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t=e.node,n=e.input,i=n.name,r=this.terminalForInput(n);r.multiple||this.setupMappingView(r),this.el.terminal=r,r.node=t,r.name=i,t.input_terminals[i]=r},events:{dropinit:"onDropInit",dropstart:"onDropStart",dropend:"onDropEnd",drop:"onDrop",hover:"onHover"},onDropInit:function(e,t){var n=this.el.terminal;return r(t.drag).hasClass("output-terminal")&&n.canAccept(t.drag.terminal)},onDropStart:function(e,t){t.proxy.terminal&&(t.proxy.terminal.connectors[0].inner_color="#BBFFBB")},onDropEnd:function(e,t){t.proxy.terminal&&(t.proxy.terminal.connectors[0].inner_color="#FFFFFF")},onDrop:function(e,t){var n=this.el.terminal;new c.default(t.drag.terminal,n).redraw()},onHover:function(){var e=this.el,t=e.terminal;if(t.connectors.length>0){var n=r("").css({display:"none"}).appendTo("body").append(r("").append(r("").addClass("fa-icon-button fa 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s=n.Model.extend({initialize:function(e){this.mapOver=e.mapOver||a,this.terminal=e.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(e){this.mapOver=e,this.trigger("change")}}),l=n.Model.extend({initialize:function(e){this.element=e.element,this.connectors=[]},connect:function(e){this.connectors.push(e),this.node&&this.node.markChanged()},disconnect:function(t){this.connectors.splice(e.inArray(t,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){e.each(this.connectors,function(e,t){t.redraw()})},destroy:function(){e.each(this.connectors.slice(),function(e,t){t.destroy()})},destroyInvalidConnections:function(){i.each(this.connectors,function(e){e&&e.destroyIfInvalid()})},setMapOver:function(e){this.multiple||this.mapOver().equal(e)||(this.terminalMapping.setMapOver(e),i.each(this.node.output_terminals,function(t){t.setMapOver(e)}))},mapOver:function(){return this.terminalMapping?this.terminalMapping.mapOver:a},isMappedOver:function(){return this.terminalMapping&&this.terminalMapping.mapOver.isCollection},resetMapping:function(){this.terminalMapping.disableMapOver()},resetMappingIfNeeded:function(){}}),c=l.extend({initialize:function(e){l.prototype.initialize.call(this,e),this.datatypes=e.datatypes},resetMappingIfNeeded:function(){this.node.hasConnectedOutputTerminals()||this.node.hasConnectedMappedInputTerminals()||i.each(this.node.mappedInputTerminals(),function(e){e.resetMappingIfNeeded()}),!this.node.hasMappedOverInputTerminals()&&this.resetMapping()},resetMapping:function(){this.terminalMapping.disableMapOver(),i.each(this.connectors,function(e){var t=e.handle2;t&&(t.resetMappingIfNeeded(),e.destroyIfInvalid())})}}),d=l.extend({initialize:function(e){l.prototype.initialize.call(this,e),this.update(e.input)},canAccept:function(e){return!this._inputFilled()&&this.attachable(e)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||i.each(this.node.output_terminals,function(e){e.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){var e;return this.connected()?this.multiple?this._collectionAttached()?inputsFilled=!0:e=!1:e=!0:e=!1,e},_collectionAttached:function(){if(this.connected()){var e=this.connectors[0].handle1;return!!e&&!!(e.isCollection||e.isMappedOver()||e.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var e=this.mapOver();if(e.isCollection)return[e];var t=[];return this.node.hasConnectedOutputTerminals()?t.push(i.first(i.values(this.node.output_terminals)).mapOver()):i.each(this.node.connectedMappedInputTerminals(),function(e){t.push(e.mapOver())}),t},_producesAcceptableDatatype:function(e){for(var t in this.datatypes){var n=this.datatypes[t];if("input"==n)return!0;var i=new Array;if(i=i.concat(e.datatypes),e.node.post_job_actions)for(var r in e.node.post_job_actions){var a=e.node.post_job_actions[r];"ChangeDatatypeAction"!=a.action_type||""!=a.output_name&&a.output_name!