npm - @apollo-annotation/jbrowse-plugin-apollo - Versions diffs - 1.1.0 → 1.1.2 - Mend

@apollo-annotation/jbrowse-plugin-apollo 1.1.0 → 1.1.2

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Files changed (15) hide show

package/dist/jbrowse-plugin-apollo.umd.production.min.js CHANGED Viewed

@@ -1,2 +1,2 @@
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R(this,t),D(r=T(this,t,[e,n]),"typeName","FeatureAttributeChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldAttributes:o.oldAttributes,newAttributes:o.newAttributes}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger;return new t({changedIds:W(this.changedIds).reverse(),typeName:"FeatureAttributeChange",changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldAttributes:e.newAttributes,newAttributes:e.oldAttributes}})),assembly:e},{logger:r})}}])}(ft),Ct=["__v","_id","assemblies","configuration","internetAccounts","plugins","tracks"],At=["hasRole"];function kt(e){var t,n=e.assemblies,r=e.configuration,o=e.internetAccounts,i=e.plugins,a=e.tracks,s=q(e,Ct);if(n&&(s.assemblies=n.filter((function(e){return"ApolloSequenceAdapter"!==e.sequence.adapter.type}))),null!=r&&null!==(t=r.ApolloPlugin)&&void 0!==t&&t.hasRole){var l=q(r.ApolloPlugin,At);s.configuration=B(B({},r),{},{ApolloPlugin:l})}return o&&(s.internetAccounts=o.filter((function(e){return"ApolloInternetAccount"!==e.type}))),i&&(s.plugins=i.filter((function(e){return"Apollo"!==e.name}))),a&&(s.tracks=a.filter((function(e){return"ApolloTrack"!==e.type}))),s}var Nt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","ImportJBrowseConfigChange"),D(r,"oldJBrowseConfig",void 0),D(r,"newJBrowseConfig",void 0),r.oldJBrowseConfig=e.oldJBrowseConfig,r.newJBrowseConfig=e.newJBrowseConfig,r}return M(t,e),I(t,[{key:"toJSON",value:function(){return{typeName:this.typeName,oldJBrowseConfig:this.oldJBrowseConfig,newJBrowseConfig:this.newJBrowseConfig}}},{key:"getInverse",value:function(){return new t({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:this.newJBrowseConfig,newJBrowseConfig:this.oldJBrowseConfig},{logger:this.logger})}}])}(ct),Tt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","LocationEndChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldEnd:o.oldEnd,newEnd:o.newEnd}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldEnd:e.newEnd,newEnd:e.oldEnd}})),assembly:e},{logger:r})}}])}(ft);function Rt(e){return"LocationEndChange"===e.typeName}var Et=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","LocationStartChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldStart:o.oldStart,newStart:o.newStart}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldStart:e.newStart,newStart:e.oldStart}})),assembly:e},{logger:r})}}])}(ft);function It(e){return"LocationStartChange"===e.typeName}var jt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","MergeExonsChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"notification",get:function(){return"Exons successfully merged"}},{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,firstExon:o.firstExon,secondExon:o.secondExon,parentFeatureId:o.parentFeatureId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e,t=this.assembly,n=this.changes,r=this.logger,o=W(this.changedIds).reverse(),i=W(n).reverse().map((function(e){return{exonsToRestore:[e.firstExon,e.secondExon],parentFeatureId:e.parentFeatureId}}));return null===(e=r.debug)||void 0===e||e.call(r,"INVERSE CHANGE '".concat(JSON.stringify(i),"'")),new Dt({changedIds:o,typeName:"UndoMergeExonsChange",changes:i,assembly:t},{logger:r})}}])}(ft),Dt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","UndoMergeExonsChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,exonsToRestore:o.exonsToRestore,parentFeatureId:o.parentFeatureId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,t=this.changes,n=this.logger,r=W(this.changedIds).reverse(),o=W(t).reverse().map((function(e){return{firstExon:e.exonsToRestore[0],secondExon:e.exonsToRestore[1],parentFeatureId:e.parentFeatureId}}));return new jt({changedIds:r,typeName:"MergeExonsChange",changes:o,assembly:e},{logger:n})}}])}(ft);function Ot(e,t){for(var n=[],r=0;r<e.length;r+=t){var o=e.slice(r,r+t);n.push(o)}return n}function Ft(e){var t,n,r=e,o=null===(t=r.attributes.get("gff_id"))||void 0===t?void 0:t.join(",");if(o)return"ID=".concat(o," (_id: ").concat(e._id.toString(),")");var i=null===(n=r.attributes.get("gff_name"))||void 0===n?void 0:n.join(",");return i?"Name=".concat(i," (_id: ").concat(e._id.toString(),")"):"_id: ".concat(e._id.toString())}function Mt(e){var t={};if(!e)return t;for(var n=0,r=Object.entries(e);n<r.length;n++){var o=G(r[n],2),i=o[1];t[o[0]]=null==i?void 0:i.slice()}return t}function Lt(e){if(!e)return"";for(var t=[],n=0,r=Object.entries(e);n<r.length;n++){var o=G(r[n],2),i=o[1],a=o[0];a.startsWith("gff_")&&(a=(a=a.slice(4)).charAt(0).toUpperCase()+a.slice(1)),t.push(i?"".concat(a,"=").concat(i.join(",")):a)}return encodeURIComponent(t.join(";"))}var Pt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","MergeTranscriptsChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"notification",get:function(){return"Transcripts successfully merged"}},{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,firstTranscript:o.firstTranscript,secondTranscript:o.secondTranscript,parentFeatureId:o.parentFeatureId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"mergeTranscriptsOnServer",value:function(e,t){e.min=Math.min(e.min,t.min),e.max=Math.max(e.max,t.max);var n=e.attributes?JSON.parse(JSON.stringify(e.attributes)):{};if(t.attributes&&(Object.keys(n).includes("merged_with")||(n.merged_with=[]),n.merged_with.push(Lt(Mt(t.attributes)))),e.attributes=n,t.children)for(var r=0,o=Object.entries(t.children);r<o.length;r++){var i=G(o[r],2);this.mergeFeatureIntoTranscriptOnServer(i[1],e)}}},{key:"mergeFeatureIntoTranscriptOnServer",value:function(e,t){var n,r=this;null!==(n=t.children)&&void 0!==n||(t.children=new Map);var i,a,s,l=!1,c=j(t.children);try{for(c.s();!(s=c.n()).done;){var u=G(s.value,2)[1];if(l&&i?a=!0:(a=!1,i=u),i.type===e.type&&i.type===u.type&&o.doesIntersect2(e.min,e.max,i.min,i.max)&&o.doesIntersect2(u.min,u.max,i.min,i.max)){var d,f;i.min=Math.min(e.min,i.min,u.min),i.max=Math.max(e.max,i.max,u.max),null!==(f=(d=i).attributes)&&void 0!==f||(d.attributes={});var h=JSON.parse(JSON.stringify(i.attributes));Object.keys(h).includes("merged_with")||(h.merged_with=[]);var p=h.merged_with;if(p.push(Lt(Mt(e.attributes))),a){var g=u.attributes?JSON.parse(JSON.stringify(u.attributes)):void 0;p.push(Lt(g)),t.children.delete(u._id.toString())}h.merged_with=W(new Set(p)),i.attributes=h,l=!0}}}catch(e){c.e(e)}finally{c.f()}l&&i&&e.children&&Object.entries(e.children).map((function(e){var t=G(e,2);r.addChild(i,t[1])})),this.addChild(t,l&&i?i:e)}},{key:"mergeTranscriptsOnClient",value:function(e,t){var n,r;e.setMin(Math.min(e.min,t.min)),e.setMax(Math.max(e.max,t.max));var o=null!