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October 2012

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commit/galaxy-central: greg: Galaxy admin menu option for resetting metadata on selected tool shed repositories.
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3b9db9c42066/ changeset: 3b9db9c42066 user: greg date: 2012-10-11 16:22:04 summary: Galaxy admin menu option for resetting metadata on selected tool shed repositories. affected #: 1 file diff -r b037978114caede484df1b25bd4004e0591820f5 -r 3b9db9c4206602859dee02164aa32a925138866e templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -75,6 +75,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=installing_repository_ids )}" target="galaxy_main">Monitor installing tool shed repositories</a></div> %endif %if installed_repositories: + <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" target="galaxy_main">Reset metadata for tool shed repositories</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> %endif </div> 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 abiltiy for a Galaxy admin to reset metadata on selected installed tool shed repositories.
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b037978114ca/ changeset: b037978114ca user: greg date: 2012-10-11 16:20:57 summary: Add the abiltiy for a Galaxy admin to reset metadata on selected installed tool shed repositories. affected #: 2 files diff -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b -r b037978114caede484df1b25bd4004e0591820f5 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1447,7 +1447,59 @@ status=status ) @web.expose @web.require_admin - def reset_repository_metadata( self, trans, id ): + def reset_metadata_on_selected_repositories( self, trans, **kwd ): + # TODO: merge this with the similar method in the repository controller. + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository_ids = util.listify( kwd.get( 'repository_names_by_owner', None ) ) + if 'reset_metadata_on_selected_repositories_button' in kwd: + if repository_ids: + successful_count = 0 + unsuccessful_count = 0 + for repository_id in repository_ids: + repository = get_repository( trans, repository_id ) + try: + invalid_file_tups, metadata_dict = self.reset_repository_metadata( trans, + trans.security.encode_id( repository.id ), + resetting_all_repositories=True ) + if invalid_file_tups: + unsuccessful_count += 1 + else: + successful_count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) + unsuccessful_count += 1 + message = "Successfully reset metadata on %d %s. " % ( successful_count, + inflector.cond_plural( successful_count, "repository" ) ) + if unsuccessful_count: + message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count, + inflector.cond_plural( unsuccessful_count, + "repository" ) ) + trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + message=util.sanitize_text( message ), + status=status ) ) + else: + 'Select at least one repository to on which to reset all metadata.' + status = 'error' + repositories_select_field = SelectField( name='repository_names_by_owner', + multiple=True, + display='checkboxes' ) + for repository in trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( trans.model.ToolShedRepository.table.c.uninstalled == False ) \ + .order_by( trans.model.ToolShedRepository.table.c.name, + trans.model.ToolShedRepository.table.c.owner ): + option_label = '%s (%s)' % ( repository.name, repository.owner ) + option_value = trans.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', + repositories_select_field=repositories_select_field, + message=message, + status=status ) + @web.expose + @web.require_admin + def reset_repository_metadata( self, trans, id, resetting_all_repositories=False ): """Reset all metadata on the installed tool shed repository.""" repository = get_repository( trans, id ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) @@ -1465,23 +1517,33 @@ updating_installed_repository=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: - update_in_shed_tool_config( trans.app, repository )#def update_in_shed_tool_config( trans, shed_tool_conf_dict, elem_list ): + update_in_shed_tool_config( trans.app, repository ) trans.sa_session.add( repository ) trans.sa_session.flush() - message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name - status = 'done' + if resetting_all_repositories: + log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + else: + message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name + status = 'done' else: - message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name - status = 'done' + if resetting_all_repositories: + log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + else: + message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name + status = 'done' else: - message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name - status = 'error' - new_kwd = dict( id=id, - message=message, - status=status ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repository', - **new_kwd ) ) + if resetting_all_repositories: + log.debug( 'Error locating installation directory for repository %s.' % repository.name ) + else: + message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name + status = 'error' + if resetting_all_repositories: + return invalid_file_tups, metadata_dict + else: + new_kwd = dict( id=id, message=message, status=status ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='manage_repository', + **new_kwd ) ) @web.expose @web.require_admin def reset_to_install( self, trans, **kwd ): diff -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b -r b037978114caede484df1b25bd4004e0591820f5 templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako @@ -0,0 +1,71 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="local_javascripts()"> + <script type="text/javascript"> + function checkAllFields() + { + var chkAll = document.getElementById('checkAll'); + var checks = document.getElementsByTagName('input'); + var boxLength = checks.length; + var allChecked = false; + var totalChecked = 0; + if ( chkAll.checked == true ) + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) + { + checks[i].checked = true; + } + } + } + else + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) + { + checks[i].checked = false + } + } + } + } + </script> +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${local_javascripts()} +</%def> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="warningmessage"> + Resetting metadata may take a while, so wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as + doing anything else will not be helpful. +</div> + +<div class="toolForm"> + <div class="toolFormTitle">Reset all metadata on each selected tool shed repository</div> + <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" method="post" > + <div class="form-row"> + Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="checkbox" id="checkAll" name=select_all_repositories_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_repositories_checkbox value="true"/><b>Select/unselect all repositories</b> + </div> + <div style="clear: both"></div> + <div class="form-row"> + ${repositories_select_field.get_html()} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="reset_metadata_on_selected_repositories_button" value="Reset metadata on selected repositories"/> + </div> + </form> + </div> +</div> 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: carlfeberhard: scatterplot: added stats panel, added chart config panel; dataproviders/basic.py: compute, pass gen. stats in response.meta; base-mvc: fixed bug in chrome LoggableMixin; pack scripts
by Bitbucket 10 Oct '12

10 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0684f69e527d/ changeset: 0684f69e527d user: carlfeberhard date: 2012-10-10 23:55:34 summary: scatterplot: added stats panel, added chart config panel; dataproviders/basic.py: compute, pass gen. stats in response.meta; base-mvc: fixed bug in chrome LoggableMixin; pack scripts affected #: 17 files diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -105,7 +105,12 @@ # set up the response, column lists response = {} response[ 'data' ] = data = [ [] for column in columns ] - response[ 'meta' ] = meta = [ { 'min': None, 'max': None } for column in columns ] + response[ 'meta' ] = meta = [{ + 'min' : None, + 'max' : None, + 'count' : 0, + 'sum' : 0 + } for column in columns ] column_types = [ self.original_dataset.metadata.column_types[ column ] for column in columns ] @@ -135,18 +140,39 @@ #NOTE: this will return None/null for abberrant column values (including bad indeces) for index, column in enumerate( columns ): column_val = None + column_type = column_types[ index ] if column < fields_len: - column_val = cast_val( fields[ column ], column_types[ index ] ) + column_val = cast_val( fields[ column ], column_type ) if column_val != None: - if( meta[ index ][ 'min' ] == None - or column_val < meta[ index ][ 'min' ] ): - meta[ index ][ 'min' ] = column_val - if( meta[ index ][ 'max' ] == None - or column_val > meta[ index ][ 'max' ] ): - meta[ index ][ 'max' ] = column_val + + # if numeric, maintain min, max, sum + if( column_type == 'float' or column_type == 'int' ): + if( ( meta[ index ][ 'min' ] == None ) or ( column_val < meta[ index ][ 'min' ] ) ): + meta[ index ][ 'min' ] = column_val + + if( ( meta[ index ][ 'max' ] == None ) or ( column_val > meta[ index ][ 'max' ] ) ): + meta[ index ][ 'max' ] = column_val + + meta[ index ][ 'sum' ] += column_val + + # maintain a count - for other stats + meta[ index ][ 'count' ] += 1 data[ index ].append( column_val ) response[ 'endpoint' ] = dict( last_line=( count - 1 ), file_ptr=f.tell() ) f.close() + for index, meta in enumerate( response[ 'meta' ] ): + count = meta[ 'count' ] + meta[ 'mean' ] = float( meta[ 'sum' ] ) / count + + sorted_data = sorted( response[ 'data' ][ index ] ) + # even data count - + middle_index = count / 2 - 1 + if count % 2 == 0: + meta[ 'median' ] = sum( sorted_data[ middle_index : ( middle_index + 1 ) ] ) / 2.0 + + else: + meta[ 'median' ] = sorted_data[ middle_index ] + return response diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/libs/jquery/jquery-ui-1.8.23.custom.min.js --- a/static/scripts/libs/jquery/jquery-ui-1.8.23.custom.min.js +++ b/static/scripts/libs/jquery/jquery-ui-1.8.23.custom.min.js @@ -22,4 +22,4 @@ * 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this.handles.removeClass("ui-state-active"),this._mouseSliding=!1,this._stop(a,this._handleIndex),this._change(a,this._handleIndex),this._handleIndex=null,this._clickOffset=null,this._animateOff=!1,!1},_detectOrientation:function(){this.orientation=this.options.orientation==="vertical"?"vertical":"horizontal"},_normValueFromMouse:function(a){var b,c,d,e,f;return this.orientation==="horizontal"?(b=this.elementSize.width,c=a.x-this.elementOffset.left-(this._clickOffset?this._clickOffset.left:0)):(b=this.elementSize.height,c=a.y-this.elementOffset.top-(this._clickOffset?this._clickOffset.top:0)),d=c/b,d>1&&(d=1),d<0&&(d=0),this.orientation==="vertical"&&(d=1-d),e=this._valueMax()-this._valueMin(),f=this._valueMin()+d*e,this._trimAlignValue(f)},_start:function(a,b){var c={handle:this.handles[b],value:this.value()};return this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("start",a,c)},_slide:function(a,b,c){var d,e,f;this.options.values&&this.options.values.length?(d=this.values(b?0:1),this.options.values.length===2&&this.options.range===!0&&(b===0&&c>d||b===1&&c<d)&&(c=d),c!==this.values(b)&&(e=this.values(),e[b]=c,f=this._trigger("slide",a,{handle:this.handles[b],value:c,values:e}),d=this.values(b?0:1),f!==!1&&this.values(b,c,!0))):c!==this.value()&&(f=this._trigger("slide",a,{handle:this.handles[b],value:c}),f!==!1&&this.value(c))},_stop:function(a,b){var c={handle:this.handles[b],value:this.value()};this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("stop",a,c)},_change:function(a,b){if(!this._keySliding&&!this._mouseSliding){var c={handle:this.handles[b],value:this.value()};this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("change",a,c)}},value:function(a){if(arguments.length){this.options.value=this._trimAlignValue(a),this._refreshValue(),this._change(null,0);return}return this._value()},values:function(b,c){var d,e,f;if(arguments.length>1){this.options.values[b]=this._trimAlignValue(c),this._refreshValue(),this._change(null,b);return}if(!arguments.length)return this._values();if(!a.isArray(arguments[0]))return this.options.values&&this.options.values.length?this._values(b):this.value();d=this.options.values,e=arguments[0];for(f=0;f<d.length;f+=1)d[f]=this._trimAlignValue(e[f]),this._change(null,f);this._refreshValue()},_setOption:function(b,c){var d,e=0;a.isArray(this.options.values)&&(e=this.options.values.length),a.Widget.prototype._setOption.apply(this,arguments);switch(b){case"disabled":c?(this.handles.filter(".ui-state-focus").blur(),this.handles.removeClass("ui-state-hover"),this.handles.propAttr("disabled",!0),this.element.addClass("ui-disabled")):(this.handles.propAttr("disabled",!1),this.element.removeClass("ui-disabled"));break;case"orientation":this._detectOrientation(),this.element.removeClass("ui-slider-horizontal ui-slider-vertical").addClass("ui-slider-"+this.orientation),this._refreshValue();break;case"value":this._animateOff=!0,this._refreshValue(),this._change(null,0),this._animateOff=!1;break;case"values":this._animateOff=!0,this._refreshValue();for(d=0;d<e;d+=1)this._change(null,d);this._animateOff=!1}},_value:function(){var a=this.options.value;return a=this._trimAlignValue(a),a},_values:function(a){var b,c,d;if(arguments.length)return 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b=this.options.range,c=this.options,d=this,e=this._animateOff?!1:c.animate,f,g={},h,i,j,k;this.options.values&&this.options.values.length?this.handles.each(function(b,i){f=(d.values(b)-d._valueMin())/(d._valueMax()-d._valueMin())*100,g[d.orientation==="horizontal"?"left":"bottom"]=f+"%",a(this).stop(1,1)[e?"animate":"css"](g,c.animate),d.options.range===!0&&(d.orientation==="horizontal"?(b===0&&d.range.stop(1,1)[e?"animate":"css"]({left:f+"%"},c.animate),b===1&&d.range[e?"animate":"css"]({width:f-h+"%"},{queue:!1,duration:c.animate})):(b===0&&d.range.stop(1,1)[e?"animate":"css"]({bottom:f+"%"},c.animate),b===1&&d.range[e?"animate":"css"]({height:f-h+"%"},{queue:!1,duration:c.animate}))),h=f}):(i=this.value(),j=this._valueMin(),k=this._valueMax(),f=k!==j?(i-j)/(k-j)*100:0,g[d.orientation==="horizontal"?"left":"bottom"]=f+"%",this.handle.stop(1,1)[e?"animate":"css"](g,c.animate),b==="min"&&this.orientation==="horizontal"&&this.range.stop(1,1)[e?"animate":"css"]({width:f+"%"},c.animate),b==="max"&&this.orientation==="horizontal"&&this.range[e?"animate":"css"]({width:100-f+"%"},{queue:!1,duration:c.animate}),b==="min"&&this.orientation==="vertical"&&this.range.stop(1,1)[e?"animate":"css"]({height:f+"%"},c.animate),b==="max"&&this.orientation==="vertical"&&this.range[e?"animate":"css"]({height:100-f+"%"},{queue:!1,duration:c.animate}))}}),a.extend(a.ui.slider,{version:"1.8.23"})})(jQuery);; diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -65,8 +65,10 @@ logger : null, log : function(){ - return ( this.logger )?( this.logger.log.apply( this, arguments ) ) - :( undefined ); + if( this.logger ){ + return this.logger.log.apply( this.logger, arguments ); + } + return undefined; } }; diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){return(this.logger)?(this.logger.log.apply(this,arguments)):(undefined)}};var GalaxyLocalization=jQuery.extend({},{aliasName:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){var a=b;if(_.has(this.localizedStrings,b)){a=this.localizedStrings[b]}return a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.aliasName]=function(a){return GalaxyLocalization.localize(a)};var TemplateLoader=_.extend({},LoggableMixin,{getTemplateLoadFn:function(){throw ("There is no templateLoadFn. Make sure you're using a subclass of TemplateLoader")},getTemplates:function(d,e){e=e||false;this.log(this,"getTemplates:",d,", forceReload:",e);var c={},a=this,b=this.getTemplateLoadFn();if(!d){return c}jQuery.each(d,function(f,g){jQuery.each(g,function(h,i){a.log(a+", templateFile:",f,"templateName:",h,", templateID:",i);c[h]=b.call(a,f,h,i)})});return c}});var CompiledTemplateLoader=_.extend({},TemplateLoader,{getTemplateLoadFn:function(){return this.loadCompiledHandlebarsTemplate},loadCompiledHandlebarsTemplate:function(b,a,c){this.log("getInDomTemplates, templateFile:",b,"templateName:",a,", templateID:",c);if(!Handlebars.templates||!Handlebars.templates[c]){throw ("Template not found: Handlebars."