can split + # TODO: if metadata is present, take the number of lines / 4 + if input_datasets[0].metadata is not None and input_datasets[0].metadata.sequences is not None: + total_sequences = input_datasets[0].metadata.sequences + else: + input_file = input_datasets[0].file_name + compress = is_gzip(input_file) + if compress: + # gzip is really slow before python 2.7! + in_file = gzip.GzipFile(input_file, 'r') + else: + # TODO + # if a file is not compressed, seek locations can be calculated and stored + # ideally, this would be done in metadata + # TODO + # Add BufferedReader if python 2.7? + in_file = open(input_file, 'rt') + total_sequences = long(0) + for i, line in enumerate(in_file): + total_sequences += 1 + in_file.close() + total_sequences /= 4 + + sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params) + return cls.write_split_files(input_datasets, None, subdir_generator_function, sequences_per_file) + do_slow_split = classmethod(do_slow_split) + + def do_fast_split( cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params): + data = simplejson.load(open(toc_file_datasets[0].file_name)) + sections = data['sections'] + total_sequences = long(0) + for section in sections: + total_sequences += long(section['sequences']) + sequences_per_file = cls.get_sequences_per_file(total_sequences, split_params) + return cls.write_split_files(input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file) + do_fast_split = classmethod(do_fast_split) + + def write_split_files(cls, input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file): + directories = [] + def get_subdir(idx): + if idx < len(directories): + return directories[idx] + dir = subdir_generator_function() + directories.append(dir) + return dir + + # we know how many splits and how many sequences in each. What remains is to write out instructions for the + # splitting of all the input files. To decouple the format of those instructions from this code, the exact format of + # those instructions is delegated to scripts + start_sequence=0 + for part_no in range(len(sequences_per_file)): + dir = get_subdir(part_no) + for ds_no in range(len(input_datasets)): + ds = input_datasets[ds_no] + base_name = os.path.basename(ds.file_name) + part_path = os.path.join(dir, base_name) + split_data = dict(class_name='%s.%s' % (cls.__module__, cls.__name__), + output_name=part_path, + input_name=ds.file_name, + args=dict(start_sequence=start_sequence, num_sequences=sequences_per_file[part_no])) + if toc_file_datasets is not None: + toc = toc_file_datasets[ds_no] + split_data['args']['toc_file'] = toc.file_name + f = open(os.path.join(dir, 'split_info_%s.json' % base_name), 'w') + simplejson.dump(split_data, f) + f.close() + start_sequence += sequences_per_file[part_no] + return directories + write_split_files = classmethod(write_split_files) + + def split( cls, input_datasets, subdir_generator_function, split_params): + """ + FASTQ files are split on cluster boundaries, in increments of 4 lines + """ + if split_params is None: + return None + + # first, see if there are any associated FQTOC files that will give us the split locations + # if so, we don't need to read the files to do the splitting + toc_file_datasets = [] + for ds in input_datasets: + tmp_ds = ds + fqtoc_file = None + while fqtoc_file is None and tmp_ds is not None: + fqtoc_file = tmp_ds.get_converted_files_by_type('fqtoc') + tmp_ds = tmp_ds.copied_from_library_dataset_dataset_association + + if fqtoc_file is not None: + toc_file_datasets.append(fqtoc_file) + + if len(toc_file_datasets) == len(input_datasets): + return cls.do_fast_split(input_datasets, toc_file_datasets, subdir_generator_function, split_params) + return cls.do_slow_split(input_datasets, subdir_generator_function, split_params) + split = classmethod(split) + + def process_split_file(data): + """ + This is called in the context of an external process launched by a Task (possibly not on the Galaxy machine) + to create the input files for the Task. The parameters: + data - a dict containing the contents of the split file + """ + args = data['args'] + input_name = data['input_name'] + output_name = data['output_name'] + start_sequence = long(args['start_sequence']) + sequence_count = long(args['num_sequences']) + + if 'toc_file' in args: + toc_file = simplejson.load(open(args['toc_file'], 'r')) + commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count) + else: + commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count) + for cmd in commands: + if 0 != os.system(cmd): + raise Exception("Executing '%s' failed" % cmd) + return True + process_split_file = staticmethod(process_split_file) + + def get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count): + """ + Uses a Table of Contents dict, parsed from an FQTOC file, to come up with a set of + shell commands that will extract the parts necessary + >>> three_sections=[dict(start=0, end=74, sequences=10), dict(start=74, end=148, sequences=10), dict(start=148, end=148+76, sequences=10)] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=10) + ['dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=1, sequence_count=5) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +5 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=20) + ['dd bs=1 skip=0 count=148 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=10) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', '(dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=10, sequence_count=10) + ['dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=20) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', 'dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz', '(dd bs=1 skip=148 count=76 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + """ + sections = toc_file['sections'] + result = [] + + current_sequence = long(0) + i=0 + # skip to the section that contains my starting sequence + while i < len(sections) and start_sequence >= current_sequence + long(sections[i]['sequences']): + current_sequence += long(sections[i]['sequences']) + i += 1 + if i == len(sections): # bad input data! + raise Exception('No FQTOC section contains starting sequence %s' % start_sequence) + + # These two variables act as an accumulator for consecutive entire blocks that + # can be copied verbatim (without decompressing) + start_chunk = long(-1) + end_chunk = long(-1) + copy_chunk_cmd = 'dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s' + + while sequence_count > 0 and i < len(sections): + # we need to extract partial data. So, find the byte offsets of the chunks that contain the data we need + # use a combination of dd (to pull just the right sections out) tail (to skip lines) and head (to get the + # right number of lines + sequences = long(sections[i]['sequences']) + skip_sequences = start_sequence-current_sequence + sequences_to_extract = min(sequence_count, sequences-skip_sequences) + start_copy = long(sections[i]['start']) + end_copy = long(sections[i]['end']) + if sequences_to_extract < sequences: + if start_chunk > -1: + result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name)) + start_chunk = -1 + # extract, unzip, trim, recompress + result.append('(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s' % + (start_copy, end_copy-start_copy, input_name, skip_sequences*4+1, sequences_to_extract*4, output_name)) + else: # whole section - add it to the start_chunk/end_chunk accumulator + if start_chunk == -1: + start_chunk = start_copy + end_chunk = end_copy + sequence_count -= sequences_to_extract + start_sequence += sequences_to_extract + current_sequence += sequences + i += 1 + if start_chunk > -1: + result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name)) + + if sequence_count > 0: + raise Exception('%s sequences not found in file' % sequence_count) + + return result + get_split_commands_with_toc = staticmethod(get_split_commands_with_toc) + + + def get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count): + """ + Does a brain-dead sequential scan & extract of certain sequences + >>> Sequence.get_split_commands_sequential(True, './input.gz', './output.gz', start_sequence=0, sequence_count=10) + ['zcat "./input.gz" | ( tail -n +1 2> /dev/null) | head -40 | gzip -c > "./output.gz"'] + >>> Sequence.get_split_commands_sequential(False, './input.fastq', './output.fastq', start_sequence=10, sequence_count=10) + ['tail -n +41 "./input.fastq" 2> /dev/null | head -40 > "./output.fastq"'] + """ + start_line = start_sequence * 4 + line_count = sequence_count * 4 + # TODO: verify that tail can handle 64-bit numbers + if is_compressed: + cmd = 'zcat "%s" | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c' % (input_name, start_line+1, line_count) + else: + cmd = 'tail -n +%s "%s" 2> /dev/null | head -%s' % (start_line+1, input_name, line_count) + cmd += ' > "%s"' % output_name + + return [cmd] + get_split_commands_sequential = staticmethod(get_split_commands_sequential) + + + class Alignment( data.Text ): """Class describing an alignment""" @@ -550,3 +829,4 @@ return False except: return False + --- a/lib/galaxy/jobs/__init__.