==(n=null===(r=e.attributes.get("merged_with"))||void 0===r?void 0:r.slice())&&void 0!==n?n:[],i=Lt(Mt(t.attributes));if(o.includes(i)||o.push(i),e.setAttribute("merged_with",o),t.children)for(var a=0,s=Object.entries(t.children);a<s.length;a++){var l=G(s[a],2);this.mergeFeatureIntoTranscriptOnClient(l[1],e)}}},{key:"mergeFeatureIntoTranscriptOnClient",value:function(e,t){var n;null!==(n=t.children)&&void 0!==n||(t.children=new Map);var r,i,a,s=!1,c=j(t.children);try{for(c.s();!(a=c.n()).done;){var u=G(a.value,2)[1];if(s&&r?i=!0:(i=!1,r=u),r.type===e.type&&r.type===u.type&&o.doesIntersect2(e.min,e.max,r.min,r.max)&&o.doesIntersect2(u.min,u.max,r.min,r.max)){var d,f;r.setMin(Math.min(e.min,r.min,u.min)),r.setMax(Math.max(e.max,r.max,u.max));var h=null!==(d=null===(f=r.attributes.get("merged_with"))||void 0===f?void 0:f.slice())&&void 0!==d?d:[];h.push(Lt(Mt(e.attributes))),i&&(h.push(Lt(l.getSnapshot(u).attributes)),t.deleteChild(u._id)),r.setAttribute("merged_with",W(new Set(h))),s=!0}}}catch(e){c.e(e)}finally{c.f()}s&&r&&e.children&&Object.entries(e.children).map((function(e){var t=G(e,2);r.addChild(t[1])})),t.addChild(s&&r?l.getSnapshot(r):e)}},{key:"getInverse",value:function(){var e,t=this.assembly,n=this.changes,r=this.logger,o=W(this.changedIds).reverse(),i=W(n).reverse().map((function(e){return{transcriptsToRestore:[e.firstTranscript,e.secondTranscript],parentFeatureId:e.parentFeatureId}}));return null===(e=r.debug)||void 0===e||e.call(r,"INVERSE CHANGE 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Pt({changedIds:r,typeName:"MergeTranscriptsChange",changes:o,assembly:e},{logger:n})}}])}(ft),qt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","SplitExonChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"notification",get:function(){return"Exon successfully split"}},{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,exonToBeSplit:o.exonToBeSplit,parentFeatureId:o.parentFeatureId,upstreamCut:o.upstreamCut,downstreamCut:o.downstreamCut,leftExonId:o.leftExonId,rightExonId:o.rightExonId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e,t=this.assembly,n=this.changes,r=this.logger,o=W(this.changedIds).reverse(),i=W(n).reverse().map((function(e){return{exonToRestore:e.exonToBeSplit,parentFeatureId:e.parentFeatureId,idsToDelete:[e.leftExonId,e.rightExonId],upstreamCut:e.upstreamCut,downstreamCut:e.downstreamCut,leftExonId:e.leftExonId,rightExonId:e.rightExonId}}));return null===(e=r.debug)||void 0===e||e.call(r,"INVERSE CHANGE '".concat(JSON.stringify(i),"'")),new Ut({changedIds:o,typeName:"UndoSplitExonChange",changes:i,assembly:t},{logger:r})}},{key:"makeSplitExons",value:function(e,t,n,r,o){var i=JSON.parse(JSON.stringify(e));delete i.attributes._id,delete i.attributes.gff_id;var a=structuredClone(i);a._id=r,a.max=t;var s=structuredClone(i);return s.min=n,s._id=o,[a,s]}}])}(ft),Ut=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","UndoSplitExonChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,exonToRestore:o.exonToRestore,parentFeatureId:o.parentFeatureId,idsToDelete:o.idsToDelete,upstreamCut:o.upstreamCut,downstreamCut:o.downstreamCut,leftExonId:o.leftExonId,rightExonId:o.rightExonId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,t=this.changes,n=this.logger,r=W(this.changedIds).reverse(),o=W(t).reverse().map((function(e){return{parentFeatureId:e.parentFeatureId,exonToBeSplit:e.exonToRestore,upstreamCut:e.upstreamCut,downstreamCut:e.downstreamCut,leftExonId:e.leftExonId,rightExonId:e.rightExonId}}));return new qt({changedIds:r,typeName:"SplitExonChange",changes:o,assembly:e},{logger:n})}}])}(ft),zt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","StrandChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldStrand:o.oldStrand,newStrand:o.newStrand}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldStrand:e.newStrand,newStrand:e.oldStrand}})),assembly:e},{logger:r})}}])}(ft),$t=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","TypeChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldType:o.oldType,newType:o.newType}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldType:e.newType,newType:e.oldType}})),assembly:e},{logger:r})}}])}(ft),Ht=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","UserChange"),D(r,"changes",void 0),D(r,"userId",void 0),r.changes="changes"in e?e.changes:[e],r.userId=e.userId,r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.changes,t=this.typeName,n=this.userId;return 1===e.length?{typeName:t,userId:n,role:G(e,1)[0].role}:{typeName:t,userId:n,changes:e}}},{key:"getInverse",value:function(){return new 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location&&"https:"===location.protocol,r.hostname&&!r.port&&(r.port=n.secure?"443":"80"),n.hostname=r.hostname||("undefined"!=typeof location?location.hostname:"localhost"),n.port=r.port||("undefined"!=typeof location&&location.port?location.port:n.secure?"443":"80"),n.transports=r.transports||["polling","websocket","webtransport"],n.writeBuffer=[],n.prevBufferLen=0,n.opts=Object.assign({path:"/engine.io",agent:!1,withCredentials:!1,upgrade:!0,timestampParam:"t",rememberUpgrade:!1,addTrailingSlash:!0,rejectUnauthorized:!0,perMessageDeflate:{threshold:1024},transportOptions:{},closeOnBeforeunload:!1},r),n.opts.path=n.opts.path.replace(/\/$/,"")+(n.opts.addTrailingSlash?"/":""),"string"==typeof n.opts.query&&(n.opts.query=function(e){for(var t={},n=e.split("&"),r=0,o=n.length;r<o;r++){var i=n[r].split("=");t[decodeURIComponent(i[0])]=decodeURIComponent(i[1])}return t}(n.opts.query)),n.id=null,n.upgrades=null,n.pingInterval=null,n.pingTimeout=null,n.pingTimeoutTimer=null,"function"==typeof addEventListener&&(n.opts.closeOnBeforeunload&&(n.beforeunloadEventListener=function(){n.transport&&(n.transport.removeAllListeners(),n.transport.close())},addEventListener("beforeunload",n.beforeunloadEventListener,!1)),"localhost"!==n.hostname&&(n.offlineEventListener=function(){n.onClose("transport close",{description:"network connection lost"})},addEventListener("offline",n.offlineEventListener,!1))),n.open(),n}return M(t,e),I(t,[{key:"createTransport",value:function(e){var t=Object.assign({},this.opts.query);t.EIO=4,t.transport=e,this.id&&(t.sid=this.id);var n=Object.assign({},this.opts,{query:t,socket:this,hostname:this.hostname,secure:this.secure,port:this.port},this.opts.transportOptions[e]);return new jr[e](n)}},{key:"open",value:function(){var e,n=this;if(this.opts.rememberUpgrade&&t.priorWebsocketSuccess&&-1!