=e.name||!a.action_arguments||i.push(a.action_arguments.newtype)}for(var o in i){var s=i[o];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(i[o],n))return!0}}return!1},_otherCollectionType:function(e){var t=a;e.isCollection&&(t=e.collectionType);var n=e.mapOver();return n.isCollection&&(t=n.append(t)),t}}),u=d.extend({update:function(e){this.datatypes=e.extensions,this.multiple=e.multiple,this.collection=!1},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._otherCollectionType(t);n.isCollection&&this.setMapOver(n)}},attachable:function(e){var t=this._otherCollectionType(e),n=this.mapOver();if(t.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==t.rank&&this._producesAcceptableDatatype(e));if(n.isCollection&&n.canMatch(t))return this._producesAcceptableDatatype(e);return!!this._mappingConstraints().every(i.bind(t.canMatch,t))&&this._producesAcceptableDatatype(e)}return!n.isCollection&&this._producesAcceptableDatatype(e)}}),h=d.extend({update:function(e){this.multiple=!1,this.collection=!0,this.datatypes=e.extensions;var t=[];e.collection_types?i.each(e.collection_types,function(e){t.push(new r(e))}):t.push(o),this.collectionTypes=t},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._effectiveMapOver(t);this.setMapOver(n)}},_effectiveMapOver:function(e){var t=this.collectionTypes,n=this._otherCollectionType(e);if(!i.some(t,function(e){return e.canMatch(n)}))for(var r in t){var o=t[r];if(n.canMapOver(o)){var s=n.effectiveMapOver(o);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var e=this.mapOver();return i.map(this.collectionTypes,function(t){return e.append(t)})},attachable:function(e){var t=this._otherCollectionType(e);if(t.isCollection){var n=this._effectiveCollectionTypes(),r=this.mapOver();if(i.some(n,function(e){return e.canMatch(t)}))return this._producesAcceptableDatatype(e);if(r.isCollection)return!1;if(i.some(this.collectionTypes,function(e){return t.canMapOver(e)})){var a=this._effectiveMapOver(e);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(e)}}return!1}}),f=l.extend({initialize:function(e){if(l.prototype.initialize.call(this,e),this.datatypes=e.datatypes,e.collection_type)this.collectionType=new r(e.collection_type);else{e.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=o}this.isCollection=!0},update:function(e){var t;if(e.collection_type)t=new r(e.collection_type);else{e.collection_type_source||console.log("Warning: No collection type or collection type source defined."),t=o}t.collectionType!=this.collectionType.collectionType&&i.each(this.connectors,function(e){e.destroy()}),this.collectionType=t}});t.default={InputTerminal:u,OutputTerminal:c,InputCollectionTerminal:h,OutputCollectionTerminal:f,TerminalMapping:s,CollectionTypeDescription:r,NULL_COLLECTION_TYPE_DESCRIPTION:a,ANY_COLLECTION_TYPE_DESCRIPTION:o}}).call(t,n(0),n(2),n(1))},292:function(e,t,n){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0}),window.workflow_globals=window.workflow_globals||{};var i=e.View.extend({className:"form-row dataRow 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a({label:i,output:t,node:r});this.calloutView=o,this.$el.append(o.el),this.$el.hover(function(){o.hoverImage()},function(){o.resetImage()})}this.$el.css({position:"absolute",left:-1e3,top:-1e3,display:"none"}),n("body").append(this.el),this.nodeView.updateMaxWidth(this.$el.outerWidth()+17),this.$el.css({position:"",left:"",top:"",display:""}).detach()},redrawWorkflowOutput:function(){this.calloutView&&this.calloutView.resetImage()}}),a=e.View.extend({tagName:"div",initialize:function(e){this.label=e.label,this.node=e.node,this.output=e.output;var t=this,i=this.node;this.$el.attr("class","callout "+this.label).css({display:"none"}).append(n("").append(n("| ',' | ',' | name | ','description | ','data type | ','size | ','time updated (UTC) | ','state | ','',"",'',' |