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/jobs/__init__.py Wed Oct 12 12:51:09 2011 -0500 @@ -327,6 +327,7 @@ self.working_directory = \ os.path.join( self.app.config.job_working_directory, str( self.job_id ) ) self.output_paths = None + self.output_dataset_paths = None self.tool_provided_job_metadata = None # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) @@ -719,23 +720,35 @@ def get_session_id( self ): return self.session_id + def get_input_dataset_fnames( self, ds ): + filenames = [] + filenames = [ ds.file_name ] + #we will need to stage in metadata file names also + #TODO: would be better to only stage in metadata files that are actually needed (found in command line, referenced in config files, etc.) + for key, value in ds.metadata.items(): + if isinstance( value, model.MetadataFile ): + filenames.append( value.file_name ) + return filenames + def get_input_fnames( self ): job = self.get_job() filenames = [] for da in job.input_datasets + job.input_library_datasets: #da is JobToInputDatasetAssociation object if da.dataset: - filenames.append( da.dataset.file_name ) - #we will need to stage in metadata file names also - #TODO: would be better to only stage in metadata files that are actually needed (found in command line, referenced in config files, etc.) - for key, value in da.dataset.metadata.items(): - if isinstance( value, model.MetadataFile ): - filenames.append( value.file_name ) + filenames.extend(self.get_input_dataset_fnames(da.dataset)) return filenames def get_output_fnames( self ): - if self.output_paths is not None: - return self.output_paths + if self.output_paths is None: + self.compute_outputs() + return self.output_paths + def get_output_datasets_and_fnames( self ): + if self.output_dataset_paths is None: + self.compute_outputs() + return self.output_dataset_paths + + def compute_outputs( self ) : class DatasetPath( object ): def __init__( self, dataset_id, real_path, false_path = None ): self.dataset_id = dataset_id @@ -746,23 +759,27 @@ return self.real_path else: return self.false_path - job = self.get_job() # Job output datasets are combination of output datasets, library datasets, and jeha datasets. jeha = self.sa_session.query( model.JobExportHistoryArchive ).filter_by( job=job ).first() + jeha_false_path = None if self.app.config.outputs_to_working_directory: self.output_paths = [] + output_dataset_paths = {} for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) ) - self.output_paths.append( DatasetPath( data.id, data.file_name, false_path ) ) + dsp = DatasetPath( data.id, data.file_name, false_path ) + self.output_paths.append( dsp ) + self.output_dataset_paths[name] = data, dsp if jeha: - false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % jeha.dataset.id ) ) - self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name, false_path ) ) + jeha_false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % jeha.dataset.id ) ) else: - self.output_paths = [ DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) for da in job.output_datasets + job.output_library_datasets ] - if jeha: - self.output_paths.append( DatasetPath( jeha.dataset.id, jeha.dataset.file_name ) ) - + results = [ (da.name, da.dataset, DatasetPath( da.dataset.dataset.id, da.dataset.file_name )) for da in job.output_datasets + job.output_library_datasets ] + self.output_paths = [t[2] for t in results] + self.output_dataset_paths = dict([(t[0], t[1:]) for t in results]) + if jeha: + dsp = DatasetPath( jeha.dataset.id, jeha.dataset.file_name, jeha_false_path ) + self.output_paths.append( dsp ) return self.output_paths def get_output_file_id( self, file ): @@ -872,12 +889,11 @@ def __init__(self, task, queue): super(TaskWrapper, self).__init__(task.job, queue) self.task_id = task.id - self.parallelism = None - if task.part_file: - #do this better - self.working_directory = os.path.dirname(task.part_file) + self.working_directory = task.working_directory + if task.prepare_input_files_cmd is not None: + self.prepare_input_files_cmds = [ task.prepare_input_files_cmd ] else: - self.working_directory = None + self.prepare_input_files_cmds = None self.status = task.states.NEW def get_job( self ): @@ -1252,4 +1268,3 @@ return def shutdown( self ): return - --- a/lib/galaxy/jobs/runners/__init__.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/jobs/runners/__init__.py Wed Oct 12 12:51:09 2011 -0500 @@ -6,6 +6,7 @@ Compose the sequence of commands necessary to execute a job. This will currently include: - environment settings corresponding to any requirement tags + - preparing input files - command line taken from job wrapper - commands to set metadata (if include_metadata is True) """ @@ -17,10 +18,13 @@ # Prepend version string if job_wrapper.version_string_cmd: commands = "%s &> %s; " % ( job_wrapper.version_string_cmd, job_wrapper.get_version_string_path() ) + commands + # prepend getting input files (if defined) + if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: + commands = "; ".join( job_wrapper.prepare_input_files_cmds + [ commands ] ) # Prepend dependency injection if job_wrapper.dependency_shell_commands: commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) - + # Append metadata setting commands, we don't want to overwrite metadata # that was copied over in init_meta(), as per established behavior if include_metadata and self.app.config.set_metadata_externally: --- a/lib/galaxy/jobs/runners/lwr.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/jobs/runners/lwr.py Wed Oct 12 12:51:09 2011 -0500 @@ -249,6 +249,12 @@ try: job_wrapper.prepare() + if hasattr(job_wrapper, 'prepare_input_files_cmds') and job_wrapper.prepare_input_files_cmds is not None: + for cmd in job_wrapper.prepare_input_file_cmds: # run the commands to stage the input files + #log.debug( 'executing: %s' % cmd ) + if 0 != os.system(cmd): + raise Exception('Error running file staging command: %s' % cmd) + job_wrapper.prepare_input_files_cmds = None # prevent them from being used in-line command_line = self.build_command_line( job_wrapper, include_metadata=False ) except: job_wrapper.fail( "failure preparing job", exception=True ) --- a/lib/galaxy/jobs/runners/tasks.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/jobs/runners/tasks.py Wed Oct 12 12:51:09 2011 -0500 @@ -60,71 +60,58 @@ if command_line: try: # DBTODO read tool info and use the right kind of parallelism. - # For now, the only splitter is the 'basic' one, n-ways split on one input, one output. - # This is incredibly simplified. Parallelism ultimately needs to describe which inputs, how, etc. + # For now, the only splitter is the 'basic' one job_wrapper.change_state( model.Job.states.RUNNING ) self.sa_session.flush() - parent_job = job_wrapper.get_job() # Split with the tool-defined method. - if job_wrapper.tool.parallelism == "basic": - from galaxy.jobs.splitters import basic - if len(job_wrapper.get_input_fnames()) > 1 or len(job_wrapper.get_output_fnames()) > 1: - log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.") - job_wrapper.change_state( model.Job.states.ERROR ) - job_wrapper.fail("Job Splitting Failed, the basic splitter only handles tools with one input and one output") - # Requeue as a standard job? - return - input_file = job_wrapper.get_input_fnames()[0] - working_directory = job_wrapper.working_directory - # DBTODO execute an external task to do the splitting, this should happen at refactor. - # Regarding number of ways split, use "hints" in tool config? - # If the number of tasks is sufficiently high, we can use it to calculate job completion % and give a running status. - basic.split(input_file, working_directory, - 20, #Needs serious experimentation to find out what makes the most sense. - parent_job.input_datasets[0].dataset.ext) - # Tasks in this parts list are in alphabetical listdir order (15 before 5), but that should not matter. - parts = [os.path.join(os.path.abspath(job_wrapper.working_directory), p, os.path.basename(input_file)) - for p in os.listdir(job_wrapper.working_directory) - if p.startswith('task_')] - else: + try: + splitter = getattr(__import__('galaxy.jobs.splitters', globals(), locals(), [job_wrapper.tool.parallelism.method]), job_wrapper.tool.parallelism.method) + except: job_wrapper.change_state( model.Job.states.ERROR ) job_wrapper.fail("Job Splitting Failed, no match for '%s'" % job_wrapper.tool.parallelism) - # Assemble parts into task_wrappers + return + tasks = splitter.do_split(job_wrapper) # Not an option for now. Task objects don't *do* anything useful yet, but we'll want them tracked outside this thread to do anything. # if track_tasks_in_database: - tasks = [] task_wrappers = [] - for part in parts: - task = model.Task(parent_job, part) + for task in tasks: self.sa_session.add(task) - tasks.append(task) self.sa_session.flush() + # Must flush prior to the creation and queueing of task wrappers. for task in tasks: tw = TaskWrapper(task, job_wrapper.queue) task_wrappers.append(tw) self.app.job_manager.dispatcher.put(tw) tasks_incomplete = False + count_complete = 0 sleep_time = 1 + # sleep/loop until no more progress can be made. That is when + # all tasks are one of { OK, ERROR, DELETED } + completed_states = [ model.Task.states.OK, \ + model.Task.states.ERROR, \ + model.Task.states.DELETED ] + # TODO: Should we report an error (and not merge outputs) if one of the subtasks errored out? + # Should we prevent any that are pending from being started in that case? while tasks_incomplete is False: + count_complete = 0 tasks_incomplete = True for tw in task_wrappers: - if not tw.get_state() == model.Task.states.OK: + task_state = tw.get_state() + if not task_state in completed_states: tasks_incomplete = False - sleep( sleep_time ) - if sleep_time < 8: - sleep_time *= 2 - output_filename = job_wrapper.get_output_fnames()[0].real_path - basic.merge(working_directory, output_filename) - log.debug('execution finished: %s' % command_line) - for tw in task_wrappers: - # Prevent repetitive output, e.g. "Sequence File Aligned"x20 - # Eventually do a reduce for jobs that output "N reads mapped", combining all N for tasks. - if stdout.strip() != tw.get_task().stdout.strip(): - stdout += tw.get_task().stdout - if stderr.strip() != tw.get_task().stderr.strip(): - stderr += tw.get_task().stderr + else: + count_complete = count_complete + 1 + if tasks_incomplete is False: + # log.debug('Tasks complete: %s. Sleeping %s' % (count_complete, sleep_time)) + sleep( sleep_time ) + if sleep_time < 8: + sleep_time *= 2 + + log.debug('execution finished - beginning merge: %s' % command_line) + stdout, stderr = splitter.do_merge(job_wrapper, task_wrappers) + except Exception: job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) --- a/lib/galaxy/jobs/splitters/basic.