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September 2013

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commit/galaxy-central: Dave Bouvier: Fix for tool shed repository metadata API value mappers when time_last_tested is null for a metadata record.
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e1c5eeed1bd6/ Changeset: e1c5eeed1bd6 User: Dave Bouvier Date: 2013-09-11 22:36:52 Summary: Fix for tool shed repository metadata API value mappers when time_last_tested is null for a metadata record. Affected #: 2 files diff -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de -r e1c5eeed1bd6ba5c66dce308e69e44e6edea920f lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -96,9 +96,6 @@ ] } """ - metadata_value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id, - 'time_last_tested' : time_ago } repository_value_mapper = { 'id' : trans.security.encode_id, 'user_id' : trans.security.encode_id } # Example URL: http://localhost:9009/api/repositories/get_repository_revision_install_info… @@ -123,7 +120,7 @@ if repository_metadata: encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id ) repository_metadata_dict = repository_metadata.to_dict( view='collection', - value_mapper=metadata_value_mapper ) + value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=encoded_repository_metadata_id ) @@ -194,3 +191,10 @@ log.error( message, exc_info=True ) trans.response.status = 500 return message + + def __get_value_mapper( self, trans, repository_metadata ): + value_mapper = { 'id' : trans.security.encode_id, + 'repository_id' : trans.security.encode_id } + if repository_metadata.time_last_tested is not None: + value_mapper[ 'time_last_tested' ] = time_ago + return value_mapper diff -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de -r e1c5eeed1bd6ba5c66dce308e69e44e6edea920f lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -72,9 +72,6 @@ GET /api/repository_revisions Displays a collection (list) of repository revisions. """ - value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id, - 'time_last_tested' : time_ago } # Example URL: http://localhost:9009/api/repository_revisions repository_metadata_dicts = [] # Build up an anded clause list of filters. @@ -124,7 +121,7 @@ .all() for repository_metadata in query: repository_metadata_dict = repository_metadata.to_dict( view='collection', - value_mapper=value_mapper ) + value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=trans.security.encode_id( repository_metadata.id ) ) @@ -144,13 +141,10 @@ :param id: the encoded id of the `RepositoryMetadata` object """ - value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id, - 'time_last_tested' : time_ago } # Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620 try: repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) - repository_metadata_dict = repository_metadata.to_dict( value_mapper=value_mapper ) + repository_metadata_dict = repository_metadata.to_dict( value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=trans.security.encode_id( repository_metadata.id ) ) @@ -167,7 +161,6 @@ PUT /api/repository_revisions/{encoded_repository_metadata_id}/{payload} Updates the value of specified columns of the repository_metadata table based on the key / value pairs in payload. """ - value_mapper = dict( id=trans.security.encode_id, repository_id=trans.security.encode_id, time_last_tested=time_ago ) repository_metadata_id = kwd.get( 'id', None ) try: repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -188,8 +181,15 @@ log.error( message, exc_info=True ) trans.response.status = 500 return message - repository_metadata_dict = repository_metadata.to_dict( value_mapper=value_mapper ) + repository_metadata_dict = repository_metadata.to_dict( value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=trans.security.encode_id( repository_metadata.id ) ) return repository_metadata_dict + + def __get_value_mapper( self, trans, repository_metadata ): + value_mapper = { 'id' : trans.security.encode_id, + 'repository_id' : trans.security.encode_id } + if repository_metadata.time_last_tested is not None: + value_mapper[ 'time_last_tested' ] = time_ago + return value_mapper 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: Style: fix tooltips in history panel; pack scripts
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/18745fd87025/ Changeset: 18745fd87025 User: carlfeberhard Date: 2013-09-11 22:36:01 Summary: Style: fix tooltips in history panel; pack scripts Affected #: 15 files diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -174,7 +174,7 @@ // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) //TODO: we can potentially skip this step and call popupmenu directly on the download button make_popup_menus( $container ); - $container.find( '.tooltip' ).tooltip({ placement : 'bottom' }); + $container.find( '[title]' ).tooltip({ placement : 'bottom' }); }, // ................................................................................ RENDER titlebar diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -271,7 +271,7 @@ // render the main template, tooltips //NOTE: this is done before the items, since item views should handle theirs themselves newRender.append( HistoryPanel.templates.historyPanel( modelJson ) ); - newRender.find( '.tooltip' ).tooltip({ placement: 'bottom' }); + newRender.find( '[title]' ).tooltip({ placement: 'bottom' }); // render hda views (if any and any shown (show_deleted/hidden) //TODO: this seems too elaborate @@ -485,7 +485,7 @@ success: function(tag_elt_html) { //view.log( view + ' tag elt html (ajax)', tag_elt_html ); tagElt.html(tag_elt_html); - tagElt.find(".tooltip").tooltip(); + tagElt.find("[title]").tooltip(); tagArea.slideDown("fast"); } }); diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(a){var b=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(d){a.load_file("static/style/galaxy.modal.css");if(!d){d=this.options}else{d=_.defaults(d,this.options)}this.setElement(this.template(d.title,d.body));$(this.el_main).append($(this.el));var e=(this.$el).find(".footer");var c=this;if(d.buttons){$.each(d.buttons,function(f,g){e.append($("<button></button>").text(f).click(g)).append(" ")})}else{e.append($("<button></button>").text("Close").click(function(){c.hide()})).append(" ")}$(this.el).hide()},events:{"mousedown .dialog":"event_default","mousedown .background":"hide"},event_default:function(c){c.preventDefault()},show:function(){this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},destroy:function(){this.$el.remove()},template:function(d,c){return'<div class="galaxy-modal"><div class="background"></div><div class="dialog galaxy-corner"><div class="header"><span><h3 class="title">'+d+'</h3></span></div><div class="body">'+c+'</div><div class="footer"></div></div></div>'}});return{GalaxyModal:b}}); \ No newline at end of file +define(["utils/galaxy.css","libs/backbone/backbone-relational"],function(a){var b=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(d){if(!d){d=this.options}else{d=_.defaults(d,this.options)}this.setElement(this.template(d.title,d.body));$(this.el_main).append($(this.el));var e=(this.$el).find(".footer");var c=this;if(d.buttons){$.each(d.buttons,function(f,g){e.append($("<button></button>").text(f).click(g)).append(" ")})}else{e.append($("<button></button>").text("Close").click(function(){c.hide()})).append(" ")}$(this.el).hide()},events:{"mousedown .dialog":"event_default","mousedown .background":"hide"},event_default:function(c){c.preventDefault()},show:function(){this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},destroy:function(){this.$el.remove()},template:function(d,c){return'<div class="modal"><div class="modal-backdrop"></div><div class="modal-dialog galaxy-corner"><div class="modal-content"><div class="header"><span><h3 class="title">'+d+'</h3></span></div><div class="body">'+c+'</div><div class="footer"></div></div</div></div>'}});return{GalaxyModal:b}}); \ No newline at end of file diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(_.keys(b).length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<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=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",function(d,c){var b=_.omit(this.model.changedAttributes(),"display_apps","display_types");if(_.keys(b).length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find("[title]").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<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=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var b={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){b.enabled=false;b.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD){b.enabled=false;b.title=_l("This dataset must finish uploading before it can be viewed")}else{b.title=_l("View data");b.href=this.urls.display;var a=this;b.on_click=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer",type:"url",location:"center",content:a.urls.display})}}}this.displayButton=new IconButtonView({model:new IconButton(b)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a.trim())},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayAppArea:function(){return $("<div/>").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');this._setUpBehaviors(a)},_render_body_new:function(b){var a=_l("This is a new dataset and not all of its data are available yet");b.append($("<div>"+_l(a)+"</div>"))},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+"</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to resume")+"</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+"</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred with this dataset")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();a.off();if(b){b()}})},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find(".tooltip").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find("[title]").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de 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(m,C,A,s,J){this.compilerInfo=[4,">= 1.0.0"];A=this.merge(A,m.helpers);J=J||{};var B="",p,l,h,x=this,e="function",c=A.blockHelperMissing,d=this.escapeExpression;function v(O,N){var K="",M,L;K+='\n <div id="history-name" class="editable-text"\n title="';L={hash:{},inverse:x.noop,fn:x.program(2,u,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+='">';if(M=A.name){M=M.call(O,{hash:{},data:N})}else{M=O.name;M=typeof M===e?M.apply(O):M}K+=d(M)+"</div>\n ";return K}function u(L,K){return"Click to rename history"}function t(O,N){var K="",M,L;K+='\n <div id="history-name"\n title="';L={hash:{},inverse:x.noop,fn:x.program(5,r,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof 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\ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(m,C,A,s,J){this.compilerInfo=[4,">= 1.0.0"];A=this.merge(A,m.helpers);J=J||{};var B="",p,l,h,x=this,e="function",c=A.blockHelperMissing,d=this.escapeExpression;function v(O,N){var K="",M,L;K+='\n <div id="history-name" class="editable-text"\n title="';L={hash:{},inverse:x.noop,fn:x.program(2,u,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+='">';if(M=A.name){M=M.call(O,{hash:{},data:N})}else{M=O.name;M=typeof M===e?M.apply(O):M}K+=d(M)+"</div>\n ";return K}function u(L,K){return"Click to rename history"}function t(O,N){var K="",M,L;K+='\n <div id="history-name"\n title="';L={hash:{},inverse:x.noop,fn:x.program(5,r,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+='">';if(M=A.name){M=M.call(O,{hash:{},data:N})}else{M=O.name;M=typeof M===e?M.apply(O):M}K+=d(M)+"</div>\n ";return K}function r(L,K){return"You must be logged in to edit your history name"}function q(O,N){var K="",M,L;K+='\n <a id="history-tag" title="';L={hash:{},inverse:x.noop,fn:x.program(8,o,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+='"\n class="icon-button tags" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';L={hash:{},inverse:x.noop,fn:x.program(10,I,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+='"\n class="icon-button annotate" target="galaxy_main" href="javascript:void(0)"></a>\n ';return K}function o(L,K){return"Edit history tags"}function I(L,K){return"Edit history annotation"}function H(O,N){var K="",M,L;K+='\n <div id="history-tag-annotation">\n\n <div id="history-tag-area" style="display: none">\n <strong>';L={hash:{},inverse:x.noop,fn:x.program(13,G,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+=':</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>';L={hash:{},inverse:x.noop,fn:x.program(15,F,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+=':</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="editable-text"\n title="';L={hash:{},inverse:x.noop,fn:x.program(17,E,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+='">\n ';M=A["if"].call(O,O.annotation,{hash:{},inverse:x.program(21,n,N),fn:x.program(19,D,N),data:N});if(M||M===0){K+=M}K+="\n </div>\n </div>\n </div>\n </div>\n ";return K}function G(L,K){return"Tags"}function F(L,K){return"Annotation"}function E(L,K){return"Click to edit annotation"}function D(N,M){var K="",L;K+="\n ";if(L=A.annotation){L=L.call(N,{hash:{},data:M})}else{L=N.annotation;L=typeof L===e?L.apply(N):L}K+=d(L)+"\n ";return K}function n(O,N){var K="",M,L;K+="\n <em>";L={hash:{},inverse:x.noop,fn:x.program(22,k,N),data:N};if(M=A.local){M=M.call(O,L)}else{M=O.local;M=typeof M===e?M.apply(O):M}if(!A.local){M=c.call(O,M,L)}if(M||M===0){K+=M}K+="</em>\n ";return K}function k(L,K){return"Describe or add notes to history"}function j(O,N){var K="",M,L;K+="\n ";L={hash:{},inverse:x.noop,fn:x.program(25,i,N),data:N};if(M=A.warningmessagesmall){M=M.call(O,L)}else{M=O.warningmessagesmall;M=typeof M===e?M.apply(O):M}if(!A.warningmessagesmall){M=c.call(O,M,L)}if(M||M===0){K+=M}K+="\n ";return K}function i(N,M){var L,K;K={hash:{},inverse:x.noop,fn:x.program(26,g,M),data:M};if(L=A.local){L=L.call(N,K)}else{L=N.local;L=typeof L===e?L.apply(N):L}if(!A.local){L=c.call(N,L,K)}if(L||L===0){return L}else{return""}}function g(L,K){return"You are currently viewing a deleted history!"}function f(N,M){var K="",L;K+='\n <div class="';if(L=A.status){L=L.call(N,{hash:{},data:M})}else{L=N.status;L=typeof L===e?L.apply(N):L}K+=d(L)+'message">';if(L=A.message){L=L.call(N,{hash:{},data:M})}else{L=N.message;L=typeof L===e?L.apply(N):L}K+=d(L)+"</div>\n ";return K}function z(L,K){return"You are over your disk quota"}function y(L,K){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function w(L,K){return"Your history is empty. 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If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.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(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.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(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;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 ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}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 ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.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.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);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;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[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(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);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=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);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(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".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 q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){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(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:new X.Dataset(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(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 ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.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 W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;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)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.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(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.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:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.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=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);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:j.get_random_color()},{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:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);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:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{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:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#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:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{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:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",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:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");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()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){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(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.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(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#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:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}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 ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.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.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<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 ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);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=1/this.resolution_b_px;var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);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(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".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 q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){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(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ah,af,ae,ag){this.track=ad;this.region=ah;this.low=ah.get("start");this.high=ah.get("end");this.resolution=af;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ah,af,ae,ag){b.call(this,ad,ah,af,ae,ag)};M.prototype.predisplay_actions=function(){};var O=function(ag,ao,ah,af,aj,aq,ak,ar,ae,an){b.call(this,ag,ao,ah,af,aj);this.mode=ak;this.all_slotted=ae;this.feature_mapper=an;this.has_icons=false;if(ar){this.has_icons=true;var al=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var am=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ap=aj.length,ai=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ap+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ai.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()});ad.click(function(){al.stale=true;ag.data_manager.get_more_data(am,ag.mode,al.resolution,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(at){at.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:X.Dataset.findOrCreate(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(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 ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.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 W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;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)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.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(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ad*S*ag)<ah){am=this._get_tile_bounds(ad,ag);ai=this.draw_helper(am,ag,ap,aq);aj.push(ai);$.when(ai).then(function(ar){ao.push(ar)});ad+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ao=ac.filter(ao,function(ar){return ar!==null});if(ao.length!==0){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,ak.resolution,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ag,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],ag,am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.LinePainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new M(this,ai,ah,ag,ad.data)},draw_tile:function(ad,ae,ai,ag,ah,aj,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(ad,ae){var ag=Math.floor(ad*S*ae),ah=Math.ceil(S*ae),af=(ag+ah<=this.view.max_high?ag+ah:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:ag,end:af})},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.dataset_type==="bigwig"||ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.dataset_type==="bigwig"||ad.message||ad.extra_info==="no_detail"){return false}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.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:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,ag.resolution,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.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=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(af,ae,ag,ad){if(ag>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,af,ae,ag,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(ag,am,ah,ae,aj,an){var af=this.data_manager.subset_entry(ag,aj),al=af.data;var ad=am.canvas;am.font=am.canvas.manager.default_font;am.textAlign="center";for(var ai=0,ak=al.length;ai<ak;ai++){am.fillStyle=this.view.get_base_color(al[ai]);am.fillText(al[ai],Math.floor(ai*an),10)}return new b(this,aj,ae,ad,af)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);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:j.get_random_color()},{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:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ah,af,ag,ai){return this._draw_line_track_tile(ad,ae,ah,af,ag,ai)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);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:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{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:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,aj,ah,ai,ak){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj);ae.draw(af,ag.width,ag.height,ak);return new b(this,ai,ah,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#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:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{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:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",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:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");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()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){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(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.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(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,at,ag,ak,af){var aq=this,ae=ar.canvas,az=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,at,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ai=an.data[au];var av=false;var am;for(var ay=0,aD=al.length;ay<aD;ay++){am=al[ay];am.update_attrs(ai);if(!am.keep(ai)){av=true;break}}if(!av){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aC=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),aA=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aB=new (this.painter)(aj,az,ad,this.prefs,ap,aC,aA,af,function(aE){return aq.view.get_base_color(aE)});var ax=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ax=aB.draw(ar,ae.width,ae.height,ak,ao);ax.translation=-ah}return new O(aq,ag,at,ae,an.data,ak,ap,an.message,all_slotted,ax)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,aj,ah,ai,ak){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,ai,ak)}else{var af=this.view,ae=new (this.painter)(ad.data,ai.get("start"),ai.get("end"),this.prefs,aj,function(al){return af.get_base_color(al)});ae.draw(ag,ag.canvas.width,ag.canvas.height,ak);return new b(this,ai,ah,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#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:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de 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 @@ -58,13 +58,13 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; + buffer += "\"\n class=\"icon-button tags\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; options = {hash:{},inverse:self.noop,fn:self.program(10, program10, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; + buffer += "\"\n class=\"icon-button annotate\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n "; return buffer; } function program8(depth0,data) { @@ -94,7 +94,7 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\"\n title=\""; + buffer += ":</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"editable-text\"\n title=\""; options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -24,9 +24,9 @@ <div id="history-secondary-links" style="float: right;"> {{#if user.email}} <a id="history-tag" title="{{#local}}Edit history tags{{/local}}" - class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a> + class="icon-button tags" 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="javascript:void(0)"></a> + class="icon-button annotate" target="galaxy_main" href="javascript:void(0)"></a> {{/if}} </div><div style="clear: both;"></div> @@ -45,7 +45,7 @@ <div id="history-annotation-area" style="display: none"><strong>{{#local}}Annotation{{/local}}:</strong><div id="history-annotation-container"> - <div id="history-annotation" class="tooltip editable-text" + <div id="history-annotation" class="editable-text" title="{{#local}}Click to edit annotation{{/local}}"> {{#if annotation}} {{annotation}} diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1341,6 +1341,7 @@ .icon-button.link-broken{background:url(../images/silk/link_break.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px} body.historyPage{background:#dfe5f9;color:#000;margin:5px;border:0;padding:0} +body.historyPage>*{margin:0px;padding:0px} div.historyLinks{margin:5px 5px} div.historyItem{margin:0 -5px;padding:8px 10px;border-top:solid #bfbfbf 1px;border-right:none;word-wrap:break-word;background:#eee}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat} div.historyItem .historyItemTitle{font-weight:bold;line-height:16px} diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/style/blue/sprite-fugue.png Binary file static/style/blue/sprite-fugue.png has changed diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/style/blue/sprite-history-buttons.png Binary file static/style/blue/sprite-history-buttons.png has changed diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/style/blue/sprite-history-states.png Binary file static/style/blue/sprite-history-states.png has changed diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1358,6 +1358,11 @@ padding: 0; } +body.historyPage > * { + margin: 0px; + padding: 0px; +} + // Control links at top of history div.historyLinks { margin: 5px 5px; @@ -1754,4 +1759,4 @@ } .icon-button.chevron-expand { .sprite(@chevron-expand-bw); -} \ No newline at end of file +} diff -r 5432c6f3fe421b820673d6096cc039085555b44c -r 18745fd87025971fb7f8a3bc9cd9e54a5f5759de templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -342,13 +342,6 @@ margin: 0px; } - #history-subtitle-area { - } - #history-size { - } - #history-secondary-links { - } - #history-secondary-links #history-refresh { text-decoration: none; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: make compatible with recent Backbone-relational update by using findOrCreate rather than creating new dataset objects each time. This fixes composite tracks and readding tracks.