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e=this;r("#changeset").on("change",function(){e.options.current_changeset=r("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset],e.checkInstalled(e.options.current_metadata),e.reDraw()}),r("#tool_panel_section_select").on("change",function(){e.tpsSelection()}),r("#install_repository").on("click",function(t){r("#repository_installation");t.preventDefault();var n={};n.repositories=JSON.stringify([[r("#install_repository").attr("data-tsrid"),r("#changeset").find("option:selected").val()]]),n.tool_shed_repository_ids=JSON.stringify([r("#install_repository").attr("data-tsrid")]),n.tool_shed_url=e.model.tool_shed_url,n.install_tool_dependencies=r("#install_tool_dependencies").val(),n.install_repository_dependencies=r("#install_repository_dependencies").val(),n.install_resolver_dependencies=r("#install_resolver_dependencies").val();e.panelSelect(n);n.tool_panel_section=JSON.stringify(e.panelSelect(n)),n.shed_tool_conf=r("select[name='shed_tool_conf']").find("option:selected").val(),n.changeset=r("#changeset").find("option:selected").val();var i=r("#repository_installation").attr("action");e.prepareInstall(n,i)}),r("#queue_install").on("click",function(t){e.options.current_changeset=r("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset];var n=(e.options.current_changeset,{});i.each(Object.keys(e.options.current_metadata),function(t){n[t]||(n[t]=e.options.current_metadata[t])}),n.install_tool_dependencies=r("#install_tool_dependencies").val(),n.install_repository_dependencies=r("#install_repository_dependencies").val(),n.install_resolver_dependencies=r("#install_resolver_dependencies").val(),n.tool_panel_section=JSON.stringify(e.panelSelect({})),n.shed_tool_conf=r("select[name='shed_tool_conf']").find("option:selected").val(),n.tool_shed_url=e.model.tool_shed_url,"/"==n.tool_shed_url.substr(-1)&&(n.tool_shed_url=n.tool_shed_url.substr(0,n.tool_shed_url.length-1)),g.default.addToQueue(n),e.checkInstalled(n)}),r(".tool_panel_section_picker").on("change",function(){r(this).find("option:selected").val()==r("#tool_panel_section_select").find("option:selected").val()?r(this).attr("default","active"):r(this).removeAttr("default")}),r(function(){r("#repository_dependencies").jstree()}),r(".tool_form").on("click",function(){var t=r(this).attr("data-guid"),n=(r(this).attr("data-clean"),r(this).attr("data-name")),i=r(this).attr("data-desc"),a=e.model.tool_shed_url,o=r("#repository_details").attr("data-tsrid"),s=r("#changeset").find("option:selected").val(),l=Galaxy.root+"api/tool_shed/tool_json",c={guid:t,tool_shed_url:a,tsr_id:o,changeset:s};r.get(l,c,function(e){e.cls="ui-portlet-plain";var t=new p.default(e);d.default.deepeach(e.inputs,function(e){e.type&&-1!=["data","data_collection"].indexOf(e.type)&&(e.type="hidden",e.info="Data input '"+e.name+"' ("+d.default.textify(e.extensions)+")")});var r=new h.default.View,a=""+n+" "+i;r.show({closing_events:!0,title:a,body:t.$el,buttons:{Close:function(){r.hide()}}})})})},checkInstalled:function(e){var t=this,n={name:e.name,owner:e.owner},i=!1;t.repoQueued(e);r.get(Galaxy.root+"api/tool_shed_repositories",n,function(n){for(var a=0;a','","
",'','','',"
","
","| Owner | ','Name | ',"Synopsis | ",'Type | ',"
|---|---|---|---|
| <%= repository.owner %> | ","",'"," | ","<%= repository.description %> | ","<%= repository.type %> | ","
Repository information for <%= repository.name %> from <%= repository.owner %>
','',"",'','","
"].join("")),templateRepoDependencies:i.template(['Repository Dependencies
','',"
"].join("")),templateRepoDependency:i.template(['- ","
- Repository installation requires the following","<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","<% } %>"," ","
- ',"<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","
Shed tool configuration file:
','','
"].join("")),templateToolDependency:i.template(["<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% if (dependency.includes_tool_dependencies) { %>","<% dependency.tool_dependency_template = tool_dependency_template %>","<%= tool_dependency_template(dependency) %>","<% } %>","<% }); %>","<% } %>"].join("")),templateGlobalSectionCreate:i.template(['',"<%= stc_html %>",'
","Select the file whose tool_path setting you want used for installing repositories.