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/jobs/splitters/basic.py Wed Oct 12 12:51:09 2011 -0500 @@ -1,91 +1,23 @@ -import os, logging +import logging +import multi + log = logging.getLogger( __name__ ) -def _file_len(fname): - i = 0 - f = open(fname) - for i, l in enumerate(f): - pass - f.close() - return i + 1 +def set_basic_defaults(job_wrapper): + parent_job = job_wrapper.get_job() + job_wrapper.tool.parallelism.attributes['split_inputs'] = parent_job.input_datasets[0].name + job_wrapper.tool.parallelism.attributes['merge_outputs'] = job_wrapper.get_output_datasets_and_fnames().keys()[0] -def _fq_seq_count(fname): - count = 0 - f = open(fname) - for i, l in enumerate(f): - if l.startswith('@'): - count += 1 - f.close() - return count - -def split_fq(input_file, working_directory, parts): - # Temporary, switch this to use the fq reader in lib/galaxy_utils/sequence. - outputs = [] - length = _fq_seq_count(input_file) - if length < 1: - return outputs - if length < parts: - parts = length - len_each, remainder = divmod(length, parts) - f = open(input_file, 'rt') - for p in range(0, parts): - part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) - if not os.path.exists( part_dir ): - os.mkdir( part_dir ) - part_path = os.path.join(part_dir, os.path.basename(input_file)) - part_file = open(part_path, 'w') - for l in range(0, len_each): - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - if remainder > 0: - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - part_file.write(f.readline()) - remainder -= 1 - outputs.append(part_path) - part_file.close() - f.close() - return outputs - -def split_txt(input_file, working_directory, parts): - outputs = [] - length = _file_len(input_file) - if length < parts: - parts = length - len_each, remainder = divmod(length, parts) - f = open(input_file, 'rt') - for p in range(0, parts): - part_dir = os.path.join( os.path.abspath(working_directory), 'task_%s' % p) - if not os.path.exists( part_dir ): - os.mkdir( part_dir ) - part_path = os.path.join(part_dir, os.path.basename(input_file)) - part_file = open(part_path, 'w') - for l in range(0, len_each): - part_file.write(f.readline()) - if remainder > 0: - part_file.write(f.readline()) - remainder -= 1 - outputs.append(part_path) - part_file.close() - f.close() - return outputs +def do_split (job_wrapper): + if len(job_wrapper.get_input_fnames()) > 1 or len(job_wrapper.get_output_fnames()) > 1: + log.error("The basic splitter is not capable of handling jobs with multiple inputs or outputs.") + raise Exception, "Job Splitting Failed, the basic splitter only handles tools with one input and one output" + # add in the missing information for splitting the one input and merging the one output + set_basic_defaults(job_wrapper) + return multi.do_split(job_wrapper) -def split( input_file, working_directory, parts, file_type = None): - #Implement a better method for determining how to split. - if file_type.startswith('fastq'): - return split_fq(input_file, working_directory, parts) - else: - return split_txt(input_file, working_directory, parts) +def do_merge( job_wrapper, task_wrappers): + # add in the missing information for splitting the one input and merging the one output + set_basic_defaults(job_wrapper) + return multi.do_merge(job_wrapper, task_wrappers) -def merge( working_directory, output_file ): - output_file_name = os.path.basename(output_file) - task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] - task_dirs.sort(key = lambda x: int(x.split('task_')[-1])) - for task_dir in task_dirs: - try: - os.system( 'cat %s >> %s' % ( os.path.join(task_dir, output_file_name), output_file ) ) - except Exception, e: - log.error(str(e)) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/jobs/splitters/multi.py Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,158 @@ +import os, logging, shutil +from galaxy import model, util + + +log = logging.getLogger( __name__ ) + +def do_split (job_wrapper): + parent_job = job_wrapper.get_job() + working_directory = os.path.abspath(job_wrapper.working_directory) + + parallel_settings = job_wrapper.tool.parallelism.attributes + # Syntax: split_inputs="input1,input2" shared_inputs="genome" + # Designates inputs to be split or shared + split_inputs=parallel_settings.get("split_inputs") + if split_inputs is None: + split_inputs = [] + else: + split_inputs = [x.strip() for x in split_inputs.split(",")] + + shared_inputs=parallel_settings.get("shared_inputs") + if shared_inputs is None: + shared_inputs = [] + else: + shared_inputs = [x.strip() for x in shared_inputs.split(",")] + illegal_inputs = [x for x in shared_inputs if x in split_inputs] + if len(illegal_inputs) > 0: + raise Exception("Inputs have conflicting parallelism attributes: %s" % str( illegal_inputs )) + + subdir_index = [0] # use a list to get around Python 2.x lame closure support + task_dirs = [] + def get_new_working_directory_name(): + dir=os.path.join(working_directory, 'task_%d' % subdir_index[0]) + subdir_index[0] = subdir_index[0] + 1 + if not os.path.exists(dir): + os.makedirs(dir) + task_dirs.append(dir) + return dir + + # For things like paired end alignment, we need two inputs to be split. Since all inputs to all + # derived subtasks need to be correlated, allow only one input type to be split + type_to_input_map = {} + for input in parent_job.input_datasets: + if input.name in split_inputs: + type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name) + elif input.name in shared_inputs: + pass # pass original file name + else: + log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) + log.error(log_error) + raise Exception(log_error) + + if len(type_to_input_map) > 1: + log_error = "The multi splitter does not support splitting inputs of more than one type" + log.error(log_error) + raise Exception(log_error) + + # split the first one to build up the task directories + input_datasets = [] + for input in parent_job.input_datasets: + if input.name in split_inputs: + this_input_files = job_wrapper.get_input_dataset_fnames(input.dataset) + if len(this_input_files) > 1: + log_error = "The input '%s' is composed of multiple files - splitting is not allowed" % str(input.name) + log.error(log_error) + raise Exception(log_error) + input_datasets.append(input.dataset) + + input_type = type_to_input_map.keys()[0] + # DBTODO execute an external task to do the splitting, this should happen at refactor. + # If the number of tasks is sufficiently high, we can use it to calculate job completion % and give a running status. + try: + input_type.split(input_datasets, get_new_working_directory_name, parallel_settings) + except AttributeError: + log_error = "The type '%s' does not define a method for splitting files" % str(input_type) + log.error(log_error) + raise + log.debug('do_split created %d parts' % len(task_dirs)) + # next, after we know how many divisions there are, add the shared inputs via soft links + for input in parent_job.input_datasets: + if input and input.name in shared_inputs: + names = job_wrapper.get_input_dataset_fnames(input.dataset) + for dir in task_dirs: + for file in names: + os.symlink(file, os.path.join(dir, os.path.basename(file))) + tasks = [] + prepare_files = os.path.join(util.galaxy_directory(), 'extract_dataset_parts.sh') + ' %s' + for dir in task_dirs: + task = model.Task(parent_job, dir, prepare_files % dir) + tasks.append(task) + return tasks + + +def do_merge( job_wrapper, task_wrappers): + parent_job = job_wrapper.get_job() + parallel_settings = job_wrapper.tool.parallelism.attributes + # Syntax: merge_outputs="export" pickone_outputs="genomesize" + # Designates outputs to be merged, or selected from as a representative + merge_outputs = parallel_settings.get("merge_outputs") + if merge_outputs is None: + merge_outputs = [] + else: + merge_outputs = [x.strip() for x in merge_outputs.split(",")] + pickone_outputs = parallel_settings.get("pickone_outputs") + if pickone_outputs is None: + pickone_outputs = [] + else: + pickone_outputs = [x.strip() for x in pickone_outputs.split(",")] + + illegal_outputs = [x for x in merge_outputs if x in pickone_outputs] + if len(illegal_outputs) > 0: + return ('Tool file error', 'Outputs have conflicting parallelism attributes: %s' % str( illegal_outputs )) + + stdout = '' + stderr = '' + + try: + working_directory = job_wrapper.working_directory + task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] + # TODO: Output datasets can be very complex. This doesn't handle metadata files + outputs = job_wrapper.get_output_datasets_and_fnames() + pickone_done = [] + task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] + for output in outputs: + output_file_name = str(outputs[output][1]) + base_output_name = os.path.basename(output_file_name) + if output in merge_outputs: + output_type = outputs[output][0].datatype + output_files = [os.path.join(dir,base_output_name) for dir in task_dirs] + log.debug('files %s ' % output_files) + output_type.merge(output_files, output_file_name) + log.debug('merge finished: %s' % output_file_name) + pass # TODO: merge all the files + elif output in pickone_outputs: + # just pick one of them + if output not in pickone_done: + task_file_name = os.path.join(task_dirs[0], base_output_name) + shutil.move( task_file_name, output_file_name ) + pickone_done.append(output) + else: + log_error = "The output '%s' does not define a method for implementing parallelism" % output + log.error(log_error) + raise Exception(log_error) + except Exception, e: + stdout = 'Error merging files'; + stderr = str(e) + + + for tw in task_wrappers: + # Prevent repetitive output, e.g. "Sequence File Aligned"x20 + # Eventually do a reduce for jobs that output "N reads mapped", combining all N for tasks. + out = tw.get_task().stdout.strip() + err = tw.get_task().stderr.strip() + if len(out) > 0: + stdout += tw.working_directory + ':\n' + out + if len(err) > 0: + stderr += tw.working_directory + ':\n' + err + return (stdout, stderr) + --- a/lib/galaxy/model/__init__.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/model/__init__.py Wed Oct 12 12:51:09 2011 -0500 @@ -204,18 +204,19 @@ ERROR = 'error', DELETED = 'deleted' ) - def __init__( self, job, part_file = None ): + def __init__( self, job, working_directory, prepare_files_cmd ): self.command_line = None self.parameters = [] self.state = Task.states.NEW self.info = None - self.part_file = part_file + self.working_directory = working_directory self.task_runner_name = None self.task_runner_external_id = None self.job = job self.stdout = None self.stderr = None - + self.prepare_input_files_cmd = prepare_files_cmd + def set_state( self, state ): self.state = state @@ -896,7 +897,9 @@ def get_converted_files_by_type( self, file_type ): for assoc in self.implicitly_converted_datasets: if not assoc.deleted and assoc.type == file_type: - return assoc.dataset + if assoc.dataset: + return assoc.dataset + return assoc.dataset_ldda return None def get_converted_dataset_deps(self, trans, target_ext): """ @@ -1588,7 +1591,12 @@ class ImplicitlyConvertedDatasetAssociation( object ): def __init__( self, id = None, parent = None, dataset = None, file_type = None, deleted = False, purged = False, metadata_safe = True ): self.id = id - self.dataset = dataset + if isinstance(dataset, HistoryDatasetAssociation): + self.dataset = dataset + elif isinstance(dataset, LibraryDatasetDatasetAssociation): + self.dataset_ldda = dataset + else: + raise AttributeError, 'Unknown dataset type provided for dataset: %s' % type( dataset ) if isinstance(parent, HistoryDatasetAssociation): self.parent_hda = parent elif isinstance(parent, LibraryDatasetDatasetAssociation): --- a/lib/galaxy/model/mapping.