==this.transports.indexOf("websocket"))e="websocket";else{if(0===this.transports.length)return void this.setTimeoutFn((function(){n.emitReserved("error","No transports available")}),0);e=this.transports[0]}this.readyState="opening";try{e=this.createTransport(e)}catch(e){return this.transports.shift(),void this.open()}e.open(),this.setTransport(e)}},{key:"setTransport",value:function(e){var t=this;this.transport&&this.transport.removeAllListeners(),this.transport=e,e.on("drain",this.onDrain.bind(this)).on("packet",this.onPacket.bind(this)).on("error",this.onError.bind(this)).on("close",(function(e){return t.onClose("transport close",e)}))}},{key:"probe",value:function(e){var n=this,r=this.createTransport(e),o=!1;t.priorWebsocketSuccess=!1;var i=function(){o||(r.send([{type:"ping",data:"probe"}]),r.once("packet",(function(e){if(!o)if("pong"===e.type&&"probe"===e.data){if(n.upgrading=!0,n.emitReserved("upgrading",r),!r)return;t.priorWebsocketSuccess="websocket"===r.name,n.transport.pause((function(){o||"closed"!==n.readyState&&(d(),n.setTransport(r),r.send([{type:"upgrade"}]),n.emitReserved("upgrade",r),r=null,n.upgrading=!1,n.flush())}))}else{var i=new Error("probe error");i.transport=r.name,n.emitReserved("upgradeError",i)}})))};function a(){o||(o=!0,d(),r.close(),r=null)}var s=function(e){var t=new Error("probe error: "+e);t.transport=r.name,a(),n.emitReserved("upgradeError",t)};function l(){s("transport closed")}function c(){s("socket closed")}function u(e){r&&e.name!==r.name&&a()}var d=function(){r.removeListener("open",i),r.removeListener("error",s),r.removeListener("close",l),n.off("close",c),n.off("upgrading",u)};r.once("open",i),r.once("error",s),r.once("close",l),this.once("close",c),this.once("upgrading",u),-1!==this.upgrades.indexOf("webtransport")&&"webtransport"!==e?this.setTimeoutFn((function(){o||r.open()}),200):r.open()}},{key:"onOpen",value:function(){if(this.readyState="open",t.priorWebsocketSuccess="websocket"===this.transport.name,this.emitReserved("open"),this.flush(),"open"===this.readyState&&this.opts.upgrade)for(var e=0,n=this.upgrades.length;e<n;e++)this.probe(this.upgrades[e])}},{key:"onPacket",value:function(e){if("opening"===this.readyState||"open"===this.readyState||"closing"===this.readyState)switch(this.emitReserved("packet",e),this.emitReserved("heartbeat"),this.resetPingTimeout(),e.type){case"open":this.onHandshake(JSON.parse(e.data));break;case"ping":this.sendPacket("pong"),this.emitReserved("ping"),this.emitReserved("pong");break;case"error":var t=new Error("server error");t.code=e.data,this.onError(t);break;case"message":this.emitReserved("data",e.data),this.emitReserved("message",e.data)}}},{key:"onHandshake",value:function(e){this.emitReserved("handshake",e),this.id=e.sid,this.transport.query.sid=e.sid,this.upgrades=this.filterUpgrades(e.upgrades),this.pingInterval=e.pingInterval,this.pingTimeout=e.pingTimeout,this.maxPayload=e.maxPayload,this.onOpen(),"closed"!==this.readyState&&this.resetPingTimeout()}},{key:"resetPingTimeout",value:function(){var e=this;this.clearTimeoutFn(this.pingTimeoutTimer),this.pingTimeoutTimer=this.setTimeoutFn((function(){e.onClose("ping timeout")}),this.pingInterval+this.pingTimeout),this.opts.autoUnref&&this.pingTimeoutTimer.unref()}},{key:"onDrain",value:function(){this.writeBuffer.splice(0,this.prevBufferLen),this.prevBufferLen=0,0===this.writeBuffer.length?this.emitReserved("drain"):this.flush()}},{key:"flush",value:function(){if("closed"!==this.readyState&&this.transport.writable&&!this.upgrading&&this.writeBuffer.length){var e=this.getWritablePackets();this.transport.send(e),this.prevBufferLen=e.length,this.emitReserved("flush")}}},{key:"getWritablePackets",value:function(){if(!(this.maxPayload&&"polling"===this.transport.name&&this.writeBuffer.length>1))return this.writeBuffer;for(var e,t=1,n=0;n<this.writeBuffer.length;n++){var r=this.writeBuffer[n].data;if(r&&(t+="string"==typeof(e=r)?function(e){for(var t=0,n=0,r=0,o=e.length;r<o;r++)(t=e.charCodeAt(r))<128?n+=1:t<2048?n+=2:t<55296||t>=57344?n+=3:(r++,n+=4);return n}(e):Math.ceil(1.33*(e.byteLength||e.size))),n>0&&t>this.maxPayload)return this.writeBuffer.slice(0,n);t+=2}return this.writeBuffer}},{key:"write",value:function(e,t,n){return this.sendPacket("message",e,t,n),this}},{key:"send",value:function(e,t,n){return this.sendPacket("message",e,t,n),this}},{key:"sendPacket",value:function(e,t,n,r){if("function"==typeof t&&(r=t,t=void 0),"function"==typeof n&&(r=n,n=null),"closing"!==this.readyState&&"closed"!==this.readyState){(n=n||{}).compress=!1!==n.compress;var o={type:e,data:t,options:n};this.emitReserved("packetCreate",o),this.writeBuffer.push(o),r&&this.once("flush",r),this.flush()}}},{key:"close",value:function(){var e=this,t=function(){e.onClose("forced close"),e.transport.close()},n=function(){e.off("upgrade",n),e.off("upgradeError",n),t()},r=function(){e.once("upgrade",n),e.once("upgradeError",n)};return"opening"!==this.readyState&&"open"!==this.readyState||(this.readyState="closing",this.writeBuffer.length?this.once("drain",(function(){e.upgrading?r():t()})):this.upgrading?r():t()),this}},{key:"onError",value:function(e){t.priorWebsocketSuccess=!1,this.emitReserved("error",e),this.onClose("transport error",e)}},{key:"onClose",value:function(e,t){"opening"!==this.readyState&&"open"!==this.readyState&&"closing"!==this.readyState||(this.clearTimeoutFn(this.pingTimeoutTimer),this.transport.removeAllListeners("close"),this.transport.close(),this.transport.removeAllListeners(),"function"==typeof removeEventListener&&(removeEventListener("beforeunload",this.beforeunloadEventListener,!1),removeEventListener("offline",this.offlineEventListener,!1)),this.readyState="closed",this.id=null,this.emitReserved("close",e,t),this.writeBuffer=[],this.prevBufferLen=0)}},{key:"filterUpgrades",value:function(e){for(var t=[],n=0,r=e.length;n<r;n++)~this.transports.indexOf(e[n])&&t.push(e[n]);return t}}])}(ir);Mr.protocol=4;var Lr="function"==typeof ArrayBuffer,Pr=function(e){return"function"==typeof ArrayBuffer.isView?ArrayBuffer.isView(e):e.buffer instanceof ArrayBuffer},Br=Object.prototype.toString,qr="function"==typeof Blob||"undefined"!=typeof Blob&&"[object BlobConstructor]"===Br.call(Blob),Ur="function"==typeof File||"undefined"!=typeof File&&"[object FileConstructor]"===Br.call(File);function zr(e){return Lr&&(e instanceof ArrayBuffer||Pr(e))||qr&&e instanceof Blob||Ur&&e instanceof File}function $r(e,t){if(!e||"object"!==K(e))return!1;if(Array.isArray(e)){for(var n=0,r=e.length;n<r;n++)if($r(e[n]))return!0;return!1}if(zr(e))return!0;if(e.toJSON&&"function"==typeof e.toJSON&&1===arguments.length)return $r(e.toJSON(),!0);for(var o in e)if(Object.prototype.hasOwnProperty.call(e,o)&&$r(e[o]))return!0;return!1}function Hr(e){var t=[],n=e;return n.data=Gr(e.data,t),n.attachments=t.length,{packet:n,buffers:t}}function Gr(e,t){if(!e)return e;if(zr(e)){var n={_placeholder:!0,num:t.length};return t.push(e),n}if(Array.isArray(e)){for(var r=new Array(e.length),o=0;o<e.length;o++)r[o]=Gr(e[o],t);return r}if("object"===K(e)&&!