+c+". Check your h.templates() call in the mako file that rendered this page")}this.log("found template function:",c);return Handlebars.templates[c]}});var InDomTemplateLoader=_.extend({},TemplateLoader,{compileTemplate:function(a){if(!Handlebars||!Handlebars.compile){throw ("No Handlebars.compile found. You may only have Handlebars.runtime loaded.Include handlebars.full for this to work")}this.log("compiling template:",a);return Handlebars.compile(a)},findTemplateInDom:function(b,a,c){return $("script#"+c).last()},getTemplateLoadFn:function(){return this.loadInDomTemplate},loadInDomTemplate:function(b,a,c){this.log("getInDomTemplate, templateFile:",b,"templateName:",a,", templateID:",c);var d=this.findTemplateInDom(b,a,c);if(!d||!d.length){throw ("Template not found within the DOM: "+c+". Check that this template has been included in the page")}this.log("found template in dom:",d.html());return this.compileTemplate(d.html())}});var RemoteTemplateLoader=_.extend({},InDomTemplateLoader,{templateBaseURL:"static/scripts/templates/",getTemplateLoadFn:function(){return this.loadViaHttpGet},loadViaHttpGet:function(d,c,f){var b="static/scripts/templates/";this.log("loadViaHttpGet, templateFile:",d,"templateName:",c,", templateID:",f,"templateBaseURL:",this.templateBaseURL);var h=null;try{h=this.loadInDomTemplate(d,c,f)}catch(g){this.log("getInDomTemplate exception:"+g);if(!Handlebars.compile){throw (g)}this.log("Couldn't locate template in DOM: "+f);var a=this;var e=b+d;jQuery.ajax(e,{method:"GET",async:false,success:function(i){a.log(d+" loaded via GET. Attempting compile...");$("body").append(i);h=a.loadInDomTemplate(d,c,f)},error:function(j,i,k){throw ("Failed to fetch "+e+":"+i)}})}if(!h){throw ("Couldn't load or fetch template: "+f)}return h}}); \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){var a=b;if(_.has(this.localizedStrings,b)){a=this.localizedStrings[b]}return a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;var e=function(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this.save();return this},deleteKey:function(j){delete i[j];this.save();return this},save:function(){return h.save()},toString:function(){return("StorageRecursionHelper("+i+")")}}};var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);f.save=function(h){c(g,f.get())};f.destroy=function(){a(g)};f.toString=function(){return"PersistantStorage("+data+")"};return f}; \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/mvc/history.js --- a/static/scripts/packed/mvc/history.js +++ b/static/scripts/packed/mvc/history.js @@ -1,1 +1,1 @@ -var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",downloadLinks:"template-history-downloadLinks",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea",displayApps:"template-history-displayApps"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(c){a.log(a+".render_items:",c);b.prepend(c.render())});return b},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates=CompiledTemplateLoader.getTemplates({"history-templates.html":{historyPanel:"template-history-historyPanel"}}); \ No newline at end of file +var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",this,this.model);this.visible=a.visible},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}if(this.visible){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b){var a=this.$el.find(".historyItemBody");if(b===undefined){a.toggle()}else{if(b){a.show()}else{a.hide()}}this.trigger("toggleBodyVisibility",this.model.get("id"),a.is(":visible"))},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HistoryItemView("+a+")"}});HistoryItemView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{visibleItems:{}});this.initializeItems()},initializeItems:function(){this.itemViews={};var a=this;this.model.items.each(function(c){var e=c.get("id"),d=a.storage.get("visibleItems").get(e),b=new HistoryItemView({model:c,visible:d});a.setUpItemListeners(b);a.itemViews[e]=b})},setUpItemListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("visibleItems").set(d,true)}else{a.storage.get("visibleItems").deleteKey(d)}})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");async_save_text("history-name-container","history-name",this.model.get("renameURL"),"new_name",18);this.$el.find(".tooltip").tooltip();var b=this.$el.find("#history-annotation-area");$("#history-annotate").click(function(){if(b.is(":hidden")){b.slideDown("fast")}else{b.slideUp("fast")}return false});async_save_text("history-annotation-container","history-annotation",this.model.get("annotateURL"),"new_annotation",18,true,4);if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(d,c){a.log(a+".render_items:",c,d);b.prepend(d.render())});return b},events:{"click #history-collapse-all":"hideAllItemBodies","click #history-tag":"loadAndDisplayTags"},hideAllItemBodies:function(){_.each(this.itemViews,function(a){a.toggleBodyVisibility(false)})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:this.model.get("tagURL"),error:function(){alert("Tagging failed")},success:function(e){a.log(a+" tag elt html (ajax)",e);b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,C,A,s,J){A=A||k.helpers;var B="",o,n,y=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(L,K){return"refresh"}function t(L,K){return"collapse all"}function r(O,N){var L="",M,K;L+='\n <div style="width: 40px; float: right; white-space: nowrap;">\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="';K=A.tagURL;if(K){M=K.call(O,{hash:{}})}else{M=O.tagURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n <a id="history-annotate" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="';K=A.annotateURL;if(K){M=K.call(O,{hash:{}})}else{M=O.annotateURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n </div>\n ';return L}function q(L,K){return"Edit history tags"}function m(L,K){return"Edit history annotation"}function I(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideDeletedURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideDeletedURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function H(L,K){return"hide deleted"}function G(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideHiddenURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideHiddenURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function F(L,K){return"hide hidden"}function E(O,N){var L="",M,K;L+="\n ";L+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+'</div>\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n \n ";return L}function D(O,N){var L="",M,K;L+='\n <div id="history-size">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function p(O,N){var L="",M,K;L+="\n";K=A.warningmessagesmall;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}else{M=O.warningmessagesmall;M=typeof M===f?M():M}if(!A.warningmessagesmall){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}if(M||M===0){L+=M}L+="\n";return L}function l(N,M){var L,K;K=A.local;if(K){L=K.call(N,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}else{L=N.local;L=typeof L===f?L():L}if(!A.local){L=c.call(N,L,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}if(L||L===0){return L}else{return""}}function j(L,K){return"You are currently viewing a deleted history!"}function i(N,M){var K="",L;K+="\n";K+='\n<div style="margin: 0px 5px 10px 5px">\n\n <div id="history-tag-area" style="display: none">\n <b>Tags:</b>\n ';K+="\n ";K+='\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';L=N.annotation;L=A["if"].call(N,L,{hash:{},inverse:y.program(27,g,M),fn:y.program(25,h,M)});if(L||L===0){K+=L}K+="\n </div>\n </div>\n </div>\n</div>\n";return K}function h(O,N){var L="",M,K;L+="\n ";K=A.annotation;if(K){M=K.call(O,{hash:{}})}else{M=O.annotation;M=typeof M===f?M():M}L+=e(M)+"\n ";return L}function g(L,K){return"\n <em>Describe or add notes to history</em>\n "}function d(O,N){var L="",M,K;L+='\n<div id="message-container">\n <div class="';K=A.status;if(K){M=K.call(O,{hash:{}})}else{M=O.status;M=typeof M===f?M():M}L+=e(M)+'message">\n ';K=A.message;if(K){M=K.call(O,{hash:{}})}else{M=O.message;M=typeof M===f?M():M}L+=e(M)+"\n </div><br />\n</div>\n";return L}function z(L,K){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota.\n </div>\n <br/>\n '}function x(O,N){var L="",M,K;L+='\n<div id="';K=A.id;if(K){M=K.call(O,{hash:{}})}else{M=O.id;M=typeof M===f?M():M}L+=e(M)+'-datasets" class="history-datasets-list">\n ';L+="\n</div>\n\n";return L}function w(O,N){var L="",M,K;L+='\n<div class="infomessagesmall" id="emptyHistoryMessage">\n';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(36,v,N)})}if(M||M===0){L+=M}L+="\n</div>\n";return L}function v(L,K){return"Your history is empty. Click 'Get Data' on the left pane to start"}B+='<div id="top-links" class="historyLinks">\n <a title="';n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(1,u,J)})}if(o||o===0){B+=o}B+='" class="icon-button arrow-circle tooltip" href="';n=A.baseURL;if(n){o=n.call(C,{hash:{}})}else{o=C.baseURL;o=typeof o===f?o():o}B+=e(o)+"\"></a>\n <a title='";n=A.local;if(n){o=n.call(C,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}else{o=C.local;o=typeof o===f?o():o}if(!A.local){o=c.call(C,o,{hash:{},inverse:y.noop,fn:y.program(3,t,J)})}if(o||o===0){B+=o}B+="' class='icon-button toggle tooltip' href='#' style=\"display: none\"></a>\n ";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(5,r,J)});if(o||o===0){B+=o}B+='\n</div>\n<div class="clear"></div>\n\n';B+="\n";o=C.showDeleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(10,I,J)});if(o||o===0){B+=o}B+="\n\n";o=C.showHidden;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(13,G,J)});if(o||o===0){B+=o}B+="\n\n";B+='\n<div id="history-name-area" class="historyLinks">\n <div id="history-name-container" style="position: relative;">\n ';o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.program(18,D,J),fn:y.program(16,E,J)});if(o||o===0){B+=o}B+='\n </div> \n</div>\n<div style="clear: both;"></div>\n\n';o=C.deleted;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(20,p,J)});if(o||o===0){B+=o}B+="\n\n";B+="\n";B+="\n";o=C.userRoles;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(24,i,J)});if(o||o===0){B+=o}B+="\n\n";o=C.message;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(29,d,J)});if(o||o===0){B+=o}B+='\n\n<div id="quota-message-container">\n ';o=C.over_quota;o=A["if"].call(C,o,{hash:{},inverse:y.noop,fn:y.program(31,z,J)});if(o||o===0){B+=o}B+="\n</div>\n\n";o=C.itemsLength;o=A["if"].call(C,o,{hash:{},inverse:y.program(35,w,J),fn:y.program(33,x,J)});if(o||o===0){B+=o}return B})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,C,A,s,J){A=A||k.helpers;var B="",o,n,y=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(L,K){return"refresh"}function t(L,K){return"collapse all"}function r(O,N){var L="",M,K;L+='\n <div style="width: 40px; float: right; white-space: nowrap;">\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n </div>\n ';return L}function q(L,K){return"Edit history tags"}function m(L,K){return"Edit history annotation"}function I(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideDeletedURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideDeletedURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function H(L,K){return"hide deleted"}function G(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideHiddenURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideHiddenURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function F(L,K){return"hide hidden"}function E(O,N){var L="",M,K;L+="\n ";L+='\n <div id="history-size" style="position: absolute; top: 3px; right: 0px;">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+'</div>\n <div id="history-name" style="margin-right: 50px;" class="tooltip editable-text" title="Click to rename history">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n \n ";return L}function D(O,N){var L="",M,K;L+='\n <div id="history-size">';K=A.diskSize;if(K){M=K.call(O,{hash:{}})}else{M=O.diskSize;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function p(O,N){var L="",M,K;L+="\n";K=A.warningmessagesmall;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}else{M=O.warningmessagesmall;M=typeof M===f?M():M}if(!A.warningmessagesmall){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(21,l,N)})}if(M||M===0){L+=M}L+="\n";return L}function l(N,M){var L,K;K=A.local;if(K){L=K.call(N,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}else{L=N.local;L=typeof L===f?L():L}if(!A.local){L=c.call(N,L,{hash:{},inverse:y.noop,fn:y.program(22,j,M)})}if(L||L===0){return L}else{return""}}function j(L,K){return"You are currently viewing a deleted history!"}function i(N,M){var K="",L;K+="\n";K+='\n<div style="margin: 0px 5px 10px 5px">\n\n <div id="history-tag-area" style="display: none">\n ';K+="\n ";K+='\n <strong>Tags:</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>Annotation / Notes:</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation">\n ';L=N.annotation;L=A["if"].call(N,L,{hash:{},inverse:y.program(27,g,M),fn:y.program(25,h,M)});if(L||L===0){K+=L}K+="\n </div>\n </div>\n </div>\n</div>\n";return K}function h(O,N){var L="",M,K;L+="\n ";K=A.annotation;if(K){M=K.call(O,{hash:{}})}else{M=O.annotation;M=typeof M===f?M():M}L+=e(M)+"\n ";return L}function g(L,K){return"\n <em>Describe or add notes to history</em>\n "}function d(O,N){var L="",M,K;L+='\n<div id="message-container">\n <div class="';K=A.status;if(K){M=K.call(O,{hash:{}})}else{M=O.status;M=typeof M===f?M():M}L+=e(M)+'message">\n ';K=A.message;if(K){M=K.call(O,{hash:{}})}else{M=O.message;M=typeof M===f?M():M}L+=e(M)+"\n </div><br />\n</div>\n";return L}function z(L,K){return'\n <div id="quota-message" class="errormessage">\n You are over your disk quota. 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\ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/templates/compiled/template-visualization-chartSettings.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-chartSettings.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-chartSettings"]=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,n=this;function d(p,o){return"checked"}i+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n </p>\n \n <div id="maxDataPoints" class="form-input numeric-slider-input">\n <label for="maxDataPoints">Maximum data points allowed on graph: </label>\n <div class="slider-output">';h=e.maxDataPoints;if(h){c=h.call(m,{hash:{}})}else{c=m.maxDataPoints;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">';h=e.datapointSize;if(h){c=h.call(m,{hash:{}})}else{c=m.datapointSize;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id="entryAnimDuration" class="form-input checkbox-input">\n <label for="animated">Animate graph transitions?: </label>\n <input type="checkbox" id="animated" class="checkbox control" value="';c=m.entryAnimDuration;c=e["if"].call(m,c,{hash:{},inverse:n.noop,fn:n.program(1,d,k)});if(c||c===0){i+=c}i+='" />\n <p class="form-help help-text-small">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id="width" class="form-input numeric-slider-input">\n <label for="width">Graph width: </label>\n <div class="slider-output">';h=e.width;if(h){c=h.call(m,{hash:{}})}else{c=m.width;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="height" class="form-input numeric-slider-input">\n <label for="height">Graph height: </label>\n <div class="slider-output">';h=e.height;if(h){c=h.call(m,{hash:{}})}else{c=m.height;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="';h=e.xLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.xLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <div id="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="';h=e.yLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.yLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <input id="render-button" type="button" value="Draw" />';return i})})(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/templates/compiled/template-visualization-statsTable.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-statsTable.