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/model/mapping.py Wed Oct 12 12:51:09 2011 -0500 @@ -148,6 +148,7 @@ Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), + Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), Column( "hda_parent_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), Column( "deleted", Boolean, index=True, default=False ), @@ -467,11 +468,13 @@ Column( "runner_name", String( 255 ) ), Column( "stdout", TEXT ), Column( "stderr", TEXT ), + Column( "info", TrimmedString ( 255 ) ), Column( "traceback", TEXT ), Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ), - Column( "part_file", String(1024)), + Column( "working_directory", String(1024)), Column( "task_runner_name", String( 255 ) ), - Column( "task_runner_external_id", String( 255 ) ) ) + Column( "task_runner_external_id", String( 255 ) ), + Column( "prepare_input_files_cmd", TEXT ) ) PostJobAction.table = Table("post_job_action", metadata, Column("id", Integer, primary_key=True), @@ -1206,11 +1209,12 @@ properties=dict( parent_hda=relation( HistoryDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), - parent_ldda=relation( LibraryDatasetDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id ) ), - + dataset_ldda=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_id == LibraryDatasetDatasetAssociation.table.c.id ) ), dataset=relation( HistoryDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_id == HistoryDatasetAssociation.table.c.id ) ) ) ) @@ -1594,7 +1598,7 @@ annotations=relation( PageAnnotationAssociation, order_by=PageAnnotationAssociation.table.c.id, backref="pages" ), ratings=relation( PageRatingAssociation, order_by=PageRatingAssociation.table.c.id, backref="pages" ) ) ) - + assign_mapper( context, ToolShedRepository, ToolShedRepository.table ) # Set up proxy so that --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,63 @@ +""" +Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column. +""" + +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 ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + task_table = Table( "task", metadata, autoload=True ) + c = Column( "prepare_input_files_cmd", TEXT, nullable=True ) + c.create( task_table ) + assert c is task_table.c.prepare_input_files_cmd + except Exception, e: + print "Adding prepare_input_files_cmd column to task table failed: %s" % str( e ) + log.debug( "Adding prepare_input_files_cmd column to task table failed: %s" % str( e ) ) + try: + task_table = Table( "task", metadata, autoload=True ) + c = Column( "working_directory", String ( 1024 ), nullable=True ) + c.create( task_table ) + assert c is task_table.c.working_directory + except Exception, e: + print "Adding working_directory column to task table failed: %s" % str( e ) + log.debug( "Adding working_directory column to task table failed: %s" % str( e ) ) + + # remove the 'part_file' column - nobody used tasks before this, so no data needs to be migrated + try: + task_table.c.part_file.drop() + except Exception, e: + log.debug( "Deleting column 'part_file' from the 'task' table failed: %s" % ( str( e ) ) ) + +def downgrade(): + metadata.reflect() + try: + task_table = Table( "task", metadata, autoload=True ) + task_table.c.prepare_input_files_cmd.drop() + except Exception, e: + print "Dropping prepare_input_files_cmd column from task table failed: %s" % str( e ) + log.debug( "Dropping prepare_input_files_cmd column from task table failed: %s" % str( e ) ) + try: + task_table = Table( "task", metadata, autoload=True ) + task_table.c.working_directory.drop() + except Exception, e: + print "Dropping working_directory column from task table failed: %s" % str( e ) + log.debug( "Dropping working_directory column from task table failed: %s" % str( e ) ) + try: + task_table = Table( "task", metadata, autoload=True ) + c = Column( "part_file", String ( 1024 ), nullable=True ) + c.create( task_table ) + assert c is task_table.c.part_file + except Exception, e: + print "Adding part_file column to task table failed: %s" % str( e ) + log.debug( "Adding part_file column to task table failed: %s" % str( e ) ) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,35 @@ +""" +Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table. +""" + +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 ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + Implicitly_converted_table = Table( "implicitly_converted_dataset_association", metadata, autoload=True ) + c = Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ) + c.create( Implicitly_converted_table ) + assert c is Implicitly_converted_table.c.ldda_id + except Exception, e: + print "Adding ldda_id column to implicitly_converted_dataset_association table failed: %s" % str( e ) + log.debug( "Adding ldda_id column to implicitly_converted_dataset_association table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + Implicitly_converted_table = Table( "implicitly_converted_dataset_association", metadata, autoload=True ) + Implicitly_converted_table.c.ldda_id.drop() + except Exception, e: + print "Dropping ldda_id column from implicitly_converted_dataset_association table failed: %s" % str( e ) + log.debug( "Dropping ldda_id column from implicitly_converted_dataset_association table failed: %s" % str( e ) ) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0085_add_task_info.py Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,36 @@ +""" +Migration script to add 'info' column to the task table. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) +from galaxy.model.custom_types import TrimmedString + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + task_table = Table( "task", metadata, autoload=True ) + c = Column( "info", TrimmedString (255) , nullable=True ) + c.create( task_table ) + assert c is task_table.c.info + except Exception, e: + print "Adding info column to table table failed: %s" % str( e ) + log.debug( "Adding info column to task table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + task_table = Table( "task", metadata, autoload=True ) + task_table.c.info.drop() + except Exception, e: + print "Dropping info column from task table failed: %s" % str( e ) + log.debug( "Dropping info column from task table failed: %s" % str( e ) ) --- a/lib/galaxy/tools/__init__.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/tools/__init__.py Wed Oct 12 12:51:09 2011 -0500 @@ -352,6 +352,21 @@ self.fabfile = fabfile self.method = method +class ToolParallelismInfo(object): + """ + Stores the information (if any) for running multiple instances of the tool in parallel + on the same set of inputs. + """ + def __init__(self, tag): + self.method = tag.get('method') + self.attributes = dict([item for item in tag.attrib.items() if item[0] != 'method' ]) + if len(self.attributes) == 0: + # legacy basic mode - provide compatible defaults + self.attributes['split_size'] = 20 + self.attributes['split_mode'] = 'number_of_parts' + + + class Tool: """ Represents a computational tool that can be executed through Galaxy. @@ -442,7 +457,7 @@ # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): - self.parallelism = parallelism.get("method") + self.parallelism = ToolParallelismInfo(parallelism) else: self.parallelism = None if self.app.config.start_job_runners is None: --- a/lib/galaxy/util/__init__.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/util/__init__.py Wed Oct 12 12:51:09 2011 -0500 @@ -623,6 +623,9 @@ gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) genetrack_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "genetrack", "genetrack_sites.txt" ), check_builds=False ) +def galaxy_directory(): + return os.path.abspath(galaxy_root_path) + if __name__ == '__main__': import doctest, sys doctest.testmod(sys.modules[__name__], verbose=False) --- a/lib/galaxy/web/controllers/dataset.py Wed Oct 12 08:30:14 2011 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Wed Oct 12 12:51:09 2011 -0500 @@ -1141,9 +1141,6 @@ num_source = len( source_dataset_ids ) - invalid_datasets num_target = len(target_histories) done_msg = "%i %s copied to %i %s: %s." % (num_source, inflector.cond_plural(num_source, "dataset"), num_target, inflector.cond_plural(num_target, "history"), hist_names_str ) - if new_history is not None: - done_msg += " <a href=\"%s\" target=\"_top\">Switch to the new history.</a>" % url_for( - controller="history", action="switch_to_history", hist_id=trans.security.encode_id( new_history.id ) ) trans.sa_session.refresh( history ) source_datasets = history.visible_datasets target_histories = [history] --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/extract_dataset_part.py Wed Oct 12 12:51:09 2011 -0500 @@ -0,0 +1,48 @@ +""" +Reads a JSON file and uses it to call into a datatype class to extract +a subset of a dataset for processing. + +Used by jobs that split large files into pieces to be processed concurrently +on a gid in a scatter-gather mode. This does part of the scatter. + +""" +import os +import sys +import logging +logging.basicConfig() +log = logging.getLogger( __name__ ) + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path + +from galaxy import eggs +import pkg_resources +pkg_resources.require("simplejson") +import simplejson + +# This junk is here to prevent loading errors +import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers +galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here +galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid + +def __main__(): + """ + Argument: a JSON file + """ + file_path = sys.argv.pop( 1 ) + data = simplejson.load(open(file_path, 'r')) + try: + class_name_parts = data['class_name'].split('.') + module_name = '.'.join(class_name_parts[:-1]) + class_name = class_name_parts[-1] + mod = __import__(module_name, globals(), locals(), [class_name]) + cls = getattr(mod, class_name) + if not cls.process_split_file(data): + sys.stderr.write('Writing split file failed\n') + sys.exit(1) + except Exception, e: + sys.stderr.write(str(e)) + sys.exit(1) + +__main__() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Workflows: Fix for 5cfec3f4f17c to accommodate workflows with 'input dataset' steps.
by Bitbucket 14 Oct '11

14 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a0fc8c81ff09/ changeset: a0fc8c81ff09 user: dannon date: 2011-10-14 20:21:07 summary: Workflows: Fix for 5cfec3f4f17c to accommodate workflows with 'input dataset' steps. affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/workflow.py Fri Oct 14 12:14:54 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Fri Oct 14 14:21:07 2011 -0400 @@ -1764,7 +1764,7 @@ # FIXME: Position should be handled inside module step.position = step_dict['position'] module = module_factory.from_dict( trans, step_dict, secure=False ) - if module.tool is None: + if module.type == 'tool' and module.tool is None: # A required tool is not available in the local Galaxy instance. missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) if missing_tool_tup not in missing_tool_tups: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to upload exported Galaxy workflow files. Makew a first pass at fixing bugs when importing a workflow into a Galaxy instance that does not have all of the required tools. This code is still full of bugs.