(e instanceof Date)){var i={};for(var a in e)Object.prototype.hasOwnProperty.call(e,a)&&(i[a]=Gr(e[a],t));return i}return e}function Vr(e,t){return e.data=Wr(e.data,t),delete e.attachments,e}function Wr(e,t){if(!e)return e;if(e&&!0===e._placeholder){if("number"==typeof e.num&&e.num>=0&&e.num<t.length)return t[e.num];throw new Error("illegal attachments")}if(Array.isArray(e))for(var n=0;n<e.length;n++)e[n]=Wr(e[n],t);else if("object"===K(e))for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&(e[r]=Wr(e[r],t));return e}var Jr,Kr=["connect","connect_error","disconnect","disconnecting","newListener","removeListener"];!function(e){e[e.CONNECT=0]="CONNECT",e[e.DISCONNECT=1]="DISCONNECT",e[e.EVENT=2]="EVENT",e[e.ACK=3]="ACK",e[e.CONNECT_ERROR=4]="CONNECT_ERROR",e[e.BINARY_EVENT=5]="BINARY_EVENT",e[e.BINARY_ACK=6]="BINARY_ACK"}(Jr||(Jr={}));var Yr=function(){return I((function e(t){R(this,e),this.replacer=t}),[{key:"encode",value:function(e){return e.type!==Jr.EVENT&&e.type!==Jr.ACK||!$r(e)?[this.encodeAsString(e)]:this.encodeAsBinary({type:e.type===Jr.EVENT?Jr.BINARY_EVENT:Jr.BINARY_ACK,nsp:e.nsp,data:e.data,id:e.id})}},{key:"encodeAsString",value:function(e){var t=""+e.type;return e.type!==Jr.BINARY_EVENT&&e.type!==Jr.BINARY_ACK||(t+=e.attachments+"-"),e.nsp&&"/"!==e.nsp&&(t+=e.nsp+","),null!=e.id&&(t+=e.id),null!=e.data&&(t+=JSON.stringify(e.data,this.replacer)),t}},{key:"encodeAsBinary",value:function(e){var t=Hr(e),n=this.encodeAsString(t.packet),r=t.buffers;return r.unshift(n),r}}])}();function Xr(e){return"[object Object]"===Object.prototype.toString.call(e)}var Zr=function(e){function t(e){var n;return R(this,t),(n=T(this,t)).reviver=e,n}return M(t,e),I(t,[{key:"add",value:function(e){var n;if("string"==typeof e){if(this.reconstructor)throw new Error("got plaintext data when reconstructing a packet");var r=(n=this.decodeString(e)).type===Jr.BINARY_EVENT;r||n.type===Jr.BINARY_ACK?(n.type=r?Jr.EVENT:Jr.ACK,this.reconstructor=new Qr(n),0===n.attachments&&V(t,"emitReserved",this,3)(["decoded",n])):V(t,"emitReserved",this,3)(["decoded",n])}else{if(!zr(e)&&!e.base64)throw new Error("Unknown type: "+e);if(!this.reconstructor)throw new Error("got binary data when not reconstructing a packet");(n=this.reconstructor.takeBinaryData(e))&&(this.reconstructor=null,V(t,"emitReserved",this,3)(["decoded",n]))}}},{key:"decodeString",value:function(e){var n=0,r={type:Number(e.charAt(0))};if(void 0===Jr[r.type])throw new Error("unknown packet type "+r.type);if(r.type===Jr.BINARY_EVENT||r.type===Jr.BINARY_ACK){for(var o=n+1;"-"!==e.charAt(++n)&&n!=e.length;);var i=e.substring(o,n);if(i!=Number(i)||"-"!==e.charAt(n))throw new Error("Illegal attachments");r.attachments=Number(i)}if("/"===e.charAt(n+1)){for(var a=n+1;++n&&","!==e.charAt(n)&&n!==e.length;);r.nsp=e.substring(a,n)}else r.nsp="/";var s=e.charAt(n+1);if(""!==s&&Number(s)==s){for(var l=n+1;++n;){var c=e.charAt(n);if(null==c||Number(c)!=c){--n;break}if(n===e.length)break}r.id=Number(e.substring(l,n+1))}if(e.charAt(++n)){var u=this.tryParse(e.substr(n));if(!t.isPayloadValid(r.type,u))throw new Error("invalid payload");r.data=u}return r}},{key:"tryParse",value:function(e){try{return JSON.parse(e,this.reviver)}catch(e){return!1}}},{key:"destroy",value:function(){this.reconstructor&&(this.reconstructor.finishedReconstruction(),this.reconstructor=null)}}],[{key:"isPayloadValid",value:function(e,t){switch(e){case Jr.CONNECT:return Xr(t);case Jr.DISCONNECT:return void 0===t;case Jr.CONNECT_ERROR:return"string"==typeof t||Xr(t);case Jr.EVENT:case Jr.BINARY_EVENT:return Array.isArray(t)&&("number"==typeof t[0]||"string"==typeof t[0]&&-1===Kr.indexOf(t[0]));case Jr.ACK:case Jr.BINARY_ACK:return Array.isArray(t)}}}])}(ir),Qr=function(){return I((function e(t){R(this,e),this.packet=t,this.buffers=[],this.reconPack=t}),[{key:"takeBinaryData",value:function(e){if(this.buffers.push(e),this.buffers.length===this.reconPack.attachments){var t=Vr(this.reconPack,this.buffers);return this.finishedReconstruction(),t}return null}},{key:"finishedReconstruction",value:function(){this.reconPack=null,this.buffers=[]}}])}(),eo={__proto__:null,Decoder:Zr,Encoder:Yr,get PacketType(){return Jr}};function to(e,t,n){return e.on(t,n),function(){e.off(t,n)}}var no=Object.freeze({connect:1,connect_error:1,disconnect:1,disconnecting:1,newListener:1,removeListener:1}),ro=function(e){function t(e,n,r){var o;return R(this,t),(o=T(this,t)).connected=!1,o.recovered=!1,o.receiveBuffer=[],o.sendBuffer=[],o._queue=[],o._queueSeq=0,o.ids=0,o.acks={},o.flags={},o.io=e,o.nsp=n,r&&r.auth&&(o.auth=r.auth),o._opts=Object.assign({},r),o.io._autoConnect&&o.open(),o}return M(t,e),I(t,[{key:"disconnected",get:function(){return!this.connected}},{key:"subEvents",value:function(){if(!this.subs){var e=this.io;this.subs=[to(e,"open",this.onopen.bind(this)),to(e,"packet",this.onpacket.bind(this)),to(e,"error",this.onerror.bind(this)),to(e,"close",this.onclose.bind(this))]}}},{key:"active",get:function(){return!!this.subs}},{key:"connect",value:function(){return this.connected||(this.subEvents(),this.io._reconnecting||this.io.open(),"open"===this.io._readyState&&this.onopen()),this}},{key:"open",value:function(){return this.connect()}},{key:"send",value:function(){for(var e=arguments.length,t=new Array(e),n=0;n<e;n++)t[n]=arguments[n];return t.unshift("message"),this.emit.apply(this,t),this}},{key:"emit",value:function(e){if(no.hasOwnProperty(e))throw new Error('"'+e.toString()+'" is a reserved event name');for(var t=arguments.length,n=new Array(t>1?t-1:0),r=1;r<t;r++)n[r-1]=arguments[r];if(n.unshift(e),this._opts.retries&&!this.flags.fromQueue&&!this.flags.volatile)return this._addToQueue(n),this;var o={type:Jr.EVENT,data:n,options:{}};if(o.options.compress=!1!==this.flags.compress,"function"==typeof n[n.length-1]){var i=this.ids++,a=n.pop();this._registerAckCallback(i,a),o.id=i}return this.flags.volatile&&(!(this.io.engine&&this.io.engine.transport&&this.io.engine.transport.writable)||!this.connected)||(this.connected?(this.notifyOutgoingListeners(o),this.packet(o)):this.sendBuffer.push(o)),this.flags={},this}},{key:"_registerAckCallback",value:function(e,t){var n,r=this,o=null!==(n=this.flags.timeout)&&void 0!==n?n:this._opts.ackTimeout;if(void 0!==o){var i=this.io.setTimeoutFn((function(){delete r.acks[e];for(var n=0;n<r.sendBuffer.length;n++)r.sendBuffer[n].id===e&&r.sendBuffer.splice(n,1);t.call(r,new Error("operation has timed out"))}),o);this.acks[e]=function(){r.io.clearTimeoutFn(i);for(var e=arguments.length,n=new Array(e),o=0;o<e;o++)n[o]=arguments[o];t.apply(r,[null].concat(n))}}else this.acks[e]=t}},{key:"emitWithAck",value:function(e){for(var t=this,n=arguments.length,r=new Array(n>1?n-1:0),o=1;o<n;o++)r[o-1]=arguments[o];var i=void 0!==this.flags.timeout||void 0!==this._opts.ackTimeout;return new Promise((function(n,o){r.push((function(e,t){return i?e?o(e):n(t):n(e)})),t.emit.apply(t,[e].concat(r))}))}},{key:"_addToQueue",value:function(e){var t,n=this;"function"==typeof e[e.length-1]&&(t=e.pop());var r={id:this._queueSeq++,tryCount:0,pending:!1,args:e,flags:Object.assign({fromQueue:!0},this.flags)};e.push((function(e){if(r===n._queue[0]){if(null!