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-statsTable"]=b(function(f,l,e,k,j){e=e||f.helpers;var h="",c,g="function",i=this.escapeExpression,m=this;function d(r,q){var o="",p,n;o+="\n <tr><td>";n=e.name;if(n){p=n.call(r,{hash:{}})}else{p=r.name;p=typeof p===g?p():p}o+=i(p)+"</td><td>";n=e.xval;if(n){p=n.call(r,{hash:{}})}else{p=r.xval;p=typeof p===g?p():p}o+=i(p)+"</td><td>";n=e.yval;if(n){p=n.call(r,{hash:{}})}else{p=r.yval;p=typeof p===g?p():p}o+=i(p)+"</td></tr>\n </tr>\n ";return o}h+='<p class="help-text">By column:</p>\n <table id="chart-stats-table">\n <thead><th></th><th>X</th><th>Y</th></thead>\n ';c=l.stats;c=e.each.call(l,c,{hash:{},inverse:m.noop,fn:m.program(1,d,j)});if(c||c===0){h+=c}h+="\n </table>";return h})})(); 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t=s.enter().insert("svg:g","g.node").attr("class","completeLink");t.append("svg:path").attr("class","link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1});var r=s.transition().duration(500);r.select("path.link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1+" L "+w.pos2});var p=s.exit().remove()},selectNode:function(n){var m=this;l.selectAll("g.node").classed("selectedHighlight",function(o){if(n.id===o.id){if(n._selected){delete n._selected;return false}else{n._selected=true;return true}}return false});m.model.set("selectedNode",n);$("#phyloVizSelectedNodeName").val(n.name);$("#phyloVizSelectedNodeDist").val(n.dist);$("#phyloVizSelectedNodeAnnotation").val(n.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var n=this.__data__,m=n.annotation||"None";return n?(n.name?n.name+"<br/>":"")+"Dist: "+n.dist+" <br/>Annotation: "+m:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(n){var m=this;m.margins=n.margins;m.layoutMode="Linear";m.stdInit(n);m.layout();m.updateAndRender(m.model.root)},layout:function(){var m=this;m.tree=new g().layoutMode("Linear");m.diagonal=l.svg.diagonal().projection(function(n){return[n.y,n.x]})},renderNodes:function(m){var t=this,u=t.model.get("fontSize")+"px";t.tree.separation(t.model.get("separation")).leafHeight(t.model.get("leafHeight"));var p=500,n=t.tree.separation(t.model.get("separation")).nodes(t.model.root);var o=t.vis.selectAll("g.node").data(n,function(v){return v.name+v.id||(v.id=++t.i)});t.nodes=n;t.duration=p;var q=o.enter().append("svg:g").attr("class","node").on("dblclick",function(){l.event.stopPropagation()}).on("click",function(v){if(l.event.altKey){t.selectNode(v)}else{if(v.children&&v.children.length===0){return}t.model.toggle(v);t.updateAndRender(v)}});q.attr("transform",function(v){return"translate("+m.y0+","+m.x0+")"});q.append("svg:circle").attr("r",0.000001).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});q.append("svg:text").attr("class","nodeLabel").attr("x",function(v){return v.children||v._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(v){return v.children||v._children?"end":"start"}).style("fill-opacity",0.000001);var r=o.transition().duration(p);r.attr("transform",function(v){return"translate("+v.y+","+v.x+")"});r.select("circle").attr("r",t.defaults.nodeRadius).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});r.select("text").style("fill-opacity",1).style("font-size",u).text(function(v){return v.name});var s=o.exit().transition().duration(p).remove();s.select("circle").attr("r",0.000001);s.select("text").style("fill-opacity",0.000001);n.forEach(function(v){v.x0=v.x;v.y0=v.y})}});var i=Backbone.View.extend({className:"phyloviz",initialize:function(n){var m=this;m.MIN_SCALE=0.05;m.MAX_SCALE=5;m.MAX_DISPLACEMENT=500;m.margins=[10,60,10,80];m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.radius=m.width;m.data=n.data;$(window).resize(function(){m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.render()});m.phyloTree=new b(n.config);m.phyloTree.root=m.data;m.zoomFunc=l.behavior.zoom().scaleExtent([m.MIN_SCALE,m.MAX_SCALE]);m.zoomFunc.translate(m.phyloTree.get("translate"));m.zoomFunc.scale(m.phyloTree.get("scaleFactor"));m.navMenu=new c(m);m.settingsMenu=new h({phyloTree:m.phyloTree});m.nodeSelectionView=new e({phyloTree:m.phyloTree});m.search=new j();setTimeout(function(){m.zoomAndPan()},1000)},render:function(){var n=this;$("#PhyloViz").empty();n.mainSVG=l.select("#PhyloViz").append("svg:svg").attr("width",n.width).attr("height",n.height).attr("pointer-events","all").call(n.zoomFunc.on("zoom",function(){n.zoomAndPan()}));n.boundingRect=n.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",n.width).attr("height",n.height).attr("stroke","black").attr("fill","white");n.vis=n.mainSVG.append("svg:g").attr("class","vis");n.layoutOptions={model:n.phyloTree,width:n.width,height:n.height,vis:n.vis,margins:n.margins};$("#title").text("Phylogenetic Tree from "+n.phyloTree.get("title")+":");var m=new a(n.layoutOptions)},zoomAndPan:function(m){var s,o;if(typeof m!=="undefined"){s=m.zoom;o=m.translate}var v=this,q=v.zoomFunc.scale(),u=v.zoomFunc.translate(),r="",t="";switch(s){case"reset":q=1;u=[0,0];break;case"+":q*=1.1;break;case"-":q*=0.9;break;default:if(typeof s==="number"){q=s}else{if(l.event!==null){q=l.event.scale}}}if(q<v.MIN_SCALE||q>v.MAX_SCALE){return}v.zoomFunc.scale(q);r="translate("+v.margins[3]+","+v.margins[0]+") scale("+q+")";if(l.event!==null){t="translate("+l.event.translate+")"}else{if(typeof o!=="undefined"){var p=o.split(",")[0];var n=o.split(",")[1];if(!isNaN(p)&&!isNaN(n)){u=[u[0]+parseFloat(p),u[1]+parseFloat(n)]}}v.zoomFunc.translate(u);t="translate("+u+")"}v.phyloTree.set("scaleFactor",q);v.phyloTree.set("translate",u);v.vis.attr("transform",t+r)},reloadViz:function(){var n=this,p=$("#phylovizNexSelector :selected").val(),m=n.phyloTree.get("dataset_id"),o="phyloviz/getJsonData?dataset_id="+m+"&treeIndex="+String(p);$.getJSON(o,function(q){window.initPhyloViz(q.data,q.config)})}});var c=Backbone.View.extend({initialize:function(n){var m=this;m.phylovizView=n;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();m.initNavBtns();m.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){m.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var m=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();m.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var n=$("#phylovizNexSelector option:selected").text();if(n){m.phylovizView.phyloTree.set("title",n)}m.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz 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m=this;m.phyloTree=n.phyloTree;m.el=$("#SettingsMenu");m.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){m.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){m.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){m.apply()})},apply:function(){var m=this;if(!m.isAcceptableValue(m.inputs.separation,50,2500)||!m.isAcceptableValue(m.inputs.leafHeight,5,30)||!m.isAcceptableValue(m.inputs.fontSize,5,20)){return}$.each(m.inputs,function(n,o){m.phyloTree.set(n,o.val())})},updateUI:function(){var m=this;$.each(m.inputs,function(n,o){o.val(m.phyloTree.get(n))})},resetToDefaults:function(){$(".bs-tooltip").remove();var m=this;$.each(m.phyloTree.defaults,function(n,o){m.phyloTree.set(n,o)});m.updateUI()},render:function(){}});var e=k.extend({className:"Settings",initialize:function(n){var m=this;m.el=$("#nodeSelectionView");m.phyloTree=n.phyloTree;m.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};m.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){m.el.hide()});m.UI.saveChanges.off().on("click",function(){m.updateNodes()});m.UI.cancelChanges.off().on("click",function(){m.cancelChanges()});(function(o){o.fn.enable=function(p){return o(this).each(function(){if(p){o(this).removeAttr("disabled")}else{o(this).attr("disabled","disabled")}})}})(jQuery);m.UI.enableEdit.off().on("click",function(){m.toggleUI()})},toggleUI:function(){var m=this,n=m.UI.enableEdit.is(":checked");if(!n){m.cancelChanges()}$.each(m.valuesOfConcern,function(o,p){m.UI[o].enable(n)});if(n){m.UI.saveChanges.show();m.UI.cancelChanges.show()}else{m.UI.saveChanges.hide();m.UI.cancelChanges.hide()}},cancelChanges:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){$.each(m.valuesOfConcern,function(o,p){m.UI[o].val(n[o])})}},updateNodes:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){if(!m.isAcceptableValue(m.UI.dist,0,1)||m.hasIllegalJsonCharacters(m.UI.name)||m.hasIllegalJsonCharacters(m.UI.annotation)){return}$.each(m.valuesOfConcern,function(o,p){(n[o])=m.UI[o].val()});m.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var j=k.extend({initialize:function(){var m=this;$("#phyloVizSearchBtn").on("click",function(){var o=$("#phyloVizSearchTerm"),p=$("#phyloVizSearchCondition").val().split("-"),n=p[0],q=p[1];m.hasIllegalJsonCharacters(o);if(n==="dist"){m.isAcceptableValue(o,0,1)}m.searchTree(n,q,o.val())})},searchTree:function(m,o,n){l.selectAll("g.node").classed("searchHighlight",function(q){var p=q[m];if(typeof p!=="undefined"&&p!==null){if(m==="dist"){switch(o){case"greaterEqual":return p>=+n;case"lesserEqual":return p<=+n;default:return}}else{if(m==="name"||m==="annotation"){return p.toLowerCase().indexOf(n.toLowerCase())!==-1}}}})}});return{PhylovizView:i}}); \ No newline at end of file +define(["libs/d3","viz/visualization","mvc/data"],function(m,f,g){var l=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(r,p,n){var o=this,s=r.val(),t=r.attr("displayLabel")||r.attr("id").replace("phyloViz","");function q(u){return !isNaN(parseFloat(u))&&isFinite(u)}if(!q(s)){alert(t+" is not a number!");return false}if(s>n){alert(t+" is too large.");return false}else{if(s<p){alert(t+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(n){if(n.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). 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C=B.dist||p;C=C>1?1:C;B.dist=C;if(z!==null){B.y0=z.y0+C*s}else{B.y0=n}if(!y){B.x0=t++*A}else{y.forEach(function(E){E.parent=B;x+=o(E,D,A,B)});B.x0=x/y.length}B.x=B.x0;B.y=B.y0;return B.x0}return w}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},initialize:function(n){this.set("dataset",new g.Dataset({id:n.dataset_id}))},root:{},toggle:function(n){if(typeof n==="undefined"){return}if(n.children){n._children=n.children;n.children=null}else{n.children=n._children;n._children=null}},toggleAll:function(n){if(n.children&&n.children.length!==0){n.children.forEach(this.toggleAll);toggle(n)}},getData:function(){return this.root},save:function(){var n=this.root;o(n);this.set("root",n);function o(q){delete q.parent;if(q._selected){delete q._selected}if(q.children){q.children.forEach(o)}if(q._children){q._children.forEach(o)}}var p=jQuery.extend(true,{},this.attributes);p.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(p)},success:function(q){var r=q.url.split("id=")[1].split("&")[0],s="/visualization?id="+r;window.history.pushState({},"",s+window.location.hash);hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(o){var n=this;n.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",n.updateAndRender,n);n.vis=o.vis;n.i=0;n.maxDepth=-1;n.width=o.width;n.height=o.height},updateAndRender:function(p){var o=m.select(".vis"),n=this;p=p||n.model.root;n.renderNodes(p);n.renderLinks(p);n.addTooltips()},renderLinks:function(n){var w=this;var o=w.diagonal;var p=w.duration;var r=w.layoutMode;var t=w.vis.selectAll("g.completeLink").data(w.tree.links(w.nodes),function(x){return x.target.id});var v=function(x){x.pos0=x.source.y0+" "+x.source.x0;x.pos1=x.source.y0+" "+x.target.x0;x.pos2=x.target.y0+" "+x.target.x0};var u=t.enter().insert("svg:g","g.node").attr("class","completeLink");u.append("svg:path").attr("class","link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1});var s=t.transition().duration(500);s.select("path.link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1+" L "+x.pos2});var q=t.exit().remove()},selectNode:function(o){var n=this;m.selectAll("g.node").classed("selectedHighlight",function(p){if(o.id===p.id){if(o._selected){delete o._selected;return false}else{o._selected=true;return true}}return false});n.model.set("selectedNode",o);$("#phyloVizSelectedNodeName").val(o.name);$("#phyloVizSelectedNodeDist").val(o.dist);$("#phyloVizSelectedNodeAnnotation").val(o.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var o=this.__data__,n=o.annotation||"None";return o?(o.name?o.name+"<br/>":"")+"Dist: "+o.dist+" <br/>Annotation: "+n:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(o){var n=this;n.margins=o.margins;n.layoutMode="Linear";n.stdInit(o);n.layout();n.updateAndRender(n.model.root)},layout:function(){var n=this;n.tree=new h().layoutMode("Linear");n.diagonal=m.svg.diagonal().projection(function(o){return[o.y,o.x]})},renderNodes:function(n){var u=this,v=u.model.get("fontSize")+"px";u.tree.separation(u.model.get("separation")).leafHeight(u.model.get("leafHeight"));var q=500,o=u.tree.separation(u.model.get("separation")).nodes(u.model.root);var p=u.vis.selectAll("g.node").data(o,function(w){return w.name+w.id||(w.id=++u.i)});u.nodes=o;u.duration=q;var r=p.enter().append("svg:g").attr("class","node").on("dblclick",function(){m.event.stopPropagation()}).on("click",function(w){if(m.event.altKey){u.selectNode(w)}else{if(w.children&&w.children.length===0){return}u.model.toggle(w);u.updateAndRender(w)}});r.attr("transform",function(w){return"translate("+n.y0+","+n.x0+")"});r.append("svg:circle").attr("r",0.000001).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});r.append("svg:text").attr("class","nodeLabel").attr("x",function(w){return w.children||w._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(w){return w.children||w._children?"end":"start"}).style("fill-opacity",0.000001);var s=p.transition().duration(q);s.attr("transform",function(w){return"translate("+w.y+","+w.x+")"});s.select("circle").attr("r",u.defaults.nodeRadius).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});s.select("text").style("fill-opacity",1).style("font-size",v).text(function(w){return w.name});var t=p.exit().transition().duration(q).remove();t.select("circle").attr("r",0.000001);t.select("text").style("fill-opacity",0.000001);o.forEach(function(w){w.x0=w.x;w.y0=w.y})}});var j=Backbone.View.extend({className:"phyloviz",initialize:function(o){var n=this;n.MIN_SCALE=0.05;n.MAX_SCALE=5;n.MAX_DISPLACEMENT=500;n.margins=[10,60,10,80];n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.radius=n.width;n.data=o.data;$(window).resize(function(){n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.render()});n.phyloTree=new b(o.config);n.phyloTree.root=n.data;n.zoomFunc=m.behavior.zoom().scaleExtent([n.MIN_SCALE,n.MAX_SCALE]);n.zoomFunc.translate(n.phyloTree.get("translate"));n.zoomFunc.scale(n.phyloTree.get("scaleFactor"));n.navMenu=new c(n);n.settingsMenu=new i({phyloTree:n.phyloTree});n.nodeSelectionView=new e({phyloTree:n.phyloTree});n.search=new k();setTimeout(function(){n.zoomAndPan()},1000)},render:function(){var o=this;$("#PhyloViz").empty();o.mainSVG=m.select("#PhyloViz").append("svg:svg").attr("width",o.width).attr("height",o.height).attr("pointer-events","all").call(o.zoomFunc.on("zoom",function(){o.zoomAndPan()}));o.boundingRect=o.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",o.width).attr("height",o.height).attr("stroke","black").attr("fill","white");o.vis=o.mainSVG.append("svg:g").attr("class","vis");o.layoutOptions={model:o.phyloTree,width:o.width,height:o.height,vis:o.vis,margins:o.margins};$("#title").text("Phylogenetic Tree from "+o.phyloTree.get("title")+":");var n=new a(o.layoutOptions)},zoomAndPan:function(n){var t,p;if(typeof n!=="undefined"){t=n.zoom;p=n.translate}var w=this,r=w.zoomFunc.scale(),v=w.zoomFunc.translate(),s="",u="";switch(t){case"reset":r=1;v=[0,0];break;case"+":r*=1.1;break;case"-":r*=0.9;break;default:if(typeof t==="number"){r=t}else{if(m.event!==null){r=m.event.scale}}}if(r<w.MIN_SCALE||r>w.MAX_SCALE){return}w.zoomFunc.scale(r);s="translate("+w.margins[3]+","+w.margins[0]+") scale("+r+")";if(m.event!==null){u="translate("+m.event.translate+")"}else{if(typeof p!=="undefined"){var q=p.split(",")[0];var o=p.split(",")[1];if(!isNaN(q)&&!isNaN(o)){v=[v[0]+parseFloat(q),v[1]+parseFloat(o)]}}w.zoomFunc.translate(v);u="translate("+v+")"}w.phyloTree.set("scaleFactor",r);w.phyloTree.set("translate",v);w.vis.attr("transform",u+s)},reloadViz:function(){var n=this,o=$("#phylovizNexSelector :selected").val();$.getJSON(n.phyloTree.get("dataset").url(),{tree_index:o,data_type:"raw_data"},function(p){n.data=p.data;n.config=p;n.render()})}});var c=Backbone.View.extend({initialize:function(o){var n=this;n.phylovizView=o;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();n.initNavBtns();n.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){n.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var n=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();n.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var o=$("#phylovizNexSelector option:selected").text();if(o){n.phylovizView.phyloTree.set("title",o)}n.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("http://wiki.g2.bx.psu.edu/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var n=this,o=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){n.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){n.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){n.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(o.