by Bitbucket 14 Oct '11

14 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5cfec3f4f17c/ changeset: 5cfec3f4f17c user: greg date: 2011-10-14 18:14:54 summary: Add the ability to upload exported Galaxy workflow files. Makew a first pass at fixing bugs when importing a workflow into a Galaxy instance that does not have all of the required tools. This code is still full of bugs. affected #: 8 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Oct 14 12:14:54 2011 -0400 @@ -1299,9 +1299,8 @@ @web.require_admin def index( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'galaxy' ) - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if webapp == 'galaxy': cloned_repositories = trans.sa_session.query( trans.model.ToolShedRepository ) \ .filter( trans.model.ToolShedRepository.deleted == False ) \ @@ -1320,10 +1319,16 @@ @web.require_admin def center( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'galaxy' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if webapp == 'galaxy': - return trans.fill_template( '/webapps/galaxy/admin/center.mako' ) + return trans.fill_template( '/webapps/galaxy/admin/center.mako', + message=message, + status=status ) else: - return trans.fill_template( '/webapps/community/admin/center.mako' ) + return trans.fill_template( '/webapps/community/admin/center.mako', + message=message, + status=status ) @web.expose @web.require_admin def reload_tool( self, trans, **kwd ): --- a/lib/galaxy/web/controllers/workflow.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Fri Oct 14 12:14:54 2011 -0400 @@ -792,10 +792,10 @@ 'data_outputs': [], 'form_html': invalid_tool_form_html, 'annotation' : annotation_str, + 'input_connections' : {}, 'post_job_actions' : {}, 'workflow_outputs' : [] } - step_dict['input_connections'] = input_conn_dict # Position step_dict['position'] = step.position # Add to return value @@ -958,19 +958,13 @@ """ stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True ) return trans.fill_template( "/workflow/export.mako", item=stored, use_panels=True ) - - @web.expose @web.require_login( "use workflows" ) def import_from_myexp( self, trans, myexp_id, myexp_username=None, myexp_password=None ): """ Imports a workflow from the myExperiment website. """ - - # # Get workflow XML. - # - # Get workflow content. conn = httplib.HTTPConnection( self.__myexp_url ) # NOTE: blocks web thread. @@ -985,17 +979,16 @@ parser = SingleTagContentsParser( "content" ) parser.feed( workflow_xml ) workflow_content = base64.b64decode( parser.tag_content ) - - # # Process workflow XML and create workflow. - # parser = SingleTagContentsParser( "galaxy_json" ) parser.feed( workflow_content ) workflow_dict = from_json_string( parser.tag_content ) - # Create workflow. - workflow = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ).latest_workflow - + workflow, missing_tool_tups = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ).latest_workflow + if missing_tool_tups: + # TODO: handle the case where the imported workflow requires tools that are not available in + # the local Galaxy instance. + pass # Provide user feedback. if workflow.has_errors: return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors" ) @@ -1003,7 +996,6 @@ return trans.show_warn_message( "Imported, but this workflow contains cycles" ) else: return trans.show_message( "Workflow '%s' imported" % workflow.name ) - @web.expose @web.require_login( "use workflows" ) def export_to_myexp( self, trans, id, myexp_username, myexp_password ): @@ -1102,40 +1094,91 @@ return stored_dict @web.expose - def import_workflow( self, trans, workflow_text=None, url=None ): - if workflow_text is None and url is None: - return form( url_for(), "Import Workflow", submit_text="Import", use_panels=True ) \ - .add_text( "url", "Workflow URL", "" ) \ - .add_input( "textarea", "Encoded workflow (as generated by export workflow)", "workflow_text", "" ) - if url: - # Load workflow from external URL - # NOTE: blocks the web thread. - try: - workflow_data = urllib2.urlopen( url ).read() - except Exception, e: - return trans.show_error_message( "Failed to open URL %s<br><br>Message: %s" % ( url, str( e ) ) ) - else: - workflow_data = workflow_text - # Convert incoming workflow data from json - try: - data = simplejson.loads( workflow_data ) - except Exception, e: - return trans.show_error_message( "Data at '%s' does not appear to be a Galaxy workflow<br><br>Message: %s" % ( url, str( e ) ) ) - - # Create workflow. - workflow = self._workflow_from_dict( trans, data, source="uploaded file" ).latest_workflow - - # Provide user feedback and show workflow list. - if workflow.has_errors: - trans.set_message( "Imported, but some steps in this workflow have validation errors", - type="warning" ) - if workflow.has_cycles: - trans.set_message( "Imported, but this workflow contains cycles", - type="warning" ) - else: - trans.set_message( "Workflow '%s' imported" % workflow.name ) - return self.list( trans ) - + def import_workflow( self, trans, **kwd ): + url = kwd.get( 'url', '' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + if kwd.get( 'import_button', False ): + workflow_data = None + if url: + # Load workflow from external URL + # NOTE: blocks the web thread. + try: + workflow_data = urllib2.urlopen( url ).read() + except Exception, e: + message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) ) + status = 'error' + else: + # Load workflow from browsed file. + file_data = kwd.get( 'file_data', '' ) + if file_data in ( '', None ): + message = 'No exported Galaxy workflow files were selected.' + status = 'error' + else: + uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = file_data.filename + if os.path.getsize( os.path.abspath( uploaded_file_name ) ) > 0: + # We're reading the file as text so we can re-use the existing code below. + # This may not be ideal... + workflow_data = uploaded_file.read() + else: + message= 'You attempted to upload an empty file.' + status = 'error' + if workflow_data: + # Convert incoming workflow data from json + try: + data = simplejson.loads( workflow_data ) + except Exception, e: + data = None + message = "The data content does not appear to be a Galaxy workflow.<br/>Exception: %s" % str( e ) + status = 'error' + if data: + # Create workflow if possible. If a required tool is not available in the local + # Galaxy instance, the tool information will be available in the step_dict. + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="uploaded file" ) + workflow = workflow.latest_workflow + # Provide user feedback and show workflow list. + if workflow.has_errors: + message += "Imported, but some steps in this workflow have validation errors. " + status = "error" + if workflow.has_cycles: + message += "Imported, but this workflow contains cycles. " + status = "error" + else: + message += "Workflow '%s' imported successfully. " % workflow.name + if missing_tool_tups: + if trans.user_is_admin(): + # A required tool is not available in the local Galaxy instance. + # TODO: It would sure be nice to be able to redirec to a mako tempalte here that displays a nice + # page including the links to the configured tool shed instead of this stupd message, but trying + # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone + #involved in workflow development needs to figure out what it will take to get the Galaxy panels back... + galaxy_url = trans.request.host + message += "The workflow requires the following tools that are not available in this Galaxy instance." + message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" + for missing_tool_tup in missing_tool_tups: + missing_tool_id = missing_tool_tup[0] + for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if tool_shed_url.endswith( '/' ): + tool_shed_url = tool_shed_url.rstrip( '/' ) + url = '%s/repository/find_tools?tool_id=%s&galaxy_url=%s&webapp=community' % ( tool_shed_url, missing_tool_id, galaxy_url ) + message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) + status = 'error' + return trans.response.send_redirect( web.url_for( controller='admin', + action='index', + webapp='galaxy', + message=message, + status=status ) ) + else: + # TODO: Figure out what to do here... + pass + return self.list( trans ) + return trans.fill_template( "workflow/import.mako", + url=url, + message=message, + status=status, + use_panels=True ) @web.json def get_datatypes( self, trans ): ext_to_class_name = dict() @@ -1605,8 +1648,7 @@ step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" if step_annotation: - annotation_str = step_annotation.annotation - + annotation_str = step_annotation.annotation # Step info step_dict = { 'id': step.order_index, @@ -1620,7 +1662,6 @@ ## 'data_outputs': module.get_data_outputs(), 'annotation' : annotation_str } - # Add post-job actions to step dict. if module.type == 'tool': pja_dict = {} @@ -1629,7 +1670,6 @@ output_name = pja.output_name, action_arguments = pja.action_arguments ) step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs step_dict['inputs'] = [] if module.type == "data_input": @@ -1647,7 +1687,6 @@ for partname, partval in val.items(): if type( partval ) == RuntimeValue: step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - # User outputs step_dict['user_outputs'] = [] """ @@ -1668,7 +1707,6 @@ if type( module ) is ToolModule: for output in module.get_data_outputs(): step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections input_connections = step.input_connections if step.type is None or step.type == 'tool': @@ -1692,7 +1730,6 @@ # Add to return value data['steps'][step.order_index] = step_dict return data - def _workflow_from_dict( self, trans, data, source=None ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. @@ -1714,8 +1751,12 @@ # The editor will provide ids for each step that we don't need to save, # but do need to use to make connections steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the local Galaxy instance. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] # First pass to build step objects and populate basic values - for key, step_dict in data['steps'].iteritems(): + for key, step_dict in data[ 'steps' ].iteritems(): # Create the model class for the step step = model.WorkflowStep() steps.append( step ) @@ -1723,6 +1764,11 @@ # FIXME: Position should be handled inside module step.position = step_dict['position'] module = module_factory.from_dict( trans, step_dict, secure=False ) + if module.tool is None: + # A required tool is not available in the local Galaxy instance. + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) module.save_to_step( step ) if step.tool_errors: workflow.has_errors = True @@ -1761,7 +1807,7 @@ # Persist trans.sa_session.add( stored ) trans.sa_session.flush() - return stored + return stored, missing_tool_tups ## ---- Utility methods ------------------------------------------------------- --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Oct 14 12:14:54 2011 -0400 @@ -251,8 +251,7 @@ RevisionColumn( "Revision" ), UserColumn( "Owner", model_class=model.User, - attach_popup=False, - key="User.username" ) + attach_popup=False ) ] operations = [] standard_filters = [] --- a/lib/galaxy/workflow/modules.py Fri Oct 14 09:58:59 2011 -0400 +++ b/lib/galaxy/workflow/modules.py Fri Oct 14 12:14:54 2011 -0400 @@ -8,6 +8,9 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.jobs.actions.post import ActionBox from galaxy.model import PostJobAction +import logging + +log = logging.getLogger( __name__ ) class WorkflowModule( object ): @@ -163,29 +166,46 @@ def __init__( self, trans, tool_id ): self.trans = trans self.tool_id = tool_id - self.tool = trans.app.toolbox.tools_by_id[ tool_id ] + try: + self.tool = trans.app.toolbox.tools_by_id[ tool_id ] + except KeyError, e: + # Handle the case where the workflow requires a tool not available in the local Galaxy instance. + self.tool = None + # TODO: Instead of parsing the guid, get the tool_id and version from the shed_tool_conf.xml, + # which requires enhancements to the tool loading process. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if available_tool_id.find( tool_id ) >=0: + # We're attempting to match tool id against a tool guid. + # TODO: match by tool_id (and version if we attempt that, but + # workflows will break) is not good enough because + # 2 tools installed from a tool shed could both match this. We + # need to present a select list here. + self.tool = available_tool + break self.post_job_actions = {} self.workflow_outputs = [] self.state = None - self.errors = None - + if self.tool: + self.errors = None + else: + self.errors = {} + self.errors[ tool_id ] = 'Tool unavailable' @classmethod def new( Class, trans, tool_id=None ): module = Class( trans, tool_id ) module.state = module.tool.new_state( trans, all_pages=True ) return module - @classmethod def from_dict( Class, trans, d, secure=True ): - tool_id = d['tool_id'] + tool_id = d[ 'tool_id' ] module = Class( trans, tool_id ) module.state = DefaultToolState() - module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=secure ) + if module.tool is not None: + module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) module.errors = d.get( "tool_errors", None ) - module.post_job_actions = d.get("post_job_actions", {}) - module.workflow_outputs = d.get("workflow_outputs", []) + module.post_job_actions = d.get( "post_job_actions", {} ) + module.workflow_outputs = d.get( "workflow_outputs", [] ) return module - @classmethod def from_workflow_step( Class, trans, step ): tool_id = step.tool_id @@ -203,12 +223,15 @@ pjadict[pja.action_type] = pja module.post_job_actions = pjadict return module - def save_to_step( self, step ): step.type = self.type step.tool_id = self.tool_id - step.tool_version = self.get_tool_version() - step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) + if self.tool: + step.tool_version = self.get_tool_version() + step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) + else: + step.tool_version = None + step.tool_inputs = None step.tool_errors = self.errors for k, v in self.post_job_actions.iteritems(): # Must have action_type, step. output and a_args are optional. @@ -221,7 +244,6 @@ else: action_arguments = None n_p = PostJobAction(v['action_type'], step, output_name, action_arguments) - def get_name( self ): return self.tool.name def get_tool_id( self ): @@ -234,7 +256,6 @@ return self.errors def get_tooltip( self ): return self.tool.help - def get_data_inputs( self ): data_inputs = [] def callback( input, value, prefixed_name, prefixed_label ): @@ -268,15 +289,12 @@ formats.append( format ) data_outputs.append( dict( name=name, extensions=formats ) ) return data_outputs - def get_post_job_actions( self ): return self.post_job_actions - def get_config_form( self ): self.add_dummy_datasets() return self.trans.fill_template( "workflow/editor_tool_form.mako", tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) ) - def update_state( self, incoming ): # Build a callback that handles setting an input to be required at # runtime. We still process all other parameters the user might have @@ -306,10 +324,8 @@ # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) self.errors = errors or None - def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans ) - def add_dummy_datasets( self, connections=None): if connections: # Store onnections by input name @@ -324,8 +340,7 @@ if connections is None or prefixed_name in input_connections_by_name: return DummyDataset() visit_input_values( self.tool.inputs, self.state.inputs, callback ) - - + class WorkflowModuleFactory( object ): def __init__( self, module_types ): self.module_types = module_types --- a/templates/webapps/galaxy/admin/center.mako Fri Oct 14 09:58:59 2011 -0400 +++ b/templates/webapps/galaxy/admin/center.mako Fri Oct 14 12:14:54 2011 -0400 @@ -1,187 +1,192 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /><%def name="title()">Galaxy Administration</%def><h2>Administration</h2> -<p>The menu on the left provides the following features</p> -<ul> - <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details +%if message: + ${render_msg( message, status )} +%else: + <p>The menu on the left provides the following features</p> + <ul> + <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details + <p/> + <ul> + <li> + <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated + with each user. + </li> + <p/> + <li> + <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with + each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and + roles that are associated with the group. + </li> + <p/> + <li> + <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that + are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated + with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied + to each dataset. + </li> + </ul> + </li><p/> - <ul> - <li> - <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated - with each user. - </li> + <li><strong>Data</strong><p/> - <li> - <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with - each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and - roles that are associated with the group. - </li> + <ul> + <li> + <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library. Currently, + only administrators can create data libraries. + <p/> + When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even + those that are not logged in. The Galaxy administrator can restrict access to a data library by associating roles with the data library's + "access library" permission. This permission will conservatively override the [dataset] "access" permission for the data library's contained + datasets. + <p/> + For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the + data library will still only be displayed to those users that have Role1. However, if the data library's "access library" permission is + associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, + then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission + is associated with only Role1. + <p/> + In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can + be granted to users (a library item is one of: a data library, a library folder, a library dataset). + <p/> + <ul> + <li><strong>add library item</strong> - Users that have the role can add library items to this data library or folder</li> + <li><strong>modify library item</strong> - Users that have the role can modify this library item</li> + <li><strong>manage library permissions</strong> - Users that have the role can manage permissions applied to this library item</li> + </ul> + <p/> + The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception + of the "access library" permission, which is only available on the data library itself). Because of this, it is important to set desired permissions + on a new data library when it is created. When this is done, new folders and datasets added to the data library will automatically inherit those + permissions. In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders. + <p/> + The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them. + Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk. This + approach allows for multiple users to use a single (possibly very large) dataset file. + </li> + </ul> + </li> + <p/> + <li><strong>Server</strong><p/> - <li> - <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that - are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated - with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied - to each dataset. - </li> - </ul> - </li> + <ul> + <li> + <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running + </li> + <p/> + <li> + <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions + </li> + <p/> + <li> + <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or + running). Administrators are able to cleanly stop long-running jobs. + </li> + </ul> + </li> + <p/> + <li><strong>Forms</strong> + <p/>To be completed + </li> + <p/> + <li><strong>Sequencing Requests</strong> + <p/>To be completed + </li> + <p/> + <li><strong>Cloud</strong> + <p/>To be completed + </li> + </ul><p/> - <li><strong>Data</strong> + <p><strong>Data Security and Data Libraries</strong></p> + <p/> + <strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found + here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security + process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" + and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and + the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference + in the way Galaxy has behaved in the past. + <ul> + <li> + <strong>Users</strong> - registered Galaxy users that have created a Galaxy account. Users can belong to groups and can + be associated with 1 or more roles. If a user is not authenticated during a Galaxy session, they will not have access to any + of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they + will be considered "public", and no one will be allowed to change permissions on them). + </li><p/> - <ul> - <li> - <strong>Manage data libraries</strong> - Data libraries enable a Galaxy administrator to upload datasets into a data library. Currently, - only administrators can create data libraries. - <p/> - When a data library is first created, it is considered "public" since it will be displayed in the "Data Libraries" view for any user, even - those that are not logged in. The Galaxy administrator can restrict access to a data library by associating roles with the data library's - "access library" permission. This permission will conservatively override the [dataset] "access" permission for the data library's contained - datasets. - <p/> - For example, if a data library's "access library" permission is associated with Role1 and the data library contains "public" datasets, the - data library will still only be displayed to those users that have Role1. However, if the data library's "access library" permission is - associated with both Role1 and Role2 and the data library contains datasets whose [dataset] "access" permission is associated with only Role1, - then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission - is associated with only Role1. - <p/> - In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can - be granted to users (a library item is one of: a data library, a library folder, a library dataset). - <p/> - <ul> - <li><strong>add library item</strong> - Users that have the role can add library items to this data library or folder</li> - <li><strong>modify library item</strong> - Users that have the role can modify this library item</li> - <li><strong>manage library permissions</strong> - Users that have the role can manage permissions applied to this library item</li> - </ul> - <p/> - The default behavior is for no permissions to be applied to a data library item, but applied permissions are inherited downward (with the exception - of the "access library" permission, which is only available on the data library itself). Because of this, it is important to set desired permissions - on a new data library when it is created. When this is done, new folders and datasets added to the data library will automatically inherit those - permissions. In the same way, permissions can be applied to a folder, which will be automatically inherited by all contained datasets and sub-folders. - <p/> - The "Data Libraries" menu item allows users to access the datasets in a data library as long as they are not restricted from accessing them. - Importing a library dataset into a history will not make a copy of the dataset, but will be a "pointer" to the dataset on disk. This - approach allows for multiple users to use a single (possibly very large) dataset file. - </li> - </ul> - </li> - <p/> - <li><strong>Server</strong> + <li> + <strong>Groups</strong> - a set of 0 or more users which are considered members of the group. Groups can be associated with 0 + or more roles, simplifying the process of applying permissions to the data between a select group of users. + </li><p/> - <ul> - <li> - <strong>Reload a tool's configuration</strong> - allows a new version of a tool to be loaded while the server is running - </li> - <p/> - <li> - <strong>Profile memory usage</strong> - measures system memory used for certain Galaxy functions - </li> - <p/> - <li> - <strong>Manage jobs</strong> - displays all jobs that are currently not finished (i.e., their state is new, waiting, queued, or - running). Administrators are able to cleanly stop long-running jobs. - </li> - </ul> - </li> - <p/> - <li><strong>Forms</strong> - <p/>To be completed - </li> - <p/> - <li><strong>Sequencing Requests</strong> - <p/>To be completed - </li> - <p/> - <li><strong>Cloud</strong> - <p/>To be completed - </li> -</ul> -<p/> -<p><strong>Data Security and Data Libraries</strong></p> -<p/> -<strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found -here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security -process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" -and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and -the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference -in the way Galaxy has behaved in the past. -<ul> - <li> - <strong>Users</strong> - registered Galaxy users that have created a Galaxy account. Users can belong to groups and can - be associated with 1 or more roles. If a user is not authenticated during a Galaxy session, they will not have access to any - of the security features, and datasets they create during that session will have no permissions applied to them (i.e., they - will be considered "public", and no one will be allowed to change permissions on them). - </li> - <p/> - <li> - <strong>Groups</strong> - a set of 0 or more users which are considered members of the group. Groups can be associated with 0 - or more roles, simplifying the process of applying permissions to the data between a select group of users. - </li> - <p/> - <li> - <strong>Roles</strong> - associate users and groups with specific permissions on datasets. For example, users in groups A and B - can be associated with role C which gives them the "access" permission on datasets D, E and F. Roles have a type which is currently - one of the following: - <ul> - <li> - <strong>private</strong> - every user is associated automatically with their own private role. Administrators cannot - manage private roles. - </li> - <li> - <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role - and this will be it's type. - </li> - <li> - <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with - another user. This can generally be considered a temporary role. - </li> - <li><strong>admin</strong> - a role created by a Galaxy administrator.