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5432c6f3fe42/ Changeset: 5432c6f3fe42 User: jgoecks Date: 2013-09-11 22:27:16 Summary: Trackster: make compatible with recent Backbone-relational update by using findOrCreate rather than creating new dataset objects each time. This fixes composite tracks and readding tracks. Affected #: 1 file diff -r bfcb397e240947dead624e730c3bc1ebb9fbf933 -r 5432c6f3fe421b820673d6096cc039085555b44c static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2321,7 +2321,7 @@ this.dataset = null; if (obj_dict.dataset) { // Dataset can be a Backbone model or a dict that can be used to create a model. - this.dataset = (obj_dict.dataset instanceof Backbone.Model ? obj_dict.dataset : new data.Dataset(obj_dict.dataset) ); + this.dataset = (obj_dict.dataset instanceof Backbone.Model ? obj_dict.dataset : data.Dataset.findOrCreate(obj_dict.dataset) ); } this.dataset_check_type = 'converted_datasets_state'; this.data_url_extra_params = {}; 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.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bfcb397e2409/ Changeset: bfcb397e2409 User: jgoecks Date: 2013-09-11 22:00:19 Summary: Trackster: fix data-mode compatibility test; this fixes mode changing from coverage to dense/squish/pack. Affected #: 1 file diff -r c90e760da0fdc89f2e6b9e42dfaa7b365c8eeea4 -r bfcb397e240947dead624e730c3bc1ebb9fbf933 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3421,7 +3421,8 @@ return data.dataset_type === "bigwig"; } // All other modes--Dense, Squish, Pack--require data + details. - else if (data.extra_info === "no_detail") { + else if (data.dataset_type === "bigwig" || + data.extra_info === "no_detail") { return false; } else { https://bitbucket.org/galaxy/galaxy-central/commits/185e24997925/ Changeset: 185e24997925 Branch: stable User: jgoecks Date: 2013-09-11 22:00:19 Summary: Trackster: fix data-mode compatibility test; this fixes mode changing from coverage to dense/squish/pack. Affected #: 1 file diff -r 055ef20e662a4e0806df7832625792cd5da17c44 -r 185e24997925d70a287243fac83530208819fac2 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3444,7 +3444,8 @@ return data.dataset_type === "bigwig"; } // All other modes--Dense, Squish, Pack--require data + details. - else if (data.extra_info === "no_detail") { + else if (data.dataset_type === "bigwig" || + data.extra_info === "no_detail") { return false; } else { https://bitbucket.org/galaxy/galaxy-central/commits/1f34ec186fcf/ Changeset: 1f34ec186fcf Branch: stable User: jgoecks Date: 2013-09-11 22:06:32 Summary: Pack script. Affected #: 1 file diff -r 185e24997925d70a287243fac83530208819fac2 -r 1f34ec186fcf79e5d82ea2a7e73ba5f537fb80f9 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(ab,w,k,t,L,X,i){var p=ab.extend;var m={};var j=function(ac,ad){m[ac.attr("id")]=ad};var l=function(ac,ae,ag,af){ag=".group";var ad={};m[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=m[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}m[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);m[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));m[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,n="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",R=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(y.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=o(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var Q=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);j(this.container_div,this);j(this.content_div,this);l(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 af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(Q.prototype,q.prototype,y.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}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 ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){p(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.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.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;j(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(o(ah,ac,ac))})})});this.nav_labeltrack=$("<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 ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]||this.config.values.n_color}});p(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);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(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.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 r=function(ae,aj,af){this.track=ae;this.id=aj.id;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new O(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: 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ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new w.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:this.id,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new Q(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new X.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new k.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var O=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){O.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){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(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(F.prototype,{set_param_default_value:function(ad,ac){var ae=ab.find(this.params,function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.params,function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.values[ac]!==ad){this.values[ac]=ad;return true}else{return false}},restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(k.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ad=ae.set_param_value(ah.key,ag)||ad}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ac,ag,ae,ad,af){b.call(this,ac,ag,ae,ad,af)};M.prototype.predisplay_actions=function(){};var P=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.dataset=new X.Dataset(ae.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(g.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(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 ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.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 W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(n);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;l(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new w.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(N.prototype,q.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,ag=this.view.high,aj=ag-ak,ad=this.view.container.width(),ao=this.view.resolution_px_b,af=this.view.resolution_b_px;if(this.is_overview){ak=this.view.max_low;ag=this.view.max_high;af=(view.max_high-view.max_low)/ad;ao=1/af}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(ak/(af*S)),al,ah,ai=[],an=[];while((ac*S*af)<ag){al=this._get_tile_bounds(ac,af);ah=this.draw_helper(al,af,ao,ap);ai.push(ah);$.when(ah).then(function(aq){an.push(aq)});ac+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();an=ab.filter(an,function(aq){return aq!==null});if(an.length!==0){ae.postdraw_actions(an,ad,ao,am)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ah=ah||function(){ad.request_draw({clear_tile_cache:true})},ae=this.container_div.find(".yaxislabel."+ag);if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".bs-tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,aj.resolution,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,af,ao,ap){if(!ap){ap={}}var ad=ap.force,an=!(ap.data_fetch===false),ai=ap.mode||this.mode,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(ao,al),ah=function(aq){return(aq&&"track" in aq)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,ao)}return aj}if(!an){return null}var ak=function(){var aq=(ab.find(A,function(at){return at===ai})?"Coverage":ai);var ar=ab.map(ag,function(at){return at.data_manager.get_data(al,aq,af,ae.data_url_extra_params)});if(view.reference_track){ar.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return ar};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var aq=ak(),aw=aq,aC;if(view.reference_track){aC=view.reference_track.data_manager.subset_entry(aq.pop(),al)}var ax=[],au=[];ab.each(ag,function(aH,aE){var aG=aH.mode,aF=aw[aE];if(aG==="Auto"){aG=aH.get_mode(aF);aH.update_auto_mode(aG)}ax.push(aG);au.push(aH.get_canvas_height(aF,aG,ao,ar))});var av=ae.view.canvas_manager.new_canvas(),ay=al.get("start"),aD=al.get("end"),at=0,ar=Math.ceil((aD-ay)*ao)+ae.left_offset,aA=ab.max(au),az;av.width=ar;av.height=(ap.height||aA);var aB=av.getContext("2d");aB.translate(ae.left_offset,0);if(ag.length>1){aB.globalAlpha=0.5;aB.globalCompositeOperation="source-over"}ab.each(ag,function(aF,aE){az=aF.draw_tile(aw[aE],aB,ax[aE],af,al,ao,aC)});if(az!==undefined){ae.tile_cache.set_elt(am,az);ae.show_tile(az,ao)}ac.resolve(az)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.LinePainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new M(this,ah,ag,af,ac.data)},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ae.html_elt.height("auto");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(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="bigwig"||ac.message||ac.extra_info==="no_detail"){return false}return true},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(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new k.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda")},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){this.display_modes=A;N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=o(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};p(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.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:q.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new Q(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1;for(var ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(var ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,af.resolution,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.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 w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};p(B.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:q.prototype.can_draw,draw_helper:function(ae,ad,af,ac){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,ad,af,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=A;this.mode="Histogram";N.call(this,ae,ad,af);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:k.get_random_color()},{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:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(h.prototype,q.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ac,ad,ag,ae,af,ah){return this._draw_line_track_tile(ac,ad,ag,ae,af,ah)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var s=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ae,ad,af);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:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{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:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(s.prototype,q.prototype,N.prototype,{draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,af,ae,ah);var ag=k.get_random_color(),ac=k.get_random_color([ag,"#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:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{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:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",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:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.set_painter_from_config();ad.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");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()};p(c.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters;for(var aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(var aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof P){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){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(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (t.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.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(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,ar,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new P(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)}});var Z=function(ad,ac,ae){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:k.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};p(Z.prototype,q.prototype,N.prototype,{draw_tile:function(ac,af,ai,ag,ah,aj){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ah,aj)}else{var ae=this.view,ad=new (this.painter)(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return ae.get_base_color(ak)});ad.draw(af,af.canvas.width,af.canvas.height,aj);return new b(this,ah,ag,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=new (this.painter)(null,null,null,this.prefs,ag);var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(af,ag,ai,ad){N.prototype.postdraw_actions.call(this,af,ag,ai,ad);var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length===0&&this.prefs.show_labels){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ah=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=k.get_random_color(),ac=k.get_random_color([af,"#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:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(ae.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};p(T.prototype,q.prototype,N.prototype,c.prototype);var d={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:s,FeatureTrack:c,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var o=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:s,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:o}}); \ 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(ab,w,k,t,L,X,i){var p=ab.extend;var m={};var j=function(ac,ad){m[ac.attr("id")]=ad};var l=function(ac,ae,ag,af){ag=".group";var ad={};m[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=m[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}m[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);m[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));m[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,n="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",R=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.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(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];p(q.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(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;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 ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(y.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=o(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad]._draw(ac)}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var Q=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);j(this.container_div,this);j(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(Q.prototype,q.prototype,y.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}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 ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ad=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac){ab.each(this.drawables,function(ad){ad.request_draw(ac)})}});var Y=Backbone.View.extend({initialize:function(ac){p(ac,{obj_type:"View"});y.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.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.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ac.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);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;j(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(o(ah,ac,ac))})})});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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[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(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]||this.config.values.n_color}});p(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){y.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(ac<this.max_low){ac=this.max_low}if(ag>this.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad<this.min_separation){ag=ac+this.min_separation}this.low=Math.floor(ac);this.high=Math.ceil(ag);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:af,width:Math.max(ae,ah)}).show();if(ah<ae){this.overview_box.css("left",af-(ae-ah)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:ah})}ab.each(this.tracks_to_be_redrawn,function(ak){var ai=ak[0],aj=ak[1];if(ai){ai._draw(aj)}});this.tracks_to_be_redrawn=[];ab.each(this.label_tracks,function(ai){ai._draw()})},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);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(ae){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ae.dataset.id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.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 r=function(ae,aj,af){this.track=ae;this.id=aj.id;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new O(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new w.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:this.id,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new Q(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new X.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new k.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var O=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){O.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){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(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(F.prototype,{set_param_default_value:function(ad,ac){var ae=ab.find(this.params,function(af){return af.key===ad});if(ae){ae.default_value=ac}},set_param_value:function(ac,ad){var ae=ab.find(this.params,function(af){return af.key===ac});if(ae){if(typeof ad==="string"||ad instanceof String){if(ad.trim()===""){ad=ae.default_value}else{if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad,10)}}}}}if(this.values[ac]!==ad){this.values[ac]=ad;return true}else{return false}},restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(k.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ad=ae.set_param_value(ah.key,ag)||ad}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ac,ag,ae,ad,af){b.call(this,ac,ag,ae,ad,af)};M.prototype.predisplay_actions=function(){};var P=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.dataset=new X.Dataset(ae.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(g.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter 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class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(n);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;l(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new w.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(N.prototype,q.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,ag=this.view.high,aj=ag-ak,ad=this.view.container.width(),ao=this.view.resolution_px_b,af=this.view.resolution_b_px;if(this.is_overview){ak=this.view.max_low;ag=this.view.max_high;af=(view.max_high-view.max_low)/ad;ao=1/af}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(ak/(af*S)),al,ah,ai=[],an=[];while((ac*S*af)<ag){al=this._get_tile_bounds(ac,af);ah=this.draw_helper(al,af,ao,ap);ai.push(ah);$.when(ah).then(function(aq){an.push(aq)});ac+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ae=this;$.when.apply($,ai).then(function(){ae.tiles_div.children(".remove").remove();an=ab.filter(an,function(aq){return aq!==null});if(an.length!==0){ae.postdraw_actions(an,ad,ao,am)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ah=ah||function(){ad.request_draw({clear_tile_cache:true})},ae=this.container_div.find(".yaxislabel."+ag);if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".bs-tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,aj.resolution,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,af,ao,ap){if(!ap){ap={}}var ad=ap.force,an=!(ap.data_fetch===false),ai=ap.mode||this.mode,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(ao,al),ah=function(aq){return(aq&&"track" in aq)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,ao)}return aj}if(!an){return null}var ak=function(){var aq=(ab.find(A,function(at){return at===ai})?"Coverage":ai);var ar=ab.map(ag,function(at){return at.data_manager.get_data(al,aq,af,ae.data_url_extra_params)});if(view.reference_track){ar.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return ar};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var aq=ak(),aw=aq,aC;if(view.reference_track){aC=view.reference_track.data_manager.subset_entry(aq.pop(),al)}var ax=[],au=[];ab.each(ag,function(aH,aE){var aG=aH.mode,aF=aw[aE];if(aG==="Auto"){aG=aH.get_mode(aF);aH.update_auto_mode(aG)}ax.push(aG);au.push(aH.get_canvas_height(aF,aG,ao,ar))});var av=ae.view.canvas_manager.new_canvas(),ay=al.get("start"),aD=al.get("end"),at=0,ar=Math.ceil((aD-ay)*ao)+ae.left_offset,aA=ab.max(au),az;av.width=ar;av.height=(ap.height||aA);var aB=av.getContext("2d");aB.translate(ae.left_offset,0);if(ag.length>1){aB.globalAlpha=0.5;aB.globalCompositeOperation="source-over"}ab.each(ag,function(aF,aE){az=aF.draw_tile(aw[aE],aB,ax[aE],af,al,ao,aC)});if(az!==undefined){ae.tile_cache.set_elt(am,az);ae.show_tile(az,ao)}ac.resolve(az)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.LinePainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new M(this,ah,ag,af,ac.data)},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ae.html_elt.height("auto");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(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="bigwig"||ac.message||ac.extra_info==="no_detail"){return false}return true},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(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new k.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda")},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ai=(ac-ae.low)/af*ah;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){this.display_modes=A;N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=o(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};p(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.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:q.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new Q(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1;for(var ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(var ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(af.region,af.resolution,al,{force:true,height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){N.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.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 w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};p(B.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:q.prototype.can_draw,draw_helper:function(ae,ad,af,ac){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,ad,af,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=A;this.mode="Histogram";N.call(this,ae,ad,af);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:k.get_random_color()},{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:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(h.prototype,q.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ac,ad,ag,ae,af,ah){return this._draw_line_track_tile(ac,ad,ag,ae,af,ah)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var s=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ae,ad,af);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:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{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:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(s.prototype,q.prototype,N.prototype,{draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,af,ae,ah);var ag=k.get_random_color(),ac=k.get_random_color([ag,"#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:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{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:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",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:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.set_painter_from_config();ad.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");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()};p(c.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters;for(var aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(var aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof P){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){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(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (t.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.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(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,ar,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new P(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)}});var Z=function(ad,ac,ae){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:k.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};p(Z.prototype,q.prototype,N.prototype,{draw_tile:function(ac,af,ai,ag,ah,aj){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ah,aj)}else{var ae=this.view,ad=new (this.painter)(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return ae.get_base_color(ak)});ad.draw(af,af.canvas.width,af.canvas.height,aj);return new b(this,ah,ag,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=new (this.painter)(null,null,null,this.prefs,ag);var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(af,ag,ai,ad){N.prototype.postdraw_actions.call(this,af,ag,ai,ad);var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length===0&&this.prefs.show_labels){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ah=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=k.get_random_color(),ac=k.get_random_color([af,"#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:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(ae.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};p(T.prototype,q.prototype,N.prototype,c.prototype);var d={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:s,FeatureTrack:c,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var o=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:s,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:o}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: style: do not word wrap in pre blocks