==e)r.tryCount>n._opts.retries&&(n._queue.shift(),t&&t(e));else if(n._queue.shift(),t){for(var o=arguments.length,i=new Array(o>1?o-1:0),a=1;a<o;a++)i[a-1]=arguments[a];t.apply(void 0,[null].concat(i))}return r.pending=!1,n._drainQueue()}})),this._queue.push(r),this._drainQueue()}},{key:"_drainQueue",value:function(){if(this.connected&&0!==this._queue.length){var e=this._queue[0];e.pending&&!(arguments.length>0&&void 0!==arguments[0]&&arguments[0])||(e.pending=!0,e.tryCount++,this.flags=e.flags,this.emit.apply(this,e.args))}}},{key:"packet",value:function(e){e.nsp=this.nsp,this.io._packet(e)}},{key:"onopen",value:function(){var e=this;"function"==typeof this.auth?this.auth((function(t){e._sendConnectPacket(t)})):this._sendConnectPacket(this.auth)}},{key:"_sendConnectPacket",value:function(e){this.packet({type:Jr.CONNECT,data:this._pid?Object.assign({pid:this._pid,offset:this._lastOffset},e):e})}},{key:"onerror",value:function(e){this.connected||this.emitReserved("connect_error",e)}},{key:"onclose",value:function(e,t){this.connected=!1,delete this.id,this.emitReserved("disconnect",e,t)}},{key:"onpacket",value:function(e){if(e.nsp===this.nsp)switch(e.type){case Jr.CONNECT:e.data&&e.data.sid?this.onconnect(e.data.sid,e.data.pid):this.emitReserved("connect_error",new Error("It seems you are trying to reach a Socket.IO server in v2.x with a v3.x client, but they are not compatible (more information here: https://socket.io/docs/v3/migrating-from-2-x-to-3-0/)"));break;case Jr.EVENT:case Jr.BINARY_EVENT:this.onevent(e);break;case Jr.ACK:case Jr.BINARY_ACK:this.onack(e);break;case Jr.DISCONNECT:this.ondisconnect();break;case Jr.CONNECT_ERROR:this.destroy();var t=new Error(e.data.message);t.data=e.data.data,this.emitReserved("connect_error",t)}}},{key:"onevent",value:function(e){var t=e.data||[];null!=e.id&&t.push(this.ack(e.id)),this.connected?this.emitEvent(t):this.receiveBuffer.push(Object.freeze(t))}},{key:"emitEvent",value:function(e){if(this._anyListeners&&this._anyListeners.length){var n,r=j(this._anyListeners.slice());try{for(r.s();!(n=r.n()).done;)n.value.apply(this,e)}catch(e){r.e(e)}finally{r.f()}}V(t,"emit",this,1).apply(this,e),this._pid&&e.length&&"string"==typeof e[e.length-1]&&(this._lastOffset=e[e.length-1])}},{key:"ack",value:function(e){var t=this,n=!1;return function(){if(!n){n=!0;for(var r=arguments.length,o=new Array(r),i=0;i<r;i++)o[i]=arguments[i];t.packet({type:Jr.ACK,id:e,data:o})}}}},{key:"onack",value:function(e){var t=this.acks[e.id];"function"==typeof t&&(t.apply(this,e.data),delete this.acks[e.id])}},{key:"onconnect",value:function(e,t){this.id=e,this.recovered=t&&this._pid===t,this._pid=t,this.connected=!0,this.emitBuffered(),this.emitReserved("connect"),this._drainQueue(!0)}},{key:"emitBuffered",value:function(){var e=this;this.receiveBuffer.forEach((function(t){return e.emitEvent(t)})),this.receiveBuffer=[],this.sendBuffer.forEach((function(t){e.notifyOutgoingListeners(t),e.packet(t)})),this.sendBuffer=[]}},{key:"ondisconnect",value:function(){this.destroy(),this.onclose("io server disconnect")}},{key:"destroy",value:function(){this.subs&&(this.subs.forEach((function(e){return e()})),this.subs=void 0),this.io._destroy(this)}},{key:"disconnect",value:function(){return this.connected&&this.packet({type:Jr.DISCONNECT}),this.destroy(),this.connected&&this.onclose("io client disconnect"),this}},{key:"close",value:function(){return this.disconnect()}},{key:"compress",value:function(e){return this.flags.compress=e,this}},{key:"volatile",get:function(){return this.flags.volatile=!0,this}},{key:"timeout",value:function(e){return this.flags.timeout=e,this}},{key:"onAny",value:function(e){return this._anyListeners=this._anyListeners||[],this._anyListeners.push(e),this}},{key:"prependAny",value:function(e){return this._anyListeners=this._anyListeners||[],this._anyListeners.unshift(e),this}},{key:"offAny",value:function(e){if(!this._anyListeners)return this;if(e){for(var t=this._anyListeners,n=0;n<t.length;n++)if(e===t[n])return t.splice(n,1),this}else this._anyListeners=[];return this}},{key:"listenersAny",value:function(){return this._anyListeners||[]}},{key:"onAnyOutgoing",value:function(e){return this._anyOutgoingListeners=this._anyOutgoingListeners||[],this._anyOutgoingListeners.push(e),this}},{key:"prependAnyOutgoing",value:function(e){return this._anyOutgoingListeners=this._anyOutgoingListeners||[],this._anyOutgoingListeners.unshift(e),this}},{key:"offAnyOutgoing",value:function(e){if(!this._anyOutgoingListeners)return this;if(e){for(var 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34:this.$=a[l]}},table:[{3:1,4:[1,2],6:3,13:4,15:[1,5],16:[1,6],17:[1,7],18:[1,8],19:[1,9]},{1:[3]},{1:[2,1],5:10,7:11,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,3],5:21,7:11,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,12],12:[2,12],14:[2,12],22:[2,12]},{1:[2,14],12:[2,14],14:[2,14],22:[2,14]},{1:[2,15],12:[2,15],14:[2,15],22:[2,15]},{1:[2,16],12:[2,16],14:[2,16],22:[2,16]},{1:[2,17],12:[2,17],14:[2,17],22:[2,17]},{1:[2,18],12:[2,18],14:[2,18],22:[2,18]},{1:[2,2],7:22,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,5],12:[2,5],14:[2,5],22:[2,5]},{1:[2,7],12:[2,7],14:[2,7],22:[2,7]},{1:[2,8],12:[2,8],14:[2,8],22:[2,8]},{1:[2,9],12:[2,9],14:[2,9],22:[2,9]},{1:[2,10],12:[2,10],14:[2,10],22:[2,10]},{1:[2,19],12:[2,19],14:[2,19],22:[2,19]},{1:[2,20],12:[2,20],14:[2,20],22:[2,20]},{13:23,15:[1,5],16:[1,6],17:[1,7],18:[1,8],19:[1,9]},{13:24,15:[1,5],16:[1,6],17:[1,7],18:[1,8],19:[1,9],22:[1,25]},{15:[1,29],17:[1,30],18:[1,33],23:26,25:27,26:28,27:32,29:34,30:[1,35],31:[1,31],32:[1,36],33:[1,37]},{1:[2,4],7:22,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,6],12:[2,6],14:[2,6],22:[2,6]},{1:[2,11],12:[2,11],14:[2,11],22:[2,11]},{1:[2,13],12:[2,13],14:[2,13],22:[2,13]},{15:[1,29],17:[1,30],18:[1,33],23:38,25:27,26:28,27:32,29:34,30:[1,35],31:[1,31],32:[1,36],33:[1,37]},{24:[1,39]},{24:[2,23]},{24:[2,24],28:[1,40]},{24:[2,30]},{24:[2,31]},{24:[2,32]},{24:[2,25],28:[2,25]},{24:[2,27],28:[2,27]},{24:[2,28],28:[2,28]},{24:[2,29],28:[2,29]},{24:[2,33],28:[2,33]},{24:[2,34],28:[2,34]},{24:[1,41]},{1:[2,21],12:[2,21],14:[2,21],22:[2,21]},{18:[1,33],27:42,29:34,30:[1,35],32:[1,36],33:[1,37]},{1:[2,22],12:[2,22],14:[2,22],22:[2,22]},{24:[2,26],28:[2,26]}],defaultActions:{27:[2,23],29:[2,30],30:[2,31],31:[2,32]},parseError:function(e,t){if(!t.recoverable)throw new Error(e);this.trace(e)},parse:function(e){var t=this,n=[0],r=[null],o=[],i=this.table,a="",s=0,l=0,c=o.slice.call(arguments,1);this.lexer.setInput(e),this.lexer.yy=this.yy,this.yy.lexer=this.lexer,this.yy.parser=this,void 0===this.lexer.yylloc&&(this.lexer.yylloc={});var u=this.lexer.yylloc;o.push(u);var d=this.lexer.options&&this.lexer.options.ranges;function f(){var e;return"number"!