</li> - </ul> - </li> - <p/> - <li> - <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described. - <ul> - <li> - <strong>access</strong> - users associated with the role can import this dataset into their history for analysis. - <p> - If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone - that can access the data library in which it is contained. See the <strong>Manage data libraries</strong> section above for - details. Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in - during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected. - </p> - <p> - Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it. - For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users - and groups who are associated with 'Role A' may access the dataset. - </p> - <p> - If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived - from the intersection of the users associated with the roles. For example, if 'Role A' and 'Role B' are associated with - a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset. When - the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and - roles associated with the "access" permission (otherwise the dataset would be restricted from everyone). - </p> - <p> - In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with - their private role (the role identical to their Galaxy user name / email address). Associating additional roles that - include the "access" permission is not possible, since it would render the dataset inaccessible to everyone. - <p> - To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset - with that role, not their "private role". Galaxy makes this easy by telling the user they are about to share a private dataset - and giving them the option of doing so. If they respond positively, the sharing role is automatically created for them. - </p> - <p> - Private data (data associated with roles that include the "access" permission) must be made public in order to be used - with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" - tool. Being made publically accessible means removing the association of all roles that include the "access" permission - from the dataset. - <p> - </li> - <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li> - </ul> - </li> -</ul> -<br/> + <li> + <strong>Roles</strong> - associate users and groups with specific permissions on datasets. For example, users in groups A and B + can be associated with role C which gives them the "access" permission on datasets D, E and F. Roles have a type which is currently + one of the following: + <ul> + <li> + <strong>private</strong> - every user is associated automatically with their own private role. Administrators cannot + manage private roles. + </li> + <li> + <strong>user</strong> - this is currently not used, but eventually any registered user will be able to create a new role + and this will be it's type. + </li> + <li> + <strong>sharing</strong> - a role created automatically during a Galaxy session that enables a user to share data with + another user. This can generally be considered a temporary role. + </li> + <li><strong>admin</strong> - a role created by a Galaxy administrator.</li> + </ul> + </li> + <p/> + <li> + <strong>Dataset Permissions</strong> - applying the following permissions will to a dataset will result in the behavior described. + <ul> + <li> + <strong>access</strong> - users associated with the role can import this dataset into their history for analysis. + <p> + If no roles with the "access" permission are associated with a dataset, the dataset is "public" and may be accessed by anyone + that can access the data library in which it is contained. See the <strong>Manage data libraries</strong> section above for + details. Public datasets contained in public data libraries will be accessible to all users (as well as anyone not logged in + during a Galaxy session) from the list of data libraries displayed when the "Data Libraries" menu item is selected. + </p> + <p> + Associating a dataset with a role that includes the "access" permission restricts the set of users that can access it. + For example, if 'Role A' includes the "access" permission and 'Role A' is associated with the dataset, only those users + and groups who are associated with 'Role A' may access the dataset. + </p> + <p> + If multiple roles that include the "access" permission are associated with a dataset, access to the dataset is derived + from the intersection of the users associated with the roles. For example, if 'Role A' and 'Role B' are associated with + a dataset, only those users and groups who are associated with both 'Role A' AND 'Role B' may access the dataset. When + the "access" permission is applied to a dataset, Galaxy checks to make sure that at least 1 user belongs to all groups and + roles associated with the "access" permission (otherwise the dataset would be restricted from everyone). + </p> + <p> + In order for a user to make a dataset private (i.e., only they can access it), they should associate the dataset with + their private role (the role identical to their Galaxy user name / email address). Associating additional roles that + include the "access" permission is not possible, since it would render the dataset inaccessible to everyone. + <p> + To make a dataset private to themselves and one or more other users, the user can create a new role and associate the dataset + with that role, not their "private role". Galaxy makes this easy by telling the user they are about to share a private dataset + and giving them the option of doing so. If they respond positively, the sharing role is automatically created for them. + </p> + <p> + Private data (data associated with roles that include the "access" permission) must be made public in order to be used + with external applications like the "view at UCSC" link, or the "Perform genome analysis and prediction with EpiGRAPH" + tool. Being made publically accessible means removing the association of all roles that include the "access" permission + from the dataset. + <p> + </li> + <li><strong>manage permissions</strong> - Role members can manage the permissions applied to this dataset</li> + </ul> + </li> + </ul> + <br/> +%endif --- a/templates/webapps/galaxy/admin/index.mako Fri Oct 14 09:58:59 2011 -0400 +++ b/templates/webapps/galaxy/admin/index.mako Fri Oct 14 12:14:54 2011 -0400 @@ -1,4 +1,5 @@ <%inherit file="/webapps/galaxy/base_panels.mako"/> +<%namespace file="/message.mako" import="render_msg" /> ## Default title <%def name="title()">Galaxy Administration</%def> @@ -102,6 +103,6 @@ </%def><%def name="center_panel()"> - <% center_url = h.url_for( action='center', webapp='galaxy' ) %> + <% center_url = h.url_for( controller='admin', action='center', webapp='galaxy', message=message, status=status ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> --- a/templates/workflow/list.mako Fri Oct 14 09:58:59 2011 -0400 +++ b/templates/workflow/list.mako Fri Oct 14 12:14:54 2011 -0400 @@ -37,7 +37,7 @@ </a></li><li> - <a class="action-button" href="${h.url_for( action='import_workflow' )}"> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow' )}"><img src="${h.url_for('/static/images/fugue/arrow-090.png')}" /><span>Upload or import workflow</span></a> @@ -63,22 +63,20 @@ ## <td>${str(workflow.update_time)[:19]}</td><td><div popupmenu="wf-${i}-popup"> - <a class="action-button" href="${h.url_for( action='editor', id=trans.security.encode_id(workflow.id) )}" target="_parent">Edit</a> - <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(workflow.id) )}" target="_parent">Run</a> - <a class="action-button" href="${h.url_for( action='sharing', id=trans.security.encode_id(workflow.id) )}">Share or Publish</a> - <a class="action-button" href="${h.url_for( action='export', id=trans.security.encode_id(workflow.id) )}">Download or Export</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a> - <a class="action-button" href="${h.url_for( action='rename', id=trans.security.encode_id(workflow.id) )}">Rename</a> - <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( action='delete', id=trans.security.encode_id(workflow.id) )}">Delete</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id( workflow.id ) )}" target="_parent">Edit</a> + <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id( workflow.id ) )}" target="_parent">Run</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='sharing', id=trans.security.encode_id( workflow.id ) )}">Share or Publish</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='export', id=trans.security.encode_id( workflow.id ) )}">Download or Export</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='rename', id=trans.security.encode_id( workflow.id ) )}">Rename</a> + <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='delete', id=trans.security.encode_id( workflow.id ) )}">Delete</a></div></td></tr> %endfor </table> %else: - You have no workflows. - %endif <h2>Workflows shared with you by others</h2> @@ -101,18 +99,16 @@ <td>${len(workflow.latest_workflow.steps)}</td><td><div popupmenu="shared-${i}-popup"> - <a class="action-button" href="${h.url_for( action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug)}" target="_top">View</a> - <a class="action-button" href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">Run</a> - <a class="action-button" href="${h.url_for( action='clone', id=trans.security.encode_id(workflow.id) )}">Clone</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='clone', id=trans.security.encode_id( workflow.id ) )}">Clone</a></div></td></tr> %endfor </table> %else: - No workflows have been shared with you. - %endif <h2>Other options</h2> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Remove incorrect #-S /bin/bash (SGE shell override) from drmaa job runner. If you were depending on this to get jobs to run on your SGE cluster under bash, please add '-S /bin/bash' to your Galaxy user's ~/.sge_request.
by Bitbucket 14 Oct '11

14 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d711a9201414/ changeset: d711a9201414 user: natefoo date: 2011-10-14 15:58:59 summary: Remove incorrect #-S /bin/bash (SGE shell override) from drmaa job runner. If you were depending on this to get jobs to run on your SGE cluster under bash, please add '-S /bin/bash' to your Galaxy user's ~/.sge_request. affected #: 1 file (-1 bytes) --- a/lib/galaxy/jobs/runners/drmaa.py Thu Oct 13 16:09:28 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Oct 14 09:58:59 2011 -0400 @@ -33,7 +33,6 @@ } drm_template = """#!/bin/sh -#$ -S /bin/sh GALAXY_LIB="%s" if [ "$GALAXY_LIB" != "None" ]; then if [ -n "$PYTHONPATH" ]; then Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Clarify tool searches in the tool shed. Searches are retricted to only tools that properly load in Galaxy.