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c90e760da0fd/ Changeset: c90e760da0fd User: james_taylor Date: 2013-09-11 21:47:26 Summary: style: do not word wrap in pre blocks Affected #: 3 files diff -r 669dd89d39c410688d5c6201fcdb9d30f2259787 -r c90e760da0fdc89f2e6b9e42dfaa7b365c8eeea4 lib/galaxy/__init__.py --- a/lib/galaxy/__init__.py +++ b/lib/galaxy/__init__.py @@ -106,4 +106,6 @@ class NullHandler( logging.Handler ): def emit( self, record ): pass - logging.NullHandler = NullHandler \ No newline at end of file + logging.NullHandler = NullHandler + +import galaxy.eggs \ No newline at end of file diff -r 669dd89d39c410688d5c6201fcdb9d30f2259787 -r c90e760da0fdc89f2e6b9e42dfaa7b365c8eeea4 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -752,6 +752,7 @@ .text-hide{font:0/0 a;color:transparent;text-shadow:none;background-color:transparent;border:0} .affix{position:fixed} .navbar-fixed-top .navbar-brand{font-family:Verdana;font-weight:bold;font-size:160%} +pre{overflow:auto;word-wrap:normal;white-space:pre} .btn.active,.btn:active{color:inherit} .dropdown-menu{max-width:auto} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex} diff -r 669dd89d39c410688d5c6201fcdb9d30f2259787 -r c90e760da0fdc89f2e6b9e42dfaa7b365c8eeea4 static/style/src/less/galaxy_bootstrap/overrides.less --- a/static/style/src/less/galaxy_bootstrap/overrides.less +++ b/static/style/src/less/galaxy_bootstrap/overrides.less @@ -1,9 +1,17 @@ .navbar-fixed-top .navbar-brand { - font-family: Verdana; - font-weight: bold; - font-size: 160%; + font-family: Verdana; + font-weight: bold; + font-size: 160%; } +// Don't wrap text inside pre +pre { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + + .btn.hover { @btn:hover(); } 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.

1 0

commit/galaxy-central: jgoecks: Remove TODO because it is not needed--any Backbone object can be a mixin.
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ff34b0a0f9d/ Changeset: 4ff34b0a0f9d User: jgoecks Date: 2013-09-11 20:45:06 Summary: Remove TODO because it is not needed--any Backbone object can be a mixin. Affected #: 1 file diff -r 5c606445f35e6328e92e70a2c55eb148086696e1 -r 4ff34b0a0f9dc763b87ce20bcb39c75447aed94d static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -3,7 +3,6 @@ /** * Utility class for working with SVG. */ -// TODO: make into a mixin. var SVGUtils = Backbone.Model.extend({ /** 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/63c492b8f6da/ Changeset: 63c492b8f6da User: dannon Date: 2013-09-11 20:35:33 Summary: Touch. Affected #: 1 file diff -r fe1a800dfcb6d842c3769c3334d602ce95095570 -r 63c492b8f6da79d7ecc4459419c4e90fe4bf4fc6 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -42,7 +42,7 @@ # Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. threadpool_kill_thread_limit = 10800 - + # ---- Filters -------------------------------------------------------------- # Filters sit between Galaxy and the HTTP server. https://bitbucket.org/galaxy/galaxy-central/commits/5c606445f35e/ Changeset: 5c606445f35e User: dannon Date: 2013-09-11 20:36:00 Summary: Merge Affected #: 1 file diff -r 63c492b8f6da79d7ecc4459419c4e90fe4bf4fc6 -r 5c606445f35e6328e92e70a2c55eb148086696e1 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -344,7 +344,7 @@ required_repository_tups.append( components_list ) else: # We have a single repository with no dependencies. - components_list = [ tool_shed_url, repository_name, repository_owner, changeset_revision, 'False', 'False' ] + components_list = [ tool_shed_url, repository_name, repository_owner, changeset_revision ] required_repository_tups.append( components_list ) if required_repository_tups: # The value of required_repository_tups is a list of tuples, so we need to encode it. 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.

1 0

commit/galaxy-central: Dave Bouvier: Backward compatibility fix for installing repositories without repository dependencies.
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/48191107fd2d/ Changeset: 48191107fd2d User: Dave Bouvier Date: 2013-09-11 20:16:52 Summary: Backward compatibility fix for installing repositories without repository dependencies. Affected #: 1 file diff -r fe1a800dfcb6d842c3769c3334d602ce95095570 -r 48191107fd2da06e10af5e7d83e197585e859f06 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -344,7 +344,7 @@ required_repository_tups.append( components_list ) else: # We have a single repository with no dependencies. - components_list = [ tool_shed_url, repository_name, repository_owner, changeset_revision, 'False', 'False' ] + components_list = [ tool_shed_url, repository_name, repository_owner, changeset_revision ] required_repository_tups.append( components_list ) if required_repository_tups: # The value of required_repository_tups is a list of tuples, so we need to encode it. 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.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/055ef20e662a/ Changeset: 055ef20e662a Branch: stable User: jgoecks Date: 2013-09-11 18:22:16 Summary: Close branch 10517:97d020901403 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/684ef8edd1d4/ Changeset: 684ef8edd1d4 Branch: dataset-cleanup User: jgoecks Date: 2013-09-11 18:24:00 Summary: Close branch 10525:e4734c99812a Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/fe1a800dfcb6/ Changeset: fe1a800dfcb6 User: jgoecks Date: 2013-09-11 18:25:02 Summary: Close branch 10558:dcd9809d0239 Affected #: 0 files 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.

1 0

commit/galaxy-central: 25 new changesets
by commits-noreply＠bitbucket.org 11 Sep '13

11 Sep '13

25 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a37731994c9/ Changeset: 0a37731994c9 User: saketkc Date: 2013-06-19 08:51:46 Summary: Adding a small check to skip the assertion of tagNumber being an integer for VCF4.1 files. I am not sure if there are better ways or beter checks that can be implemen= ted to do this. So, this should require discussions. The description of ##INFO and ##FORMAT tag as given on [http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-varia= nt-call-format-version-41] is : ##INFO=3D<ID=3DID,Number=3Dnumber,Type=3Dtype,Description=3D=E2=80=9Ddescri= ption=E2=80=9D> Possible Types for INFO fields are: Integer, Float, Flag, Character, and St= ring. The Number entry is an Integer that describes the number of values that can= be included with the INFO field. For example, if the INFO field contains a single number, then this value sh= ould be 1; if the INFO field describes a pair of numbers, then this value should be 2 = and so on. If the field has one value per alternate allele then this value should be '= A'; if the field has one value for each possible genotype (more relevant to the= FORMAT tags) then this value should be 'G'. If the number of possible values varies, is unknown, or is unbounded, then = this value should be '.'. The 'Flag' type indicates that the INFO field does not contain a Value entr= y, and hence the Number should be 0 in this case. The Description value must be surrounded by double-quote= s. Double-quote character can be escaped with backslash (\") and backslash as = \\. Affected #: 1 file diff -r 81a2bb351c1a0f545a1f69b5514a29d96eb4575a -r 0a37731994c91fd59d2d31f= 79156abb58cc76d75 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/ebdaa310677b/ Changeset: ebdaa310677b User: saketkc Date: 2013-06-19 08:52:22 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 170dd4c157b8b5e010804ba4a1ef3b5da08fa49d -r ebdaa310677b57337f5fcc0= aa2ac475379bf271c tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/493bee44220a/ Changeset: 493bee44220a User: saketkc Date: 2013-06-20 05:58:14 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 36d9e5bcd2cbcd5b34b2ae0e7839a71a55350011 -r 493bee44220a54f4d0595bf= 3fd49efdf8a8795bd tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/a52434fb61a8/ Changeset: a52434fb61a8 User: saketkc Date: 2013-06-20 18:32:29 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 7362302b2c638d377931fa710d40ba2f86f25dba -r a52434fb61a8968735ed1b5= 03b6a5b2b253963ea tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/b1bb5b64dd8e/ Changeset: b1bb5b64dd8e User: saketkc Date: 2013-06-20 18:58:11 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 13b5283f964cfa7364b653f2c578b4d7cc27c6e5 -r b1bb5b64dd8eb871451b6bd= 489cc26a6c08dbb7e tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/caa8fd7a0dcf/ Changeset: caa8fd7a0dcf User: saketkc Date: 2013-06-20 19:02:55 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 89e7db1cd8098fd6191ab3b4af92e4af32e4c651 -r caa8fd7a0dcf279fec70c3d= 1581296610fc6f636 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/adb63b769897/ Changeset: adb63b769897 User: saketkc Date: 2013-06-21 07:01:54 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r cf58e35b3a973311ab291e90b501c6f4bc31b6d3 -r adb63b769897f2d2f34b935= d1a9597df6d1a9cdf tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/b092c9d9a17b/ Changeset: b092c9d9a17b User: saketkc Date: 2013-06-21 12:18:18 Summary: Automated merge with ssh://bitbucket.org/saketkc/galaxy-central Affected #: 1 file diff -r adb63b769897f2d2f34b935d1a9597df6d1a9cdf -r b092c9d9a17b448e5cb7249= 828dbcd90ab27f1f1 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -246,8 +246,8 @@ return module_factory.from_dict(trans, from_json_string(st= ep.config), secure=3DFalse) module =3D Class( trans, tool_id ) module.state =3D galaxy.tools.DefaultToolState() - if step.tool_version and (step.tool_version !=3D tool.version= ): - module.version_changes.append("%s: using version '%s' inst= ead of version '%s' indicated in this workflow." % (tool_id, tool.version, = step.tool_version)) + if step.tool_version and (step.tool_version !=3D module.tool.v= ersion): + module.version_changes.append("%s: using version '%s' inst= ead of version '%s' indicated in this workflow." % (tool_id, module.tool.ve= rsion, step.tool_version)) module.state.inputs =3D module.tool.params_from_strings( step.= tool_inputs, trans.app, ignore_errors=3DTrue ) module.errors =3D step.tool_errors # module.post_job_actions =3D step.post_job_actions https://bitbucket.org/galaxy/galaxy-central/commits/46f4beebb766/ Changeset: 46f4beebb766 User: saketkc Date: 2013-06-22 12:02:56 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 4f7b7e4ca213498824d5fba7526676ddf976b823 -r 46f4beebb766fd75edb59bc= 3598342ef95775af9 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/1ff57c7a9deb/ Changeset: 1ff57c7a9deb User: saketkc Date: 2013-06-26 21:44:43 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 62 files diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -267,25 +267,25 @@ # bam does not use '#' to indicate comments/headers - we need to strip= out those headers from the std. providers #TODO:?? seems like there should be an easier way to do/inherit this -= metadata.comment_char? #TODO: incorporate samtools options to control output: regions first, = then flags, etc. - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.= line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): samtools_source =3D dataproviders.dataset.SamtoolsDataProvider( da= taset ) settings[ 'comment_char' ] =3D '@' return dataproviders.line.FilteredLineDataProvider( samtools_sourc= e, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataprov= iders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): samtools_source =3D dataproviders.dataset.SamtoolsDataProvider( da= taset ) settings[ 'comment_char' ] =3D '@' return dataproviders.line.RegexLineDataProvider( samtools_source, = **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataprovider= s.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): samtools_source =3D dataproviders.dataset.SamtoolsDataProvider( da= taset ) settings[ 'comment_char' ] =3D '@' return dataproviders.column.ColumnarDataProvider( samtools_source,= **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.c= olumn.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): samtools_source =3D dataproviders.dataset.SamtoolsDataProvider( da= taset ) settings[ 'comment_char' ] =3D '@' @@ -293,30 +293,30 @@ =20 # these can't be used directly - may need BamColumn, BamMap (Bam metad= ata -> column/map) # OR - see genomic_region_dataprovider - #(a)dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + #(a)dataproviders.decorators.dataprovider_factory( 'dataset-column', dat= aproviders.column.ColumnarDataProvider.settings ) #def dataset_column_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] =3D '@' # return super( Sam, self ).dataset_column_dataprovider( dataset, *= *settings ) =20 - #(a)dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + #(a)dataproviders.decorators.dataprovider_factory( 'dataset-map', datapr= oviders.column.MapDataProvider.settings ) #def dataset_map_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] =3D '@' # return super( Sam, self ).dataset_map_dataprovider( dataset, **se= ttings ) =20 - @dataproviders.decorators.dataprovider_factory( 'header' ) + @dataproviders.decorators.dataprovider_factory( 'header', dataprovider= s.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): # in this case we can use an option of samtools view to provide ju= st what we need (w/o regex) samtools_source =3D dataproviders.dataset.SamtoolsDataProvider( da= taset, '-H' ) return dataproviders.line.RegexLineDataProvider( samtools_source, = **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual' ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', datapro= viders.column.MapDataProvider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] =3D [ 0, 9, 10 ] settings[ 'column_types' ] =3D [ 'str', 'str', 'str' ] settings[ 'column_names' ] =3D [ 'id', 'seq', 'qual' ] return self.map_dataprovider( dataset, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', data= providers.column.ColumnarDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): # GenomicRegionDataProvider currently requires a dataset as source= - may not be necc. #TODO:?? consider (at least) the possible use of a kwarg: metadata= _source (def. to source.dataset), @@ -330,7 +330,7 @@ settings[ 'column_types' ] =3D [ 'str', 'int', 'int' ] return self.column_dataprovider( dataset, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', = dataproviders.column.MapDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] =3D [ 2, 3, 3 ] settings[ 'column_types' ] =3D [ 'str', 'int', 'int' ] diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -593,7 +593,6 @@ Base dataprovider factory for all datatypes that returns the prope= r provider for the given `data_format` or raises a `NoProviderAvailable`. """ - #TODO:?? is this handling super class providers? if self.has_dataprovider( data_format ): return self.dataproviders[ data_format ]( self, dataset, **set= tings ) raise dataproviders.exceptions.NoProviderAvailable( self, data_for= mat ) @@ -603,12 +602,12 @@ dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) return dataproviders.base.DataProvider( dataset_source, **settings= ) =20 - @dataproviders.decorators.dataprovider_factory( 'chunk' ) + @dataproviders.decorators.dataprovider_factory( 'chunk', dataproviders= .chunk.ChunkDataProvider.settings ) def chunk_dataprovider( self, dataset, **settings ): dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) return dataproviders.chunk.ChunkDataProvider( dataset_source, **se= ttings ) =20 - @dataproviders.decorators.dataprovider_factory( 'chunk64' ) + @dataproviders.decorators.dataprovider_factory( 'chunk64', dataprovide= rs.chunk.Base64ChunkDataProvider.settings ) def chunk64_dataprovider( self, dataset, **settings ): dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) return dataproviders.chunk.Base64ChunkDataProvider( dataset_source= , **settings ) @@ -785,7 +784,7 @@ split =3D classmethod(split) =20 # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.= line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): """ Returns an iterator over the dataset's lines (that have been `stri= p`ed) @@ -794,7 +793,7 @@ dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) return dataproviders.line.FilteredLineDataProvider( dataset_source= , **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataprov= iders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): """ Returns an iterator over the dataset's lines diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/dataproviders/base.py --- a/lib/galaxy/datatypes/dataproviders/base.py +++ b/lib/galaxy/datatypes/dataproviders/base.py @@ -22,8 +22,13 @@ =20 icorporate existing visualization/dataproviders some of the sources (esp. in datasets) don't need to be re-created +YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvid= er =20 -YAGNI: InterleavingMultiSourceDataProvider, CombiningMultiSourceDataProvid= er +datasets API entry point: + kwargs should be parsed from strings 2 layers up (in the DatasetsAPI) = - that's the 'proper' place for that. + but how would it know how/what to parse if it doesn't have access to t= he classes used in the provider? + Building a giant list by sweeping all possible dprov classes doesn= 't make sense + For now - I'm burying them in the class __init__s - but I don't like t= hat """ =20 import logging @@ -31,6 +36,31 @@ =20 =20 # ------------------------------------------------------------------------= ----- base classes +class HasSettings( type ): + """ + Metaclass for data providers that allows defining and inheriting + a dictionary named 'settings'. + + Useful for allowing class level access to expected variable types + passed to class `__init__` functions so they can be parsed from a quer= y string. + """ + # yeah - this is all too acrobatic + def __new__( cls, name, base_classes, attributes ): + settings =3D {} + # get settings defined in base classes + for base_class in base_classes: + base_settings =3D getattr( base_class, 'settings', None ) + if base_settings: + settings.update( base_settings ) + # get settings defined in this class + new_settings =3D attributes.pop( 'settings', None ) + if new_settings: + settings.update( new_settings ) + attributes[ 'settings' ] =3D settings + return type.__new__( cls, name, base_classes, attributes ) + + +# ------------------------------------------------------------------------= ----- base classes class DataProvider( object ): """ Base class for all data providers. Data providers: @@ -39,6 +69,12 @@ (c) do not allow write methods (but otherwise implement the other file object interface metho= ds) """ + # a definition of expected types for keyword arguments sent to __init__ + # useful for controlling how query string dictionaries can be parsed= into correct types for __init__ + # empty in this base class + __metaclass__ =3D HasSettings + settings =3D {} + def __init__( self, source, **kwargs ): """ :param source: the source that this iterator will loop over. @@ -130,13 +166,16 @@ - `num_valid_data_read`: how many data have been returned from `fi= lter`. - `num_data_returned`: how many data has this provider yielded. """ + # not useful here - we don't want functions over the query string + #settings.update({ 'filter_fn': 'function' }) + def __init__( self, source, filter_fn=3DNone, **kwargs ): """ :param filter_fn: a lambda or function that will be passed a datum= and return either the (optionally modified) datum or None. """ super( FilteredDataProvider, self ).__init__( source, **kwargs ) - self.filter_fn =3D filter_fn + self.filter_fn =3D filter_fn if hasattr( filter_fn, '__call__' ) e= lse None # count how many data we got from the source self.num_data_read =3D 0 # how many valid data have we gotten from the source @@ -179,6 +218,12 @@ =20 Useful for grabbing sections from a source (e.g. pagination). """ + # define the expected types of these __init__ arguments so they can be= parsed out from query strings + settings =3D { + 'limit' : 'int', + 'offset': 'int' + } + #TODO: may want to squash this into DataProvider def __init__( self, source, offset=3D0, limit=3DNone, **kwargs ): """ diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/dataproviders/chunk.py --- a/lib/galaxy/datatypes/dataproviders/chunk.py +++ b/lib/galaxy/datatypes/dataproviders/chunk.py @@ -26,6 +26,10 @@ """ MAX_CHUNK_SIZE =3D 2**16 DEFAULT_CHUNK_SIZE =3D MAX_CHUNK_SIZE + settings =3D { + 'chunk_index' : 'int', + 'chunk_size' : 'int' + } =20 #TODO: subclass from LimitedOffsetDataProvider? # see web/framework/base.iterate_file, util/__init__.file_reader, and = datatypes.tabular @@ -38,8 +42,8 @@ (gen. in bytes). """ super( ChunkDataProvider, self ).__init__( source, **kwargs ) - self.chunk_size =3D chunk_size - self.chunk_pos =3D chunk_index * self.chunk_size + self.chunk_size =3D int( chunk_size ) + self.chunk_pos =3D int( chunk_index ) * self.chunk_size =20 def validate_source( self, source ): """ diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/dataproviders/column.py --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -29,6 +29,14 @@ the same number of columns as the number of indeces asked for (even if= they are filled with None). """ + settings =3D { + 'indeces' : 'list:int', + 'column_count' : 'int', + 'column_types' : 'list:str', + 'parse_columns' : 'bool', + 'deliminator' : 'str' + } + def __init__( self, source, indeces=3DNone, column_count=3DNone, column_types=3DNone, parsers=3DNone, pars= e_columns=3DTrue, deliminator=3D'\t', **kwargs ): @@ -91,11 +99,11 @@ # how/whether to parse each column value self.parsers =3D {} if parse_columns: - self.parsers =3D self._get_default_parsers() + self.parsers =3D self.get_default_parsers() # overwrite with user desired parsers self.parsers.update( parsers or {} ) =20 - def _get_default_parsers( self ): + def get_default_parsers( self ): """ Return parser dictionary keyed for each columnar type (as defined in datatypes). @@ -132,7 +140,7 @@ #'gffstrand': # -, +, ?, or '.' for None, etc. } =20 - def _parse_value( self, val, type ): + def parse_value( self, val, type ): """ Attempt to parse and return the given value based on the given typ= e. =20 @@ -153,7 +161,7 @@ return None return val =20 - def _get_column_type( self, index ): + def get_column_type( self, index ): """ Get the column type for the parser from `self.column_types` or `No= ne` if the type is unavailable. @@ -165,18 +173,18 @@ except IndexError, ind_err: return None =20 - def _parse_column_at_index( self, columns, parser_index, index ): + def parse_column_at_index( self, columns, parser_index, index ): """ Get the column type for the parser from `self.column_types` or `No= ne` if the type is unavailable. """ try: - return self._parse_value( columns[ index ], self._get_column_t= ype( parser_index ) ) + return self.parse_value( columns[ index ], self.get_column_typ= e( parser_index ) ) # if a selected index is not within columns, return None except IndexError, index_err: return None =20 - def _parse_columns_from_line( self, line ): + def parse_columns_from_line( self, line ): """ Returns a list of the desired, parsed columns. :param line: the line to parse @@ -188,13 +196,13 @@ selected_indeces =3D self.selected_column_indeces or list( xrange(= len( all_columns ) ) ) parsed_columns =3D [] for parser_index, column_index in enumerate( selected_indeces ): - parsed_columns.append( self._parse_column_at_index( all_column= s, parser_index, column_index ) ) + parsed_columns.append( self.parse_column_at_index( all_columns= , parser_index, column_index ) ) return parsed_columns =20 def __iter__( self ): parent_gen =3D super( ColumnarDataProvider, self ).__iter__() for line in parent_gen: - columns =3D self._parse_columns_from_line( line ) + columns =3D self.parse_columns_from_line( line ) yield columns =20 #TODO: implement column filters here and not below - flatten hierarchy @@ -223,6 +231,10 @@ .. note: that the subclass constructors are passed kwargs - so they're params (limit, offset, etc.) are also applicable here. """ + settings =3D { + 'column_names' : 'list:str', + } + def __init__( self, source, column_names=3DNone, **kwargs ): """ :param column_names: an ordered list of strings that will be used = as the keys diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -141,7 +141,7 @@ """ # metadata columns are 1-based indeces column =3D getattr( self.dataset.metadata, name ) - return ( column - 1 ) if isinstance( column, int ) else None + return ( column - 1 ) if ( isinstance( column, int ) and column > = 0 ) else None =20 def get_genomic_region_indeces( self, check=3DFalse ): """ @@ -271,6 +271,12 @@ """ # dictionary keys when named_columns=3DTrue COLUMN_NAMES =3D [ 'chrom', 'start', 'end' ] + settings =3D { + 'chrom_column' : 'int', + 'start_column' : 'int', + 'end_column' : 'int', + 'named_columns' : 'bool', + } =20 def __init__( self, dataset, chrom_column=3DNone, start_column=3DNone,= end_column=3DNone, named_columns=3DFalse, **kwargs ): """ @@ -333,6 +339,14 @@ 'chrom', 'start', 'end' (and 'strand' and 'name' if available). """ COLUMN_NAMES =3D [ 'chrom', 'start', 'end', 'strand', 'name' ] + settings =3D { + 'chrom_column' : 'int', + 'start_column' : 'int', + 'end_column' : 'int', + 'strand_column' : 'int', + 'name_column' : 'int', + 'named_columns' : 'bool', + } =20 def __init__( self, dataset, chrom_column=3DNone, start_column=3DNone,= end_column=3DNone, strand_column=3DNone, name_column=3DNone, named_columns= =3DFalse, **kwargs ): @@ -349,25 +363,40 @@ dataset_source =3D DatasetDataProvider( dataset ) =20 # get genomic indeces and add strand and name + self.column_names =3D [] + indeces =3D [] + #TODO: this is sort of involved and oogly if chrom_column =3D=3D None: chrom_column =3D dataset_source.get_metadata_column_index_by_n= ame( 'chromCol' ) + if chrom_column !=3D None: + self.column_names.append( 'chrom' ) + indeces.append( chrom_column ) if start_column =3D=3D None: start_column =3D dataset_source.get_metadata_column_index_by_n= ame( 'startCol' ) + if start_column !=3D None: + self.column_names.append( 'start' ) + indeces.append( start_column ) if end_column =3D=3D None: end_column =3D dataset_source.get_metadata_column_index_by_nam= e( 'endCol' ) + if end_column !=3D None: + self.column_names.append( 'end' ) + indeces.append( end_column ) if strand_column =3D=3D None: strand_column =3D dataset_source.get_metadata_column_index_by_= name( 'strandCol' ) + if strand_column !=3D None: + self.column_names.append( 'strand' ) + indeces.append( strand_column ) if name_column =3D=3D None: name_column =3D dataset_source.get_metadata_column_index_by_na= me( 'nameCol' ) - indeces =3D [ chrom_column, start_column, end_column, strand_colum= n, name_column ] + if name_column !=3D None: + self.column_names.append( 'name' ) + indeces.append( name_column ) + kwargs.update({ 'indeces' : indeces }) - if not kwargs.get( 'column_types', None ): kwargs.update({ 'column_types' : dataset_source.get_metadata_c= olumn_types( indeces=3Dindeces ) }) =20 self.named_columns =3D named_columns - if self.named_columns: - self.column_names =3D self.COLUMN_NAMES =20 super( IntervalDataProvider, self ).