',"','
"].join("")),templateGlobalSectionSelect:i.template(['','','','
","',"Add a new tool panel section to contain the installed tools (optional).","
","','
"].join("")),templateToolSectionCreate:i.template(['Tool Panel Section
','','
","','",'','
","',"Select an existing tool panel section to contain the installed tools (optional).","
","','','',"
"].join("")),templateToolSectionSelect:i.template(['','",'','',"
"].join("")),templatePanelSelectOptions:i.template(["<% _.each(sections, function(section) { %>",'',"<% }); %>"].join(""))});t.default={RepoDetails:m}}).call(t,n(2),n(1),n(0))},311:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(17),s=a(o),l=n(18),c=a(l),d=e.View.extend({el:"#center",defaults:[{}],initialize:function(e){var t=this;this.model=new s.default.RepoQueue,this.listenTo(this.model,"sync",this.render),this.model.fetch(),t.render()},render:function(e){var t=this,n=t.templateRepoQueue,r=t.model.models;t.$el.html(n({title:"Repository Installation Queue",repositories:r,queue:c.default.queueLength()})),i("#center").css("overflow","auto"),t.bindEvents()},bindEvents:function(){var t=this;i(".install_one").on("click",function(){var e=t.loadFromQueue(i(this).attr("data-repokey"));t.installFromQueue(e,i(this).attr("data-repokey"))}),i(".remove_one").on("click",function(){var e=i(this).attr("data-repokey"),t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e)){var n=t[e].repository.id;delete t[e],i("#queued_repository_"+n).remove()}localStorage.repositories=JSON.stringify(t)}),i("#clear_queue").on("click",function(){localStorage.repositories="{}"}),i("#from_workflow").on("click",function(){e.history.navigate("workflows",{trigger:!0,replace:!0})})},installFromQueue:function(t,n){var r=Object();r.install_tool_dependencies=t.install_tool_dependencies,r.install_repository_dependencies=t.install_repository_dependencies,r.install_resolver_dependencies=t.install_resolver_dependencies,r.tool_panel_section=t.tool_panel_section,r.shed_tool_conf=t.shed_tool_conf,r.repositories=JSON.stringify([[t.repository.id,t.changeset_revision]]),r.tool_shed_repository_ids=JSON.stringify([t.repository.id]),r.tool_shed_url=n.split("|")[0],r.changeset=t.changeset_revision;var a=Galaxy.root+"api/tool_shed_repositories/install?async=True";if(i("#queued_repository_"+t.repository.id).remove(),localStorage.repositories){void 0===n&&(n=c.default.queueKey(t));var o=JSON.parse(localStorage.repositories);o.hasOwnProperty(n)&&(delete o[n],localStorage.repositories=JSON.stringify(o))}i.post(a,r,function(t){var n=JSON.parse(t),r=n.repositories,a="status/r/"+r.join("|");i.post(Galaxy.root+"admin_toolshed/install_repositories",n,function(e){console.log("Initializing repository installation succeeded")}),e.history.navigate(a,{trigger:!0,replace:!0})})},loadFromQueue:function(e){var t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e))return t[e]},reDraw:function(e){this.$el.empty(),this.initialize(e),this.model.fetch(),this.render(e)},templateRepoQueue:r.template(['','
",'<%= title %>
','',"','','',"
",'',"
"].join(""))});t.default={RepoQueueView:d}}).call(t,n(2),n(0),n(1))},312:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(17),s=a(o),l=n(18),c=a(l),d=e.View.extend({el:"#center",initialize:function(e){this.options=i.defaults(this.options||[{}],e,this.defaults),this.model=new s.default.RepoStatus,this.listenTo(this.model,"sync",this.render),this.model.url+="?repositories="+this.options.repositories.join("|"),this.model.fetch(),this.timer=setInterval(function(e){var t=["installed","error"],n=!0;i.some(e.model.models,function(e){repo_id=e.get("id");var i=e.get("status").toLowerCase();if(-1===t.indexOf(i))return n=!1,!0}),n?clearInterval(e.timer):e.model.fetch()},2e3,this)},close:function(){clearInterval(this.timer)},render:function(e){this.options=i.extend(this.options,e);var t=this.templateRepoStatus;this.$el.html(t({title:"Repository Status",repositories:this.model.models,queue:c.default.queueLength()})),r("#center").css("overflow","auto"),this.bindEvents()},bindEvents:function(){},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateRepoStatus:i.template(['| Name | ','Owner | ','Revision | ','ToolShed | ','Install | ',''," |
|---|---|---|---|---|---|
| <%= repository.get("repository").name %> | ','<%= repository.get("repository").owner %> | ','<%= repository.get("changeset_revision") %> | ','<%= repository.get("tool_shed_url") %> | ','','" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />'," | ",'','" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />'," | ","
','
",'",'<%= title %>
','',"| Name | ','Description | ','Owner | ','Revision | ','Installation Status | ',"
|---|---|---|---|---|
| ",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","
','
",'",'<%= title %>
','',"