=typeof(e=t.lexer.lex()||1)&&(e=t.symbols_[e]||e),e}this.parseError="function"==typeof this.yy.parseError?this.yy.parseError:Object.getPrototypeOf(this).parseError;for(var h,p,g,m,y,_,v,b={};;){if(this.defaultActions[p=n[n.length-1]]?g=this.defaultActions[p]:(null==h&&(h=f()),g=i[p]&&i[p][h]),void 0===g||!g.length||!g[0]){var x;for(y in v=[],i[p])this.terminals_[y]&&y>2&&v.push("'"+this.terminals_[y]+"'");x=this.lexer.showPosition?"Parse error on line "+(s+1)+":\n"+this.lexer.showPosition()+"\nExpecting "+v.join(", ")+", got '"+(this.terminals_[h]||h)+"'":"Parse error on line "+(s+1)+": Unexpected "+(1==h?"end of input":"'"+(this.terminals_[h]||h)+"'"),this.parseError(x,{text:this.lexer.match,token:this.terminals_[h]||h,line:this.lexer.yylineno,loc:u,expected:v})}if(g[0]instanceof Array&&g.length>1)throw new Error("Parse Error: multiple actions possible at state: "+p+", token: "+h);switch(g[0]){case 1:n.push(h),r.push(this.lexer.yytext),o.push(this.lexer.yylloc),n.push(g[1]),h=null,l=this.lexer.yyleng,a=this.lexer.yytext,s=this.lexer.yylineno,u=this.lexer.yylloc;break;case 2:if(b.$=r[r.length-(_=this.productions_[g[1]][1])],b._$={first_line:o[o.length-(_||1)].first_line,last_line:o[o.length-1].last_line,first_column:o[o.length-(_||1)].first_column,last_column:o[o.length-1].last_column},d&&(b._$.range=[o[o.length-(_||1)].range[0],o[o.length-1].range[1]]),void 0!==(m=this.performAction.apply(b,[a,l,s,this.yy,g[1],r,o].concat(c))))return m;_&&(n=n.slice(0,-1*_*2),r=r.slice(0,-1*_),o=o.slice(0,-1*_)),n.push(this.productions_[g[1]][0]),r.push(b.$),o.push(b._$),n.push(i[n[n.length-2]][n[n.length-1]]);break;case 3:return!0}}return!0}},t={initialize:function(){this._nodes=[],this._node={},this._stash=[]},set:function(e){for(var t in e)this._node[t]=e[t];return this._node},node:function(e){return arguments.length&&(this._node=e),this._node},push:function(){this._nodes.push(this._node),this._node={}},unshift:function(){this._nodes.unshift(this._node),this._node={}},yield:function(){var e=this._nodes;return this.initialize(),e}},n=function(){var e={EOF:1,parseError:function(e,t){if(!this.yy.parser)throw new Error(e);this.yy.parser.parseError(e,t)},setInput:function(e){return this._input=e,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var e=this._input[0];return this.yytext+=e,this.yyleng++,this.offset++,this.match+=e,this.matched+=e,e.match(/(?:\r\n?|\n).*/g)?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),e},unput:function(e){var t=e.length,n=e.split(/(?:\r\n?|\n)/g);this._input=e+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-t-1),this.offset-=t;var r=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),n.length-1&&(this.yylineno-=n.length-1);var o=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:n?(n.length===r.length?this.yylloc.first_column:0)+r[r.length-n.length].length-n[0].length:this.yylloc.first_column-t},this.options.ranges&&(this.yylloc.range=[o[0],o[0]+this.yyleng-t]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){return this.options.backtrack_lexer?(this._backtrack=!0,this):this.parseError("Lexical error on line "+(this.yylineno+1)+". You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},less:function(e){this.unput(this.match.slice(e))},pastInput:function(){var e=this.matched.substr(0,this.matched.length-this.match.length);return(e.length>20?"...":"")+e.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var e=this.match;return e.length<20&&(e+=this._input.substr(0,20-e.length)),(e.substr(0,20)+(e.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var e=this.pastInput(),t=new Array(e.length+1).join("-");return e+this.upcomingInput()+"\n"+t+"^"},test_match:function(e,t){var n,r,o;if(this.options.backtrack_lexer&&(o={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(o.yylloc.range=this.yylloc.range.slice(0))),(r=e[0].match(/(?:\r\n?|\n).*/g))&&(this.yylineno+=r.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:r?r[r.length-1].length-r[r.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+e[0].length},this.yytext+=e[0],this.match+=e[0],this.matches=e,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(e[0].length),this.matched+=e[0],n=this.performAction.call(this,this.yy,this,t,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),n)return n;if(this._backtrack){for(var i in o)this[i]=o[i];return!1}return!1},next:function(){if(this.done)return this.EOF;var e,t,n,r;this._input||(this.done=!0),this._more||(this.yytext="",this.match="");for(var o=this._currentRules(),i=0;i<o.length;i++)if((n=this._input.match(this.rules[o[i]]))&&(!t||n[0].length>t[0].length)){if(t=n,r=i,this.options.backtrack_lexer){if(!1!==(e=this.test_match(n,o[i])))return e;if(this._backtrack){t=!1;continue}return!1}if(!this.options.flex)break}return t?!1!==(e=this.test_match(t,o[r]))&&e:""===this._input?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){return this.next()||this.lex()},begin:function(e){this.conditionStack.push(e)},popState:function(){return this.conditionStack.length-1>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(e){return(e=this.conditionStack.length-1-Math.abs(e||0))>=0?this.conditionStack[e]:"INITIAL"},pushState:function(e){this.begin(e)},stateStackSize:function(){return this.conditionStack.length},options:{},performAction:function(e,t,n,r){switch(n){case 0:return 4;case 1:return 14;case 2:return 12;case 3:return 15;case 4:return 16;case 5:return 22;case 6:return 24;case 7:return 28;case 8:return 30;case 9:return 18;case 10:return t.yytext=t.yytext.substr(1,t.yyleng-2),32;case 11:return t.yytext=t.yytext.substr(1,t.yyleng-2),33;case 12:return 17;case 13:return 31}},rules:[/^(?:\$)/,/^(?:\.\.)/,/^(?:\.)/,/^(?:\*)/,/^(?:[a-zA-Z_]+[a-zA-Z0-9_]*)/,/^(?:\[)/,/^(?:\])/,/^(?:,)/,/^(?:((-?(?:0|[1-9][0-9]*)))?\:((-?(?:0|[1-9][0-9]*)))?(\:((-?(?:0|[1-9][0-9]*)))?)?)/,/^(?:(-?(?:0|[1-9][0-9]*)))/,/^(?:"(?:\\["bfnrt/\\]|\\u[a-fA-F0-9]{4}|[^"\\])*")/,/^(?:'(?:\\['bfnrt/\\]|\\u[a-fA-F0-9]{4}|[^'\\])*')/,/^(?:\(.+?\)(?=\]))/,/^(?:\?\(.+?\)(?=\]))/],conditions:{INITIAL:{rules:[0,1,2,3,4,5,6,7,8,9,10,11,12,13],inclusive:!0}}};return e}();function r(){this.yy={}}return e.lexer=n,r.prototype=e,e.Parser=r,new r}();void 0!==e&&void 0!==n&&(n.parser=o,n.Parser=o.Parser,n.parse=function(){return o.parse.apply(o,arguments)},n.main=function(t){t[1]||(console.log("Usage: "+t[0]+" FILE"),r.exit(1));var o=e("fs").readFileSync(e("path").normalize(t[1]),"utf8");return n.parser.parse(o)},void 0!==t&&e.main===t&&n.main(r.argv.slice(1)))}).call(this,e("_process"))},{_process:14,fs:12,path:13}],2:[function(e,t,n){t.exports={identifier:"[a-zA-Z_]+[a-zA-Z0-9_]*",integer:"-?(?:0|[1-9][0-9]*)",qq_string:'"(?:\\\\["bfnrt/\\\\]|\\\\u[a-fA-F0-9]{4}|[^"\\\\])*"',q_string:"'(?:\\\\['bfnrt/\\\\]|\\\\u[a-fA-F0-9]{4}|[^'\\\\])*'"}},{}],3:[function(e,t,n){var r=e("./dict"),o=e("fs"),i={lex:{macros:{esc:"\\\\",int:r.integer},rules:[["\\$","return 'DOLLAR'"],["\\.\\.","return 'DOT_DOT'"],["\\.","return 'DOT'"],["\\*","return 'STAR'"],[r.identifier,"return 'IDENTIFIER'"],["\\[","return '['"],["\\]","return ']'"],[",","return ','"],["({int})?\\:({int})?(\\:({int})?)?","return 'ARRAY_SLICE'"],["{int}","return 'INTEGER'"],[r.qq_string,"yytext = yytext.substr(1,yyleng-2); return 'QQ_STRING';"],[r.q_string,"yytext = yytext.substr(1,yyleng-2); return 'Q_STRING';"],["\\(.