__init__( dataset_source, **kw= args ) =20 @@ -390,6 +419,10 @@ sequence: <joined lines of nucleotide/amino data> } """ + settings =3D { + 'ids' : 'list:str', + } + def __init__( self, source, ids=3DNone, **kwargs ): """ :param ids: optionally return only ids (and sequences) that are in= this list. @@ -419,6 +452,10 @@ sequence: <joined lines of nucleotide/amino data> } """ + settings =3D { + 'ids' : 'list:str', + } + def __init__( self, source, ids=3DNone, **kwargs ): """ :param ids: optionally return only ids (and sequences) that are in= this list. @@ -445,6 +482,10 @@ Class that returns chrom, pos, data from a wiggle source. """ COLUMN_NAMES =3D [ 'chrom', 'pos', 'value' ] + settings =3D { + 'named_columns' : 'bool', + 'column_names' : 'list:str', + } =20 def __init__( self, source, named_columns=3DFalse, column_names=3DNone= , **kwargs ): """ @@ -483,6 +524,10 @@ Class that returns chrom, pos, data from a wiggle source. """ COLUMN_NAMES =3D [ 'chrom', 'pos', 'value' ] + settings =3D { + 'named_columns' : 'bool', + 'column_names' : 'list:str', + } =20 def __init__( self, source, chrom, start, end, named_columns=3DFalse, = column_names=3DNone, **kwargs ): """ diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/dataproviders/decorators.py --- a/lib/galaxy/datatypes/dataproviders/decorators.py +++ b/lib/galaxy/datatypes/dataproviders/decorators.py @@ -87,17 +87,40 @@ # log.debug( '\t\t ', fn.__doc__ ) return cls =20 -def dataprovider_factory( name ): +def dataprovider_factory( name, settings=3DNone ): """ - Wraps a class method and marks it as a dataprovider factory. + Wraps a class method and marks it as a dataprovider factory and create= s a + function to parse query strings to __init__ arguments as the + `parse_query_string_settings` attribute of the factory function. + + An example use of the `parse_query_string_settings`: + ..example:: + kwargs =3D dataset.datatype.dataproviders[ provider ].parse_query_stri= ng_settings( query_kwargs ) + return list( dataset.datatype.dataprovider( dataset, provider, **kwarg= s ) ) =20 :param name: what name/key to register the factory under in `cls.datap= roviders` - :param type: any hashable var + :type name: any hashable var + :param settings: dictionary containing key/type pairs for parsing quer= y strings + to __init__ arguments + :type settings: dictionary """ + #TODO:?? use *args for settings allowing mulitple dictionaries + # make a function available through the name->provider dispatch to par= se query strings + # callable like: + # settings_dict =3D dataproviders[ provider_name ].parse_query_string_= settings( query_kwargs ) + #TODO: ugh - overly complicated but the best I could think of + def parse_query_string_settings( query_kwargs ): + return _parse_query_string_settings( query_kwargs, settings ) + #log.debug( 'dataprovider:', name ) def named_dataprovider_factory( func ): #log.debug( 'named_dataprovider_factory:', name, '->', func.__name= __ ) setattr( func, _DATAPROVIDER_METHOD_NAME_KEY, name ) + + setattr( func, 'parse_query_string_settings', parse_query_string_s= ettings ) + setattr( func, 'settings', settings ) + #TODO: I want a way to inherit settings from the previous provider= ( this_name ) instead of defining over and over + #log.debug( '\t setting:', getattr( func, _DATAPROVIDER_METHOD_NAM= E_KEY ) ) @wraps( func ) def wrapped_dataprovider_factory( self, *args, **kwargs ): @@ -105,3 +128,38 @@ return func( self, *args, **kwargs ) return wrapped_dataprovider_factory return named_dataprovider_factory + +def _parse_query_string_settings( query_kwargs, settings=3DNone ): + """ + Parse the values in `query_kwargs` from strings to the proper types + listed in the same key in `settings`. + """ + def list_from_query_string( s ): + # assume csv + return s.split( ',' ) + + parsers =3D { + 'int' : int, + 'float' : float, + 'bool' : bool, + 'list:str' : lambda s: list_from_query_string( s ), + 'list:int' : lambda s: [ int( i ) for i in list_from_query_string= ( s ) ], + } + settings =3D settings or {} + # yay! yet another set of query string parsers! <-- sarcasm + # work through the keys in settings finding matching keys in query_kwa= rgs + # if found in both, get the expected/needed type from settings and s= tore the new parsed value + # if we can't parse it (no parser, bad value), delete the key from q= uery_kwargs so the provider will use the defaults + for key in settings: + if key in query_kwargs: + #TODO: this would be the place to sanitize any strings + query_value =3D query_kwargs[ key ] + needed_type =3D settings[ key ] + try: + query_kwargs[ key ] =3D parsers[ needed_type ]( query_valu= e ) + except ( KeyError, ValueError ): + del query_kwargs[ key ] + + #TODO:?? do we want to remove query_kwarg entries NOT in settings? + return query_kwargs + diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/dataproviders/line.py --- a/lib/galaxy/datatypes/dataproviders/line.py +++ b/lib/galaxy/datatypes/dataproviders/line.py @@ -27,6 +27,12 @@ to return. """ DEFAULT_COMMENT_CHAR =3D '#' + settings =3D { + 'string_lines' : 'bool', + 'provide_blank' : 'bool', + 'comment_char' : 'str', + } + def __init__( self, source, strip_lines=3DTrue, provide_blank=3DFalse,= comment_char=3DDEFAULT_COMMENT_CHAR, **kwargs ): """ :param strip_lines: remove whitespace from the beginning an ending @@ -78,6 +84,11 @@ .. note:: the regex matches are effectively OR'd (if **any** regex mat= ches the line it is considered valid and will be provided). """ + settings =3D { + 'regex_list' : 'list:str', + 'invert' : 'bool', + } + def __init__( self, source, regex_list=3DNone, invert=3DFalse, **kwarg= s ): """ :param regex_list: list of strings or regular expression strings t= hat will diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -334,20 +334,24 @@ return None =20 # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, *= *settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] =3D True return self.genomic_region_dataprovider( dataset, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'interval' ) + @dataproviders.decorators.dataprovider_factory( 'interval', + dataproviders.dataset.= IntervalDataProvider.settings ) def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, **sett= ings ) =20 - @dataproviders.decorators.dataprovider_factory( 'interval-map' ) + @dataproviders.decorators.dataprovider_factory( 'interval-map', + dataproviders.dataset.= IntervalDataProvider.settings ) def interval_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] =3D True return self.interval_dataprovider( dataset, **settings ) @@ -809,20 +813,24 @@ =20 # ------------- Dataproviders # redefine bc super is Tabular - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0= , 3, 4, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] =3D True return self.genomic_region_dataprovider( dataset, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'interval' ) + @dataproviders.decorators.dataprovider_factory( 'interval', + dataproviders.dataset.= IntervalDataProvider.settings ) def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, 0, 3, = 4, 6, 2, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'interval-map' ) + @dataproviders.decorators.dataprovider_factory( 'interval-map', + dataproviders.dataset.= IntervalDataProvider.settings ) def interval_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] =3D True return self.interval_dataprovider( dataset, **settings ) @@ -1193,12 +1201,12 @@ return resolution =20 # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'wiggle' ) + @dataproviders.decorators.dataprovider_factory( 'wiggle', dataprovider= s.dataset.WiggleDataProvider.settings ) def wiggle_dataprovider( self, dataset, **settings ): dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) return dataproviders.dataset.WiggleDataProvider( dataset_source, *= *settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'wiggle-map' ) + @dataproviders.decorators.dataprovider_factory( 'wiggle-map', dataprov= iders.dataset.WiggleDataProvider.settings ) def wiggle_map_dataprovider( self, dataset, **settings ): dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) settings[ 'named_columns' ] =3D True diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -15,8 +15,6 @@ from galaxy import util from sniff import * =20 -from galaxy.datatypes import dataproviders - import pkg_resources pkg_resources.require("simplejson") import simplejson @@ -399,15 +397,6 @@ f.close() _count_split =3D classmethod(_count_split) =20 - def provider( self, dataset, data_format, **settings ): - from galaxy.dataproviders import dataset as dataset_providers - - if data_format =3D=3D 'id_seq': - source =3D dataset_providers.DatasetDataProvider( dataset ) - return dataset_providers.FastaDataProvider( source, **settings= ) - - return super( Fasta, self ).provider( dataset, data_format, **sett= ings ) - =20 class csFasta( Sequence ): """ Class representing the SOLID Color-Space sequence ( csfasta ) """ diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -6,6 +6,7 @@ from galaxy import util from galaxy.datatypes.checkers import * from encodings import search_function as encodings_search_function +from binary import Binary =20 log =3D logging.getLogger(__name__) =20 diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -345,26 +345,25 @@ return vizs =20 # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataprovider= s.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): """Uses column settings that are passed in""" - print 'Tabular.comment_char:', settings.get( 'comment_char', None ) - dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) return dataproviders.column.ColumnarDataProvider( dataset_source, = **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-column', + dataproviders.column.C= olumnarDataProvider.settings ) def dataset_column_dataprovider( self, dataset, **settings ): """Attempts to get column settings from dataset.metadata""" return dataproviders.dataset.DatasetColumnarDataProvider( dataset,= **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.c= olumn.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): """Uses column settings that are passed in""" dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) return dataproviders.column.MapDataProvider( dataset_source, **set= tings ) =20 - @dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-map', datapro= viders.column.MapDataProvider.settings ) def dataset_map_dataprovider( self, dataset, **settings ): """Attempts to get column settings from dataset.metadata""" return dataproviders.dataset.DatasetMapDataProvider( dataset, **se= ttings ) @@ -502,55 +501,58 @@ # ------------- Dataproviders # sam does not use '#' to indicate comments/headers - we need to strip= out those headers from the std. providers #TODO:?? seems like there should be an easier way to do this - metadat= a.comment_char? - @dataproviders.decorators.dataprovider_factory( 'line' ) + @dataproviders.decorators.dataprovider_factory( 'line', dataproviders.= line.FilteredLineDataProvider.settings ) def line_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return super( Sam, self ).line_dataprovider( dataset, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'regex-line' ) + @dataproviders.decorators.dataprovider_factory( 'regex-line', dataprov= iders.line.RegexLineDataProvider.settings ) def regex_line_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return super( Sam, self ).regex_line_dataprovider( dataset, **sett= ings ) =20 - @dataproviders.decorators.dataprovider_factory( 'column' ) + @dataproviders.decorators.dataprovider_factory( 'column', dataprovider= s.column.ColumnarDataProvider.settings ) def column_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return super( Sam, self ).column_dataprovider( dataset, **settings= ) =20 - @dataproviders.decorators.dataprovider_factory( 'dataset-column' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-column', + dataproviders.column.C= olumnarDataProvider.settings ) def dataset_column_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return super( Sam, self ).dataset_column_dataprovider( dataset, **= settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'map' ) + @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.c= olumn.MapDataProvider.settings ) def map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return super( Sam, self ).map_dataprovider( dataset, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'dataset-map' ) + @dataproviders.decorators.dataprovider_factory( 'dataset-map', datapro= viders.column.MapDataProvider.settings ) def dataset_map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return super( Sam, self ).dataset_map_dataprovider( dataset, **set= tings ) =20 - @dataproviders.decorators.dataprovider_factory( 'header' ) + @dataproviders.decorators.dataprovider_factory( 'header', dataprovider= s.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): dataset_source =3D dataproviders.dataset.DatasetDataProvider( data= set ) headers_source =3D dataproviders.line.RegexLineDataProvider( datas= et_source, regex_list=3D[ '^@' ] ) return dataproviders.line.RegexLineDataProvider( headers_source, *= *settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual' ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', map_dat= aprovider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): # provided as an example of a specified column map (w/o metadata) settings[ 'indeces' ] =3D [ 0, 9, 10 ] settings[ 'column_names' ] =3D [ 'id', 'seq', 'qual' ] return self.map_dataprovider( dataset, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2= , 3, 3, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] =3D '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2= , 3, 3, True, **settings ) @@ -621,11 +623,13 @@ return False =20 # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, *= *settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] =3D True return self.genomic_region_dataprovider( dataset, **settings ) @@ -668,11 +672,13 @@ dataset.metadata.sample_names =3D line.split()[ 9: ] =20 # ------------- Dataproviders - @dataproviders.decorators.dataprovider_factory( 'genomic-region' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0= , 1, 1, **settings ) =20 - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map' ) + @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + dataproviders.dataset.= GenomicRegionDataProvider.settings ) def genomic_region_map_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] =3D True return self.genomic_region_dataprovider( dataset, **settings ) diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -32,7 +32,7 @@ "bigwig": genome.BigWigDataProvider, "bigbed": genome.BigBedDataProvider, =20 - "column": ColumnDataProvider + "column_with_stats": ColumnDataProvider } =20 def get_data_provider( self, trans, name=3DNone, source=3D'data', raw= =3DFalse, original_dataset=3DNone ): diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -15,22 +15,27 @@ log =3D logging.getLogger( __name__ ) =20 __TODO__ =3D """ - BUGS: - anon users clicking a viz link gets 'must be' msg in galaxy_main (= w/ masthead) - should not show visualizations (no icon)? - newick files aren't being sniffed prop? - datatype is txt +BUGS: + anon users clicking a viz link gets 'must be' msg in galaxy_main (w/ m= asthead) + should not show visualizations (no icon)? + newick files aren't being sniffed prop? - datatype is txt =20 - have parsers create objects instead of dicts - allow data_sources with no model_class but have tests (isAdmin, etc.) - maybe that's an instance of User model_class? - some confused vocabulary in docs, var names - tests: - anding, grouping, not - data_sources: - lists of - add description element to visualization. +have parsers create objects instead of dicts +allow data_sources with no model_class but have tests (isAdmin, etc.) + maybe that's an instance of User model_class? +some confused vocabulary in docs, var names +tests: + anding, grouping, not +data_sources: + lists of +add description element to visualization. + +TESTS to add: + has dataprovider + user is admin """ =20 +# ------------------------------------------------------------------- the = registry class VisualizationsRegistry( object ): """ Main responsibilities are: @@ -93,6 +98,45 @@ """ self.listings =3D VisualizationsConfigParser.parse( self.configura= tion_filepath ) =20 + def get_visualization( self, trans, visualization_name, target_object = ): + """ + Return data to build a url to the visualization with the given + `visualization_name` if it's applicable to `target_object` or + `None` if it's not. + """ + # a little weird to pass trans because this registry is part of th= e trans.app + listing_data =3D self.listings.get( visualization_name, None ) + if not listing_data: + return None + + data_sources =3D listing_data[ 'data_sources' ] + for data_source in data_sources: + # currently a model class is required + model_class =3D data_source[ 'model_class' ] + if not isinstance( target_object, model_class ): + continue + + # tests are optional - default is the above class test + tests =3D data_source[ 'tests' ] + if tests and not self.is_object_applicable( trans, target_obje= ct, tests ): + continue + + param_data =3D data_source[ 'to_params' ] + url =3D self.get_visualization_url( trans, target_object, visu= alization_name, param_data ) + link_text =3D listing_data.get( 'link_text', None ) + if not link_text: + # default to visualization name, titlecase, and replace un= derscores + link_text =3D visualization_name.title().replace( '_', ' '= ) + render_location =3D listing_data.get( 'render_location' ) + # remap some of these vars for direct use in ui.js, PopupMenu = (e.g. text->html) + return { + 'href' : url, + 'html' : link_text, + 'target': render_location + } + + return None + # -- building links to visualizations from objects -- def get_visualizations( self, trans, target_object ): """ @@ -100,36 +144,11 @@ the urls to call in order to render the visualizations. """ #TODO:?? a list of objects? YAGNI? - # a little weird to pass trans because this registry is part of th= e trans.app applicable_visualizations =3D [] - for vis_name, listing_data in self.listings.items(): - - data_sources =3D listing_data[ 'data_sources' ] - for data_source in data_sources: - # currently a model class is required - model_class =3D data_source[ 'model_class' ] - if not isinstance( target_object, model_class ): - continue - - # tests are optional - default is the above class test - tests =3D data_source[ 'tests' ] - if tests and not self.is_object_applicable( trans, target_= object, tests ): - continue - - param_data =3D data_source[ 'to_params' ] - url =3D self.get_visualization_url( trans, target_object, = vis_name, param_data ) - link_text =3D listing_data.get( 'link_text', None ) - if not link_text: - # default to visualization name, titlecase, and replac= e underscores - link_text =3D vis_name.title().replace( '_', ' ' ) - render_location =3D listing_data.get( 'render_location' ) - # remap some of these vars for direct use in ui.js, PopupM= enu (e.g. text->html) - applicable_visualizations.append({ - 'href' : url, - 'html' : link_text, - 'target': render_location - }) - + for vis_name in self.listings: + url_data =3D self.get_visualization( trans, vis_name, target_o= bject ) + if url_data: + applicable_visualizations.append( url_data ) return applicable_visualizations =20 def is_object_applicable( self, trans, target_object, data_source_test= s ): @@ -151,10 +170,11 @@ # convert datatypes to their actual classes (for use w= ith isinstance) test_result =3D trans.app.datatypes_registry.get_datat= ype_class_by_name( test_result ) if not test_result: - # warn if can't find class, but continue + # warn if can't find class, but continue (with oth= er tests) log.warn( 'visualizations_registry cannot find cla= ss (%s) for applicability test', test_result ) continue =20 + #NOTE: tests are OR'd, if any test passes - the visualization = can be applied if test_fn( target_object, test_result ): #log.debug( 'test passed' ) return True diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -6,6 +6,7 @@ from galaxy.web.base.controller import BaseAPIController, UsesVisualizatio= nMixin, UsesHistoryDatasetAssociationMixin from galaxy.web.base.controller import UsesHistoryMixin from galaxy.web.framework.helpers import is_true +from galaxy.datatypes import dataproviders =20 import logging log =3D logging.getLogger( __name__ ) @@ -217,10 +218,24 @@ return msg =20 registry =3D trans.app.data_provider_registry + # allow the caller to specifiy which provider is used - if provider and provider in registry.dataset_type_name_to_data_pro= vider: - data_provider =3D registry.dataset_type_name_to_data_provider[= provider ]( dataset ) - # or have it look up by datatype + # pulling from the original providers if possible, then the new = providers + if provider: + if provider in registry.dataset_type_name_to_data_provider: + data_provider =3D registry.dataset_type_name_to_data_provi= der[ provider ]( dataset ) + + elif dataset.datatype.has_dataprovider( provider ): + kwargs =3D dataset.datatype.dataproviders[ provider ].pars= e_query_string_settings( kwargs ) + # use dictionary to allow more than the data itself to be = returned (data totals, other meta, etc.) + return { + 'data': list( dataset.datatype.dataprovider( dataset, = provider, **kwargs ) ) + } + + else: + raise dataproviders.exceptions.NoProviderAvailable( datase= t.datatype, provider ) + + # no provider name: look up by datatype else: data_provider =3D registry.get_data_provider( trans, raw=3DTru= e, original_dataset=3Ddataset ) =20 diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -179,6 +179,11 @@ # Get the information about the Galaxy components (e.g., tool pane= section, tool config file, etc) that will contain the repository informati= on. install_repository_dependencies =3D payload.get( 'install_reposito= ry_dependencies', False ) install_tool_dependencies =3D payload.get( 'install_tool_dependenc= ies', False ) + if install_tool_dependencies: + if trans.app.config.tool_dependency_dir is None: + no_tool_dependency_dir_message =3D "Tool dependencies can = be automatically installed only if you set the value of your 'tool_dependen= cy_dir' " + no_tool_dependency_dir_message +=3D "setting in your Galax= y configuration file (universe_wsgi.ini) and restart your Galaxy server." + raise HTTPBadRequest( detail=3Dno_tool_dependency_dir_mess= age ) new_tool_panel_section =3D payload.get( 'new_tool_panel_section_la= bel', '' ) shed_tool_conf =3D payload.get( 'shed_tool_conf', None ) if shed_tool_conf: @@ -211,13 +216,8 @@ tool_path=3Dtool_path, tool_shed_url=3Dtool_shed_url ) # Create the tool_shed_repository database records and gather addi= tional information for repository installation. - created_or_updated_tool_shed_repositories, tool_panel_section_keys= , repo_info_dicts, filtered_repo_info_dicts, message =3D \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys= , repo_info_dicts, filtered_repo_info_dicts =3D \ repository_util.handle_tool_shed_repositories( trans, installa= tion_dict, using_api=3DTrue ) - if message and len( repo_info_dicts ) =3D=3D 1: - # We're attempting to install a single repository that has alr= eady been installed into this Galaxy instance. - log.error( message, exc_info=3DTrue ) - trans.response.status =3D 500 - return dict( status=3D'error', error=3Dmessage ) if created_or_updated_tool_shed_repositories: # Build the dictionary of information necessary for installing= the repositories. installation_dict =3D dict( created_or_updated_tool_shed_repos= itories=3Dcreated_or_updated_tool_shed_repositories, @@ -266,11 +266,7 @@ acti= on=3D'show', id= =3Dtrans.security.encode_id( tool_shed_repository.id ) ) installed_tool_shed_repositories.append( tool_shed_rep= ository_dict ) - elif message: - log.error( message, exc_info=3DTrue ) - trans.response.status =3D 500 - return dict( status=3D'error', error=3Dmessage ) - elif not created_or_updated_tool_shed_repositories and not message: + else: # We're attempting to install more than 1 repository, and all = of them have already been installed. return dict( status=3D'error', error=3D'All repositories that = you are attempting to install have been previously installed.' ) # Display the list of installed repositories. diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 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 @@ -155,7 +155,8 @@ def browse_tool_dependency( self, trans, **kwd ): message =3D kwd.get( 'message', '' ) status =3D kwd.get( 'status', 'done' ) - tool_dependency =3D tool_dependency_util.get_tool_dependency( tran= s, kwd[ 'id' ] ) + tool_dependency_ids =3D tool_dependency_util.get_tool_dependency_i= ds( as_string=3DFalse, **kwd ) + tool_dependency =3D tool_dependency_util.get_tool_dependency( tran= s, tool_dependency_ids[ 0 ] ) if tool_dependency.in_error_state: message =3D "This tool dependency is not installed correctly (= see the <b>Tool dependency installation error</b> below). " message +=3D "Choose <b>Uninstall this tool dependency</b> fro= m the <b>Repository Actions</b> menu, correct problems " @@ -482,9 +483,7 @@ def install_tool_dependencies( self, trans, **kwd ): message =3D kwd.get( 'message', '' ) status =3D kwd.get( 'status', 'done' ) - tool_dependency_ids =3D util.listify( kwd.get( 'tool_dependency_id= s', None ) ) - if not tool_dependency_ids: - tool_dependency_ids =3D util.listify( kwd.get( 'id', None ) ) + tool_dependency_ids =3D tool_dependency_util.get_tool_dependency_i= ds( as_string=3DFalse, **kwd ) tool_dependencies =3D [] for tool_dependency_id in tool_dependency_ids: tool_dependency =3D tool_dependency_util.get_tool_dependency( = trans, tool_dependency_id ) @@ -731,11 +730,11 @@ kwd[ 'status' ] =3D 'error' installed_tool_dependencies_select_field =3D suc.build_tool_depend= encies_select_field( trans, = tool_shed_repository=3Dtool_shed_repository, - = name=3D'tool_dependency_ids', + = name=3D'inst_td_ids', = uninstalled=3DFalse ) uninstalled_tool_dependencies_select_field =3D suc.build_tool_depe= ndencies_select_field( trans, = tool_shed_repository=3Dtool_shed_repository, - = name=3D'tool_dependency_ids', + = name=3D'uninstalled_tool_dependency_ids', = uninstalled=3DTrue ) return trans.fill_template( '/admin/tool_shed_repository/manage_re= pository_tool_dependencies.mako', repository=3Dtool_shed_repository, @@ -886,15 +885,8 @@ tool_panel_section=3Dtool_panel_sect= ion, tool_path=3Dtool_path, tool_shed_url=3Dtool_shed_url ) - created_or_updated_tool_shed_repositories, tool_panel_section_= keys, repo_info_dicts, filtered_repo_info_dicts, message =3D \ + created_or_updated_tool_shed_repositories, tool_panel_section_= keys, repo_info_dicts, filtered_repo_info_dicts =3D \ repository_util.handle_tool_shed_repositories( trans, inst= allation_dict, using_api=3DFalse ) - if message and len( repo_info_dicts ) =3D=3D 1: - # We're undoubtedly attempting to install a repository tha= t has been previously installed. - return trans.response.send_redirect( web.url_for( controll= er=3D'admin_toolshed', - action= =3D'browse_repositories', - message= =3Dmessage, - status= =3D'error' ) ) - if created_or_updated_tool_shed_repositories: installation_dict =3D dict( created_or_updated_tool_shed_r= epositories=3Dcreated_or_updated_tool_shed_repositories, filtered_repo_info_dicts=3Dfilte= red_repo_info_dicts, @@ -1128,7 +1120,7 @@ reposi= tory_dependencies=3Drepository_dependencies ) repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. - created_or_updated_tool_shed_repositories, tool_panel_section_keys= , repo_info_dicts, filtered_repo_info_dicts, message =3D \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys= , repo_info_dicts, filtered_repo_info_dicts =3D \ repository_dependency_util.create_repository_dependency_object= s( trans=3Dtrans, = tool_path=3Dtool_path, = tool_shed_url=3Dtool_shed_url, @@ -1175,6 +1167,18 @@ initiate_repository_installation_ids= =3Dencoded_repository_ids, reinstalling=3DTrue ) =20 + @web.expose + @web.require_admin + def repair_repository( self, trans, **kwd ): + """ + Inspect the repository dependency hierarchy for a specified reposi= tory and attempt to make sure they are all properly installed as well as + each repository's tool dependencies. + """ + message =3D kwd.get( 'message', '' ) + status =3D kwd.get( 'status', 'done' ) + repository_id =3D kwd[ 'id' ] + tool_shed_repository =3D suc.get_installed_tool_shed_repository( t= rans, repository_id ) + @web.json def repository_installation_status_updates( self, trans, ids=3DNone, s= tatus_list=3DNone ): # Avoid caching @@ -1517,7 +1521,7 @@ def uninstall_tool_dependencies( self, trans, **kwd ): message =3D kwd.get( 'message', '' ) status =3D kwd.get( 'status', 'done' ) - tool_dependency_ids =3D util.listify( kwd.get( 'tool_dependency_id= s', None ) ) + tool_dependency_ids =3D tool_dependency_util.get_tool_dependency_i= ds( as_string=3DFalse, **kwd ) if not tool_dependency_ids: tool_dependency_ids =3D util.listify( kwd.get( 'id', None ) ) tool_dependencies =3D [] diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -358,7 +358,7 @@ tool_panel_section =3D installation_dict[ 'tool_panel_section' ] tool_path =3D installation_dict[ 'tool_path' ] tool_shed_url =3D installation_dict[ 'tool_shed_url' ] - created_or_updated_tool_shed_repositories, tool_panel_section_keys, re= po_info_dicts, filtered_repo_info_dicts, message =3D \ + created_or_updated_tool_shed_repositories, tool_panel_section_keys, re= po_info_dicts, filtered_repo_info_dicts =3D \ repository_dependency_util.create_repository_dependency_objects( t= rans=3Dtrans, t= ool_path=3Dtool_path, t= ool_shed_url=3Dtool_shed_url, @@ -368,11 +368,7 @@ n= o_changes_checked=3Dno_changes_checked, t= ool_panel_section=3Dtool_panel_section, n= ew_tool_panel_section=3Dnew_tool_panel_section ) - if message and len( repo_info_dicts ) =3D=3D 1 and not using_api: - installed_tool_shed_repository =3D created_or_updated_tool_shed_re= positories[ 0 ] - message +=3D 'Click <a href=3D"%s">here</a> to manage the reposito= ry. ' % \ - ( web.url_for( controller=3D'admin_toolshed', action=3D'manage= _repository', id=3Dtrans.security.encode_id( installed_tool_shed_repository= .id ) ) ) - return created_or_updated_tool_shed_repositories, tool_panel_section_k= eys, repo_info_dicts, filtered_repo_info_dicts, message + return created_or_updated_tool_shed_repositories, tool_panel_section_k= eys, repo_info_dicts, filtered_repo_info_dicts =20 def initiate_repository_installation( trans, installation_dict ): # The following installation_dict entries are all required. diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/tool_shed/galaxy_install/tool_dependencies/common_uti= l.