by Bitbucket 13 Oct '11

13 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/98041300775e/ changeset: 98041300775e user: greg date: 2011-10-13 22:09:28 summary: Clarify tool searches in the tool shed. Searches are retricted to only tools that properly load in Galaxy. affected #: 3 files (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 15:35:45 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 16:09:28 2011 -0400 @@ -293,7 +293,12 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/index.mako', message=message, status=status ) + # See if there are any RepositoryMetadata records since menu items require them. + repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first() + return trans.fill_template( '/webapps/community/index.mako', + repository_metadata=repository_metadata, + message=message, + status=status ) @web.expose def browse_categories( self, trans, **kwd ): if 'f-free-text-search' in kwd: @@ -400,7 +405,7 @@ exact_matches_checked = CheckboxField.is_checked( exact_matches ) match_tuples = [] if tool_id or tool_name or tool_version: - for repository_metadata in trans.sa_session.query( model.RepositoryMetadata.table ).all(): + for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): metadata = repository_metadata.metadata tools = metadata[ 'tools' ] found = False --- a/templates/webapps/community/index.mako Thu Oct 13 15:35:45 2011 -0400 +++ b/templates/webapps/community/index.mako Thu Oct 13 16:09:28 2011 -0400 @@ -61,9 +61,11 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div> %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for tools</a> - </div> + %if repository_metadata: + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> + </div> + %endif </div></div><div class="toolSectionBody"> --- a/templates/webapps/community/repository/find_tools.mako Thu Oct 13 15:35:45 2011 -0400 +++ b/templates/webapps/community/repository/find_tools.mako Thu Oct 13 16:09:28 2011 -0400 @@ -15,10 +15,10 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Search repositories for tools</div> + <div class="toolFormTitle">Search repositories for valid tools</div><div class="toolFormBody"><div class="form-row"> - Enter any combination of the following tool attributes to locate matching tools. + Valid tools are those that properly load in Galaxy. Enter any combination of the following tool attributes to locate matching valid tools. </div><div style="clear: both"></div><form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" > Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Sort the list of tool shed repositories by name when populating the grid for matching tools, but eliminate all grid column sorting.
by Bitbucket 13 Oct '11

13 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8953f799206e/ changeset: 8953f799206e user: greg date: 2011-10-13 21:35:45 summary: Sort the list of tool shed repositories by name when populating the grid for matching tools, but eliminate all grid column sorting. affected #: 1 file (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 15:21:18 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 15:35:45 2011 -0400 @@ -239,16 +239,14 @@ title = "Matched repositories" model_class = model.RepositoryMetadata template='/webapps/community/repository/grid.mako' - default_sort_key = "name" + default_sort_key = "Repository.name" columns = [ NameColumn( "Name", - key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id, webapp="community" ) ), attach_popup=True ), DescriptionColumn( "Synopsis", - key="description", attach_popup=False ), RevisionColumn( "Revision" ), UserColumn( "Owner", @@ -272,14 +270,11 @@ int( repository_id ), self.model_class.table.c.changeset_revision, changeset_revision ) ) - q = trans.sa_session.query( self.model_class ) \ - .join( model.Repository ) \ - .join( model.User.table ) \ - .filter( or_( *clause_list ) ) return trans.sa_session.query( self.model_class ) \ .join( model.Repository ) \ .join( model.User.table ) \ - .filter( or_( *clause_list ) ) + .filter( or_( *clause_list ) ) \ + .order_by( model.Repository.name ) # Return an empty query return trans.sa_session.query( self.model_class ) \ .join( model.Repository ) \ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Keep track ot the changeset revision when viewing tool shed repositories retrieved from tool searches.
by Bitbucket 13 Oct '11

13 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7117e30b95b5/ changeset: 7117e30b95b5 user: greg date: 2011-10-13 21:21:18 summary: Keep track ot the changeset revision when viewing tool shed repositories retrieved from tool searches. affected #: 1 file (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 14:47:13 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 15:21:18 2011 -0400 @@ -244,7 +244,7 @@ NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", - id=item.repository.id, + id=item.id, webapp="community" ) ), attach_popup=True ), DescriptionColumn( "Synopsis", @@ -373,11 +373,23 @@ @web.expose def find_tools( self, trans, **kwd ): if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - **kwd ) ) + repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + is_admin = trans.user_is_admin() + # The received id is a RepositoryMetadata.id, so we have to get the repository id. + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if is_admin or repository.user == trans.user: + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + **kwd ) ) + else: + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_repository', + **kwd ) ) params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the ability to search for tools within tool shed repositories by any combination of tool id, name and version (exact or partial matches).
by Bitbucket 13 Oct '11

13 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7fe346183e46/ changeset: 7fe346183e46 user: greg date: 2011-10-13 20:47:13 summary: Add the ability to search for tools within tool shed repositories by any combination of tool id, name and version (exact or partial matches). affected #: 4 files (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 10:59:14 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Oct 13 14:47:13 2011 -0400 @@ -189,7 +189,7 @@ def get_value( self, trans, grid, repository ): """ Display a SelectField whose options are the changeset_revision - strings of all downloadable_revisions of this repository. + strings of all download-able revisions of this repository. """ select_field = build_changeset_revision_select_field( trans, repository ) if len( select_field.options ) > 1: @@ -220,8 +220,75 @@ .join( model.RepositoryMetadata.table ) \ .join( model.User.table ) +class MatchedRepositoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.description + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.changeset_revision + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.user: + return repository_metadata.repository.user.username + return 'no user' + # Grid definition + title = "Matched repositories" + model_class = model.RepositoryMetadata + template='/webapps/community/repository/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.repository.id, + webapp="community" ) ), + attach_popup=True ), + DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RevisionColumn( "Revision" ), + UserColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ) + ] + operations = [] + standard_filters = [] + default_filter = {} + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + match_tuples = kwd.get( 'match_tuples', [] ) + clause_list = [] + if match_tuples: + for match_tuple in match_tuples: + repository_id, changeset_revision = match_tuple + clause_list.append( "%s=%d and %s='%s'" % ( self.model_class.table.c.repository_id, + int( repository_id ), + self.model_class.table.c.changeset_revision, + changeset_revision ) ) + q = trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( or_( *clause_list ) ) + return trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( or_( *clause_list ) ) + # Return an empty query + return trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( self.model_class.table.c.repository_id == 0 ) + class RepositoryController( BaseUIController, ItemRatings ): + matched_repository_list_grid = MatchedRepositoryListGrid() downloadable_repository_list_grid = DownloadableRepositoryListGrid() repository_list_grid = RepositoryListGrid() category_list_grid = CategoryListGrid() @@ -304,6 +371,76 @@ # Render the list view return self.downloadable_repository_list_grid( trans, **kwd ) @web.expose + def find_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + **kwd ) ) + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # Set the toolshedgalaxyurl cookie so we can get back + # to the calling local Galaxy instance. + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + tool_id = kwd.get( 'tool_id', '' ).lower() + tool_name = kwd.get( 'tool_name', '' ).lower() + tool_version = kwd.get( 'tool_version', '' ).lower() + exact_matches = params.get( 'exact_matches', '' ) + exact_matches_checked = CheckboxField.is_checked( exact_matches ) + match_tuples = [] + if tool_id or tool_name or tool_version: + for repository_metadata in trans.sa_session.query( model.RepositoryMetadata.table ).all(): + metadata = repository_metadata.metadata + tools = metadata[ 'tools' ] + found = False + for tool_dict in tools: + if tool_id and not tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) + elif tool_name and not tool_id and not tool_version: + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and not tool_id and not tool_name: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_id and tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_id and tool_version and not tool_name: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_version and tool_name and not tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + if found: + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + kwd[ 'match_tuples' ] = match_tuples + kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ + ( tool_id, tool_name, tool_version, str( exact_matches_checked ) ) + # Render the list view + return self.matched_repository_list_grid( trans, **kwd ) + exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + return trans.fill_template( '/webapps/community/repository/find_tools.mako', + tool_id=tool_id, + tool_name=tool_name, + tool_version=tool_version, + exact_matches_check_box=exact_matches_check_box, + message=message, + status=status ) + @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) --- a/templates/webapps/community/admin/center.mako Thu Oct 13 10:59:14 2011 -0400 +++ b/templates/webapps/community/admin/center.mako Thu Oct 13 14:47:13 2011 -0400 @@ -1,7 +1,13 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + <%def name="title()">Galaxy Administration</%def> +%if message: + ${render_msg( message, status )} +%endif + <h2>Administration</h2><p>The menu on the left provides the following features</p> --- a/templates/webapps/community/index.mako Thu Oct 13 10:59:14 2011 -0400 +++ b/templates/webapps/community/index.mako Thu Oct 13 14:47:13 2011 -0400 @@ -61,6 +61,9 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div> %endif + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for tools</a> + </div></div></div><div class="toolSectionBody"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Make implicit dataset conversion work with changes in 1827729ed37e.
by Bitbucket 13 Oct '11

13 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/24270f172fc8/ changeset: 24270f172fc8 user: jgoecks date: 2011-10-13 16:59:14 summary: Make implicit dataset conversion work with changes in 1827729ed37e. affected #: 1 file (-1 bytes) --- a/lib/galaxy/model/__init__.py Wed Oct 12 15:50:02 2011 -0400 +++ b/lib/galaxy/model/__init__.py Thu Oct 13 10:59:14 2011 -0400 @@ -948,12 +948,11 @@ raise NoConverterException("A dependency (%s) is missing a converter." % dependency) except KeyError: pass # No deps - assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, metadata_safe=False ) new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] new_dataset.name = self.name + assoc = ImplicitlyConvertedDatasetAssociation( parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False ) session = trans.sa_session session.add( new_dataset ) - assoc.dataset = new_dataset session.add( assoc ) session.flush() return None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Force absolute path when creating temporary directory used when importing histories. Fixes #667
by Bitbucket 12 Oct '11

12 Oct '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ac84504bc6a1/ changeset: ac84504bc6a1 user: jgoecks date: 2011-10-12 21:50:02 summary: Force absolute path when creating temporary directory used when importing histories. Fixes #667 affected #: 1 file (-1 bytes) --- a/lib/galaxy/tools/actions/history_imp_exp.py Wed Oct 12 11:19:58 2011 -0400 +++ b/lib/galaxy/tools/actions/history_imp_exp.py Wed Oct 12 15:50:02 2011 -0400 @@ -28,7 +28,10 @@ # # Add association for keeping track of job, history relationship. - archive_dir = tempfile.mkdtemp() + + # Use abspath because mkdtemp() does not, contrary to the documentation, + # always return an absolute path. + archive_dir = os.path.abspath( tempfile.mkdtemp() ) jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir ) trans.sa_session.add( jiha ) job_wrapper = JobImportHistoryArchiveWrapper( job ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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