+?\\)(?=\\])","return 'SCRIPT_EXPRESSION'"],["\\?\\(.+?\\)(?=\\])","return 'FILTER_EXPRESSION'"]]},start:"JSON_PATH",bnf:{JSON_PATH:[["DOLLAR",'yy.ast.set({ expression: { type: "root", value: $1 } }); yy.ast.unshift(); return yy.ast.yield()'],["DOLLAR PATH_COMPONENTS",'yy.ast.set({ expression: { type: "root", value: $1 } }); yy.ast.unshift(); return yy.ast.yield()'],["LEADING_CHILD_MEMBER_EXPRESSION","yy.ast.unshift(); return yy.ast.yield()"],["LEADING_CHILD_MEMBER_EXPRESSION PATH_COMPONENTS",'yy.ast.set({ operation: "member", scope: "child", expression: { type: "identifier", value: $1 }}); yy.ast.unshift(); return yy.ast.yield()']],PATH_COMPONENTS:[["PATH_COMPONENT",""],["PATH_COMPONENTS PATH_COMPONENT",""]],PATH_COMPONENT:[["MEMBER_COMPONENT",'yy.ast.set({ operation: "member" }); yy.ast.push()'],["SUBSCRIPT_COMPONENT",'yy.ast.set({ operation: "subscript" }); yy.ast.push() ']],MEMBER_COMPONENT:[["CHILD_MEMBER_COMPONENT",'yy.ast.set({ scope: "child" })'],["DESCENDANT_MEMBER_COMPONENT",'yy.ast.set({ scope: "descendant" })']],CHILD_MEMBER_COMPONENT:[["DOT MEMBER_EXPRESSION",""]],LEADING_CHILD_MEMBER_EXPRESSION:[["MEMBER_EXPRESSION",'yy.ast.set({ scope: "child", operation: "member" })']],DESCENDANT_MEMBER_COMPONENT:[["DOT_DOT MEMBER_EXPRESSION",""]],MEMBER_EXPRESSION:[["STAR",'yy.ast.set({ expression: { type: "wildcard", value: $1 } })'],["IDENTIFIER",'yy.ast.set({ expression: { type: "identifier", value: $1 } })'],["SCRIPT_EXPRESSION",'yy.ast.set({ expression: { type: "script_expression", value: $1 } })'],["INTEGER",'yy.ast.set({ expression: { type: "numeric_literal", value: parseInt($1) } })'],["END",""]],SUBSCRIPT_COMPONENT:[["CHILD_SUBSCRIPT_COMPONENT",'yy.ast.set({ scope: "child" })'],["DESCENDANT_SUBSCRIPT_COMPONENT",'yy.ast.set({ scope: "descendant" })']],CHILD_SUBSCRIPT_COMPONENT:[["[ SUBSCRIPT ]",""]],DESCENDANT_SUBSCRIPT_COMPONENT:[["DOT_DOT [ SUBSCRIPT ]",""]],SUBSCRIPT:[["SUBSCRIPT_EXPRESSION",""],["SUBSCRIPT_EXPRESSION_LIST",'$1.length > 1? yy.ast.set({ expression: { type: "union", value: $1 } }) : $$ = $1']],SUBSCRIPT_EXPRESSION_LIST:[["SUBSCRIPT_EXPRESSION_LISTABLE","$$ = [$1]"],["SUBSCRIPT_EXPRESSION_LIST , SUBSCRIPT_EXPRESSION_LISTABLE","$$ = $1.concat($3)"]],SUBSCRIPT_EXPRESSION_LISTABLE:[["INTEGER",'$$ = { expression: { type: "numeric_literal", value: parseInt($1) } }; yy.ast.set($$)'],["STRING_LITERAL",'$$ = { expression: { type: "string_literal", value: $1 } }; yy.ast.set($$)'],["ARRAY_SLICE",'$$ = { expression: { type: "slice", value: $1 } }; yy.ast.set($$)']],SUBSCRIPT_EXPRESSION:[["STAR",'$$ = { expression: { type: "wildcard", value: $1 } }; yy.ast.set($$)'],["SCRIPT_EXPRESSION",'$$ = { expression: { type: "script_expression", value: $1 } }; yy.ast.set($$)'],["FILTER_EXPRESSION",'$$ = { expression: { type: "filter_expression", value: $1 } }; yy.ast.set($$)']],STRING_LITERAL:[["QQ_STRING","$$ = $1"],["Q_STRING","$$ = $1"]]}};o.readFileSync&&(i.moduleInclude=o.readFileSync(e.resolve("../include/module.js")),i.actionInclude=o.readFileSync(e.resolve("../include/action.js"))),t.exports=i},{"./dict":2,fs:12}],4:[function(e,t,n){var r=e("./aesprim"),o=e("./slice"),i=e("static-eval"),a=e("underscore").uniq,s=function(){return this.initialize.apply(this,arguments)};function l(t,n,o){var i=e("./index"),a=h(r.parse(n).body[0].expression,{"@":t.value}),s=o.replace(/\{\{\s*value\s*\}\}/g,a),l=i.nodes(t.value,s);return l.forEach((function(e){e.path=t.path.concat(e.path.slice(1))})),l}function c(e){return Array.isArray(e)}function u(e){return function(t,n,r,o){var i=t.value,a=t.path,s=[],l=function(t,i){var a;c(t)?(t.forEach((function(e,t){s.length>=o||r(t,e,n)&&s.push({path:i.concat(t),value:e})})),t.forEach((function(t,n){s.length>=o||e&&l(t,i.concat(n))}))):(a=t)&&!(a instanceof Array)&&a instanceof 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Function)throw new Error("handler must be a function");this._fns[e]=t},s.prototype._fns={"member-child-identifier":function(e,t){var n=e.expression.value,r=t.value;if(r instanceof Object&&n in r)return[{value:r[n],path:t.path.concat(n)}]},"member-descendant-identifier":f((function(e,t,n){return e==n})),"subscript-child-numeric_literal":d((function(e,t,n){return e===n})),"member-child-numeric_literal":d((function(e,t,n){return String(e)===String(n)})),"subscript-descendant-numeric_literal":f((function(e,t,n){return e===n})),"member-child-wildcard":d((function(){return!0})),"member-descendant-wildcard":f((function(){return!0})),"subscript-descendant-wildcard":f((function(){return!0})),"subscript-child-wildcard":d((function(){return!0})),"subscript-child-slice":function(e,t){if(c(t.value)){var n=e.expression.value.split(":").map(g),r=t.value.map((function(e,n){return{value:e,path:t.path.concat(n)}}));return o.apply(null,[r].concat(n))}},"subscript-child-union":function(e,t){var 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t(e.oldVersion,e)})),Pa(n).then((function(){}))}(this.dbName),e}}async termCount(e){const t=await this.db;return(e??t.transaction("nodes")).objectStore("nodes").count()}unique(e){const t=new Map,n=[];for(const r of e)t.has(r.id)||(t.set(r.id,!0),n.push(r));return n}async getTermsWithLabelOrSynonym(e,t,n){const r=t?.includeSubclasses??!0,o=await this.db,i=n??o.transaction(["nodes","edges"]),a=i.objectStore("nodes"),s=[...await a.index("by-label").getAll(e),...await a.index("by-synonym").getAll(e)];if(r){const e=await this.recurseEdges("by-object",s.map((e=>e.id)),(e=>"is_a"===e.pred),"sub",i);for(const t of e){const e=await a.get(t);e&&s.push(e)}}return s}async getPropertiesByLabel(e,t,n){const r=t?.includeSubProperties??!0,o=await this.db,i=n??o.transaction(["nodes","edges"]),a=(await this.getTermsWithLabelOrSynonym(e,{includeSubclasses:!1},i)).filter((e=>As(e)));if(r){const e=await 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at).toHexString(),l={_id:s,refSeq:o.refSeq,min:Number(c)-1,max:Number(a),type:f};o.strand&&(l.strand=o.strand);const u=new ht({changedIds:[o._id],typeName:"AddFeatureChange",assembly:r,addedFeature:l,parentFeatureId:o._id});e.submit(u).then((()=>{n.apolloSetSelectedFeature(s)})),t(),i.preventDefault()},children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[i.jsx(s.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:c,onChange:e=>{d(e.target.value)}}),i.jsx(s.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:a,onChange:e=>{l(e.target.value)},error:_,helperText:_?'"End" must be greater than "Start"':null}),i.jsx(qs,{session:n,ontologyName:"Sequence Ontology",style:{width:170},value:f,filterTerms:Cs,fetchValidTerms:async function(e,t,n){const r=await Ms(e,t);if(r)return r;y(`Type "${e?.type}" does not have any children in the 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Vs({changeManager:e,handleClose:t,selectedFeature:n,session:r,setSelectedFeature:o,sourceAssemblyId:a,sourceFeature:c}){const[d,f]=u.useState(""),{ontologyManager:h}=r.apolloDataStore,{featureTypeOntology:p}=h;function g(e){if(!e.parent?.children||1===e.parent.children.size)return;const t=[];for(const n of e.parent.children.values())p?.isTypeOf(n.type,"CDS")||t.push(n);t.sort(((e,t)=>e.min-t.min));const n=[];for(const t of e.parent.children.values())p?.isTypeOf(t.type,"CDS")||n.push(t);if(n.sort(((e,t)=>t.max-e.max)),e.min===t[0].min){let n;for(const r of t)if(r._id!