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -216,7 +216,7 @@ return os.path.abspath( file_path ) raise ValueError( 'Could not find path to file %s' % os.path.abspath( = os.path.join( file_path, file_name ) ) ) =20 -def url_download( install_dir, downloaded_file_name, download_url ): +def url_download( install_dir, downloaded_file_name, download_url, extract= =3DTrue ): file_path =3D os.path.join( install_dir, downloaded_file_name ) src =3D None dst =3D None @@ -236,7 +236,22 @@ src.close() if dst: dst.close() - return os.path.abspath( file_path ) + if extract: + if istar( file_path ): + # <action type=3D"download_by_url">http://sourceforge.net/proj= ects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> + extract_tar( file_path, install_dir ) + dir =3D tar_extraction_directory( install_dir, downloaded_file= _name ) + elif isjar( file_path ): + dir =3D os.path.curdir + elif iszip( file_path ): + # <action type=3D"download_by_url">http://downloads.sourceforg= e.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</action> + zip_archive_extracted =3D extract_zip( file_path, install_dir ) + dir =3D zip_extraction_directory( install_dir, downloaded_file= _name ) + else: + dir =3D install_dir + else: + dir =3D install_dir + return dir =20 def zip_extraction_directory( file_path, file_name ): """Try to return the correct extraction directory.""" diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/tool_shed/galaxy_install/tool_dependencies/fabric_uti= l.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -180,19 +180,7 @@ downloaded_filename =3D action_dict[ 'target_filen= ame' ] else: downloaded_filename =3D os.path.split( url )[ -1 ] - downloaded_file_path =3D common_util.url_download( wor= k_dir, downloaded_filename, url ) - if common_util.istar( downloaded_file_path ): - # <action type=3D"download_by_url">http://sourcefo= rge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</ac= tion> - common_util.extract_tar( downloaded_file_path, wor= k_dir ) - dir =3D common_util.tar_extraction_directory( work= _dir, downloaded_filename ) - elif common_util.isjar( downloaded_file_path ): - dir =3D os.path.curdir - elif common_util.iszip( downloaded_file_path ): - # <action type=3D"download_by_url">http://download= s.sourceforge.net/project/picard/picard-tools/1.56/picard-tools-1.56.zip</a= ction> - zip_archive_extracted =3D common_util.extract_zip(= downloaded_file_path, work_dir ) - dir =3D common_util.zip_extraction_directory( work= _dir, downloaded_filename ) - else: - dir =3D os.path.curdir + dir =3D common_util.url_download( work_dir, downloaded= _filename, url, extract=3DTrue ) elif action_type =3D=3D 'shell_command': # <action type=3D"shell_command">git clone --recursive= git://github.com/ekg/freebayes.git</action> # Eliminate the shell_command clone action so remainin= g actions can be processed correctly. @@ -206,7 +194,7 @@ # Download a single file to the working directory. filtered_actions =3D actions[ 1: ] url =3D action_dict[ 'url' ] - if action_dict[ 'target_filename' ]: + if 'target_filename' in action_dict: # Sometimes compressed archives extracts their con= tent to a folder other than the default defined file name. Using this # attribute will ensure that the file name is set = appropriately and can be located after download, decompression and extracti= on. filename =3D action_dict[ 'target_filename' ] @@ -227,10 +215,10 @@ if not os.path.exists( full_path_to_dir ): os.makedirs( full_path_to_dir ) # The package has been down-loaded, so we can now perform = all of the actions defined for building it. - with lcd( dir ): - for action_tup in filtered_actions: + for action_tup in filtered_actions: + current_dir =3D os.path.abspath( os.path.join( work_di= r, dir ) ) + with lcd( current_dir ): action_type, action_dict =3D action_tup - current_dir =3D os.path.abspath( os.path.join( wor= k_dir, dir ) ) if action_type =3D=3D 'make_directory': common_util.make_directory( full_path=3Daction= _dict[ 'full_path' ] ) elif action_type =3D=3D 'move_directory_files': @@ -316,13 +304,20 @@ if return_code: return elif action_type =3D=3D 'download_file': - # Download a single file to the current direct= ory. + # Download a single file to the current workin= g directory. url =3D action_dict[ 'url' ] - if action_dict[ 'target_filename' ]: + if 'target_filename' in action_dict: filename =3D action_dict[ 'target_filename= ' ] else: filename =3D url.split( '/' )[ -1 ] - common_util.url_download( current_dir, filenam= e, url ) + extract =3D action_dict.get( 'extract', False ) + common_util.url_download( current_dir, filenam= e, url, extract=3Dextract ) + elif action_type =3D=3D 'change_directory': + target_directory =3D os.path.realpath( os.path= .join( current_dir, action_dict[ 'directory' ] ) ) + if target_directory.startswith( os.path.realpa= th( current_dir ) ) and os.path.exists( target_directory ): + dir =3D target_directory + else: + log.error( 'Invalid or nonexistent directo= ry %s specified, ignoring change_directory action.', target_directory ) =20 def log_results( command, fabric_AttributeString, file_path ): """ diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/tool_shed/galaxy_install/tool_dependencies/install_ut= il.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -13,6 +13,7 @@ from tool_shed.util import xml_util from galaxy.model.orm import and_ from galaxy.web import url_for +from galaxy.util import asbool =20 log =3D logging.getLogger( __name__ ) =20 @@ -390,15 +391,19 @@ # <action type=3D"download_by_url">http://sourceforge.net/proj= ects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> if action_elem.text: action_dict[ 'url' ] =3D action_elem.text - if 'target_filename' in action_elem.attrib: - action_dict[ 'target_filename' ] =3D action_elem.attri= b[ 'target_filename' ] + target_filename =3D action_elem.get( 'target_filename', No= ne ) + if target_filename: + action_dict[ 'target_filename' ] =3D target_filename else: continue elif action_type =3D=3D 'download_file': # <action type=3D"download_file">http://effectors.org/download= /version/TTSS_GUI-1.0.1.jar</action> if action_elem.text: action_dict[ 'url' ] =3D action_elem.text - action_dict[ 'target_filename' ] =3D action_elem.attrib.ge= t( 'target_filename', None ) + target_filename =3D action_elem.get( 'target_filename', No= ne ) + if target_filename: + action_dict[ 'target_filename' ] =3D target_filename + action_dict[ 'extract' ] =3D asbool( action_elem.get( 'ext= ract', False ) ) else: continue elif action_type =3D=3D 'make_directory': @@ -407,6 +412,12 @@ action_dict[ 'full_path' ] =3D evaluate_template( action_e= lem.text ) else: continue + elif action_type =3D=3D 'change_directory': + # <action type=3D"change_directory">PHYLIP-3.6b</action> + if action_elem.text: + action_dict[ 'directory' ] =3D action_elem.text + else: + continue elif action_type in [ 'move_directory_files', 'move_file' ]: # <action type=3D"move_file"> # <source>misc/some_file</source> diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -103,7 +103,6 @@ the dependency relationships between installed repositories. This met= hod is called when new repositories are being installed into a Galaxy instance and when uninstalled repositories are being reinstalled. """ - message =3D '' # The following list will be maintained within this method to contain = all created or updated tool shed repositories, including repository depende= ncies # that may not be installed. all_created_or_updated_tool_shed_repositories =3D [] @@ -241,7 +240,7 @@ filtered_repo_info_dicts.append( repo_info_dict ) # Build repository dependency relationships even if the user chose to = not install repository dependencies. build_repository_dependency_relationships( trans, all_repo_info_dicts,= all_created_or_updated_tool_shed_repositories ) - return created_or_updated_tool_shed_repositories, tool_panel_section_k= eys, all_repo_info_dicts, filtered_repo_info_dicts, message + return created_or_updated_tool_shed_repositories, tool_panel_section_k= eys, all_repo_info_dicts, filtered_repo_info_dicts =20 def generate_message_for_invalid_repository_dependencies( metadata_dict ): """Return the error message associated with an invalid repository depe= ndency for display in the caller.""" diff -r 46f4beebb766fd75edb59bc3598342ef95775af9 -r 1ff57c7a9debe0ced8bd216= a33789218190f1f47 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -220,9 +220,16 @@ =20 def get_tool_dependency_ids( as_string=3DFalse, **kwd ): tool_dependency_id =3D kwd.get( 'tool_dependency_id', None ) - tool_dependency_ids =3D util.listify( kwd.get( 'tool_dependency_ids', = None ) ) - if not tool_dependency_ids: - tool_dependency_ids =3D util.listify( kwd.get( 'id', None ) ) + if 'tool_dependency_ids' in kwd: + tool_dependency_ids =3D util.listify( kwd[ 'tool_dependency_ids' ]= ) + elif 'id' in kwd: + tool_dependency_ids =3D util.listify( kwd[ 'id' ] ) + elif 'inst_td_ids' in kwd: + tool_dependency_ids =3D util.listify( kwd[ 'inst_td_ids' ] ) + elif 'uninstalled_tool_dependency_ids' in kwd: + tool_dependency_ids =3D util.listify( kwd[ 'uninstalled_tool_depen= dency_ids' ] ) + else: + tool_dependency_ids =3D [] if tool_dependency_id and tool_dependency_id not in tool_dependency_id= s: tool_dependency_ids.append( tool_dependency_id ) if as_string: This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/f1e5dfbbea46/ Changeset: f1e5dfbbea46 User: saketkc Date: 2013-06-27 06:35:20 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 3fa9df444b4b81f94b1c42a033c685a6e23827be -r f1e5dfbbea46f0957ce4849= 4996444eb61f4a818 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/7e13235ae59a/ Changeset: 7e13235ae59a User: saketkc Date: 2013-06-28 07:00:22 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r b89b721a0b3db47cdeddef35f03ce4c2ffcb47b5 -r 7e13235ae59a1fb5eaa795c= 0797b4afa38001a38 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/8a88c559d596/ Changeset: 8a88c559d596 User: saketkc Date: 2013-06-29 11:41:22 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 019ad31c3c2502005846dadc5c0457bbb6f80712 -r 8a88c559d5961d41c630b8e= 2dd1dafe6f275b9b2 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/13dc3f5865da/ Changeset: 13dc3f5865da User: saketkc Date: 2013-07-01 22:14:34 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 2cabbf3687634090fbbc024726f15f43db4ff314 -r 13dc3f5865da864c3823b31= df455b5f6f1acb9f3 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/868bfd34f465/ Changeset: 868bfd34f465 User: saketkc Date: 2013-07-09 10:41:15 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 868bfd34f465dc1b6176d02= fce93baecf3129279 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/f8c0c28b902e/ Changeset: f8c0c28b902e User: saketkc Date: 2013-07-10 21:30:38 Summary: vcfclass change merged Affected #: 1 file diff -r 4cc057df762c219406af27dd04ac725a07a5a6eb -r f8c0c28b902ecad5821ece5= 5030a9e7d02f779cf tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/4ff5c8a3ff34/ Changeset: 4ff5c8a3ff34 User: saketkc Date: 2013-07-24 20:59:58 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r b42dfe74e237ea7f9c77059e427db92d9859bc67 -r 4ff5c8a3ff347824b430c99= 3303f2d97d907e2ed tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/28bad82d523b/ Changeset: 28bad82d523b User: saketkc Date: 2013-07-25 15:07:54 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 2abd0819d354d3d11182297c7206408d299f0d16 -r 28bad82d523b2053fa69c70= 301de69a74e57f323 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/a360e1b7b506/ Changeset: a360e1b7b506 User: saketkc Date: 2013-07-31 15:48:50 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 951e853b0bcd2c62cedee0b95d46c9e36ab6c605 -r a360e1b7b506450385be74b= 2c6b7762d3e794bbd tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/79ae7df72fba/ Changeset: 79ae7df72fba User: saketkc Date: 2013-08-02 19:20:58 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 24 files diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c .hgignore --- a/.hgignore +++ b/.hgignore @@ -85,6 +85,7 @@ .coverage htmlcov run_unit_tests.html +test/unit/**.log =20 # Project files *.kpf diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -475,6 +475,9 @@ =20 def sniff(self, filename): try: + # All twobit files start with a 16-byte header. If the file is= smaller than 16 bytes, it's obviously not a valid twobit file. + if os.path.getsize(filename) < 16: + return False input =3D file(filename) magic =3D struct.unpack(">L", input.read(TWOBIT_MAGIC_SIZE))[0] if magic =3D=3D TWOBIT_MAGIC_NUMBER or magic =3D=3D TWOBIT_MAG= IC_NUMBER_SWAP: diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1514,8 +1514,8 @@ NOTE: This is wasteful since dynamic options and dataset collection happens twice (here and when generating HTML).=20 """ - # Can't look at history in workflow mode - if trans is None or trans.workflow_building_mode: + # Can't look at history in workflow mode. Tool shed has no histori= es. + if trans is None or trans.workflow_building_mode or trans.webapp.n= ame =3D=3D 'tool_shed': return DummyDataset() assert trans is not None, "DataToolParameter requires a trans" history =3D trans.get_history() diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -13,6 +13,7 @@ from galaxy.util.json import from_json_string from bx.interval_index_file import Indexes from bx.bbi.bigwig_file import BigWigFile +from bx.bbi.bigbed_file import BigBedFile from galaxy.util.lrucache import LRUCache from galaxy.visualization.data_providers.basic import BaseDataProvider from galaxy.visualization.data_providers.cigar import get_ref_based_read_s= eq_and_cigar @@ -861,14 +862,14 @@ """ Returns an iterator that provides data in the region chrom:start-e= nd """ - start, end =3D int(start), int(end) + start, end =3D int( start ), int( end ) orig_data_filename =3D self.original_dataset.file_name index_filename =3D self.converted_dataset.file_name =20 # Attempt to open the BAM file with index bamfile =3D csamtools.Samfile( filename=3Dorig_data_filename, mode= =3D'rb', index_filename=3Dindex_filename ) try: - data =3D bamfile.fetch(start=3Dstart, end=3Dend, reference=3Dc= hrom) + data =3D bamfile.fetch( start=3Dstart, end=3Dend, reference=3D= chrom ) except ValueError, e: # Try alternative chrom naming. chrom =3D _convert_between_ucsc_and_ensemble_naming( chrom ) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -1,5 +1,7 @@ """ API operations on a history. + +.. seealso:: :class:`galaxy.model.History` """ =20 import pkg_resources @@ -21,17 +23,28 @@ @web.expose_api_anonymous def index( self, trans, deleted=3D'False', **kwd ): """ - GET /api/histories - GET /api/histories/deleted - Displays a collection (list) of histories. + index( trans, deleted=3D'False' ) + * GET /api/histories: + return undeleted histories for the current user + * GET /api/histories/deleted: + return deleted histories for the current user + .. note:: Anonymous users are allowed to get their current history + + :type deleted: boolean + :param deleted: if True, show only deleted histories, if False, n= on-deleted + + :rtype: list + :returns: list of dictionaries containing summary history inform= ation """ #TODO: query (by name, date, etc.) rval =3D [] deleted =3D string_as_bool( deleted ) try: if trans.user: - query =3D trans.sa_session.query(trans.app.model.History )= .filter_by( user=3Dtrans.user, deleted=3Ddeleted ).order_by( - desc(trans.app.model.History.table.c.update_time)).all= () + query =3D ( trans.sa_session.query( trans.app.model.Histor= y ) + .filter_by( user=3Dtrans.user, deleted=3Ddelet= ed ) + .order_by( desc( trans.app.model.History.table= .c.update_time ) ) + .all() ) for history in query: item =3D history.get_api_value(value_mapper=3D{'id':tr= ans.security.encode_id}) item['url'] =3D url_for( 'history', id=3Dtrans.securit= y.encode_id( history.id ) ) @@ -52,11 +65,25 @@ =20 @web.expose_api_anonymous def show( self, trans, id, deleted=3D'False', **kwd ): + # oh, sphinx - you bastard """ - GET /api/histories/{encoded_history_id} - GET /api/histories/deleted/{encoded_history_id} - GET /api/histories/most_recently_used - Displays information about a history. + show( trans, id, deleted=3D'False' ) + * GET /api/histories/{id}: + return the history with ``id`` + * GET /api/histories/deleted/{id}: + return the deleted history with ``id`` + * GET /api/histories/most_recently_used: + return the most recently used history + .. note:: Anonymous users are allowed to get their current history + + :type id: an encoded id string + :param id: the encoded id of the history to query or the str= ing 'most_recently_used' + :type deleted: boolean + :param deleted: if True, allow information on a deleted history t= o be shown. + + :rtype: dictionary + :returns: detailed history information from + :func:`galaxy.web.base.controller.UsesHistoryDatasetAssociatio= nMixin.get_history_dict` """ #TODO: GET /api/histories/{encoded_history_id}?as_archive=3DTrue #TODO: GET /api/histories/s/{username}/{slug} @@ -94,8 +121,16 @@ @web.expose_api def create( self, trans, payload, **kwd ): """ - POST /api/histories - Creates a new history. + create( trans, payload ) + * POST /api/histories: + create a new history + + :type payload: dict + :param payload: (optional) dictionary structure containing: + * name: the new history's name + =20 + :rtype: dict + :returns: element view of new history """ hist_name =3D None if payload.get( 'name', None ): @@ -115,8 +150,24 @@ @web.expose_api def delete( self, trans, id, **kwd ): """ - DELETE /api/histories/{encoded_history_id} - Deletes a history + delete( self, trans, id, **kwd ) + * DELETE /api/histories/{id} + delete the history with the given ``id`` + .. note:: Currently does not stop any active jobs in the history. + + :type id: str + :param id: the encoded id of the history to delete + :type kwd: dict + :param kwd: (optional) dictionary structure containing: + =20 + * payload: a dictionary itself containing: + * purge: if True, purge the history and all of it's HDAs + + :rtype: dict + :returns: an error object if an error occurred or a dictionary c= ontaining: + * id: the encoded id of the history, + * deleted: if the history was marked as deleted, + * purged: if the history was purged """ history_id =3D id # a request body is optional here @@ -175,8 +226,15 @@ @web.expose_api def undelete( self, trans, id, **kwd ): """ - POST /api/histories/deleted/{encoded_history_id}/undelete - Undeletes a history + undelete( self, trans, id, **kwd ) + * POST /api/histories/deleted/{id}/undelete: + undelete history (that hasn't been purged) with the given ``id= `` + + :type id: str + :param id: the encoded id of the history to undelete + + :rtype: str + :returns: 'OK' if the history was undeleted """ history_id =3D id history =3D self.get_history( trans, history_id, check_ownership= =3DTrue, check_accessible=3DFalse, deleted=3DTrue ) @@ -188,8 +246,21 @@ @web.expose_api def update( self, trans, id, payload, **kwd ): """ - PUT /api/histories/{encoded_history_id} - Changes an existing history. + update( self, trans, id, payload, **kwd ) + * PUT /api/histories/{id} + updates the values for the history with the given ``id`` + + :type id: str + :param id: the encoded id of the history to undelete + :type payload: dict + :param payload: a dictionary containing any or all the + fields in :func:`galaxy.model.History.get_api_value` and/or th= e following: + =20 + * annotation: an annotation for the history + + :rtype: dict + :returns: an error object if an error occurred or a dictionary c= ontaining + any values that were different from the original and, therefor= e, updated """ #TODO: PUT /api/histories/{encoded_history_id} payload =3D { ratin= g: rating } (w/ no security checks) try: @@ -255,6 +326,6 @@ raise ValueError( 'annotation must be a string or unic= ode: %s' %( str( type( val ) ) ) ) validated_payload[ 'annotation' ] =3D sanitize_html( val, = 'utf-8' ) elif key not in valid_but_uneditable_keys: - raise AttributeError( 'unknown key: %s' %( str( key ) ) ) + pass + #log.warn( 'unknown key: %s', str( key ) ) return validated_payload - diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -15,21 +15,27 @@ @web.expose_api_anonymous def index( self, trans, history_id, ids=3DNone, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents - Displays a collection (list) of history contents (HDAs) + index( self, trans, history_id, ids=3DNone, **kwd ) + * GET /api/histories/{history_id}/contents + return a list of HDA data for the history with the given ``id`` + .. note:: Anonymous users are allowed to get their current history= contents =20 - :param history_id: an encoded id string of the `History` to search - :param ids: (optional) a comma separated list of encoded `HDA` ids - - If Ids is not given, index returns a list of *summary* json object= s for - every `HDA` associated with the given `history_id`. - See _summary_hda_dict. + If Ids is not given, index returns a list of *summary* objects for + every HDA associated with the given `history_id`. =20 If ids is given, index returns a *more complete* json object for e= ach HDA in the ids list. =20 - Note: Anonymous users are allowed to get their current history con= tents - (generally useful for browser UI access of the api) + :type history_id: str + :param history_id: encoded id string of the HDA's History + :type ids: str + :param ids: (optional) a comma separated list of encoded `= HDA` ids + + :rtype: list + :returns: dictionaries containing summary or detailed HDA inform= ation + .. seealso:: + :func:`_summary_hda_dict` and + :func:`galaxy.web.base.controller.UsesHistoryDatasetAssociatio= nMixin.get_hda_dict` """ rval =3D [] try: @@ -78,13 +84,13 @@ #TODO: move to model or Mixin def _summary_hda_dict( self, trans, history_id, hda ): """ - Returns a dictionary based on the HDA in .. _summary form:: - { - 'id' : < the encoded dataset id >, - 'name' : < currently only returns 'file' >, - 'type' : < name of the dataset >, - 'url' : < api url to retrieve this datasets full data >, - } + Returns a dictionary based on the HDA in summary form:: + { + 'id' : < the encoded dataset id >, + 'name' : < currently only returns 'file' >, + 'type' : < name of the dataset >, + 'url' : < api url to retrieve this datasets full data >, + } """ api_type =3D "file" encoded_id =3D trans.security.encode_id( hda.id ) @@ -98,8 +104,19 @@ @web.expose_api_anonymous def show( self, trans, id, history_id, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_= id} - Displays information about a history content (dataset). + show( self, trans, id, history_id, **kwd ) + * GET /api/histories/{history_id}/contents/{id} + return detailed information about an HDA within a history + .. note:: Anonymous users are allowed to get their current history= contents + + :type id: str + :param ids: the encoded id of the HDA to return + :type history_id: str + :param history_id: encoded id string of the HDA's History + + :rtype: dict + :returns: dictionary containing detailed HDA information + .. seealso:: :func:`galaxy.web.base.controller.UsesHistoryDatasetA= ssociationMixin.get_hda_dict` """ hda_dict =3D {} try: @@ -135,8 +152,18 @@ @web.expose_api def create( self, trans, history_id, payload, **kwd ): """ - POST /api/histories/{encoded_history_id}/contents - Creates a new history content item (file, aka HistoryDatasetAssoci= ation). + create( self, trans, history_id, payload, **kwd ) + * POST /api/histories/{history_id}/contents + create a new HDA by copying an accessible LibraryDataset + + :type history_id: str + :param history_id: encoded id string of the new HDA's History + :type payload: dict + :param payload: dictionary structure containing:: + 'from_ld_id': the encoded id of the LibraryDataset to copy + + :rtype: dict + :returns: dictionary containing detailed information for the new= HDA """ #TODO: copy existing, accessible hda - dataset controller, copy_da= tasets #TODO: convert existing, accessible hda - model.DatasetInstance(or= hda.datatype).get_converter_types @@ -173,8 +200,24 @@ @web.expose_api def update( self, trans, history_id, id, payload, **kwd ): """ - PUT /api/histories/{encoded_history_id}/contents/{encoded_content_= id} - Changes an existing history dataset. + update( self, trans, history_id, id, payload, **kwd ) + * PUT /api/histories/{history_id}/contents/{id} + updates the values for the HDA with the given ``id`` + + :type history_id: str + :param history_id: encoded id string of the HDA's History + :type id: str + :param id: the encoded id of the history to undelete + :type payload: dict + :param payload: a dictionary containing any or all the + fields in :func:`galaxy.model.HistoryDatasetAssociation.get_ap= i_value` + and/or the following: + + * annotation: an annotation for the HDA + + :rtype: dict + :returns: an error object if an error occurred or a dictionary c= ontaining + any values that were different from the original and, therefor= e, updated """ #TODO: PUT /api/histories/{encoded_history_id} payload =3D { ratin= g: rating } (w/ no security checks) changed =3D {} @@ -251,6 +294,7 @@ raise ValueError( 'misc_info must be a string or unico= de: %s' %( str( type( val ) ) ) ) validated_payload[ 'info' ] =3D util.sanitize_html.sanitiz= e_html( val, 'utf-8' ) elif key not in valid_but_uneditable_keys: - raise AttributeError( 'unknown key: %s' %( str( key ) ) ) + pass + #log.warn( 'unknown key: %s', str( key ) ) return validated_payload =20 diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -15,9 +15,18 @@ @web.expose_api def index( self, trans, deleted=3D'False', **kwd ): """ - GET /api/libraries - GET /api/libraries/deleted - Displays a collection (list) of libraries. + index( self, trans, deleted=3D'False', **kwd ) + * GET /api/libraries: + returns a list of summary data for libraries + * GET /api/libraries/deleted: + returns a list of summary data for deleted libraries + + :type deleted: boolean + :param deleted: if True, show only deleted libraries, if False, n= on-deleted + + :rtype: list + :returns: list of dictionaries containing library information + .. seealso:: :attr:`galaxy.model.Library.api_collection_visible_ke= ys` """ log.debug( "LibrariesController.index: enter" ) query =3D trans.sa_session.query( trans.app.model.Library ) @@ -49,9 +58,20 @@ @web.expose_api def show( self, trans, id, deleted=3D'False', **kwd ): """ - GET /api/libraries/{encoded_library_id} - GET /api/libraries/deleted/{encoded_library_id} - Displays information about a library. + show( self, trans, id, deleted=3D'False', **kwd ) + * GET /api/libraries/{id}: + returns detailed information about a library + * GET /api/libraries/deleted/{id}: + returns detailed information about a deleted library + + :type id: an encoded id string + :param id: the encoded id of the library + :type deleted: boolean + :param deleted: if True, allow information on a deleted library + + :rtype: dictionary + :returns: detailed library information + .. seealso:: :attr:`galaxy.model.Library.api_element_visible_keys` """ log.debug( "LibraryContentsController.show: enter" ) library_id =3D id @@ -75,8 +95,20 @@ @web.expose_api def create( self, trans, payload, **kwd ): """ - POST /api/libraries - Creates a new library. + create( self, trans, payload, **kwd ) + * POST /api/libraries: + create a new library + .. note:: Currently, only admin users can create libraries. + + :type payload: dict + :param payload: (optional) dictionary structure containing:: + 'name': the new library's name + 'description': the new library's description + 'synopsis': the new library's synopsis + + :rtype: dict + :returns: a dictionary containing the id, name, and 'show' url + of the new library """ if not trans.user_is_admin(): raise HTTPForbidden( detail=3D'You are not authorized to creat= e a new library.' ) @@ -102,6 +134,19 @@ =20 @web.expose_api def delete( self, trans, id, **kwd ): + """ + delete( self, trans, id, **kwd ) + * DELETE /api/histories/{id} + mark the library with the given ``id`` as deleted + .. note:: Currently, only admin users can delete libraries. + + :type id: str + :param id: the encoded id of the library to delete + + :rtype: dictionary + :returns: detailed library information + .. seealso:: :attr:`galaxy.model.Library.api_element_visible_keys` + """ if not trans.user_is_admin(): raise HTTPForbidden( detail=3D'You are not authorized to delet= e libraries.' ) try: diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -19,8 +19,21 @@ # TODO: Add parameter to only get top level of datasets/subfolders. def index( self, trans, library_id, **kwd ): """ - GET /api/libraries/{encoded_library_id}/contents - Displays a collection (list) of library contents (files and folder= s). + index( self, trans, library_id, **kwd ) + * GET /api/libraries/{library_id}/contents: + return a list of library files and folders + + :type library_id: str + :param library_id: encoded id string of the library that contains= this item + + :rtype: list + :returns: list of dictionaries of the form: + + * id: the encoded id of the library item + * name: the 'libary path' + or relationship of the library item to the root + * type: 'file' or 'folder' + * url: the url to get detailed information on the library item """ rval =3D [] current_user_roles =3D trans.get_current_user_roles() @@ -80,8 +93,20 @@ @web.expose_api def show( self, trans, id, library_id, **kwd ): """ - GET /api/libraries/{encoded_library_id}/contents/{encoded_content_= id} - Displays information about a library content (file or folder). + show( self, trans, id, library_id, **kwd ) + * GET /api/libraries/{library_id}/contents/{id} + return information about library file or folder + + :type id: str + :param id: the encoded id of the library item to return + :type library_id: str + :param library_id: encoded id string of the library that contains= this item + + :rtype: dict + :returns: detailed library item information + .. seealso:: + :func:`galaxy.model.LibraryDataset.get_api_value` and + :attr:`galaxy.model.LibraryFolder.api_element_visible_keys` """ class_name, content_id =3D self.__decode_library_content_id( trans= , id ) if class_name =3D=3D 'LibraryFolder': @@ -93,8 +118,29 @@ @web.expose_api def create( self, trans, library_id, payload, **kwd ): """ - POST /api/libraries/{encoded_library_id}/contents - Creates a new library content item (file or folder). + create( self, trans, library_id, payload, **kwd ) + * POST /api/libraries/{library_id}/contents: + create a new library file or folder + + To copy an HDA into a library send ``create_type`` of 'file' and + the HDA's encoded id in ``from_hda_id`` (and optionally ``ldda_mes= sage``). + + :type library_id: str + :param library_id: encoded id string of the library that contains= this item + :type payload: dict + :param payload: dictionary structure containing: + =20 + * folder_id: the parent folder of the new item + * create_type: the type of item to create ('file' or 'folder') + * from_hda_id: (optional) the id of an accessible HDA to copy= into the + library + * ldda_message: (optional) the new message attribute of the LD= DA created + * extended_metadata: (optional) dub-dictionary containing any = extended + metadata to associate with the item + + :rtype: dict + :returns: a dictionary containing the id, name, + and 'show' url of the new item """ create_type =3D None if 'create_type' not in payload: @@ -195,10 +241,10 @@ =20 def _copy_hda_to_library_folder( self, trans, from_hda_id, library_id,= folder_id, ldda_message=3D'' ): """ - Copies hda `from_hda_id` to library folder `library_folder_id` opt= ionally - adding `ldda_message` to the new ldda's `message`. + Copies hda ``from_hda_id`` to library folder ``library_folder_id``= optionally + adding ``ldda_message`` to the new ldda's ``message``. =20 - `library_contents.create` will branch to this if called with 'from= _hda_id' + ``library_contents.create`` will branch to this if called with 'fr= om_hda_id' in it's payload. """ log.debug( '_copy_hda_to_library_folder: %s' %( str(( from_hda_id,= library_id, folder_id, ldda_message )) ) ) @@ -236,10 +282,23 @@ return rval =20 @web.expose_api - def update( self, trans, id, library_id, payload, **kwd ): + def update( self, trans, id, library_id, payload, **kwd ): """ - PUT /api/libraries/{encoded_library_id}/contents/{encoded_content_= type_and_id} - Sets relationships among items + update( self, trans, id, library_id, payload, **kwd ) + * PUT /api/libraries/{library_id}/contents/{id} + create a ImplicitlyConvertedDatasetAssociation + .. seealso:: :class:`galaxy.model.ImplicitlyConvertedDatasetAssoci= ation` + + :type id: str + :param id: the encoded id of the library item to return + :type library_id: str + :param library_id: encoded id string of the library that contains= this item + :type payload: dict + :param payload: dictionary structure containing:: + 'converted_dataset_id': + + :rtype: None + :returns: None """ if 'converted_dataset_id' in payload: converted_id =3D payload.pop( 'converted_dataset_id' ) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/tool_shed/galaxy_install/tool_dependencies/common_uti= l.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -8,6 +8,7 @@ import zipfile import tool_shed.util.shed_util_common as suc from galaxy.datatypes import checkers +from urllib2 import HTTPError =20 log =3D logging.getLogger( __name__ ) =20 @@ -70,6 +71,23 @@ __shellquote(env_shell_file_path= )) return cmd =20 +def download_binary_from_url( url, work_dir, install_dir ): + ''' + Download a pre-compiled binary from the specified URL. If the download= ed file is an archive, + extract it into install_dir and delete the archive. + ''' + downloaded_filename =3D os.path.split( url )[ -1 ] + try: + dir =3D url_download( work_dir, downloaded_filename, url, extract= =3DTrue ) + downloaded_filepath =3D os.path.join( work_dir, downloaded_filenam= e ) + if is_compressed( downloaded_filepath ): + os.remove( downloaded_filepath ) + move_directory_files( current_dir=3Dwork_dir, + source_dir=3Ddir, + destination_dir=3Dinstall_dir ) + return True + except HTTPError: + return False =20 def extract_tar( file_name, file_path ): if isgzip( file_name ) or isbz2( file_name ): @@ -190,6 +208,12 @@ def iszip( file_path ): return checkers.check_zip( file_path ) =20 +def is_compressed( file_path ): + if isjar( file_path ): + return False + else: + return iszip( file_path ) or isgzip( file_path ) or istar( file_pa= th ) or isbz2( file_path ) + def make_directory( full_path ): if not os.path.exists( full_path ): os.makedirs( full_path ) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/tool_shed/galaxy_install/tool_dependencies/fabric_uti= l.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -165,12 +165,29 @@ actions =3D actions_dict.get( 'actions', None ) filtered_actions =3D [] env_shell_file_paths =3D [] + # Default to false so that the install process will default to compili= ng. + binary_found =3D False if actions: with make_tmp_dir() as work_dir: with lcd( work_dir ): # The first action in the list of actions will be the one = that defines the installation process. There # are currently only two supported processes; download_by_= url and clone via a "shell_command" action type. action_type, action_dict =3D actions[ 0 ] + if action_type =3D=3D 'download_binary': + # Eliminate the download_binary action so remaining ac= tions can be processed correctly. + filtered_actions =3D actions[ 1: ] + url =3D action_dict[ 'url' ] + # Attempt to download a binary from the specified URL. + log.debug( 'Attempting to download from %s', url ) + binary_found =3D common_util.download_binary_from_url(= url, work_dir, install_dir ) + if binary_found: + # If the attempt succeeded, set the action_type to= binary_found, in order to skip any download_by_url or shell_command action= s. + actions =3D filtered_actions + action_type =3D 'binary_found' + else: + # No binary exists, or there was an error download= ing the binary from the generated URL. Proceed with the remaining actions. + del actions[ 0 ] + action_type, action_dict =3D actions[ 0 ] if action_type =3D=3D 'download_by_url': # Eliminate the download_by_url action so remaining ac= tions can be processed correctly. filtered_actions =3D actions[ 1: ] @@ -220,6 +237,9 @@ current_dir =3D os.path.abspath( os.path.join( work_di= r, dir ) ) with lcd( current_dir ): action_type, action_dict =3D action_tup + # If a binary was found, we only need to process e= nvironment variables, file permissions, and any other binary downloads. + if binary_found and action_type not in [ 'set_envi= ronment', 'chmod', 'download_binary' ]: + continue if action_type =3D=3D 'make_directory': common_util.make_directory( full_path=3Daction= _dict[ 'full_path' ] ) elif action_type =3D=3D 'move_directory_files': @@ -348,6 +368,18 @@ dir =3D target_directory.replace( os.path.= realpath( work_dir ), '' ).lstrip( '/' ) else: log.error( 'Invalid or nonexistent directo= ry %s specified, ignoring change_directory action.', target_directory ) + elif action_type =3D=3D 'chmod': + for target_file, mode in action_dict[ 'change_= modes' ]: + if os.path.exists( target_file ): + os.chmod( target_file, mode ) + elif action_type =3D=3D 'download_binary': + url =3D action_dict[ 'url' ] + binary_found =3D common_util.download_binary_f= rom_url( url, work_dir, install_dir ) + if binary_found: + log.debug( 'Successfully downloaded binary= from %s', url ) + else: + log.error( 'Unable to download binary from= %s', url ) + =20 =20 def log_results( command, fabric_AttributeString, file_path ): """ diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/tool_shed/galaxy_install/tool_dependencies/install_ut= il.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -1,6 +1,7 @@ import logging import os import sys +import stat import subprocess import tempfile from string import Template @@ -379,7 +380,22 @@ for action_elem in actions_elem.findall( 'action' ): action_dict =3D {} action_type =3D action_elem.get( 'type', 'shell_command' ) - if action_type =3D=3D 'shell_command': + if action_type =3D=3D 'download_binary': + platform_info_dict =3D tool_dependency_util.get_platform_info_= dict() + platform_info_dict[ 'name' ] =3D tool_dependency.name + platform_info_dict[ 'version' ] =3D tool_dependency.version + url_template_elems =3D action_elem.findall( 'url_template' ) + # Check if there are multiple url_template elements, each with= attrib entries for a specific platform. + if len( url_template_elems ) > 1: + # <base_url os=3D"darwin" extract=3D"false">http://hgdownl= oad.cse.ucsc.edu/admin/exe/macOSX.${architecture}/faToTwoBit</base_url> + # This method returns the url_elem that best matches the c= urrent platform as received from os.uname(). + # Currently checked attributes are os and architecture. + # These correspond to the values sysname and processor fro= m the Python documentation for os.uname(). + url_template_elem =3D tool_dependency_util.get_download_ur= l_for_platform( url_template_elems, platform_info_dict ) + else: + url_template_elem =3D url_template_elems[ 0 ] + action_dict[ 'url' ] =3D Template( url_template_elem.text ).sa= fe_substitute( platform_info_dict ) + elif action_type =3D=3D 'shell_command': # <action type=3D"shell_command">make</action> action_elem_text =3D evaluate_template( action_elem.text ) if action_elem_text: @@ -492,6 +508,27 @@ # lxml=3D=3D2.3.0</action> ## Manually specify contents of requirements.txt file to creat= e dynamically. action_dict[ 'requirements' ] =3D evaluate_template( action_el= em.text or 'requirements.txt' ) + elif action_type =3D=3D 'chmod': + # Change the read, write, and execute bits on a file. + file_elems =3D action_elem.findall( 'file' ) + chmod_actions =3D [] + # A unix octal mode is the sum of the following values: + # Owner: + # 400 Read 200 Write 100 Execute + # Group: + # 040 Read 020 Write 010 Execute + # World: + # 004 Read 002 Write 001 Execute + for file_elem in file_elems: + # So by the above table, owner read/write/execute and grou= p read permission would be 740. + # Python's os.chmod uses base 10 modes, convert received u= nix-style octal modes to base 10. + received_mode =3D int( file_elem.get( 'mode', 600 ), base= =3D8 ) + # For added security, ensure that the setuid and setgid bi= ts are not set. + mode =3D received_mode & ~( stat.S_ISUID | stat.S_ISGID ) + file =3D evaluate_template( file_elem.text ) + chmod_tuple =3D ( file, mode ) + chmod_actions.append( chmod_tuple ) + action_dict[ 'change_modes' ] =3D chmod_actions else: log.debug( "Unsupported action type '%s'. Not proceeding." % s= tr( action_type ) ) raise Exception( "Unsupported action type '%s' in tool depende= ncy definition." % str( action_type ) ) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -39,6 +39,37 @@ tool_dependencies[ dependency_key ] =3D requirements_dict return tool_dependencies =20 +def get_download_url_for_platform( url_templates, platform_info_dict ): + ''' + Compare the dict returned by get_platform_info() with the values speci= fied in the base_url element. Return + true if and only if all defined attributes match the corresponding dic= t entries. If an entry is not + defined in the base_url element, it is assumed to be irrelevant at thi= s stage. For example, + <base_url os=3D"darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOS= X.${architecture}/faToTwoBit</base_url> + where the OS must be 'darwin', but the architecture is filled in later= using string.Template. + ''' + os_ok =3D False + architecture_ok =3D False + for url_template in url_templates: + os_name =3D url_template.get( 'os', None ) + architecture =3D url_template.get( 'architecture', None ) + if os_name: + if os_name.lower() =3D=3D platform_info_dict[ 'os' ]: + os_ok =3D True + else: + os_ok =3D False + else: + os_ok =3D True + if architecture: + if architecture.lower() =3D=3D platform_info_dict[ 'architectu= re' ]: + architecture_ok =3D True + else: + architecture_ok =3D False + else: + architecture_ok =3D True + if os_ok and architecture_ok: + return url_template + return None + def create_or_update_tool_dependency( app, tool_shed_repository, name, ver= sion, type, status, set_status=3DTrue ): # Called from Galaxy (never the tool shed) when a new repository is be= ing installed or when an uninstalled repository is being reinstalled. sa_session =3D app.model.context.current @@ -204,6 +235,14 @@ missing_tool_dependencies =3D None return tool_dependencies, missing_tool_dependencies =20 +def get_platform_info_dict(): + '''Return a dict with information about the current platform.''' + platform_dict =3D {} + sysname, nodename, release, version, machine =3D os.uname() + platform_dict[ 'os' ] =3D sysname.lower() + platform_dict[ 'architecture' ] =3D machine.lower() + return platform_dict + def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.sa_session.query( trans.model.ToolDependency ).get( trans= .security.decode_id( id ) ) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c static/scripts/galaxy.pages.js --- a/static/scripts/galaxy.pages.js +++ b/static/scripts/galaxy.pages.js @@ -164,18 +164,19 @@ { "Make link": function() { // Get URL, name/title. - var sUrl =3D $(wym._options.hrefSelector).val(), - sName =3D $(".wym_title").val(); + var sUrl =3D $(wym._options.hrefSelector).val() || '', + sId =3D $(".wym_id").val() || '', + sName =3D $(wym._options.titleSelector).val() || '= '; =20 - if (sUrl && sName) { + if (sUrl || sId) { // Create link. wym._exec(WYMeditor.CREATE_LINK, sStamp); =20 // Set link attributes. var link =3D $("a[href=3D" + sStamp + "]", wym._do= c.body); link.attr(WYMeditor.HREF, sUrl) - .attr(WYMeditor.TITLE, $(wym._options.titleSel= ector).val()) - .attr("id", sName); + .attr(WYMeditor.TITLE, sName) + .attr("id", sId); =20 // If link's text is default (wym-...), change it = to the title. if (link.text().indexOf('wym-') =3D=3D=3D 0) { diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c static/scripts/packed/galaxy.pages.js --- a/static/scripts/packed/galaxy.pages.js +++ b/static/scripts/packed/galaxy.pages.js @@ -1,1 +1,1 @@ -var Galaxy=3D{ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM= _WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_vi= sualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_d= ataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",D= IALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_h= istory",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_w= orkflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_v= isualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_ga= laxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(fun= ction(){var b=3Da._doc.createRange();b.selectNodeContents(this);var d=3Dwin= dow.getSelection();d.removeAllRanges();d.addRange(b);var c=3D""})})}functio= n get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f=3D"Hist= ory";c=3D"Histories";b=3D"history";item_class=3D"History";break;case (Galax= 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-1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/b= ackbone-relational"],function(q,a,r){var f=3DBackbone.RelationalModel.exten= d({defaults:{name:null,hidden:false},show:function(){this.set("hidden",fals= e)},hide:function(){this.set("hidden",true)},is_visible:function(){return != this.attributes.hidden}});var k=3DBackbone.RelationalModel.extend({defaults= :{name:null,label:null,type:null,value:null,num_samples:5},initialize:funct= ion(){this.attributes.html=3Dunescape(this.attributes.html)},copy:function(= ){return new k(this.toJSON())},get_samples:function(){var u=3Dthis.get("typ= e"),t=3Dnull;if(u=3D=3D=3D"number"){t=3Dd3.scale.linear().domain([this.get(= "min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(u=3D=3D=3D"= select"){t=3Dq.map(this.get("options"),function(v){return v[0]})}}return t}= });var e=3Df.extend({defaults:{description:null,target:null,inputs:[]},rela= tions:[{type:Backbone.HasMany,key:"inputs",relatedModel:k,reverseRelation:{= key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy= :function(u){var v=3Dnew e(this.toJSON());if(u){var t=3Dnew Backbone.Collec= tion();v.get("inputs").each(function(w){if(w.get_samples()){t.push(w)}});v.= set("inputs",t)}return v},apply_search_results:function(t){(q.indexOf(t,thi= s.attributes.id)!=3D=3D-1?this.show():this.hide());return this.is_visible()= },set_input_value:function(t,u){this.get("inputs").find(function(v){return = v.get("name")=3D=3D=3Dt}).set("value",u)},set_input_values:function(u){var = t=3Dthis;q.each(q.keys(u),function(v){t.set_input_value(v,u[v])})},run:func= tion(){return this._run()},rerun:function(u,t){return this._run({action:"re= run",target_dataset_id:u.id,regions:t})},get_inputs_dict:function(){var t= =3D{};this.get("inputs").each(function(u){t[u.get("name")]=3Du.get("value")= });return t},_run:function(v){var w=3Dq.extend({tool_id:this.id,inputs:this= .get_inputs_dict()},v);var u=3D$.Deferred(),t=3Dnew a.ServerStateDeferred({= ajax_settings:{url:this.urlRoot,data:JSON.stringify(w),dataType:"json",cont= entType:"application/json",type:"POST"},interval:2000,success_fn:function(x= ){return x!=3D=3D"pending"}});$.when(t.go()).then(function(x){u.resolve(new= r.DatasetCollection().reset(x))});return u}});var i=3DBackbone.Collection.= extend({model:e});var m=3Df.extend({});var p=3Df.extend({defaults:{elems:[]= ,open:false},clear_search_results:function(){q.each(this.attributes.elems,f= unction(t){t.show()});this.show();this.set("open",false)},apply_search_resu= lts:function(u){var v=3Dtrue,t;q.each(this.attributes.elems,function(w){if(= w instanceof m){t=3Dw;t.hide()}else{if(w instanceof e){if(w.apply_search_re= sults(u)){v=3Dfalse;if(t){t.show()}}}}});if(v){this.hide()}else{this.show()= ;this.set("open",true)}}});var b=3Df.extend({defaults:{search_hint_string:"= search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search= _url:"",visible:true,query:"",results:null,clear_key:27},initialize:functio= n(){this.on("change:query",this.do_search)},do_search:function(){var v=3Dth= is.attributes.query;if(v.length<this.attributes.min_chars_for_search){this.= set("results",null);return}var u=3Dv+"*";if(this.timer){clearTimeout(this.t= imer)}$("#search-clear-btn").hide();$("#search-spinner").show();var t=3Dthi= s;this.timer=3DsetTimeout(function(){$.get(t.attributes.search_url,{query:u= },function(w){t.set("results",w);$("#search-spinner").hide();$("#search-cle= ar-btn").show()},"json")},200)},clear_search:function(){this.set("query",""= );this.set("results",null)}});var j=3DBackbone.Collection.extend({url:"/too= ls",tools:new i(),parse:function(t){var u=3Dfunction(x){var w=3Dx.type;if(w= =3D=3D=3D"tool"){return new e(x)}else{if(w=3D=3D=3D"section"){var v=3Dq.map= (x.elems,u);x.elems=3Dv;return new p(x)}else{if(w=3D=3D=3D"label"){return n= ew m(x)}}}};return q.map(t,u)},initialize:function(t){this.tool_search=3Dt.= tool_search;this.tool_search.on("change:results",this.apply_search_results,= this);this.on("reset",this.populate_tools,this)},populate_tools:function(){= var t=3Dthis;t.tools=3Dnew i();this.each(function(u){if(u instanceof p){q.e= ach(u.attributes.elems,function(v){if(v instanceof e){t.tools.push(v)}})}el= se{if(u instanceof e){t.tools.push(u)}}})},clear_search_results:function(){= this.each(function(t){if(t instanceof p){t.clear_search_results()}else{t.sh= ow()}})},apply_search_results:function(){var u=3Dthis.tool_search.attribute= s.results;if(u=3D=3D=3Dnull){this.clear_search_results();return}var t=3Dnul= l;this.each(function(v){if(v instanceof m){t=3Dv;t.hide()}else{if(v instanc= eof e){if(v.apply_search_results(u)){if(t){t.show()}}}else{t=3Dnull;v.apply= _search_results(u)}}})}});var n=3DBackbone.View.extend({initialize:function= (){this.model.on("change:hidden",this.update_visible,this);this.update_visi= ble()},update_visible:function(){(this.model.attributes.hidden?this.$el.hid= e():this.$el.show())}});var h=3Dn.extend({tagName:"div",template:Handlebars= .templates.tool_link,render:function(){this.$el.append(this.template(this.m= odel.toJSON()));return this}});var c=3Dn.extend({tagName:"div",className:"t= oolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.mod= el.attributes.name));return this}});var g=3Dn.extend({tagName:"div",classNa= me:"toolSectionWrapper",template:Handlebars.templates.panel_section,initial= ize:function(){n.prototype.initialize.call(this);this.model.on("change:open= ",this.update_open,this)},render:function(){this.$el.append(this.template(t= his.model.toJSON()));var t=3Dthis.$el.find(".toolSectionBody");q.each(this.= model.attributes.elems,function(u){if(u instanceof e){var v=3Dnew h({model:= u,className:"toolTitle"});v.render();t.append(v.$el)}else{if(u instanceof m= ){var w=3Dnew c({model:u});w.render();t.append(w.$el)}else{}}});return this= },events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.mo= del.set("open",!this.model.attributes.open)},update_open:function(){(this.m= odel.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"= ):this.