$el)}});var i=l.extend({className:"Settings",initialize:function(o){var n=this;n.phyloTree=o.phyloTree;n.el=$("#SettingsMenu");n.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){n.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){n.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){n.apply()})},apply:function(){var n=this;if(!n.isAcceptableValue(n.inputs.separation,50,2500)||!n.isAcceptableValue(n.inputs.leafHeight,5,30)||!n.isAcceptableValue(n.inputs.fontSize,5,20)){return}$.each(n.inputs,function(o,p){n.phyloTree.set(o,p.val())})},updateUI:function(){var n=this;$.each(n.inputs,function(o,p){p.val(n.phyloTree.get(o))})},resetToDefaults:function(){$(".bs-tooltip").remove();var n=this;$.each(n.phyloTree.defaults,function(o,p){n.phyloTree.set(o,p)});n.updateUI()},render:function(){}});var e=l.extend({className:"Settings",initialize:function(o){var n=this;n.el=$("#nodeSelectionView");n.phyloTree=o.phyloTree;n.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};n.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){n.el.hide()});n.UI.saveChanges.off().on("click",function(){n.updateNodes()});n.UI.cancelChanges.off().on("click",function(){n.cancelChanges()});(function(p){p.fn.enable=function(q){return p(this).each(function(){if(q){p(this).removeAttr("disabled")}else{p(this).attr("disabled","disabled")}})}})(jQuery);n.UI.enableEdit.off().on("click",function(){n.toggleUI()})},toggleUI:function(){var n=this,o=n.UI.enableEdit.is(":checked");if(!o){n.cancelChanges()}$.each(n.valuesOfConcern,function(p,q){n.UI[p].enable(o)});if(o){n.UI.saveChanges.show();n.UI.cancelChanges.show()}else{n.UI.saveChanges.hide();n.UI.cancelChanges.hide()}},cancelChanges:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){$.each(n.valuesOfConcern,function(p,q){n.UI[p].val(o[p])})}},updateNodes:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){if(!n.isAcceptableValue(n.UI.dist,0,1)||n.hasIllegalJsonCharacters(n.UI.name)||n.hasIllegalJsonCharacters(n.UI.annotation)){return}$.each(n.valuesOfConcern,function(p,q){(o[p])=n.UI[p].val()});n.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var k=l.extend({initialize:function(){var n=this;$("#phyloVizSearchBtn").on("click",function(){var p=$("#phyloVizSearchTerm"),q=$("#phyloVizSearchCondition").val().split("-"),o=q[0],r=q[1];n.hasIllegalJsonCharacters(p);if(o==="dist"){n.isAcceptableValue(p,0,1)}n.searchTree(o,r,p.val())})},searchTree:function(n,p,o){m.selectAll("g.node").classed("searchHighlight",function(r){var q=r[n];if(typeof q!=="undefined"&&q!==null){if(n==="dist"){switch(p){case"greaterEqual":return q>=+o;case"lesserEqual":return q<=+o;default:return}}else{if(n==="name"||n==="annotation"){return q.toLowerCase().indexOf(o.toLowerCase())!==-1}}}})}});return{PhylovizView:j}}); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ac,x,l,u,L,aa,i){var q=ac.extend;var Q=l.get_random_color;var ad=function(ae,ag,af){$.ajax({url:ae,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ah){show_modal("Select datasets for new tracks",ah,{Cancel:function(){hide_modal()},Add:function(){var ai=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var aj={data_type:"track_config",hda_ldda:"hda"},ak=$(this).val();if($(this).attr("name")!=="id"){aj.hda_ldda="ldda"}ai[ai.length]=$.ajax({url:ag+"/"+ak,data:aj,dataType:"json"})});$.when.apply($,ai).then(function(){var aj=(arguments[0] instanceof Array?$.map(arguments,function(ak){return ak[0]}):[arguments[0]]);af(aj)});hide_modal()}})}})};var W=function(ae){return("isResolved" in ae)};var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=m;var ab=16,G=9,D=20,A=100,I=12000,T=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",R=10,H=20;function X(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof c){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new f(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var Z=function(ae){q(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;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 x.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ac.extend(Z.prototype,Backbone.Events);q(Z.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);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;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ad(add_datasets_url,add_track_async_url,function(ai){ac.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=w;var ae=this,af=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){ae.add_label_track(new B(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+w+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+w+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-w});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+w});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw();var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){z.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,an){var ak=this,aj=(an?[an]:ak.drawables),ag;var af;for(var ai=0;ai<aj.length;ai++){af=aj[ai];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[ai][1]=ae;ak.tracks_to_be_redrawn[ai][2]=al}}if(!this.requested_redraw){requestAnimationFrame(function(){ak._redraw(am)});this.requested_redraw=true}},_redraw:function(ao){this.requested_redraw=false;var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();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();view.overview_drawable=null}});var s=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],af=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params.push(new e(af,ar,aj,(af in ah?ah[af]:au),an.min,an.max))}else{if(ap==="select"){this.params.push(new N(af,ar,aj,(af in ah?ah[af]:au)))}else{console.log("WARNING: unrecognized tool parameter type:",af,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);ae.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()});if("visible" in ah&&ah.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},state_dict:function(){var af={};for(var ae=0;ae<this.params.length;ae++){af[this.params[ae].name]=this.params[ae].value}af.visible=this.parent_div.is(":visible");return af},get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=ag});return ae},get_param_values:function(){var ae=[];this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();if(af){ae[ae.length]=ag}});return ae},run_on_dataset:function(){var ae=this;ae.run({target_dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(view,ae,{name:ag,hda_ldda:"hda"});ak.init_for_tool_data();ak.change_mode(aj.mode);ak.set_filters_manager(aj.filters_manager.copy(ak));ak.update_icons();ae.add_drawable(ak);ak.tiles_div.text("Starting job.");this.update_params();this.run(af,ak,function(al){ak.set_dataset(new aa.Dataset(al));ak.tiles_div.text("Running job.");ak.init()})},run:function(ae,ag,ah){ae.inputs=this.get_param_values_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(y+ai.message)}else{ah(ai)}}})}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=$(ag);this.value=ah};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ae,af){L.Scaler.call(this,af);this.filter=ae};C.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};q(F.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(am,ai){for(var aq=0;aq<am.length;aq++){ag=am[aq];if(ag.hidden){continue}var ak="param_"+aq;var av=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",ak).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",av))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",ak).val(av).click(function(){$(this).select()}))}else{if(ag.type==="select"){var at=$("<select />").attr("id",ak);for(var ao=0;ao<ag.options.length;ao++){$("<option/>").text(ag.options[ao].label).attr("value",ag.options[ao].value).appendTo(at)}at.val(av);ax.append(at)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),ar=$("<input />").attr("id",ak).attr("name",ak).val(av).css("float","left").appendTo(aw).click(function(az){$(".bs-tooltip").removeClass("in");var ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange();this.track.changed()}}});var b=function(ae,ai,ag,af,ah){this.track=ae;this.region=ai;this.low=ai.get("start");this.high=ai.get("end");this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af).height($(af).attr("height"));this.data=ah;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ae,aj,ag,af,ah,ai){b.call(this,ae,aj,ag,af,ah);this.max_val=ai};q(j.prototype,b.prototype);var O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new x.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?X(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=new aa.Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ac.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ac.map($(".bookmark"),function(ao){return new x.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(v);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){g.call(this,ag,af,ah);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new s(this,ah.tool,ah.tool_state):null);this.tile_cache=new x.Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict: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,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(W(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(W(al)){an=false}}if(an){q(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.after_show_tile(ag)},after_show_tile:function(ae){this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new l.ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var Y=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(Y.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(W(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(W(ap)){ar=false}}an.push(ap)}if(ar){q(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof h){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var h=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{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:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(X(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(X(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var c=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof j){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new j(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){c.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,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=L.ReadPainter};q(S.prototype,r.prototype,M.prototype,c.prototype);var U=function(ag,af,ai){c.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ai.prefs,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=L.ReadPainter;this.update_icons()};q(U.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:S,ReadTrack:U,CompositeTrack:f,DrawableGroup:P};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new d[ah](af,ae,ag)}};return{View:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:U,VcfTrack:S,CompositeTrack:f,object_from_template:p,add_datasets:ad}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ac,x,l,u,L,aa,i){var q=ac.extend;var Q=l.get_random_color;var ad=function(ae,ag,af){$.ajax({url:ae,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ah){show_modal("Select datasets for new tracks",ah,{Cancel:function(){hide_modal()},Add:function(){var ai=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var aj={data_type:"track_config",hda_ldda:"hda"},ak=$(this).val();if($(this).attr("name")!=="id"){aj.hda_ldda="ldda"}ai[ai.length]=$.ajax({url:ag+"/"+ak,data:aj,dataType:"json"})});$.when.apply($,ai).then(function(){var aj=(arguments[0] instanceof Array?$.map(arguments,function(ak){return ak[0]}):[arguments[0]]);af(aj)});hide_modal()}})}})};var W=function(ae){return("isResolved" in ae)};var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=m;var ab=16,G=9,D=20,A=100,I=12000,T=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",R=10,H=20;function X(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof c){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new f(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var Z=function(ae){q(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;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 x.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ac.extend(Z.prototype,Backbone.Events);q(Z.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);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;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ad(add_datasets_url,add_track_async_url,function(ai){ac.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=w;var ae=this,af=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){ae.add_label_track(new B(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+w+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+w+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-w});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+w});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw();var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){z.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,an){var ak=this,aj=(an?[an]:ak.drawables),ag;var af;for(var ai=0;ai<aj.length;ai++){af=aj[ai];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[ai][1]=ae;ak.tracks_to_be_redrawn[ai][2]=al}}if(!this.requested_redraw){requestAnimationFrame(function(){ak._redraw(am)});this.requested_redraw=true}},_redraw:function(ao){this.requested_redraw=false;var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();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();view.overview_drawable=null}});var s=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],af=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params.push(new e(af,ar,aj,(af in ah?ah[af]:au),an.min,an.max))}else{if(ap==="select"){this.params.push(new N(af,ar,aj,(af in ah?ah[af]:au)))}else{console.log("WARNING: unrecognized tool parameter type:",af,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);ae.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()});if("visible" in ah&&ah.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},state_dict:function(){var af={};for(var ae=0;ae<this.params.length;ae++){af[this.params[ae].name]=this.params[ae].value}af.visible=this.parent_div.is(":visible");return af},get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=ag});return ae},get_param_values:function(){var ae=[];this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();if(af){ae[ae.length]=ag}});return ae},run_on_dataset:function(){var ae=this;ae.run({target_dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(view,ae,{name:ag,hda_ldda:"hda"});ak.init_for_tool_data();ak.change_mode(aj.mode);ak.set_filters_manager(aj.filters_manager.copy(ak));ak.update_icons();ae.add_drawable(ak);ak.tiles_div.text("Starting job.");this.update_params();this.run(af,ak,function(al){ak.set_dataset(new aa.Dataset(al));ak.tiles_div.text("Running job.");ak.init()})},run:function(ae,ag,ah){ae.inputs=this.get_param_values_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(y+ai.message)}else{ah(ai)}}})}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=$(ag);this.value=ah};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ae,af){L.Scaler.call(this,af);this.filter=ae};C.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};q(F.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(am,ai){for(var aq=0;aq<am.length;aq++){ag=am[aq];if(ag.hidden){continue}var ak="param_"+aq;var av=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",ak).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",av))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",ak).val(av).click(function(){$(this).select()}))}else{if(ag.type==="select"){var at=$("<select />").attr("id",ak);for(var ao=0;ao<ag.options.length;ao++){$("<option/>").text(ag.options[ao].label).attr("value",ag.options[ao].value).appendTo(at)}at.val(av);ax.append(at)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),ar=$("<input />").attr("id",ak).attr("name",ak).val(av).css("float","left").appendTo(aw).click(function(az){$(".bs-tooltip").removeClass("in");var ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange();this.track.changed()}}});var b=function(ae,ai,ag,af,ah){this.track=ae;this.region=ai;this.low=ai.get("start");this.high=ai.get("end");this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af).height($(af).attr("height"));this.data=ah;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ae,aj,ag,af,ah,ai){b.call(this,ae,aj,ag,af,ah);this.max_val=ai};q(j.prototype,b.prototype);var O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new x.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?X(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=new aa.Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ac.