$el.children(".toolSectionBody").slideUp("fast"))}});var l=3DBackbon= e.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Hand= lebars.templates.tool_search,events:{click:"focus_and_select","keyup :input= ":"query_changed","click #search-clear-btn":"clear"},render:function(){this= .$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()= ){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_an= d_select:function(){this.$el.find(":input").focus().select()},clear:functio= n(){this.model.clear_search();this.$el.find(":input").val(this.model.attrib= utes.search_hint_string);this.focus_and_select();return false},query_change= d:function(t){if((this.model.attributes.clear_key)&&(this.model.attributes.= clear_key=3D=3D=3Dt.which)){this.clear();return false}this.model.set("query= ",this.$el.find(":input").val())}});var s=3DBackbone.View.extend({tagName:"= div",className:"toolMenu",initialize:function(){this.collection.tool_search= .on("change:results",this.handle_search_results,this)},render:function(){va= r t=3Dthis;var u=3Dnew l({model:this.collection.tool_search});u.render();t.= $el.append(u.$el);this.collection.each(function(w){if(w instanceof p){var v= =3Dnew g({model:w});v.render();t.$el.append(v.$el)}else{if(w instanceof e){= var x=3Dnew h({model:w,className:"toolTitleNoSection"});x.render();t.$el.ap= pend(x.$el)}else{if(w instanceof m){var y=3Dnew c({model:w});y.render();t.$= el.append(y.$el)}}}});t.$el.find("a.tool-link").click(function(x){var w=3D$= (this).attr("class").split(/\s+/)[0],v=3Dt.collection.tools.get(w);t.trigge= r("tool_link_click",x,v)});return this},handle_search_results:function(){va= r t=3Dthis.collection.tool_search.attributes.results;if(t&&t.length=3D=3D= =3D0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}= );var o=3DBackbone.View.extend({className:"toolForm",template:Handlebars.te= mplates.tool_form,render:function(){this.$el.children().remove();this.$el.a= ppend(this.template(this.model.toJSON()))}});var d=3DBackbone.View.extend({= className:"toolMenuAndView",initialize:function(){this.tool_panel_view=3Dne= w s({collection:this.collection});this.tool_form_view=3Dnew o()},render:fun= ction(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float",= "left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.h= ide();this.$el.append(this.tool_form_view.$el);var t=3Dthis;this.tool_panel= _view.on("tool_link_click",function(v,u){v.preventDefault();t.show_tool(u)}= )},show_tool:function(u){var t=3Dthis;u.fetch().done(function(){t.tool_form= _view.model=3Du;t.tool_form_view.render();t.tool_form_view.$el.show();$("#l= eft").width("650px")})}});return{Tool:e,ToolSearch:b,ToolPanel:j,ToolPanelV= iew:s,ToolFormView:o}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/b= ackbone-relational"],function(q,a,r){var g=3DBackbone.RelationalModel.exten= d({defaults:{name:null,hidden:false},show:function(){this.set("hidden",fals= e)},hide:function(){this.set("hidden",true)},is_visible:function(){return != this.attributes.hidden}});var c=3DBackbone.RelationalModel.extend({defaults= :{name:null,label:null,type:null,value:null,num_samples:5},initialize:funct= ion(){this.attributes.html=3Dunescape(this.attributes.html)},copy:function(= ){return new c(this.toJSON())},get_samples:function(){var u=3Dthis.get("typ= e"),t=3Dnull;if(u=3D=3D=3D"number"){t=3Dd3.scale.linear().domain([this.get(= "min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(u=3D=3D=3D"= select"){t=3Dq.map(this.get("options"),function(v){return v[0]})}}return t}= });var f=3Dg.extend({defaults:{description:null,target:null,inputs:[]},rela= tions:[{type:Backbone.HasMany,key:"inputs",relatedModel:c,reverseRelation:{= key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy= :function(u){var v=3Dnew f(this.toJSON());if(u){var t=3Dnew Backbone.Collec= tion();v.get("inputs").each(function(w){if(w.get_samples()){t.push(w)}});v.= set("inputs",t)}return v},apply_search_results:function(t){(q.indexOf(t,thi= s.attributes.id)!=3D=3D-1?this.show():this.hide());return this.is_visible()= },set_input_value:function(t,u){this.get("inputs").find(function(v){return = v.get("name")=3D=3D=3Dt}).set("value",u)},set_input_values:function(u){var = t=3Dthis;q.each(q.keys(u),function(v){t.set_input_value(v,u[v])})},run:func= tion(){return this._run()},rerun:function(u,t){return this._run({action:"re= run",target_dataset_id:u.id,regions:t})},get_inputs_dict:function(){var t= =3D{};this.get("inputs").each(function(u){t[u.get("name")]=3Du.get("value")= });return t},_run:function(v){var w=3Dq.extend({tool_id:this.id,inputs:this= .get_inputs_dict()},v);var u=3D$.Deferred(),t=3Dnew a.ServerStateDeferred({= ajax_settings:{url:this.urlRoot,data:JSON.stringify(w),dataType:"json",cont= entType:"application/json",type:"POST"},interval:2000,success_fn:function(x= ){return x!=3D=3D"pending"}});$.when(t.go()).then(function(x){u.resolve(new= r.DatasetCollection().reset(x))});return u}});var j=3DBackbone.Collection.= extend({model:f});var m=3Dg.extend({});var p=3Dg.extend({defaults:{elems:[]= ,open:false},clear_search_results:function(){q.each(this.attributes.elems,f= unction(t){t.show()});this.show();this.set("open",false)},apply_search_resu= lts:function(u){var v=3Dtrue,t;q.each(this.attributes.elems,function(w){if(= w instanceof m){t=3Dw;t.hide()}else{if(w instanceof f){if(w.apply_search_re= sults(u)){v=3Dfalse;if(t){t.show()}}}}});if(v){this.hide()}else{this.show()= ;this.set("open",true)}}});var b=3Dg.extend({defaults:{search_hint_string:"= search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search= _url:"",visible:true,query:"",results:null,clear_key:27},initialize:functio= n(){this.on("change:query",this.do_search)},do_search:function(){var v=3Dth= is.attributes.query;if(v.length<this.attributes.min_chars_for_search){this.= set("results",null);return}var u=3Dv+"*";if(this.timer){clearTimeout(this.t= imer)}$("#search-clear-btn").hide();$("#search-spinner").show();var t=3Dthi= s;this.timer=3DsetTimeout(function(){$.get(t.attributes.search_url,{query:u= },function(w){t.set("results",w);$("#search-spinner").hide();$("#search-cle= ar-btn").show()},"json")},200)},clear_search:function(){this.set("query",""= );this.set("results",null)}});var k=3DBackbone.Collection.extend({url:"/too= ls",tools:new j(),parse:function(t){var u=3Dfunction(x){var w=3Dx.type;if(w= =3D=3D=3D"tool"){return new f(x)}else{if(w=3D=3D=3D"section"){var v=3Dq.map= (x.elems,u);x.elems=3Dv;return new p(x)}else{if(w=3D=3D=3D"label"){return n= ew m(x)}}}};return q.map(t,u)},initialize:function(t){this.tool_search=3Dt.= tool_search;this.tool_search.on("change:results",this.apply_search_results,= this);this.on("reset",this.populate_tools,this)},populate_tools:function(){= var t=3Dthis;t.tools=3Dnew j();this.each(function(u){if(u instanceof p){q.e= ach(u.attributes.elems,function(v){if(v instanceof f){t.tools.push(v)}})}el= se{if(u instanceof f){t.tools.push(u)}}})},clear_search_results:function(){= this.each(function(t){if(t instanceof p){t.clear_search_results()}else{t.sh= ow()}})},apply_search_results:function(){var u=3Dthis.tool_search.attribute= s.results;if(u=3D=3D=3Dnull){this.clear_search_results();return}var t=3Dnul= l;this.each(function(v){if(v instanceof m){t=3Dv;t.hide()}else{if(v instanc= eof f){if(v.apply_search_results(u)){if(t){t.show()}}}else{t=3Dnull;v.apply= _search_results(u)}}})}});var n=3DBackbone.View.extend({initialize:function= (){this.model.on("change:hidden",this.update_visible,this);this.update_visi= ble()},update_visible:function(){(this.model.attributes.hidden?this.$el.hid= e():this.$el.show())}});var i=3Dn.extend({tagName:"div",template:Handlebars= .templates.tool_link,render:function(){this.$el.append(this.template(this.m= odel.toJSON()));return this}});var d=3Dn.extend({tagName:"div",className:"t= oolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.mod= el.attributes.name));return this}});var h=3Dn.extend({tagName:"div",classNa= me:"toolSectionWrapper",template:Handlebars.templates.panel_section,initial= ize:function(){n.prototype.initialize.call(this);this.model.on("change:open= ",this.update_open,this)},render:function(){this.$el.append(this.template(t= his.model.toJSON()));var t=3Dthis.$el.find(".toolSectionBody");q.each(this.= model.attributes.elems,function(u){if(u instanceof f){var v=3Dnew i({model:= u,className:"toolTitle"});v.render();t.append(v.$el)}else{if(u instanceof m= ){var w=3Dnew d({model:u});w.render();t.append(w.$el)}else{}}});return this= },events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.mo= del.set("open",!this.model.attributes.open)},update_open:function(){(this.m= odel.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"= ):this.$el.children(".toolSectionBody").slideUp("fast"))}});var l=3DBackbon= e.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Hand= lebars.templates.tool_search,events:{click:"focus_and_select","keyup :input= ":"query_changed","click #search-clear-btn":"clear"},render:function(){this= .$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()= ){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_an= d_select:function(){this.$el.find(":input").focus().select()},clear:functio= n(){this.model.clear_search();this.$el.find(":input").val(this.model.attrib= utes.search_hint_string);this.focus_and_select();return false},query_change= d:function(t){if((this.model.attributes.clear_key)&&(this.model.attributes.= clear_key=3D=3D=3Dt.which)){this.clear();return false}this.model.set("query= ",this.$el.find(":input").val())}});var s=3DBackbone.View.extend({tagName:"= div",className:"toolMenu",initialize:function(){this.collection.tool_search= .on("change:results",this.handle_search_results,this)},render:function(){va= r t=3Dthis;var u=3Dnew l({model:this.collection.tool_search});u.render();t.= $el.append(u.$el);this.collection.each(function(w){if(w instanceof p){var v= =3Dnew h({model:w});v.render();t.$el.append(v.$el)}else{if(w instanceof f){= var x=3Dnew i({model:w,className:"toolTitleNoSection"});x.render();t.$el.ap= pend(x.$el)}else{if(w instanceof m){var y=3Dnew d({model:w});y.render();t.$= el.append(y.$el)}}}});t.$el.find("a.tool-link").click(function(x){var w=3D$= (this).attr("class").split(/\s+/)[0],v=3Dt.collection.tools.get(w);t.trigge= r("tool_link_click",x,v)});return this},handle_search_results:function(){va= r t=3Dthis.collection.tool_search.attributes.results;if(t&&t.length=3D=3D= =3D0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}= );var o=3DBackbone.View.extend({className:"toolForm",template:Handlebars.te= mplates.tool_form,render:function(){this.$el.children().remove();this.$el.a= ppend(this.template(this.model.toJSON()))}});var e=3DBackbone.View.extend({= className:"toolMenuAndView",initialize:function(){this.tool_panel_view=3Dne= w s({collection:this.collection});this.tool_form_view=3Dnew o()},render:fun= ction(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float",= "left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.h= ide();this.$el.append(this.tool_form_view.$el);var t=3Dthis;this.tool_panel= _view.on("tool_link_click",function(v,u){v.preventDefault();t.show_tool(u)}= )},show_tool:function(u){var t=3Dthis;u.fetch().done(function(){t.tool_form= _view.model=3Du;t.tool_form_view.render();t.tool_form_view.$el.show();$("#l= eft").width("650px")})}});return{Tool:f,ToolSearch:b,ToolPanel:k,ToolPanelV= iew:s,ToolFormView:o}}); \ No newline at end of file diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c templates/webapps/tool_shed/repository/tool_form.mako --- a/templates/webapps/tool_shed/repository/tool_form.mako +++ b/templates/webapps/tool_shed/repository/tool_form.mako @@ -70,6 +70,8 @@ =20 <%def name=3D"row_for_param( prefix, param, parent_state, other_va= lues )"><% + # Disable refresh_on_change for select lists displayed in = the tool shed.=20 + param.refresh_on_change =3D False label =3D param.get_label() if isinstance( param, DataToolParameter ) or isinstance( p= aram, ColumnListParameter ) or isinstance( param, GenomeBuildParameter ): field =3D SelectField( param.name ) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c test/install_and_test_tool_shed_repositories/functional_t= ests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -6,6 +6,7 @@ =20 import os, sys, shutil, tempfile, re, string, urllib, platform from time import strftime +from ConfigParser import SafeConfigParser =20 # Assume we are run from the galaxy root directory, add lib to the python = path cwd =3D os.getcwd() @@ -73,6 +74,40 @@ default_galaxy_test_port_max =3D 10999 default_galaxy_test_host =3D '127.0.0.1' =20 +# should this serve static resources (scripts, images, styles, etc.) +STATIC_ENABLED =3D True + +def get_static_settings(): + """Returns dictionary of the settings necessary for a galaxy App + to be wrapped in the static middleware. + + This mainly consists of the filesystem locations of url-mapped + static resources. + """ + cwd =3D os.getcwd() + static_dir =3D os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.ini + return dict( + #TODO: static_enabled needed here? + static_enabled =3D True, + static_cache_time =3D 360, + static_dir =3D static_dir, + static_images_dir =3D os.path.join( static_dir, 'images', '' ), + static_favicon_dir =3D os.path.join( static_dir, 'favicon.ico' ), + static_scripts_dir =3D os.path.join( static_dir, 'scripts', '' ), + static_style_dir =3D os.path.join( static_dir, 'june_2007_style= ', 'blue' ), + static_robots_txt =3D os.path.join( static_dir, 'robots.txt' ), + ) + +def get_webapp_global_conf(): + """Get the global_conf dictionary sent as the first argument to app_fa= ctory. + """ + # (was originally sent 'dict()') - nothing here for now except static = settings + global_conf =3D dict() + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + # Optionally, set the environment variable GALAXY_INSTALL_TEST_TOOL_SHEDS_= CONF # to the location of a tool sheds configuration file that includes the too= l shed # that repositories will be installed from. @@ -219,6 +254,36 @@ success =3D result.wasSuccessful() return success =20 +def generate_config_file( input_filename, output_filename, config_items ): + ''' + Generate a config file with the configuration that has been defined fo= r the embedded web application. + This is mostly relevant when setting metadata externally, since the sc= ript for doing that does not + have access to app.config. + '''=20 + cp =3D SafeConfigParser() + cp.read( input_filename ) + config_items_by_section =3D [] + for label, value in config_items: + found =3D False + # Attempt to determine the correct section for this configuration = option. + for section in cp.sections(): + if cp.has_option( section, label ): + config_tuple =3D section, label, value + config_items_by_section.append( config_tuple ) + found =3D True + continue + # Default to app:main if no section was found. + if not found: + config_tuple =3D 'app:main', label, value + config_items_by_section.append( config_tuple ) + # Replace the default values with the provided configuration. + for section, label, value in config_items_by_section: + cp.remove_option( section, label ) + cp.set( section, label, str( value ) ) + fh =3D open( output_filename, 'w' ) + cp.write( fh ) + fh.close() + def get_api_url( base, parts=3D[], params=3DNone, key=3DNone ): if 'api' in parts and parts.index( 'api' ) !=3D 0: parts.pop( parts.index( 'api' ) ) @@ -554,48 +619,64 @@ # Generate the migrated_tool_conf.xml file. migrated_tool_conf_xml =3D tool_conf_template_parser.safe_substitute( = shed_tool_path=3Dgalaxy_migrated_tool_path ) file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_= xml ) - + # Write the embedded web application's specific configuration to a tem= porary file. This is necessary in order for + # the external metadata script to find the right datasets. + kwargs =3D dict( admin_users =3D 'test(a)bx.psu.edu', + allow_user_creation =3D True, + allow_user_deletion =3D True, + allow_library_path_paste =3D True, + database_connection =3D database_connection, + datatype_converters_config_file =3D "datatype_converter= s_conf.xml.sample", + file_path =3D galaxy_file_path, + id_secret =3D galaxy_encode_secret, + job_queue_workers =3D 5, + log_destination =3D "stdout", + migrated_tools_config =3D galaxy_migrated_tool_conf_fil= e, + new_file_path =3D galaxy_tempfiles, + running_functional_tests =3D True, + shed_tool_data_table_config =3D shed_tool_data_table_co= nf_file, + shed_tool_path =3D galaxy_shed_tool_path, + template_path =3D "templates", + tool_config_file =3D ','.join( [ galaxy_tool_conf_file,= galaxy_shed_tool_conf_file ] ), + tool_data_path =3D tool_data_path, + tool_data_table_config_path =3D galaxy_tool_data_table_= conf_file, + tool_dependency_dir =3D tool_dependency_dir, + tool_path =3D tool_path, + tool_parse_help =3D False, + tool_sheds_config_file =3D galaxy_tool_sheds_conf_file, + update_integrated_tool_panel =3D False, + use_heartbeat =3D False ) + galaxy_config_file =3D os.environ.get( 'GALAXY_INSTALL_TEST_INI_FILE',= None ) + # If the user has passed in a path for the .ini file, do not overwrite= it. + if not galaxy_config_file: + galaxy_config_file =3D os.path.join( galaxy_test_tmp_dir, 'install= _test_tool_shed_repositories_wsgi.ini' ) + config_items =3D [] + for label in kwargs: + config_tuple =3D label, kwargs[ label ] + config_items.append( config_tuple ) + # Write a temporary file, based on universe_wsgi.ini.sample, using= the configuration options defined above. + generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_fi= le, config_items ) + kwargs[ 'tool_config_file' ] =3D [ galaxy_tool_conf_file, galaxy_shed_= tool_conf_file ] + # Set the global_conf[ '__file__' ] option to the location of the temp= orary .ini file, which gets passed to set_metadata.sh. + kwargs[ 'global_conf' ] =3D get_webapp_global_conf() + kwargs[ 'global_conf' ][ '__file__' ] =3D galaxy_config_file # ---- Build Galaxy Application --------------------------------------= ------------=20 - global_conf =3D { '__file__' : 'universe_wsgi.ini.sample' } if not database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_max_overflow' ] =3D '20' kwargs[ 'database_engine_option_pool_size' ] =3D '10' - app =3D UniverseApplication( admin_users =3D 'test(a)bx.psu.edu', - allow_user_creation =3D True, - allow_user_deletion =3D True, - allow_library_path_paste =3D True, - database_connection =3D database_connection, - datatype_converters_config_file =3D "dataty= pe_converters_conf.xml.sample", - file_path =3D galaxy_file_path, - global_conf =3D global_conf, - id_secret =3D galaxy_encode_secret, - job_queue_workers =3D 5, - log_destination =3D "stdout", - migrated_tools_config =3D galaxy_migrated_t= ool_conf_file, - new_file_path =3D galaxy_tempfiles, - running_functional_tests=3DTrue, - shed_tool_data_table_config =3D shed_tool_d= ata_table_conf_file, - shed_tool_path =3D galaxy_shed_tool_path, - template_path =3D "templates", - tool_config_file =3D [ galaxy_tool_conf_fil= e, galaxy_shed_tool_conf_file ], - tool_data_path =3D tool_data_path, - tool_data_table_config_path =3D galaxy_tool= _data_table_conf_file, - tool_dependency_dir =3D tool_dependency_dir, - tool_path =3D tool_path, - tool_parse_help =3D False, - tool_sheds_config_file =3D galaxy_tool_shed= s_conf_file, - update_integrated_tool_panel =3D False, - use_heartbeat =3D False, - **kwargs ) + kwargs[ 'config_file' ] =3D galaxy_config_file + app =3D UniverseApplication( **kwargs ) =20 log.info( "Embedded Galaxy application started" ) =20 # ---- Run galaxy webserver ------------------------------------------= ------------ server =3D None - webapp =3D buildapp.app_factory( dict( database_file=3Ddatabase_connec= tion ), - use_translogger=3DFalse, - static_enabled=3DFalse, - app=3Dapp ) + global_conf =3D get_webapp_global_conf() + global_conf[ 'database_file' ] =3D database_connection + webapp =3D buildapp.app_factory( global_conf, + use_translogger=3DFalse, + static_enabled=3DSTATIC_ENABLED, + app=3Dapp ) =20 # Serve the app on a specified or random port. if galaxy_test_port is not None: @@ -976,6 +1057,7 @@ repositories_passed.append( dict( name=3Dname, own= er=3Downer, changeset_revision=3Dchangeset_revision ) ) params[ 'tools_functionally_correct' ] =3D True params[ 'do_not_test' ] =3D False + params[ 'test_install_error' ] =3D False register_test_result( galaxy_tool_shed_url,=20 metadata_revision_id,=20 repository_status,=20 @@ -1027,6 +1109,7 @@ repositories_failed.append( dict( name=3Dname, own= er=3Downer, changeset_revision=3Dchangeset_revision ) ) set_do_not_test =3D not is_latest_downloadable_rev= ision( galaxy_tool_shed_url, repository_info_dict ) params[ 'tools_functionally_correct' ] =3D False + params[ 'test_install_error' ] =3D False params[ 'do_not_test' ] =3D str( set_do_not_test ) register_test_result( galaxy_tool_shed_url,=20 metadata_revision_id,=20 diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c test/unit/datatypes/dataproviders/tempfilecache.py --- /dev/null +++ b/test/unit/datatypes/dataproviders/tempfilecache.py @@ -0,0 +1,47 @@ + +import os +import tempfile + +import logging +logging.getLogger( __name__ ) +log =3D logging + +class TempFileCache( object ): + """ + Creates and caches tempfiles with/based-on the given contents. + """ + def __init__( self, logger=3DNone ): + if logger: + global log + log =3D logger + super( TempFileCache, self ).__init__() + self.clear() + + def clear( self ): + self.delete_tmpfiles() + self._content_dict =3D {} + + def create_tmpfile( self, contents ): + if not hasattr( self, '_content_dict' ): + self.set_up_tmpfiles() + + if contents not in self._content_dict: + # create a named tmp and write contents to it, return filename + tmpfile =3D tempfile.NamedTemporaryFile( delete=3DFalse ) + tmpfile.write( contents ) + tmpfile.close() + log.debug( 'created tmpfile.name: %s', tmpfile.name ) + self._content_dict[ contents ] =3D tmpfile.name + + else: + log.debug( '(cached): %s', self._content_dict[ contents ] ) + return self._content_dict[ contents ] + + def delete_tmpfiles( self ): + if not hasattr( self, '_content_dict' ) or not self._content_dict: + return + for tmpfile_contents in self._content_dict: + tmpfile =3D self._content_dict[ tmpfile_contents ] + if os.path.exists( tmpfile ): + log.debug( 'unlinking tmpfile: %s', tmpfile ) + os.unlink( tmpfile ) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c test/unit/datatypes/dataproviders/test_base_dataproviders= .py --- /dev/null +++ b/test/unit/datatypes/dataproviders/test_base_dataproviders.py @@ -0,0 +1,370 @@ +""" +Unit tests for base DataProviders. +.. seealso:: galaxy.datatypes.dataproviders.base +""" +# currently because of dataproviders.dataset importing galaxy.model this d= oesn't work +#TODO: fix imports there after dist and retry + +#TODO: fix off by ones in FilteredDataProvider counters + +import unittest +import StringIO + +import tempfilecache +import utility + +log =3D utility.set_up_filelogger( __name__ + '.log' ) + +utility.add_galaxy_lib_to_path( '/test/unit/datatypes/dataproviders' ) +from galaxy.datatypes import dataproviders + + +class BaseTestCase( unittest.TestCase ): + default_file_contents =3D """ + One + Two + Three + """ + + @classmethod + def setUpClass( cls ): + log.debug( 'CLASS %s %s', ( '_' * 40 ), cls.__name__ ) + + @classmethod + def tearDownClass( cls ): + log.debug( 'CLASS %s %s\n\n', ( '_' * 40 ), cls.__name__ ) + + def __init__( self, *args ): + unittest.TestCase.