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ac.map($(".bookmark"),function(ao){return new x.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(v);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){g.call(this,ag,af,ah);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new s(this,ah.tool,ah.tool_state):null);this.tile_cache=new x.Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict: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,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(W(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(W(al)){an=false}}if(an){q(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,aj,ak){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ai=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}ae.css({position:"absolute",top:0,left:ai});if(ae.hasClass("remove")){ae.removeClass("remove")}else{aj.append(ae)}ag.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ag.html_elt.height());ag.html_elt.parent().children().css("height",this.max_height_px+"px");var ah=this.max_height_px;if(this.visible_height_px!==0){ah=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ah+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new l.ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var Y=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(Y.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(W(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(W(ap)){ar=false}}an.push(ap)}if(ar){q(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof h){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var h=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{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:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(X(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(X(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var c=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof j){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new j(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){c.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,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=L.ReadPainter};q(S.prototype,r.prototype,M.prototype,c.prototype);var U=function(ag,af,ai){c.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ai.prefs,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=L.ReadPainter;this.update_icons()};q(U.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:S,ReadTrack:U,CompositeTrack:f,DrawableGroup:P};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new d[ah](af,ae,ag)}};return{View:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:U,VcfTrack:S,CompositeTrack:f,object_from_template:p,add_datasets:ad}}); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"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.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=Math.min(s.level-1,2)}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=Math.min(s.level-1,2)}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],add_track:function(s){this.get("tracks").push(s)}});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BackboneTrack:r,BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/compiled/template-visualization-chartSettings.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-chartSettings.js @@ -0,0 +1,42 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-chartSettings'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + + return "checked";} + + buffer += "<p class=\"help-text\">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the 'handle' is in focus, your keyboard's arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n \n <div id=\"maxDataPoints\" class=\"form-input numeric-slider-input\">\n <label for=\"maxDataPoints\">Maximum data points allowed on graph: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.maxDataPoints; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.maxDataPoints; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.datapointSize; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.datapointSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id=\"entryAnimDuration\" class=\"form-input checkbox-input\">\n <label for=\"animated\">Animate graph transitions?: </label>\n <input type=\"checkbox\" id=\"animated\" class=\"checkbox control\" value=\""; + stack1 = depth0.entryAnimDuration; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" />\n <p class=\"form-help help-text-small\">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id=\"width\" class=\"form-input numeric-slider-input\">\n <label for=\"width\">Graph width: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.width; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.width; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"height\" class=\"form-input numeric-slider-input\">\n <label for=\"height\">Graph height: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.height; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.height; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"X-axis-label\"class=\"text-input form-input\">\n <label for=\"X-axis-label\">Re-label the X axis: </label>\n <input type=\"text\" name=\"X-axis-label\" id=\"X-axis-label\" value=\""; + foundHelper = helpers.xLabel; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.xLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <div id=\"Y-axis-label\" class=\"text-input form-input\">\n <label for=\"Y-axis-label\">Re-label the Y axis: </label>\n <input type=\"text\" name=\"Y-axis-label\" id=\"Y-axis-label\" value=\""; + foundHelper = helpers.yLabel; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.yLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <input id=\"render-button\" type=\"button\" value=\"Draw\" />"; + return buffer;}); +})(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js --- a/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js +++ b/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js @@ -32,20 +32,45 @@ buffer += escapeExpression(stack1) + "</option>\n "; return buffer;} +function program5(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <option value=\""; + foundHelper = helpers.index; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</option>\n "; + return buffer;} + + buffer += "\n\n<ul class=\"nav nav-tabs\">\n <li class=\"active\">\n <a data-toggle=\"tab\" href=\"#data-settings\">Data Controls</a>\n </li>\n <li><a data-toggle=\"tab\" href=\"#chart-settings\">Plot Controls</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart-stats\">Statistics</a></li>\n</ul>\n\n"; + buffer += "\n<div class=\"tab-content\">\n<div id=\"data-settings\" class=\"tab-pane active\">\n\n <p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n \n "; + buffer += "\n <div class=\"column-select\">\n <label for=\"X-select\">Data column for X: </label>\n <select name=\"X\" id=\"X-select\">\n "; + stack1 = depth0.numericColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n <div class=\"column-select\">\n <label for=\"Y-select\">Data column for Y: </label>\n <select name=\"Y\" id=\"Y-select\">\n "; + stack1 = depth0.numericColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n \n "; + buffer += "\n <div id=\"include-id\">\n <label for=\"include-id-checkbox\">Include a third column as data point IDs?</label>\n <input type=\"checkbox\" name=\"include-id\" id=\"include-id-checkbox\" />\n <p class=\"help-text-small\">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class=\"column-select\" style=\"display: none\">\n <label for=\"ID-select\">Data column for IDs: </label>\n <select name=\"ID\" id=\"ID-select\">\n "; + stack1 = depth0.allColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n \n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <input id=\"save-button\" type=\"button\" value=\"Download Plot as SVG\" style=\"display: none;\" />\n <div class=\"clear\"></div>\n</div>\n\n<div id=\"chart-settings\" class=\"tab-pane\">\n</div>\n\n<div id=\"chart-stats\" class=\"tab-pane\">\n</div>\n</div>"; + buffer += "\n\n"; buffer += "\n<div id=\"loading-indicator\" style=\"display: none;\">\n <img class=\"loading-img\" src=\""; foundHelper = helpers.loadingIndicatorImagePath; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.loadingIndicatorImagePath; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" />\n <span class=\"loading-message\"></span>\n</div>\n\n"; - buffer += "\n<div id=\"chart-settings\">\n\n "; - buffer += "\n <div id=\"x-column-input\">\n <label for=\"\">Data column for X: </label>\n <select name=\"x-column\">\n "; - stack1 = depth0.availableColumns; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n <div id=\"y-column-input\">\n <label for=\"\">Data column for Y: </label>\n <select name=\"y-column\">\n "; - stack1 = depth0.availableColumns; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n \n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <div class=\"clear\"></div>\n</div>"; + buffer += escapeExpression(stack1) + "\" />\n <span class=\"loading-message\">"; + foundHelper = helpers.message; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span>\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/compiled/template-visualization-statsTable.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-statsTable.js @@ -0,0 +1,31 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-statsTable'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <tr><td>"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td><td>"; + foundHelper = helpers.xval; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.xval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td><td>"; + foundHelper = helpers.yval; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.yval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td></tr>\n </tr>\n "; + return buffer;} + + buffer += "<p class=\"help-text\">By column:</p>\n <table id=\"chart-stats-table\">\n <thead><th></th><th>X</th><th>Y</th></thead>\n "; + stack1 = depth0.stats; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </table>"; + return buffer;}); +})(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/visualization-templates.html --- a/static/scripts/templates/visualization-templates.html +++ b/static/scripts/templates/visualization-templates.html @@ -1,33 +1,155 @@ <script type="text/template" class="template-visualization" id="template-visualization-scatterplotControlForm"> +{{! main controls }} -{{! loading indicator - initially hidden }} -<div id="loading-indicator" style="display: none;"> - <img class="loading-img" src="{{loadingIndicatorImagePath}}" /> - <span class="loading-message"></span> -</div> +<ul class="nav nav-tabs"> + <li class="active"> + <a data-toggle="tab" href="#data-settings">Data Controls</a> + </li> + <li><a data-toggle="tab" href="#chart-settings">Plot Controls</a></li> + <li><a data-toggle="tab" href="#chart-stats">Statistics</a></li> +</ul> -{{! main controls }} -<div id="chart-settings"> +{{! data settings }} +<div class="tab-content"> +<div id="data-settings" class="tab-pane active"> + <p class="help-text"> + Use the following controls to change the data used by the chart. + Use the 'Draw' button to render (or re-render) the chart with the current settings. + </p> + {{! column selector containers }} - <div id="x-column-input"> - <label for="">Data column for X: </label> - <select name="x-column"> - {{#each availableColumns}} + <div class="column-select"> + <label for="X-select">Data column for X: </label> + <select name="X" id="X-select"> + {{#each numericColumns}} <option value="{{index}}">{{name}}</option> {{/each}} </select></div> - <div id="y-column-input"> - <label for="">Data column for Y: </label> - <select name="y-column"> - {{#each availableColumns}} + <div class="column-select"> + <label for="Y-select">Data column for Y: </label> + <select name="Y" id="Y-select"> + {{#each numericColumns}} + <option value="{{index}}">{{name}}</option> + {{/each}} + </select> + </div> + + {{! optional id column }} + <div id="include-id"> + <label for="include-id-checkbox">Include a third column as data point IDs?</label> + <input type="checkbox" name="include-id" id="include-id-checkbox" /> + <p class="help-text-small"> + These will be displayed (along with the x and y values) when you hover over + a data point. + </p> + </div> + <div class="column-select" style="display: none"> + <label for="ID-select">Data column for IDs: </label> + <select name="ID" id="ID-select"> + {{#each allColumns}} <option value="{{index}}">{{name}}</option> {{/each}} </select></div><input id="render-button" type="button" value="Draw" /> + <input id="save-button" type="button" value="Download Plot as SVG" style="display: none;" /><div class="clear"></div></div> + +<div id="chart-settings" class="tab-pane"> +</div> + +<div id="chart-stats" class="tab-pane"> +</div> +</div>{{! class="tab-content" }} + +{{! loading indicator - initially hidden }} +<div id="loading-indicator" style="display: none;"> + <img class="loading-img" src="{{loadingIndicatorImagePath}}" /> + <span class="loading-message">{{message}}</span> +</div> + </script> + +<script type="text/template" class="template-visualization" id="template-visualization-statsTable"> + <p class="help-text">By column:</p> + <table id="chart-stats-table"> + <thead><th></th><th>X</th><th>Y</th></thead> + {{#each stats}} + <tr><td>{{name}}</td><td>{{xval}}</td><td>{{yval}}</td></tr> + </tr> + {{/each}} + </table> +</script> + +<script type="text/template" class="template-visualization" id="template-visualization-chartSettings"> + + <p class="help-text"> + Use the following controls to how the chart is displayed. + The slide controls can be moved by the mouse or, if the 'handle' is in focus, your keyboard's arrow keys. + Move the focus between controls by using the tab or shift+tab keys on your keyboard. + Use the 'Draw' button to render (or re-render) the chart with the current settings. + </p> + + <div id="maxDataPoints" class="form-input numeric-slider-input"> + <label for="maxDataPoints">Maximum data points allowed on graph: </label> + <div class="slider-output">{{maxDataPoints}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + Change the maximum number of data points displayable on this graph (higher values will + load significantly slower) + </p> + </div> + + <div id="datapointSize" class="form-input numeric-slider-input"> + <label for="datapointSize">Size of data point: </label> + <div class="slider-output">{{datapointSize}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + Size of the graphic representation of each data point + </p> + </div> + + <div id="entryAnimDuration" class="form-input checkbox-input"> + <label for="animated">Animate graph transitions?: </label> + <input type="checkbox" id="animated" class="checkbox control" value="{{#if entryAnimDuration}}checked{{/if}}" /> + <p class="form-help help-text-small"> + Uncheck this to disable the animations used on the graph + </p> + </div> + + <div id="width" class="form-input numeric-slider-input"> + <label for="width">Graph width: </label> + <div class="slider-output">{{width}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + (not including graph margins and axes) + </p> + </div> + + <div id="height" class="form-input numeric-slider-input"> + <label for="height">Graph height: </label> + <div class="slider-output">{{height}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + (not including graph margins and axes) + </p> + </div> + + <div id="X-axis-label"class="text-input form-input"> + <label for="X-axis-label">Re-label the X axis: </label> + <input type="text" name="X-axis-label" id="X-axis-label" value="{{xLabel}}" /> + <p class="form-help help-text-small"></p> + </div> + + <div id="Y-axis-label" class="text-input form-input"> + <label for="Y-axis-label">Re-label the Y axis: </label> + <input type="text" name="Y-axis-label" id="Y-axis-label" value="{{yLabel}}" /> + <p class="form-help help-text-small"></p> + </div> + + <input id="render-button" type="button" value="Draw" /> +</script> \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,54 +1,66 @@ define([ + //"../libs/jquery/jquery", + "../libs/underscore", + "../mvc/base-mvc", + "../templates/compiled/template-visualization-scatterplotControlForm", + "../templates/compiled/template-visualization-statsTable", + "../templates/compiled/template-visualization-chartSettings", + "../libs/d3", - "../mvc/base-mvc", - "../templates/compiled/template-visualization-scatterplotControlForm" + "../libs/bootstrap", + "../libs/jquery/jquery-ui-1.8.23.custom.min" ], function(){ + + + /* ============================================================================= todo: outside this: BUG: visualization menu doesn't disappear - BUG?: get column_names (from datatype if necessary) + BUG?: get metadata_column_names (from datatype if necessary) BUG: single vis in popupmenu should have tooltip with that name NOT 'Visualizations' - ??: maybe better to do this with a canvas... + wire label setters, anim setter - move renderScatter plot to obj, possibly view? + TwoVarScatterplot: + ??: maybe better to do this with a canvas... + save as visualization + to seperate file? + remove underscore dependencies + add interface to change values (seperate)? + download svg -> base64 encode + incorporate glyphs, glyph state renderers + + ScatterplotSettingsForm: + some css bug that lowers the width of settings form when plot-controls tab is open + causes chart to shift + what can be abstracted/reused for other graphs? + avoid direct manipulation of this.plot + allow option to put plot into seperate tab of interface (for small multiples) - fix x axis - adjust ticks when tick labels are long - move odds down and extend tick line - - provide callback in view to load data incrementally - for large sets - - paginate - handle rerender - use endpoint (here and on the server (fileptr)) - fetch (new?) data - handle rerender + provide callback in view to load data incrementally - for large sets + paginate + handle rerender + use endpoint (here and on the server (fileptr)) + fetch (new?) data + handle rerender + use d3.TSV? + render warning on long data (> maxDataPoints) + adjust endpoint - selectable list of preset column comparisons (rnaseq etc.) - multiple plots on one page (small multiples) - - where are bad dataprovider params handled? api/datasets? + selectable list of preset column comparisons (rnaseq etc.) + how to know what sort of Tabular the data is? + smarter about headers + validate columns selection (here or server) - config changes to the graph - render stats on the data (max, min, count) - render warning on long data (> maxDataPoints) - adjust endpoint - - loading indicator - - download svg -> base64 encode - dress up ui - - incorporate glyphs, glyph state renderers - - validate columns selection (here or server) - - ?? ensure svg styles thru d3 or css? - d3: configable (easily) - css: standard - better maintenance - ? override at config + Scatterplot.mako: + multiple plots on one page (small multiples) + ?? ensure svg styles thru d3 or css? + d3: configable (easily) + css: standard - better maintenance + ? override at config ============================================================================= */ /** @@ -61,8 +73,7 @@ * depends on: d3, underscore */ function TwoVarScatterplot( config ){ - var plot = this, - TICK_LINE_AND_PADDING = 10, + var TICK_LINE_AND_PADDING = 10, GUESS_AT_SVG_CHAR_WIDTH = 7, GUESS_AT_SVG_CHAR_HEIGHT = 10, PADDING = 8, @@ -73,7 +84,7 @@ if( this.debugging && console && console.debug ){ var args = Array.prototype.slice.call( arguments ); args.unshift( this.toString() ); - console.debug.apply( null, args ); + console.debug.apply( console, args ); } }; this.log( 'new TwoVarScatterplot:', config ); @@ -84,10 +95,10 @@ this.defaults = { id : 'TwoVarScatterplot', containerSelector : 'body', - maxDataPoints : 30000, - bubbleRadius : 4, + maxDataPoints : 10000, + datapointSize : 4, entryAnimDuration : 500, - //TODO: no effect? + //TODO: variable effect (not always exactly # of ticks set to) xNumTicks : 10, yNumTicks : 10, xAxisLabelBumpY : 40, @@ -99,10 +110,12 @@ marginRight : 50, marginBottom : 50, marginLeft : 50, + xMin : null, xMax : null, yMin : null, yMax : null, + xLabel : "X", yLabel : "Y" }; @@ -126,8 +139,9 @@ // ........................................................ initial element creation //NOTE: called on new this.svg = d3.select( this.config.containerSelector ) - .append( "svg:svg" ).attr( "class", "chart" ).style( 'display', 'none' ); - this.content = this.svg.append( "svg:g" ).attr( "class", "content" ); + .append( "svg:svg" ).attr( "class", "chart" ); + + this.content = this.svg.append( "svg:g" ).attr( "class", "content" ).attr( 'id', this.config.id ); this.xAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ); this.xAxisLabel = this.xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ); @@ -157,7 +171,9 @@ }; // ........................................................ data and scales - this.preprocessData = function( data ){ + this.preprocessData = function( data, min, max ){ + //TODO: filter by min, max if set + // set a cap on the data, limit to first n points return ( data.length > this.config.maxDataPoints )? ( data.slice( 0, this.config.maxDataPoints ) ): ( data ); }; @@ -313,63 +329,110 @@ }; - this.renderDatapoints = function( xCol, yCol ){ + this.renderDatapoints = function( xCol, yCol, ids ){ + // initial render, complete re-render (REPLACE datapoints) - var xPosFn = function( d, i ){ - return plot.xScale( xCol[ i ] ); - }; - var yPosFn = function( d, i ){ - return plot.yScale( yCol[ i ] ); - }; - - // select all existing glyphs and compare to incoming data - // enter() will yield those glyphs that need to be added - // exit() will yield existing glyphs that need to be removed - this.datapoints = this.content.selectAll( ".glyph" ) - .data( xCol ); - - // enter - new data to be added as glyphs: give them a 'entry' position and style - this.datapoints.enter() - .append( "svg:circle" ).attr( "class", "glyph" ) - // start all bubbles at corner... - .attr( "cx", xPosFn ) - .attr( "cy", 0 ) - .attr( "r", 0 ); - - // for all existing glyphs and those that need to be added: transition anim to final state - this.datapoints - // ...animate to final position - .transition().duration( this.config.entryAnimDuration ) - .attr( "cx", xPosFn ) - .attr( "cy", yPosFn ) - .attr( "r", this.config.bubbleRadius ); + this.datapoints = this.addDatapoints( xCol, yCol, ids, ".glyph" ); // glyphs that need to be removed: transition to from normal state to 'exit' state, remove from DOM this.datapoints.exit() .transition().duration( this.config.entryAnimDuration ) .attr( "cy", this.config.height ) .attr( "r", 0 ) - .style( "fill-opacity", 0 ) .remove(); - //this.log( this.datapoints, 'glyphs rendered' ); + this.log( this.datapoints, 'glyphs rendered' ); + }; + + this.addDatapoints = function( newXCol, newYCol, ids, selectorForExisting ){ + // ADD datapoints to plot that's already rendered + // if selectorForExisting === undefined (as in not passed), addDatapoints won't update existing + // pass in the class ( '.glyph' ) to update exising datapoints + var plot = this, + xPosFn = function( d, i ){ + return plot.xScale( newXCol[ i ] ); + }, + yPosFn = function( d, i ){ + return plot.yScale( newYCol[ i ] ); + }; + + // select all existing glyphs and compare to incoming data + // enter() will yield those glyphs that need to be added + var newDatapoints = this.content.selectAll( selectorForExisting ).data( newXCol ); + + // enter - new data to be added as glyphs: give them a 'entry' position and style + newDatapoints.enter() + .append( "svg:circle" ) + .classed( "glyph", true ) + // start all bubbles small... + .attr( "cx", xPosFn ) + .attr( "cy", yPosFn ) + .attr( "r", 0 ); + + // for all existing glyphs and those that need to be added: transition anim to final state + newDatapoints + // ...animate to final position + .transition().duration( this.config.entryAnimDuration ) + .attr( "r", this.config.datapointSize ); + + // attach ids + if( ids ){ + newDatapoints.attr( 'data', function( d, i ){ return ( ids[ i ] ); } ); + } + + // titles + newDatapoints.attr( 'title', function( d, i ){ + return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; + }); + + // events + newDatapoints + //TODO: remove magic numbers + .on( 'mouseover', function(){ + var datapoint = d3.select( this ); + datapoint + .style( 'fill', 'red' ) + .style( 'fill-opacity', 1 ); + + // create horiz, vert lines to axis + plot.content.append( 'line' ) + .attr( 'stroke', 'red' ) + .attr( 'stroke-width', 1 ) + .attr( 'x1', datapoint.attr( 'cx' ) ).attr( 'y1', datapoint.attr( 'cy' ) ) + .attr( 'x2', 0 ).attr( 'y2', datapoint.attr( 'cy' ) ) + .classed( 'hoverline', true ); + plot.content.append( 'line' ) + .attr( 'stroke', 'red' ) + .attr( 'stroke-width', 1 ) + .attr( 'x1', datapoint.attr( 'cx' ) ).attr( 'y1', datapoint.attr( 'cy' ) ) + .attr( 'x2', datapoint.attr( 'cx' ) ).attr( 'y2', plot.config.height ) + .classed( 'hoverline', true ); + }) + .on( 'mouseout', function(){ + d3.select( this ) + .style( 'fill', 'black' ) + .style( 'fill-opacity', 0.2 ); + + d3.selectAll( '.hoverline' ).remove(); + }); + + return newDatapoints; }; this.render = function( columnData, meta ){ //pre: columns passed are numeric //pre: at least two columns are passed - //assume: first column is x, second column is y, any remaining aren't used + //assume: first column is x, second column is y, any remaining aren't used var xCol = columnData[0], - yCol = columnData[1]; + yCol = columnData[1], + ids = ( columnData.length > 2 )?( columnData[2] ):( undefined ); this.log( 'renderScatterplot', xCol.length, yCol.length, this.config ); //pre: xCol.len == yCol.len - //TODO: ^^ isn't necessarily true with current ColumnDataProvider xCol = this.preprocessData( xCol ); yCol = this.preprocessData( yCol ); //this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); - //TODO: compute min, max on server. this.setUpDomains( xCol, yCol, meta ); this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); @@ -380,28 +443,31 @@ this.setUpYAxis(); this.renderGrid(); - this.renderDatapoints( xCol, yCol ); - //TODO: on hover red line to axes, display values + this.renderDatapoints( xCol, yCol, ids ); }; } //============================================================================== /** * Scatterplot control UI as a backbone view - * + * handles: + * getting the desired data + * configuring the plot display */ var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ //logger : console, tagName : 'form', className : 'scatterplot-settings-form', - loadingIndicatorImagePath : ( galaxy_paths.get( 'image_path' ) + '/loading_large_white_bg.gif' ), + loadingIndicatorImage : 'loading_large_white_bg.gif', events : { - 'click #render-button' : 'renderScatterplot' + 'click #render-button' : 'renderPlot', + 'click #include-id-checkbox' : 'toggleThirdColumnSelector' }, initialize : function( attributes ){ + if( !attributes || !attributes.dataset ){ throw( "ScatterplotView requires a dataset" ); } else { @@ -414,106 +480,230 @@ // set up the basic chart infrastructure with config (if any) this.chartConfig = attributes.chartConfig || {}; - this.log( 'this.chartConfig:', this.chartConfig ); + this.log( 'initial chartConfig:', this.chartConfig ); this.plot = new TwoVarScatterplot( this.chartConfig ); + this.chartConfig = this.plot.config; + + this.$statsPanel = null; + this.$chartSettingsPanel = null; + this.$dataSettingsPanel = null; + this.dataFetch = null; }, render : function(){ var view = this, - html = ''; + formData = { + config : this.chartConfig, + allColumns : [], + numericColumns : [], + loadingIndicatorImagePath : galaxy_paths.get( 'image_path' ) + '/' + this.loadingIndicatorImage + }; + + // gather column indeces (from metadata_column_types) and names (from metadata_columnnames) + _.each( this.dataset.metadata_column_types.split( ', ' ), function( type, index ){ + //TODO: using 0-based indeces + // label with the name if available (fall back on 'column <index>') + var name = 'column ' + ( index + 1 ); + if( view.dataset.metadata_column_names ){ + name = view.dataset.metadata_column_names[ index ]; + } - // build column select controls for each x, y (based on name if available) - var formData = { - loadingIndicatorImagePath : this.loadingIndicatorImagePath, - config : this.chartConfig, - availableColumns : [] - }; - _.each( this.dataset.metadata_column_types.split( ', ' ), function( type, index ){ - // use only numeric columns + // filter numeric columns to their own list if( type === 'int' || type === 'float' ){ - //TODO: using 0-based indeces - var name = 'column ' + index; - // label with the name if available - if( view.dataset.metadata_column_names ){ - name = view.dataset.metadata_column_names[ index ]; - } - formData.availableColumns.push({ index: index, name: name }); + formData.numericColumns.push({ index: index, name: name }); } + formData.allColumns.push({ index: index, name: name }); }); - //TODO: other vals: max_vals, start_val, pagination - html = ScatterplotControlForm.templates.form( formData ); - this.$el.append( html ); + //TODO: other vals: max_vals, start_val, pagination (plot-settings) + + this.$el.append( ScatterplotControlForm.templates.form( formData ) ); + this.$dataSettingsPanel = this.$el.find( '.tab-pane#data-settings' ); + this.$chartSettingsPanel = this._render_chartSettings(); + this.$statsPanel = this.$el.find( '.tab-pane#chart-stats' ); + + this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); return this; }, - showLoadingIndicator : function( message ){ + _render_chartSettings : function(){ + var chartControl = this, + $chartSettingsPanel = this.$el.find( '.tab-pane#chart-settings' ), + // limits for controls (by control/chartConfig id) + controlRanges = { + 'maxDataPoints' : { min: 1000, max: 30000, step: 100 }, + 'datapointSize' : { min: 2, max: 10, step: 1 }, + 'width' : { min: 200, max: 800, step: 20 }, + 'height' : { min: 200, max: 800, step: 20 } + }; + + // render the html + $chartSettingsPanel.append( ScatterplotControlForm.templates.chartSettings( this.chartConfig ) ); + + // set up js on controls + // sliders + $chartSettingsPanel.find( '.numeric-slider-input' ).each( function(){ + var $this = $( this ), + $output = $this.find( '.slider-output' ), + $slider = $this.find( '.slider' ), + id = $this.attr( 'id' ); + chartControl.log( 'slider set up', 'this:', $this, 'slider:', $slider, 'id', id ); + + // what to do when the slider changes: update display and update chartConfig + function onSliderChange(){ + var $this = $( this ), + newValue = $this.slider( 'value' ); + //chartControl.log( 'slider change', 'this:', $this, 'output:', $output, 'value', newValue ); + $output.text( newValue ); + chartControl.chartConfig[ id ] = newValue; + } + + $slider.slider( _.extend( controlRanges[ id ], { + value : chartControl.chartConfig[ id ], + change : onSliderChange, + slide : onSliderChange + })); + }); + + //TODO: anim checkbox + //TODO: labels -> renderPlot + + return $chartSettingsPanel; + }, + + toggleThirdColumnSelector : function(){ + this.$el.find( 'select[name="ID"]' ).parent().toggle(); + }, + + showLoadingIndicator : function( message, callback ){ message = message || ''; - this.$el.find( 'div#loading-indicator' ).children( '.loading-message' ).text( message ); - this.$el.find( 'div#loading-indicator' ).show( 'fast' ); + var indicator = this.$el.find( 'div#loading-indicator' ); + messageBox = indicator.find( '.loading-message' ); + + if( indicator.is( ':visible' ) ){ + if( message ){ + messageBox.fadeOut( 'fast', function(){ + messageBox.text( message ); + messageBox.fadeIn( 'fast', callback ); + }); + } else { + callback(); + } + + } else { + if( message ){ messageBox.text( message ); } + indicator.fadeIn( 'fast', callback ); + } }, - hideLoadingIndicator : function(){ - this.$el.find( 'div#loading-indicator' ).hide( 'fast' ); + hideLoadingIndicator : function( callback ){ + this.$el.find( 'div#loading-indicator' ).fadeOut( 'fast', callback ); }, - renderScatterplot : function(){ + getColumnVals : function(){ + // returns a map: { column-select name (eg. X) : { colIndex : column-selector val, + // colName : selected option text }, ... } + var selections = {}; + this.$el.find( 'div.column-select select' ).each( function(){ + var $this = $( this ), + val = $this.val(); + selections[ $this.attr( 'name' ) ] = { + colIndex : val, + colName : $this.children( '[value="' + val + '"]' ).text() + }; + }); + return selections; + }, + + fetchData : function( params, callbackFn ){ + var view = this, + url = this.apiDatasetsURL + '/' + this.dataset.id + '?data_type=raw_data&' + jQuery.param( params ); + this.log( 'url:', url ); + + this.showLoadingIndicator( 'Fetching data...', function(){ + jQuery.ajax({ + url : url, + dataType : 'json', + success : callbackFn, + error : function( xhr, status, error ){ + view.hideLoadingIndicator(); + alert( 'ERROR:' + status + '\n' + error ); + } + }); + }); + }, + + renderPlot : function(){ // parse the column values for both // indeces (for the data fetch) and names (for the graph) var view = this, - url = this.apiDatasetsURL + '/' + this.dataset.id + '?data_type=raw_data&', + columnSelections = this.getColumnVals(), + columns = []; + this.log( 'columnSelections:', columnSelections ); - xSelector = this.$el.find( '[name="x-column"]' ), - xVal = xSelector.val(), - xName = xSelector.children( '[value="' + xVal + '"]' ).text(), - - ySelector = this.$el.find( '[name="y-column"]' ), - yVal = ySelector.val(), - yName = ySelector.children( '[value="' + yVal + '"]' ).text(); - this.log( xName, yName ); - - this.chartConfig.xLabel = xName; - this.chartConfig.yLabel = yName; + //TODO: ?? could be moved into getColumnVals; + this.log( columnSelections.X.val, columnSelections.Y.val ); + this.xColIndex = columnSelections.X.colIndex; + this.yColIndex = columnSelections.Y.colIndex; + columns = [ this.xColIndex, this.yColIndex ]; + + // include the desired ID column + if( $( '#include-id-checkbox' ).attr( 'checked' ) ){ + columns.push( columnSelections.ID.colIndex ); + } + + this.log( columnSelections.X.colName, columnSelections.Y.colName ); + this.plot.xLabel = this.chartConfig.xLabel = columnSelections.X.colName; + this.plot.xLabel = this.chartConfig.yLabel = columnSelections.Y.colName; //TODO: alter directly - view.plot.updateConfig( this.chartConfig ); - + view.plot.updateConfig( this.chartConfig, false ); //TODO: validate columns - minimally: we can assume either set by selectors or via a good query string //TODO: other vals: max, start, page //TODO: chart config // fetch the data, sending chosen columns to the server - url += jQuery.param({ - columns : '[' + [ xVal, yVal ] + ']' + var params = { + columns : '[' + columns + ']' + }; + + //TODO: prob. better to use events rather than callback chains like this + this.fetchData( params, function( response ){ + // save the endpoint (number of next line, fileptr) for this object + //TODO: server sends back an endpoint, cache for next pagination request + view.dataFetch = response; + view.showLoadingIndicator( 'Rendering...', function(){ + view.plot.render( response.data, response.meta ); + + view.renderStats( response.data, response.meta ); + view.$el.find( 'ul.nav' ).find( 'a[href="#chart-stats"]' ).tab( 'show' ); + + view.hideLoadingIndicator(); + }); }); - this.log( 'url:', url ); - - this.showLoadingIndicator( 'Fetching data...' ); - jQuery.ajax({ - url : url, - dataType : 'json', - success : function( response ){ - // save the endpoint (number of next line, fileptr) for this object - //TODO: server sends back an endpoint, cache for next pagination request - view.endpoint = response.endpoint; - - view.showLoadingIndicator( 'Rendering...' ); - view.plot.render( response.data, response.meta ); - view.hideLoadingIndicator(); - }, - - error : function( xhr, status, error ){ - view.hideLoadingIndicator(); - alert( 'ERROR:' + status + '\n' + error ); - } - }); + }, + + renderStats : function(){ + this.$statsPanel.html( ScatterplotControlForm.templates.statsTable({ + stats: [ + { name: 'Count', xval: this.dataFetch.meta[0].count, yval: this.dataFetch.meta[1].count }, + { name: 'Min', xval: this.dataFetch.meta[0].min, yval: this.dataFetch.meta[1].min }, + { name: 'Max', xval: this.dataFetch.meta[0].max, yval: this.dataFetch.meta[1].max }, + { name: 'Mean', xval: this.dataFetch.meta[0].mean, yval: this.dataFetch.meta[1].mean }, + { name: 'Median', xval: this.dataFetch.meta[0].median, yval: this.dataFetch.meta[1].median } + ] + })); + }, + + toString : function(){ + return 'ScatterplotControlForm(' + attributes.dataset.id + ')'; } }); -ScatterplotControlForm.templates = CompiledTemplateLoader.getTemplates({ - 'visualization-templates.html' : { - form : 'template-visualization-scatterplotControlForm' - } -}); +ScatterplotControlForm.templates = { + form : Handlebars.templates[ 'template-visualization-scatterplotControlForm' ], + statsTable : Handlebars.templates[ 'template-visualization-statsTable' ], + chartSettings : Handlebars.templates[ 'template-visualization-chartSettings' ] +}; //============================================================================== return { diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -2,18 +2,45 @@ <%def name="stylesheets()"> ${parent.stylesheets()} +${h.css( + "base", + "autocomplete_tagging", + "jquery-ui/smoothness/jquery-ui-1.8.23.custom" +)} <style type="text/css"> /*TODO: use/move into base.less*/ * { margin: 0px; padding: 0px; } + +/* -------------------------------------------- layout */ +.column { + position:relative; + overflow: auto; +} + +.left-column { + float: left; + width: 30%; +} + +.right-column { + margin-left: 32%; +} + +div.tab-pane { + padding: 8px; +} + +/* -------------------------------------------- header */ +.header { + margin-bottom: 8px; +} + #chart-header { padding : 8px; background-color: #ebd9b2; } -.title { -} - #chart-header .subtitle { margin: -4px 0px 0px 4px; padding : 0; @@ -21,33 +48,121 @@ font-size: small; } +/* -------------------------------------------- all controls */ #chart-settings-form { /*from width + margin of chart?*/ - float: right; - width: 100%; - margin: 0px; padding-top: 1em; } -#chart-settings > * { - margin: 8px; +#chart-settings-form input[type=button], +#chart-settings-form select { + width: 100%; + max-width: 256px; + margin-bottom: 8px; } -#chart-settings-form input, #chart-settings-form select { - width: 30%; - max-width: 256px; +#chart-settings-form .help-text, +#chart-settings-form .help-text-small { + color: grey; } -#chart-holder { - overflow: auto; +#chart-settings-form .help-text { + padding-bottom: 16px; +} + +#chart-settings-form .help-text-small { + padding: 4px; + font-size: smaller; +} + +#chart-settings-form > * { +} + +#chart-settings-form input[value=Draw] { + display: block; + margin-top: 16px; +} + +/* -------------------------------------------- data controls */ + +/* -------------------------------------------- chart controls */ +#chart-settings .form-input { + /*display: table-row;*/ +} + +#chart-settings label { + /*text-align: right;*/ + margin-bottom: 8px; + /*display: table-cell;*/ +} + +#chart-settings .slider { + /*display: table-cell;*/ + height: 8px; + display: block; + margin: 8px 0px 0px 8px; +} + +#chart-settings .slider-output { + /*display: table-cell;*/ + float: right; +} + +#chart-settings input[type="text"] { + border: 1px solid lightgrey; +} + + +/* -------------------------------------------- statistics */ +#chart-stats table#chart-stats-table { + width: 100%; +} + +#chart-stats #chart-stats-table th { + width: 30%; + padding: 4px; + font-weight: bold; + color: grey; +} + +#chart-stats #chart-stats-table td { + border: solid lightgrey; + border-width: 1px 0px 0px 1px; + padding: 4px; +} + +#chart-stats #chart-stats-table td:nth-child(1) { + border-width: 1px 0px 0px 0px; + padding-right: 1em; + text-align: right; + font-weight: bold; + color: grey; +} + +/* -------------------------------------------- load indicators */ +#loading-indicator { + z-index: 2; + position: absolute; + top: 0; + bottom: 0; + left: 0; + right: 0; + background-color: white; + padding: 32px 0 0 32px; } #chart-settings-form #loading-indicator .loading-message { - margin-left: 16px; + margin-left: 10px; font-style: italic; color: grey; } +/* -------------------------------------------- chart area */ +#chart-holder { + overflow: auto; + margin-left: 8px; +} + svg .grid-line { fill: none; stroke: lightgrey; @@ -94,8 +209,6 @@ var hda = ${h.to_json_string( hda )}, historyID = '${historyID}' apiDatasetsURL = "${h.url_for( controller='/api/datasets' )}"; - //?? hmmmm - //kwargs = ${h.to_json_string( kwargs )}; var settingsForm = new scatterplot.ScatterplotControlForm({ dataset : hda, @@ -113,10 +226,20 @@ </%def><%def name="body()"> - <div id="chart-header"> +  + <div id="chart-header" class="header"><h2 class="title">Scatterplot of '${hda['name']}'</h2><p class="subtitle">${hda['misc_info']}</p></div> - <div id="chart-holder"></div> - <div id="chart-settings-form"></div> + <div class="outer-container"> +  + <div id="chart-settings-form" class="column left-column"></div> +  + <div class="column right-column"> + <div id="chart-holder" class="inner-container"></div> + </div> + <div style="clear: both;"></div> + </div> + <div id="test"></div> + </%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 6 new changesets
by Bitbucket 10 Oct '12

10 Oct '12

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/87641aaefe47/ changeset: 87641aaefe47 user: chapmanb date: 2012-10-08 11:32:54 summary: Consistently return list of users from users/index for case where API user is not an admin affected #: 1 file diff -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 -r 87641aaefe47d1892bbbd4a7ea56cc21cab9d68c lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -33,7 +33,7 @@ if not trans.user_is_admin(): item = trans.user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) - return item + return [item] for user in query: item = user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) https://bitbucket.org/galaxy/galaxy-central/changeset/9abbec24c356/ changeset: 9abbec24c356 user: chapmanb date: 2012-10-08 12:25:49 summary: Provide retrieval of the current user and user history via the API affected #: 2 files diff -r 87641aaefe47d1892bbbd4a7ea56cc21cab9d68c -r 9abbec24c3566393b05a0744941361fbfba1a968 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -48,6 +48,7 @@ """ GET /api/histories/{encoded_history_id} GET /api/histories/deleted/{encoded_history_id} + GET /api/histories/current Displays information about a history. """ history_id = id @@ -65,8 +66,13 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) + if history_id == "current" and len(trans.user.galaxy_sessions) > 0: + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history + else: + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: + raise return str( e ) try: item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) diff -r 87641aaefe47d1892bbbd4a7ea56cc21cab9d68c -r 9abbec24c3566393b05a0744941361fbfba1a968 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -45,11 +45,15 @@ """ GET /api/users/{encoded_user_id} GET /api/users/deleted/{encoded_user_id} + GET /api/users/current Displays information about a user. """ deleted = util.string_as_bool( deleted ) try: - user = self.get_user( trans, id, deleted=deleted ) + if id == "current": + user = trans.user + else: + user = self.get_user( trans, id, deleted=deleted ) if not trans.user_is_admin(): assert trans.user == user assert not user.deleted https://bitbucket.org/galaxy/galaxy-central/changeset/f5772000c6d9/ changeset: f5772000c6d9 user: chapmanb date: 2012-10-08 12:27:29 summary: Remove extra debugging statement affected #: 1 file diff -r 9abbec24c3566393b05a0744941361fbfba1a968 -r f5772000c6d9ea5d15b1332f2ea42330e645371d lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -72,7 +72,6 @@ else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: - raise return str( e ) try: item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) https://bitbucket.org/galaxy/galaxy-central/changeset/2bfdbe09caf7/ changeset: 2bfdbe09caf7 user: chapmanb date: 2012-10-09 11:39:15 summary: Defensively check for user and histories before retrieving current history from API affected #: 1 file diff -r f5772000c6d9ea5d15b1332f2ea42330e645371d -r 2bfdbe09caf7fd1e49fb5fcdfbb1665764ed39ed lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -66,9 +66,12 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - if history_id == "current" and len(trans.user.galaxy_sessions) > 0: - # Most recent active history for user sessions, not deleted - history = trans.user.galaxy_sessions[0].histories[-1].history + if history_id == "current": + if trans.user and len(trans.user.galaxy_sessions) > 0: + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history + else: + history = None else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: https://bitbucket.org/galaxy/galaxy-central/changeset/e7178dd7f9db/ changeset: e7178dd7f9db user: chapmanb date: 2012-10-10 12:53:33 summary: Rename history retrieval to reflect multiple sessions: most_recently_used affected #: 1 file diff -r 2bfdbe09caf7fd1e49fb5fcdfbb1665764ed39ed -r e7178dd7f9dbb22c880627c2fb9c05cb696392cf lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -48,7 +48,7 @@ """ GET /api/histories/{encoded_history_id} GET /api/histories/deleted/{encoded_history_id} - GET /api/histories/current + GET /api/histories/most_recently_used Displays information about a history. """ history_id = id @@ -66,7 +66,7 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - if history_id == "current": + if history_id == "most_recently_used": if trans.user and len(trans.user.galaxy_sessions) > 0: # Most recent active history for user sessions, not deleted history = trans.user.galaxy_sessions[0].histories[-1].history https://bitbucket.org/galaxy/galaxy-central/changeset/666e873a21a0/ changeset: 666e873a21a0 user: jgoecks date: 2012-10-10 15:43:15 summary: Merged in chapmanb/galaxy-central-apicurrent (pull request #77) affected #: 2 files diff -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -48,6 +48,7 @@ """ GET /api/histories/{encoded_history_id} GET /api/histories/deleted/{encoded_history_id} + GET /api/histories/most_recently_used Displays information about a history. """ history_id = id @@ -65,7 +66,14 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) + if history_id == "most_recently_used": + if trans.user and len(trans.user.galaxy_sessions) > 0: + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history + else: + history = None + else: + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: return str( e ) try: diff -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -33,7 +33,7 @@ if not trans.user_is_admin(): item = trans.user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) - return item + return [item] for user in query: item = user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) @@ -45,11 +45,15 @@ """ GET /api/users/{encoded_user_id} GET /api/users/deleted/{encoded_user_id} + GET /api/users/current Displays information about a user. """ deleted = util.string_as_bool( deleted ) try: - user = self.get_user( trans, id, deleted=deleted ) + if id == "current": + user = trans.user + else: + user = self.get_user( trans, id, deleted=deleted ) if not trans.user_is_admin(): assert trans.user == user assert not user.deleted 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: Create and use mixin method for getting dataset's genome data.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/220b6683e8da/ changeset: 220b6683e8da user: jgoecks date: 2012-10-10 05:49:01 summary: Create and use mixin method for getting dataset's genome data. affected #: 4 files diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -186,7 +186,6 @@ chrom_data = self.get_data( chrom, 0, chrom_len, **kwargs ) if chrom_data: chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len ) - chrom_data[ 'dataset_type' ] = self.dataset_type genome_data.append( chrom_data ) return { diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -602,6 +602,33 @@ return visualization + def _get_genome_data( self, trans, dataset, dbkey=None ): + """ + Returns genome-wide data for dataset if available; if not, message is returned. + """ + rval = None + + # Get data sources. + data_sources = dataset.get_datasources( trans ) + query_dbkey = dataset.dbkey + if query_dbkey == "?": + query_dbkey = dbkey + chroms_info = self.app.genomes.chroms( trans, dbkey=query_dbkey ) + + # If there are no messages (messages indicate data is not ready/available), preload data. + messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] + message = get_highest_priority_msg( messages_list ) + if message: + rval = message + else: + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, + source='index' ) + # HACK: pass in additional params, which are only used for summary tree data, not BBI data. + rval = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + + return rval + class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -51,6 +51,8 @@ rval = self._raw_data( trans, dataset, **kwd ) elif data_type == 'track_config': rval = self.get_new_track_config( trans, dataset ) + elif data_type == 'genome_data': + rval = self._get_genome_data( self, trans, dataset, kwd.get('dbkey', None) ) else: # Default: return dataset as API value. rval = dataset.get_api_value() diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -772,18 +772,10 @@ # Add genome-wide summary tree data to each track in viz. tracks = viz_config.get( 'tracks', [] ) for track in tracks: - # Get dataset and data sources. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) - data_sources = dataset.get_datasources( trans ) - - # If there are no messages (messages indicate data is not ready/available), preload data. - messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - if not get_highest_priority_msg( messages_list ): - data_provider = trans.app.data_provider_registry.get_data_provider( trans, - original_dataset=dataset, - source='index' ) - # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + genome_data = self._get_genome_data( trans, dataset, dbkey ) + if not isinstance( genome_data, str ): + track[ 'preloaded_data' ] = genome_data return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) 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: carlfeberhard: history.js: fix to HistoryView tagging functionality