__init__( self, *args ) + self.tmpfiles =3D tempfilecache.TempFileCache( log ) + + def setUp( self ): + log.debug( 'BEGIN %s %s', ( '.' * 40 ), self._testMethodName ) + if self._testMethodDoc: + log.debug( ' """%s"""', self._testMethodDoc.strip() ) + + def tearDown( self ): + self.tmpfiles.clear() + log.debug( 'END\n' ) + + def format_tmpfile_contents( self, contents=3DNone ): + contents =3D contents or self.default_file_contents + contents =3D utility.clean_multiline_string( contents ) + log.debug( 'file contents:\n%s', contents ) + return contents + + +class Test_BaseDataProvider( BaseTestCase ): + provider_class =3D dataproviders.base.DataProvider + + def contents_provider_and_data( self, + filename=3DNone, contents=3DNone, source=3DNone, *provider_arg= s, **provider_kwargs ): + # to remove boiler plate + # returns file content string, provider used, and data list + if not filename: + contents =3D self.format_tmpfile_contents( contents ) + filename =3D self.tmpfiles.create_tmpfile( contents ) + #TODO: if filename, contents =3D=3D None + if not source: + source =3D open( filename ) + provider =3D self.provider_class( source, *provider_args, **provid= er_kwargs ) + log.debug( 'provider: %s', provider ) + data =3D list( provider ) + log.debug( 'data: %s', str( data ) ) + return ( contents, provider, data ) + + def test_iterators( self ): + source =3D ( x for x in xrange( 1, 10 ) ) + provider =3D self.provider_class( source ) + data =3D list( provider ) + log.debug( 'data: %s', str( data ) ) + self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + + source =3D [ x for x in xrange( 1, 10 ) ] + provider =3D self.provider_class( source ) + data =3D list( provider ) + log.debug( 'data: %s', str( data ) ) + self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + + source =3D ( x for x in xrange( 1, 10 ) ) + provider =3D self.provider_class( source ) + data =3D list( provider ) + log.debug( 'data: %s', str( data ) ) + self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + + def test_validate_source( self ): + """validate_source should throw an error if the source doesn't hav= e attr '__iter__' + """ + def non_iterator_dprov( source ): + return self.provider_class( source ) + self.assertRaises( dataproviders.exceptions.InvalidDataProviderSou= rce, + non_iterator_dprov, 'one two three' ) + self.assertRaises( dataproviders.exceptions.InvalidDataProviderSou= rce, + non_iterator_dprov, 40 ) + + def test_writemethods( self ): + """should throw an error if any write methods are called + """ + source =3D ( x for x in xrange( 1, 10 ) ) + provider =3D self.provider_class( source ) + # should throw error + def call_method( provider, method_name, *args ): + method =3D getattr( provider, method_name ) + return method( *args ) + self.assertRaises( NotImplementedError, call_method, provider, 'tr= uncate', 20 ) + self.assertRaises( NotImplementedError, call_method, provider, 'wr= ite', 'bler' ) + self.assertRaises( NotImplementedError, call_method, provider, 'wr= itelines', [ 'one', 'two' ] ) + + def test_readlines( self ): + """readlines should return all the data in list form + """ + source =3D ( x for x in xrange( 1, 10 ) ) + provider =3D self.provider_class( source ) + data =3D provider.readlines() + log.debug( 'data: %s', str( data ) ) + self.assertEqual( data, [ x for x in xrange( 1, 10 ) ] ) + + def test_stringio( self ): + """should work with StringIO + """ + contents =3D utility.clean_multiline_string( """ + One + Two + Three + """ ) + source =3D StringIO.StringIO( contents ) + provider =3D self.provider_class( source ) + data =3D list( provider ) + log.debug( 'data: %s', str( data ) ) + # provider should call close on file + self.assertEqual( ''.join( data ), contents ) + self.assertTrue( source.closed ) + + def test_file( self ): + """should work with files + """ + ( contents, provider, data ) =3D self.contents_provider_and_data() + self.assertEqual( ''.join( data ), contents ) + # provider should call close on file + self.assertTrue( isinstance( provider.source, file ) ) + self.assertTrue( provider.source.closed ) + + +class Test_FilteredDataProvider( Test_BaseDataProvider ): + provider_class =3D dataproviders.base.FilteredDataProvider + + def assertCounters( self, provider, read, valid, returned ): + self.assertEqual( provider.num_data_read, read ) + self.assertEqual( provider.num_valid_data_read, valid ) + self.assertEqual( provider.num_data_returned, returned ) + + def test_counters( self ): + """should count: lines read, lines that passed the filter, lines r= eturned + """ + ( contents, provider, data ) =3D self.contents_provider_and_data() + self.assertCounters( provider, 3, 3, 3 ) + + def test_filter_fn( self ): + """should filter out lines using filter_fn and set counters proper= ly + based on filter + """ + def filter_ts( string ): + if string.lower().startswith( 't' ): + return None + return string + ( contents, provider, data ) =3D self.contents_provider_and_data( = filter_fn=3Dfilter_ts ) + self.assertCounters( provider, 3, 1, 1 ) + + +class Test_LimitedOffsetDataProvider( Test_FilteredDataProvider ): + provider_class =3D dataproviders.base.LimitedOffsetDataProvider + + def test_offset_1( self ): + """when offset is 1, should skip first + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = offset=3D1 ) + self.assertEqual( data, [ 'Two\n', 'Three\n' ] ) + self.assertCounters( provider, 3, 3, 2 ) + + def test_offset_all( self ): + """when offset >=3D num lines, should return empty list + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = offset=3D4 ) + self.assertEqual( data, [] ) + self.assertCounters( provider, 3, 3, 0 ) + + def test_offset_none( self ): + """when offset is 0, should return all + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = offset=3D0 ) + self.assertEqual( ''.join( data ), contents ) + self.assertCounters( provider, 3, 3, 3 ) + + def test_offset_negative( self ): + """when offset is negative, should return all + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = offset=3D-1 ) + self.assertEqual( ''.join( data ), contents ) + self.assertCounters( provider, 3, 3, 3 ) + + def test_limit_1( self ): + """when limit is one, should return first + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = limit=3D1 ) + self.assertEqual( data, [ 'One\n' ] ) + #TODO: currently reads 2 in all counters before ending + #self.assertCounters( provider, 1, 1, 1 ) + + def test_limit_all( self ): + """when limit >=3D num lines, should return all + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = limit=3D4 ) + self.assertEqual( ''.join( data ), contents ) + self.assertCounters( provider, 3, 3, 3 ) + + def test_limit_zero( self ): + """when limit >=3D num lines, should return empty list + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = limit=3D0 ) + self.assertEqual( data, [] ) + #TODO: currently reads 1 before ending + self.assertCounters( provider, 3, 0, 0 ) + + def test_limit_zero( self ): + """when limit is None, should return all + """ + ( contents, provider, data ) =3D self.contents_provider_and_data( = limit=3DNone ) + self.assertEqual( ''.join( data ), contents ) + self.assertCounters( provider, 3, 3, 3 ) + + #TODO: somehow re-use tmpfile here + def test_limit_with_offset( self ): + def limit_offset_combo( limit, offset, data_should_be, read, valid= , returned ): + ( contents, provider, data ) =3D self.contents_provider_and_da= ta( limit=3Dlimit, offset=3Doffset ) + self.assertEqual( data, data_should_be ) + #self.assertCounters( provider, read, valid, returned ) + test_data =3D [ + ( 0, 0, [], 0, 0, 0 ), + ( 1, 0, [ 'One\n' ], 1, 1, 1 ), + ( 2, 0, [ 'One\n', 'Two\n' ], 2, 2, 2 ), + ( 3, 0, [ 'One\n', 'Two\n', 'Three\n' ], 3, 3, 3 ), + ( 1, 1, [ 'Two\n' ], 1, 1, 1 ), + ( 2, 1, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), + ( 3, 1, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), + ( 1, 2, [ 'Three\n' ], 1, 1, 1 ), + ( 2, 2, [ 'Three\n' ], 1, 1, 1 ), + ( 3, 2, [ 'Three\n' ], 1, 1, 1 ), + ] + for test in test_data: + log.debug( 'limit_offset_combo: %s', ', '.join([ str( e ) for = e in test ]) ) + limit_offset_combo( *test ) + + def test_limit_with_offset_and_filter( self ): + def limit_offset_combo( limit, offset, data_should_be, read, valid= , returned ): + def only_ts( string ): + if not string.lower().startswith( 't' ): + return None + return string + ( contents, provider, data ) =3D self.contents_provider_and_da= ta( + limit=3Dlimit, offset=3Doffset, filter_fn=3Donly_ts ) + self.assertEqual( data, data_should_be ) + #self.assertCounters( provider, read, valid, returned ) + test_data =3D [ + ( 0, 0, [], 0, 0, 0 ), + ( 1, 0, [ 'Two\n' ], 1, 1, 1 ), + ( 2, 0, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), + ( 3, 0, [ 'Two\n', 'Three\n' ], 2, 2, 2 ), + ( 1, 1, [ 'Three\n' ], 1, 1, 1 ), + ( 2, 1, [ 'Three\n' ], 1, 1, 1 ), + ( 1, 2, [], 0, 0, 0 ), + ] + for test in test_data: + log.debug( 'limit_offset_combo: %s', ', '.join([ str( e ) for = e in test ]) ) + limit_offset_combo( *test ) + + +class Test_MultiSourceDataProvider( BaseTestCase ): + provider_class =3D dataproviders.base.MultiSourceDataProvider + + def contents_and_tmpfile( self, contents=3DNone ): + #TODO: hmmmm... + contents =3D contents or self.default_file_contents + contents =3D utility.clean_multiline_string( contents ) + return ( contents, self.tmpfiles.create_tmpfile( contents ) ) + + def test_multiple_sources( self ): + # clean the following contents, write them to tmpfiles, open them, + # and pass as a list to the provider + contents =3D [ + """ + One + Two + Three + Four + Five + """, + """ + Six + Seven + Eight + Nine + Ten + """, + """ + Eleven + Twelve! (<-- http://youtu.be/JZshZp-cxKg) + """ + ] + contents =3D [ utility.clean_multiline_string( c ) for c in conten= ts ] + source_list =3D [ open( self.tmpfiles.create_tmpfile( c ) ) for c = in contents ] + + provider =3D self.provider_class( source_list ) + log.debug( 'provider: %s', provider ) + data =3D list( provider ) + log.debug( 'data: %s', str( data ) ) + self.assertEqual( ''.join( data ), ''.join( contents) ) + + def test_multiple_compound_sources( self ): + # clean the following contents, write them to tmpfiles, open them, + # and pass as a list to the provider + contents =3D [ + """ + One + Two + Three + Four + Five + """, + """ + Six + Seven + Eight + Nine + Ten + """, + """ + Eleven + Twelve! (<-- http://youtu.be/JZshZp-cxKg) + """ + ] + contents =3D [ utility.clean_multiline_string( c ) for c in conten= ts ] + source_list =3D [ open( self.tmpfiles.create_tmpfile( c ) ) for c = in contents ] + + def no_Fs( string ): + return None if string.startswith( 'F' ) else string + def no_youtube( string ): + return None if ( 'youtu.be' in string ) else string + source_list =3D [ + dataproviders.base.LimitedOffsetDataProvider( source_list[0], = filter_fn=3Dno_Fs, limit=3D2, offset=3D1 ), + dataproviders.base.LimitedOffsetDataProvider( source_list[1], = limit=3D1, offset=3D3 ), + dataproviders.base.FilteredDataProvider( source_list[2], filte= r_fn=3Dno_youtube ), + ] + provider =3D self.provider_class( source_list ) + log.debug( 'provider: %s', provider ) + data =3D list( provider ) + log.debug( 'data: %s', str( data ) ) + self.assertEqual( ''.join( data ), 'Two\nThree\nNine\nEleven\n' ) + + +if __name__ =3D=3D '__main__': + unittest.main() diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c test/unit/datatypes/dataproviders/utility.py --- /dev/null +++ b/test/unit/datatypes/dataproviders/utility.py @@ -0,0 +1,45 @@ +""" +Unit test utilities. +""" + +import os +import sys +import logging +import textwrap + +def set_up_filelogger( logname, level=3Dlogging.DEBUG ): + """ + Sets up logging to a file named `logname` + (removing it first if it already exists). + + Usable with 'nosetests' to get logging msgs from failed tests + (no logfile created). + Usable with 'nosetests --nologcapture' to get logging msgs for all tes= ts + (in logfile). + """ + if os.path.exists( logname ): os.unlink( logname ) + logging.basicConfig( filename=3Dlogname, level=3Dlogging.DEBUG ) + return logging + +def add_galaxy_lib_to_path( this_dir_relative_to_root ): + """ + Adds `<galaxy>/lib` to `sys.path` given the scripts directory relative + to `<galaxy>`. + .. example:: + utility.add_galaxy_lib_to_path( '/test/unit/datatypes/dataprovider= s' ) + """ + glx_lib =3D os.path.join( os.getcwd().replace( this_dir_relative_to_ro= ot, '' ), 'lib' ) + sys.path.append( glx_lib ) + +def clean_multiline_string( multiline_string, sep=3D'\n' ): + """ + Dedent, split, remove first and last empty lines, rejoin. + """ + multiline_string =3D textwrap.dedent( multiline_string ) + string_list =3D multiline_string.split( sep ) + if not string_list[0]: + string_list =3D string_list[1:] + if not string_list[-1]: + string_list =3D string_list[:-1] + #return '\n'.join( docstrings ) + return ''.join([ ( s + '\n' ) for s in string_list ]) diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c test/unit/test_dataproviders.pyc Binary file test/unit/test_dataproviders.pyc has changed diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c test/unit/test_tool_loader.pyc Binary file test/unit/test_tool_loader.pyc has changed diff -r a360e1b7b506450385be74b2c6b7762d3e794bbd -r 79ae7df72fba2e141791bdb= 8fdf2bb372fa3787c tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ /dev/null @@ -1,241 +0,0 @@ -#!/usr/bin/env python - -# Wrapper supports Cuffdiff versions v1.3.0-v2.0 - -import optparse, os, shutil, subprocess, sys, tempfile - -def group_callback( option, op_str, value, parser ): - groups =3D [] - flist =3D [] - for arg in parser.rargs: - arg =3D arg.strip() - if arg[0] is "-": - break - elif arg[0] is ",": - groups.append(flist) - flist =3D [] - else: - flist.append(arg) - groups.append(flist) - - setattr(parser.values, option.dest, groups) - =20 -def label_callback( option, op_str, value, parser ): - labels =3D [] - for arg in parser.rargs: - arg =3D arg.strip() - if arg[0] is "-": - break - else: - labels.append(arg) - - setattr(parser.values, option.dest, labels) - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - =20 -# Copied from sam_to_bam.py: -def check_seq_file( dbkey, cached_seqs_pointer_file ): - seq_path =3D '' - for line in open( cached_seqs_pointer_file ): - line =3D line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ) and line.startswith( 'index= ' ): - fields =3D line.split( '\t' ) - if len( fields ) < 3: - continue - if fields[1] =3D=3D dbkey: - seq_path =3D fields[2].strip() - break - return seq_path - -def __main__(): - #Parse Command Line - parser =3D optparse.OptionParser() - =20 - # Cuffdiff options. - parser.add_option( '-s', '--inner-dist-std-dev', dest=3D'inner_dist_st= d_dev', help=3D'The standard deviation for the distribution on inner distan= ces between mate pairs. The default is 20bp.' ) - parser.add_option( '-p', '--num-threads', dest=3D'num_threads', help= =3D'Use this many threads to align reads. The default is 1.' ) - parser.add_option( '-m', '--inner-mean-dist', dest=3D'inner_mean_dist'= , help=3D'This is the expected (mean) inner distance between mate pairs. \ - = For, example, for paired end runs with fragments selected at 300bp, \ - = where each end is 50bp, you should set -r to be 200. The default is 4= 5bp.') - parser.add_option( '-c', '--min-alignment-count', dest=3D'min_alignmen= t_count', help=3D'The minimum number of alignments in a locus for needed to= conduct significance testing on changes in that locus observed between sam= ples. If no testing is performed, changes in the locus are deemed not signf= icant, and the locus\' observed changes don\'t contribute to correction for= multiple testing. The default is 1,000 fragment alignments (up to 2,000 pa= ired reads).' ) - parser.add_option( '--FDR', dest=3D'FDR', help=3D'The allowed false di= scovery rate. The default is 0.05.' ) - parser.add_option( '-u', '--multi-read-correct', dest=3D'multi_read_co= rrect', action=3D"store_true", help=3D'Tells Cufflinks to do an initial est= imation procedure to more accurately weight reads mapping to multiple locat= ions in the genome') - parser.add_option( '--library-norm-method', dest=3D'library_norm_metho= d' ) - parser.add_option( '--dispersion-method', dest=3D'dispersion_method' ) - - # Advanced Options:=09 - parser.add_option( '--num-importance-samples', dest=3D'num_importance_= samples', help=3D'Sets the number of importance samples generated for each = locus during abundance estimation. Default: 1000' ) - parser.add_option( '--max-mle-iterations', dest=3D'max_mle_iterations'= , help=3D'Sets the number of iterations allowed during maximum likelihood e= stimation of abundances. Default: 5000' ) - =20 - # Wrapper / Galaxy options. - parser.add_option( '-f', '--files', dest=3D'groups', action=3D"callbac= k", callback=3Dgroup_callback, help=3D"Groups to be processed, groups are s= eparated by spaces, replicates in a group comma separated. group1_rep1,grou= p1_rep2 group2_rep1,group2_rep2, ..., groupN_rep1, groupN_rep2" ) - parser.add_option( '-A', '--inputA', dest=3D'inputA', help=3D'A transc= ript GTF file produced by cufflinks, cuffcompare, or other source.') - parser.add_option( '-1', '--input1', dest=3D'input1', help=3D'File of = RNA-Seq read alignments in the SAM format. SAM is a standard short read ali= gnment, that allows aligners to attach custom tags to individual alignments= , and Cufflinks requires that the alignments you supply have some of these = tags. Please see Input formats for more details.' ) - parser.add_option( '-2', '--input2', dest=3D'input2', help=3D'File of = RNA-Seq read alignments in the SAM format. SAM is a standard short read ali= gnment, that allows aligners to attach custom tags to individual alignments= , and Cufflinks requires that the alignments you supply have some of these = tags. Please see Input formats for more details.' ) - - # Label options - parser.add_option('-L', '--labels', dest=3D'labels', action=3D"callbac= k", callback=3Dlabel_callback, help=3D"Labels for the groups the replicates= are in.") - =20 - # Normalization options. - parser.add_option( "-N", "--quartile-normalization", dest=3D"do_normal= ization", action=3D"store_true" ) - - # Bias correction options. - parser.add_option( '-b', dest=3D'do_bias_correction', action=3D"store_= true", help=3D'Providing Cufflinks with a multifasta file via this option i= nstructs it to run our new bias detection and correction algorithm which ca= n significantly improve accuracy of transcript abundance estimates.') - parser.add_option( '', '--dbkey', dest=3D'dbkey', help=3D'The build of= the reference dataset' ) - parser.add_option( '', '--index_dir', dest=3D'index_dir', help=3D'GALA= XY_DATA_INDEX_DIR' ) - parser.add_option( '', '--ref_file', dest=3D'ref_file', help=3D'The re= ference dataset from the history' ) - - # Outputs. - parser.add_option( "--isoforms_fpkm_tracking_output", dest=3D"isoforms= _fpkm_tracking_output" ) - parser.add_option( "--genes_fpkm_tracking_output", dest=3D"genes_fpkm_= tracking_output" ) - parser.add_option( "--cds_fpkm_tracking_output", dest=3D"cds_fpkm_trac= king_output" ) - parser.add_option( "--tss_groups_fpkm_tracking_output", dest=3D"tss_gr= oups_fpkm_tracking_output" ) - parser.add_option( "--isoforms_exp_output", dest=3D"isoforms_exp_outpu= t" ) - parser.add_option( "--genes_exp_output", dest=3D"genes_exp_output" ) - parser.add_option( "--tss_groups_exp_output", dest=3D"tss_groups_exp_o= utput" ) - parser.add_option( "--cds_exp_fpkm_tracking_output", dest=3D"cds_exp_f= pkm_tracking_output" ) - parser.add_option( "--splicing_diff_output", dest=3D"splicing_diff_out= put" ) - parser.add_option( "--cds_diff_output", dest=3D"cds_diff_output" ) - parser.add_option( "--promoters_diff_output", dest=3D"promoters_diff_o= utput" ) - =20 - (options, args) =3D parser.parse_args() - =20 - # output version # of tool - try: - tmp =3D tempfile.NamedTemporaryFile().name - tmp_stdout =3D open( tmp, 'wb' ) - proc =3D subprocess.Popen( args=3D'cuffdiff --no-update-check 2>&1= ', shell=3DTrue, stdout=3Dtmp_stdout ) - tmp_stdout.close() - returncode =3D proc.wait() - stdout =3D None - for line in open( tmp_stdout.name, 'rb' ): - if line.lower().find( 'cuffdiff v' ) >=3D 0: - stdout =3D line.strip() - break - if stdout: - sys.stdout.write( '%s\n' % stdout ) - else: - raise Exception - except: - sys.stdout.write( 'Could not determine Cuffdiff version\n' ) - =20 - # If doing bias correction, set/link to sequence file. - if options.do_bias_correction: - if options.ref_file !=3D 'None': - # Sequence data from history. - # Create symbolic link to ref_file so that index will be creat= ed in working directory. - seq_path =3D "ref.fa" - os.symlink( options.ref_file, seq_path ) - else: - # Sequence data from loc file. - cached_seqs_pointer_file =3D os.path.join( options.index_dir, = 'sam_fa_indices.loc' ) - if not os.path.exists( cached_seqs_pointer_file ): - stop_err( 'The required file (%s) does not exist.' % cache= d_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /g= alaxy/data/equCab2/sam_index/equCab2.fa, - # and the equCab2.fa file will contain fasta sequences. - seq_path =3D check_seq_file( options.dbkey, cached_seqs_pointe= r_file ) - if seq_path =3D=3D '': - stop_err( 'No sequence data found for dbkey %s, so bias co= rrection cannot be used.' % options.dbkey ) =20 - =20 - # Build command. - =20 - # Base; always use quiet mode to avoid problems with storing log outpu= t. - cmd =3D "cuffdiff --no-update-check -q" - =20 - # Add options. - if options.library_norm_method: - cmd +=3D ( " --library-norm-method %s" % options.library_norm_meth= od ) - if options.dispersion_method: - cmd +=3D ( " --dispersion-method %s" % options.dispersion_method ) - if options.inner_dist_std_dev: - cmd +=3D ( " -s %i" % int ( options.inner_dist_std_dev ) ) - if options.num_threads: - cmd +=3D ( " -p %i" % int ( options.num_threads ) ) - if options.inner_mean_dist: - cmd +=3D ( " -m %i" % int ( options.inner_mean_dist ) ) - if options.min_alignment_count: - cmd +=3D ( " -c %i" % int ( options.min_alignment_count ) ) - if options.FDR: - cmd +=3D ( " --FDR %f" % float( options.FDR ) ) - if options.multi_read_correct: - cmd +=3D ( " -u" ) - if options.num_importance_samples: - cmd +=3D ( " --num-importance-samples %i" % int ( options.num_impo= rtance_samples ) ) - if options.max_mle_iterations: - cmd +=3D ( " --max-mle-iterations %i" % int ( options.max_mle_iter= ations ) ) - if options.do_normalization: - cmd +=3D ( " -N" ) - if options.do_bias_correction: - cmd +=3D ( " -b %s" % seq_path ) - =20 - # Add inputs. - # For replicate analysis: group1_rep1,group1_rep2 groupN_rep1,groupN_r= ep2 - if options.groups: - cmd +=3D " --labels " - for label in options.labels: - cmd +=3D '"%s",' % label - cmd =3D cmd[:-1] - - cmd +=3D " " + options.inputA + " " - - for group in options.groups: - for filename in group: - cmd +=3D filename + "," - cmd =3D cmd[:-1] + " " - else:=20 - cmd +=3D " " + options.inputA + " " + options.input1 + " " + optio= ns.input2 - =20 - # Debugging. - print cmd - - # Run command. - try: - tmp_name =3D tempfile.NamedTemporaryFile().name - tmp_stderr =3D open( tmp_name, 'wb' ) - proc =3D subprocess.Popen( args=3Dcmd, shell=3DTrue, stderr=3Dtmp_= stderr.fileno() ) - returncode =3D proc.wait() - tmp_stderr.close() - =20 - # Get stderr, allowing for case where it's very large. - tmp_stderr =3D open( tmp_name, 'rb' ) - stderr =3D '' - buffsize =3D 1048576 - try: - while True: - stderr +=3D tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize !=3D 0: - break - except OverflowError: - pass - tmp_stderr.close() - =20 - # Error checking. - if returncode !=3D 0: - raise Exception, stderr - =20 - # check that there are results in the output file - if len( open( "isoforms.fpkm_tracking", 'rb' ).read().strip() ) = =3D=3D 0: - raise Exception, 'The main output file is empty, there may be = an error with your input file or settings.' - except Exception, e: - stop_err( 'Error running cuffdiff. ' + str( e ) ) - - =20 - # Copy output files to specified files. - try: - shutil.copyfile( "isoforms.fpkm_tracking", options.isoforms_fpkm_t= racking_output ) - shutil.copyfile( "genes.fpkm_tracking", options.genes_fpkm_trackin= g_output ) - shutil.copyfile( "cds.fpkm_tracking", options.cds_fpkm_tracking_ou= tput ) - shutil.copyfile( "tss_groups.fpkm_tracking", options.tss_groups_fp= km_tracking_output ) - shutil.copyfile( "isoform_exp.diff", options.isoforms_exp_output ) - shutil.copyfile( "gene_exp.diff", options.genes_exp_output ) - shutil.copyfile( "tss_group_exp.diff", options.tss_groups_exp_outp= ut ) - shutil.copyfile( "splicing.diff", options.splicing_diff_output ) - shutil.copyfile( "cds.diff", options.cds_diff_output ) - shutil.copyfile( "cds_exp.diff", options.cds_exp_fpkm_tracking_out= put ) - shutil.copyfile( "promoters.diff", options.promoters_diff_output )= =20 - except Exception, e: - stop_err( 'Error in cuffdiff:\n' + str( e ) ) - -if __name__=3D=3D"__main__": __main__() This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/40c9834811eb/ Changeset: 40c9834811eb User: saketkc Date: 2013-08-06 09:31:21 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r cf53a00bcf1d279072ec279e6531f211992b4f3e -r 40c9834811ebfbefb423155= 3c922ff4c44905c63 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/d33f8c5396a8/ Changeset: d33f8c5396a8 User: saketkc Date: 2013-08-07 15:21:51 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r f33c054d6d5b75ae545248d71ec559d74b4fa636 -r d33f8c5396a8825b450432a= 8c443e1592a360885 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/a968c0cae563/ Changeset: a968c0cae563 User: saketkc Date: 2013-08-28 19:15:32 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 22a4f03c1fe40dedcb7e6f11510d58ada8e9c458 -r a968c0cae5639f3be5ffdd9= 31df909c215f43a43 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/4c1eb0c91fc6/ Changeset: 4c1eb0c91fc6 User: saketkc Date: 2013-08-31 18:30:53 Summary: Automated merge with ssh://bitbucket.org/galaxy/galaxy-central Affected #: 1 file diff -r 0470feeb593f9797fa9fd19dfdac4751a7ca788b -r 4c1eb0c91fc6e3085948ef1= 6eb88d18ea626e7d3 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) https://bitbucket.org/galaxy/galaxy-central/commits/dcd9809d0239/ Changeset: dcd9809d0239 User: jgoecks Date: 2013-09-11 18:16:14 Summary: Merged in saketkc/galaxy-central (pull request #184) VCFTools Incompatible with VCF4.1 Affected #: 1 file diff -r 228f1b4066be9fc49f6f07ff6867566836134c67 -r dcd9809d0239c7dc80cec3b= 2a01d7bded4a8c088 tools/vcf_tools/vcfClass.py --- a/tools/vcf_tools/vcfClass.py +++ b/tools/vcf_tools/vcfClass.py @@ -12,12 +12,13 @@ self.hasHeader =3D True self.headerText =3D "" self.headerTitles =3D "" + self.vcfFormat =3D "" #self.headerInfoText =3D "" #self.headerFormatText =3D "" =20 # Store the info and format tags as well as the lines that describe # them in a dictionary. - self.numberDataSets =3D 0=20 + self.numberDataSets =3D 0 self.includedDataSets =3D {} self.infoHeaderTags =3D {} self.infoHeaderString =3D {} @@ -63,6 +64,7 @@ # Determine the type of information in the header line. def getHeaderLine(self, filename, writeOut): self.headerLine =3D self.filehandle.readline().rstrip("\n") + if self.headerLine.startswith("##fileformat"): success =3D self.getvcf= Format() if self.headerLine.startswith("##INFO"): success =3D self.headerInfo(w= riteOut, "info") elif self.headerLine.startswith("##FORMAT"): success =3D self.headerIn= fo(writeOut, "format") elif self.headerLine.startswith("##FILE"): success =3D self.headerFile= s(writeOut) @@ -72,6 +74,18 @@ =20 return success =20 +# Read VCF format + def getvcfFormat(self): + try: + self.vcfFormat =3D self.headerLine.split("=3D",1)[1] + self.vcfFormat =3D float( self.vcfFormat.split("VCFv",1)[1] )## = Extract the version number rather than the whole string + except IndexError: + print >> sys.stderr, "\nError parsing the fileformat" + print >> sys.stderr, "The following fileformat header is wrongly= formatted: ", self.headerLine + exit(1) + return True + + # Read information on an info field from the header line. def headerInfo(self, writeOut, lineType): tag =3D self.headerLine.split("=3D",1) @@ -93,11 +107,15 @@ # an integer or a '.' to indicate variable number of entries. if tagNumber =3D=3D ".": tagNumber =3D "variable" else: - try: tagNumber =3D int(tagNumber) - except ValueError: - print >> sys.stderr, "\nError parsing header. Problem with info t= ag:", tagID - print >> sys.stderr, "Number of fields associated with this tag is= not an integer or '.'" - exit(1) + if self.vcfFormat<4.1: + + try: + tagNumber =3D int(tagNumber) + + except ValueError: + print >> sys.stderr, "\nError parsing header. Problem with in= fo tag:", tagID + print >> sys.stderr, "Number of fields associated with this ta= g is not an integer or '.'" + exit(1) =20 if lineType =3D=3D "info": self.infoHeaderTags[tagID] =3D tagNumber, tagType, tagDescription @@ -161,7 +179,7 @@ return False =20 # If there is no header in the vcf file, close and reopen the -# file so that the first line is avaiable for parsing as a=20 +# file so that the first line is avaiable for parsing as a # vcf record. def noHeader(self, filename, writeOut): if writeOut: print >> sys.stdout, "No header lines present in", filena= me @@ -216,7 +234,7 @@ else: self.hasGenotypes =3D False =20 # Add the reference sequence to the dictionary. If it didn't previously -# exist append the reference sequence to the end of the list as well.=20 +# exist append the reference sequence to the end of the list as well. # This ensures that the order in which the reference sequences appeared # in the header can be preserved. if self.referenceSequence not in self.referenceSequences: @@ -274,7 +292,7 @@ # Check that there are as many fields as in the format field. If not, thi= s must # be because the information is not known. In this case, it is permitted = that # the genotype information is either . or ./. - if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo):=20 + if genotypeInfo[0] =3D=3D "./." or genotypeInfo[0] =3D=3D "." and le= n(self.genotypeFormats) !=3D len(genotypeInfo): self.genotypeFields[ self.samplesList[i] ] =3D "." else: if len(self.genotypeFormats) !=3D len(genotypeInfo): @@ -381,7 +399,7 @@ =20 # First check that the variant class (VC) is listed as SNP. vc =3D self.info.split("VC=3D",1) - if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1)=20 + if vc[1].find(";") !=3D -1: snp =3D vc[1].split(";",1) else: snp =3D [] snp.append(vc[1]) 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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