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3231b9ca8d82/ changeset: 3231b9ca8d82 user: carlfeberhard date: 2012-10-10 01:10:30 summary: history.js: fix to HistoryView tagging functionality affected #: 4 files diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -558,6 +558,14 @@ parent.append( this._render_displayApps() ); parent.append( this._render_peek() ); + + //TODO??: still needed? + //// If Mozilla, hide scrollbars in hidden items since they cause animation bugs + //if ( $.browser.mozilla ) { + // $( "div.historyItemBody" ).each( function() { + // if ( !$(this).is(":visible") ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); } + // }); + //} }, _render_body : function(){ @@ -704,7 +712,13 @@ toggleBodyVisibility : function( visible ){ var $body = this.$el.find( '.historyItemBody' ); - $body.toggle(); + if( visible === undefined ){ + $body.toggle(); + } else if( visible ){ + $body.show(); + } else { + $body.hide(); + } this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), $body.is( ':visible' ) ); }, @@ -715,9 +729,7 @@ } }); - //------------------------------------------------------------------------------ -//HistoryItemView.templates = InDomTemplateLoader.getTemplates({ HistoryItemView.templates = { warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], @@ -875,7 +887,6 @@ //------------------------------------------------------------------------------ // view for the HistoryCollection (as per current right hand panel) -//var HistoryView = BaseView.extend( LoggableMixin ).extend( UsesStorageMixin ) .extend({ var HistoryView = BaseView.extend( LoggableMixin ).extend({ // uncomment this out see log messages @@ -894,16 +905,20 @@ ); // set up the individual history items/datasets this.initializeItems(); + }, initializeItems : function(){ this.itemViews = {}; var historyPanel = this; + + // set up a view for each item, init with model and listeners, cache to map ( model.id : view ) this.model.items.each( function( item ){ var itemId = item.get( 'id' ), + visible = historyPanel.storage.get( 'visibleItems' ).get( itemId ), itemView = new HistoryItemView({ - model: item, visible: - historyPanel.storage.get( 'visibleItems' ).get( itemId ) + model: item, + visible: visible }); historyPanel.setUpItemListeners( itemView ); historyPanel.itemViews[ itemId ] = itemView; @@ -912,6 +927,7 @@ setUpItemListeners : function( itemView ){ var HistoryPanel = this; + // use storage to maintain a list of items whose bodies are visible itemView.bind( 'toggleBodyVisibility', function( id, visible ){ if( visible ){ @@ -930,7 +946,34 @@ this.itemsDiv = this.$el.find( '#' + this.model.get( 'id' ) + '-datasets' ); //TODO: set up widgets, tooltips, etc. + async_save_text( + "history-name-container", + "history-name", + this.model.get( 'renameURL' ), + "new_name", + 18 + ); + this.$el.find( '.tooltip' ).tooltip(); + var historyAnnotationArea = this.$el.find( '#history-annotation-area' ); + $( '#history-annotate' ).click( function() { + if ( historyAnnotationArea.is( ":hidden" ) ) { + historyAnnotationArea.slideDown( "fast" ); + } else { + historyAnnotationArea.slideUp( "fast" ); + } + return false; + }); + async_save_text( + "history-annotation-container", + "history-annotation", + this.model.get( 'annotateURL' ), + "new_annotation", + 18, + true, + 4 + ); + if( this.model.items.length ){ // render to temp, move all at once, remove temp holder var tempDiv = this._render_items(); @@ -950,6 +993,53 @@ return div; }, + events : { + 'click #history-collapse-all' : 'hideAllItemBodies', + 'click #history-tag' : 'loadAndDisplayTags' + }, + + hideAllItemBodies : function(){ + _.each( this.itemViews, function( item ){ + item.toggleBodyVisibility( false ); + }); + }, + + loadAndDisplayTags : function( event ){ + //BUG: broken with latest + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this + '.loadAndDisplayTags', event ); + var tagArea = this.$el.find( '#history-tag-area' ), + tagElt = tagArea.find( '.tag-elt' ); + this.log( '\t tagArea', tagArea, ' tagElt', tagElt ); + + // Show or hide tag area; if showing tag area and it's empty, fill it. + if( tagArea.is( ":hidden" ) ){ + if( !jQuery.trim( tagElt.html() ) ){ + var view = this; + // Need to fill tag element. + $.ajax({ + //TODO: the html from this breaks a couple of times + url: this.model.get( 'tagURL' ), + error: function() { alert( "Tagging failed" ); }, + success: function(tag_elt_html) { + view.log( view + ' tag elt html (ajax)', tag_elt_html ); + tagElt.html(tag_elt_html); + tagElt.find(".tooltip").tooltip(); + tagArea.slideDown("fast"); + } + }); + } else { + // Tag element is filled; show. + tagArea.slideDown("fast"); + } + + } else { + // Hide. + tagArea.slideUp("fast"); + } + return false; + }, + toString : function(){ var nameString = this.model.get( 'name' ) || ''; return 'HistoryView(' + nameString + ')'; diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -23,21 +23,13 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\""; - foundHelper = helpers.tagURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.tagURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"></a>\n <a id=\"history-annotate\" title=\""; + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\""; - foundHelper = helpers.annotateURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.annotateURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"></a>\n </div>\n "; + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; return buffer;} function program6(depth0,data) { @@ -143,9 +135,9 @@ var buffer = "", stack1; buffer += "\n"; - buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <b>Tags:</b>\n "; + buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n "; buffer += "\n "; - buffer += "\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + buffer += "\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; stack1 = depth0.annotation; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } @@ -228,7 +220,7 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "' class='icon-button toggle tooltip' href='#' style=\"display: none\"></a>\n "; + buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n "; stack1 = depth0.userRoles; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } @@ -252,7 +244,6 @@ if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; buffer += "\n"; - buffer += "\n"; stack1 = depth0.userRoles; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -103,13 +103,14 @@ <script type="text/template" class="template-history" id="template-history-historyPanel"><div id="top-links" class="historyLinks"><a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{baseURL}}"></a> - <a title='{{#local}}collapse all{{/local}}' class='icon-button toggle tooltip' href='#' style="display: none"></a> + <a title='{{#local}}collapse all{{/local}}' id="history-collapse-all" + class='icon-button toggle tooltip' href='javascript:void(0);'></a> {{#if userRoles}} <div style="width: 40px; float: right; white-space: nowrap;"><a id="history-tag" title="{{#local}}Edit history tags{{/local}}" - class="icon-button tags tooltip" target="galaxy_main" href="{{tagURL}}"></a> + class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a><a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" - class="icon-button annotate tooltip" target="galaxy_main" href="{{annotateURL}}"></a> + class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a></div> {{/if}} </div> @@ -148,15 +149,15 @@ {{/if}} {{! tags and annotations }} -{{! TODO: wire these to js events }} {{#if userRoles}} {{! TODO: move inline styles out }} <div style="margin: 0px 5px 10px 5px"><div id="history-tag-area" style="display: none"> - <b>Tags:</b> {{! load via js render_individual_tagging_element }} {{! render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") }} + <strong>Tags:</strong> + <div class="tag-elt"></div></div><div id="history-annotation-area" style="display: none"> @@ -202,6 +203,3 @@ </div> {{/if}} </script> - - - diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -291,9 +291,10 @@ ##TODO: move to API for_editing = True + encoded_history_id = trans.security.encode_id( history.id ) context_dict = { 'history' : { - 'id' : trans.security.encode_id( history.id ), + 'id' : encoded_history_id, 'name' : history.name, 'status' : status, @@ -324,11 +325,13 @@ 'annotation' : h.to_unicode( annotation ), ##TODO: broken - 'baseURL' : h.url_for( 'history', show_deleted=show_deleted ), - 'hideDeletedURL' : h.url_for( 'history', show_deleted=False ), - 'hideHiddenURL' : h.url_for( 'history', show_hidden=False ), - 'tagURL' : h.url_for( controller='history', action='tag' ), - 'annotateURL' : h.url_for( controller='history', action='annotate' ) + 'baseURL' : h.url_for( controller="/history", show_deleted=show_deleted ), + 'hideDeletedURL' : h.url_for( controller="/history", show_deleted=False ), + 'hideHiddenURL' : h.url_for( controller="/history", show_hidden=False ), + 'renameURL' : h.url_for( controller="/history", action="rename_async", id=encoded_history_id ), + 'tagURL' : h.url_for( controller='tag', action='get_tagging_elt_async', + item_class=history.__class__.__name__, item_id=encoded_history_id ), + 'annotateURL' : h.url_for( controller="/history", action="annotate_async", id=encoded_history_id ) }, 'hdas' : [ prep_hda( hda, for_editing ) for hda in datasets ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by Bitbucket 09 Oct '12

09 Oct '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9635e2cc9a24/ changeset: 9635e2cc9a24 user: jgoecks date: 2012-10-09 18:33:02 summary: Trackster: accurately calculate track/tile heights by clearing previously set height before calculating new height. affected #: 1 file diff -r 79bb2432133f9b18450e142fc6b80ddab364b57e -r 9635e2cc9a249aea5d939c0f4ca955c5faa3dd58 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3020,13 +3020,10 @@ * an existing tile rather than reshowing it. */ show_tile: function(tile, parent_element, w_scale) { - var - track = this, + var track = this, tile_element = tile.html_elt; - // - // Show/move tile element. - // + // -- Show/move tile element. -- tile.predisplay_actions(); @@ -3046,14 +3043,12 @@ // Showing new tile. parent_element.append(tile_element); } + + // -- Update track, tile heights based on new tile. -- - track.after_show_tile(tile); - }, - - /** - * Actions to be taken after showing tile. - */ - after_show_tile: function(tile) { + // Clear any previous height settings for tile. + tile.html_elt.height('auto'); + // Update max height based on current tile. this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); https://bitbucket.org/galaxy/galaxy-central/changeset/437b0d9ccb60/ changeset: 437b0d9ccb60 user: jgoecks date: 2012-10-09 20:16:16 summary: For Circster: only preload data if indexing is complete. affected #: 1 file diff -r 9635e2cc9a249aea5d939c0f4ca955c5faa3dd58 -r 437b0d9ccb60141d9378642893ce13bd50187cea lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -772,14 +772,18 @@ # Add genome-wide summary tree data to each track in viz. tracks = viz_config.get( 'tracks', [] ) for track in tracks: - # Get dataset and indexed datatype. + # Get dataset and data sources. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) data_sources = dataset.get_datasources( trans ) - data_provider = trans.app.data_provider_registry.get_data_provider( trans, - original_dataset=dataset, - source='index' ) - # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + + # If there are no messages (messages indicate data is not ready/available), preload data. + messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] + if not get_highest_priority_msg( messages_list ): + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, + source='index' ) + # HACK: pass in additional params, which are only used for summary tree data, not BBI data. + track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) https://bitbucket.org/galaxy/galaxy-central/changeset/dcb22217c175/ changeset: dcb22217c175 user: jgoecks date: 2012-10-09 20:16:27 summary: Merge affected #: 2 files diff -r 437b0d9ccb60141d9378642893ce13bd50187cea -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -345,13 +345,13 @@ def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) def get_html( self, value, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) diff -r 437b0d9ccb60141d9378642893ce13bd50187cea -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -274,12 +274,18 @@ column_names = dataset.metadata.column_names elif hasattr(dataset.datatype, 'column_names'): column_names = dataset.datatype.column_names + column_types = dataset.metadata.column_types + if not column_types: + column_types = [] + column_number = dataset.metadata.columns + if column_number is None: + column_number = 'null' return trans.fill_template( "/dataset/tabular_chunked.mako", dataset = dataset, chunk = self.get_chunk(trans, dataset, 0), - column_number = dataset.metadata.columns, + column_number = column_number, column_names = column_names, - column_types = dataset.metadata.column_types) + column_types = column_types ) def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for displaying metadata ColumnParameter type when columns is None.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6f017bc991a6/ changeset: 6f017bc991a6 user: dan date: 2012-10-09 19:57:19 summary: Fix for displaying metadata ColumnParameter type when columns is None. affected #: 1 file diff -r 8ce7bbba361a93a1a4a50029a3fd6a6266c1934d -r 6f017bc991a6e4617488768532adb56d49c1a688 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -345,13 +345,13 @@ def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) def get_html( self, value, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) 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: dan: Fix for preview display of tabular items when column_number is None.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8ce7bbba361a/ changeset: 8ce7bbba361a user: dan date: 2012-10-09 19:50:47 summary: Fix for preview display of tabular items when column_number is None. affected #: 1 file diff -r 259a4e01f105b6f7396292db3ae0971d049b6ce7 -r 8ce7bbba361a93a1a4a50029a3fd6a6266c1934d lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -277,10 +277,13 @@ column_types = dataset.metadata.column_types if not column_types: column_types = [] + column_number = dataset.metadata.columns + if column_number is None: + column_number = 'null' return trans.fill_template( "/dataset/tabular_chunked.mako", dataset = dataset, chunk = self.get_chunk(trans, dataset, 0), - column_number = dataset.metadata.columns, + column_number = column_number, column_names = column_names, column_types = column_types ) 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: dan: Fix for preview display of tabular items when column_types is None.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/259a4e01f105/ changeset: 259a4e01f105 user: dan date: 2012-10-09 19:46:19 summary: Fix for preview display of tabular items when column_types is None. affected #: 1 file diff -r 79bb2432133f9b18450e142fc6b80ddab364b57e -r 259a4e01f105b6f7396292db3ae0971d049b6ce7 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -274,12 +274,15 @@ column_names = dataset.metadata.column_names elif hasattr(dataset.datatype, 'column_names'): column_names = dataset.datatype.column_names + column_types = dataset.metadata.column_types + if not column_types: + column_types = [] return trans.fill_template( "/dataset/tabular_chunked.mako", dataset = dataset, chunk = self.get_chunk(trans, dataset, 0), column_number = dataset.metadata.columns, column_names = column_names, - column_types = dataset.metadata.column_types) + column_types = column_types ) def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) 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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