==e._id&&r.min>=e.min){n=r.min;break}if(n&&n!=e.parent.min)return{typeName:"LocationStartChange",changedId:e.parent._id,featureId:e.parent._id,oldLocation:e.parent.min,newLocation:n}}if(e.max===n[0].max){let t;for(const r of n)if(r._id!=e._id&&r.max<=e.max){t=r.max;break}if(t&&t!=e.parent.max)return{typeName:"LocationEndChange",changedId:e.parent._id,featureId:e.parent._id,oldLocation:e.parent.max,newLocation:t}}}return i.jsxs(Bs,{open:!0,title:"Delete feature",handleClose:t,maxWidth:!1,"data-testid":"delete-feature",children:[i.jsxs("form",{onSubmit:r=>{!async function(r){r.preventDefault(),f(""),n?._id===c._id&&o();const i=[],s=new pt({changedIds:[c._id],typeName:"DeleteFeatureChange",assembly:a,changes:[{deletedFeature:l.getSnapshot(c),parentFeatureId:c.parent?._id}]});if(p&&(p.isTypeOf(c.type,"transcript")||p.isTypeOf(c.type,"pseudogenic_transcript"))){const e=g(c);e&&i.push(e)}if(p?.isTypeOf(c.type,"exon")){const e=function(e){if(!p)return;if(!p.isTypeOf(e.type,"exon"))return;if(!e.parent?.cdsLocations||0===e.parent.cdsLocations.length||0===e.parent.cdsLocations[0].length)return;if(!e.parent.children)throw new Error("Unable to find parent of CDS");if(1!=e.parent.cdsLocations.length)throw new Error("Unable to handle a transcript with multiple CDSs");const t=(e.parent.cdsLocations.at(0)??[]).sort((({min:e},{min:t})=>e-t));let n;for(const r of e.parent.children.values())if(r.type===t[0].type){n=r;break}if(!n)throw new Error("Unable to find CDS");const r=t[0].min,o=t[t.length-1].max;if(!(e.min>r&&e.max<o||e.max<r||e.min>o)){if(e.min<=r&&e.max>=o)return new pt({changedIds:[n._id],typeName:"DeleteFeatureChange",assembly:a,changes:[{deletedFeature:l.getSnapshot(n),parentFeatureId:n.parent?._id}]});if(e.min<=r&&e.max>r){let r;for(const n of t)if(n.min>e.max){r=n.min;break}if(!r)throw new Error("Error setting new CDS start");return{typeName:"LocationStartChange",changedId:n._id,featureId:n._id,oldLocation:n.min,newLocation:r}}if(e.min<o&&e.max>=o){let r;for(const n of t.reverse())if(n.max<e.min){r=n.max;break}if(!r)throw new Error("Error setting new CDS end");return{typeName:"LocationEndChange",changedId:n._id,featureId:n._id,oldLocation:n.max,newLocation:r}}throw new Error("Unexpected relationship between exon and 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File can be gzip compressed.",children:i.jsx(ya,{className:o.radioIcon,sx:{fontSize:18}})})]})}),i.jsx(s.AccordionDetails,{className:o.accordionDetails,children:i.jsxs(s.Box,{style:{marginTop:20},children:[i.jsx("input",{"data-testid":"gff3-input-file",type:"file",disabled:C&&!p,onChange:e=>{const t=e.target.files?.item(0);t&&(R(t),v(fl.GFF3),t.name.endsWith(".gz")&&G(!0))}}),i.jsxs(s.FormGroup,{style:{display:"grid"},children:[i.jsx(s.FormControlLabel,{control:i.jsx(s.Checkbox,{checked:b,onChange:()=>{x(!b)},disabled:C&&!p}),label:"Load features from GFF3 file"}),i.jsx(s.FormControlLabel,{label:"Strict parsing",disabled:!b||C&&!p,control:i.jsx(s.Checkbox,{checked:k,onChange:e=>{N(e.target.checked)}})}),i.jsx(s.FormHelperText,{children:"Don't import any features if any lines in the GFF3 are unable to be processed"}),i.jsx(s.FormControlLabel,{"data-testid":"gff3-is-gzip-checkbox",control:i.jsx(s.Checkbox,{checked:H,onChange:()=>{G(!H)},disabled:C&&!p}),label:"GFF3 is gzip compressed"})]})]})})]})]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{disabled:!pl(m,w,_,T,E,j,W,J,K)||C,variant:"contained",type:"submit","data-testid":"submit-button",children:C?"Submitting...":"Submit"}),i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:t,children:"Cancel"})]})]}),p?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:p})}):null]})}const ml=[{field:"name",headerName:"Assembly Name",width:150,editable:!1},{field:"aliases",headerName:"Aliases",width:300,editable:!0}];function yl({changeManager:e,handleClose:t,session:n}){const{apolloDataStore:r}=n,{collaborationServerDriver:o}=r,a=o.getAssemblies().map((e=>({id:e.name,name:e.displayName,aliases:e.aliases.join(", ")}))),[l,c]=u.useState("");return i.jsxs(Bs,{open:!0,title:"Add assembly aliases",handleClose:t,maxWidth:"sm","data-testid":"add-assembly-alias",fullWidth:!0,children:[i.jsx(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:i.jsx(s.Box,{sx:{height:400,width:"100%"},children:i.jsx(m.DataGrid,{rows:a,columns:ml,initialState:{pagination:{paginationModel:{pageSize:5}}},pageSizeOptions:[5],processRowUpdate:(n,r)=>{const o=new gt({typeName:"AddAssemblyAliasesChange",assembly:n.id,aliases:n.aliases.split(",")});return e.submit(o).catch((()=>{c("Error submitting change")})),t(),n},disableRowSelectionOnClick:!0})})}),l?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:l})}):null]})}const _l=new Set(["TAA","TAG","TGA"]);function vl(e,t,n){let r=0;for(const o of t){const t=o.max-o.min;if(e<=r+t){const t=e-r;return 1===n?o.min+t:o.max-t}r+=t}const o=t.at(-1);if(!o)throw new Error("No exons found");return 1===n?o.max:o.min}function bl({changeManager:e,handleClose:t,refName:n,session:r,sourceAssemblyId:a,sourceFeature:l}){const[c,d]=u.useState("longest-orf"),[f,h]=u.useState(""),[p,g]=u.useState(""),[m,y]=u.useState(""),_="manual"===c&&Boolean(f)&&Boolean(p)&&Number(p)<=Number(f),v="manual"===c&&(!(f&&p)||_);return i.jsxs(Bs,{open:!0,title:"Add coding sequence",handleClose:t,maxWidth:!1,"data-testid":"add-coding-sequence",children:[i.jsxs("form",{onSubmit:i=>{!async function(i){let s,u;i.preventDefault(),y("");try{if("longest-orf"===c){const e=l.transcriptExonParts.filter((e=>"exon"===e.type));if(0===e.length)return void y("No exons found in this transcript");const i=r.apolloDataStore.getBackendDriver(a);if(!i)return void y("No backend driver found for this assembly");let c="";for(const t of e){const{seq:e}=await i.getSequence({assemblyName:a,refName:n,start:t.min,end:t.max});c+=-1===l.strand?o.revcom(e):e}const d=function(e){const t=[null,null,null];let n;for(let r=0;r<e.length-2;r++){const o=e.slice(r,r+3).toUpperCase(),i=r%3;if("ATG"===o&&null===t[i])t[i]=r;else if(_l.has(o)){const e=t[i];if(null===e)continue;(!n||n[1]-n[0]<r-e)&&(n=[e,r]),t[i]=null}}return n}(c);if(!d)return r.notify("No open reading frame found in this transcript","error"),void t();1===(l.strand??1)?(s=vl(d[0],e,1),u=vl(d[1]+3,e,1)):(u=vl(d[0],e,-1),s=vl(d[1]+3,e,-1))}else s=Number(f)-1,u=Number(p);const i=(new at).toHexString(),d={_id:i,refSeq:l.refSeq,min:s,max:u,type:"CDS"};l.strand&&(d.strand=l.strand);const h=new ht({changedIds:[l._id],typeName:"AddFeatureChange",assembly:a,addedFeature:d,parentFeatureId:l._id});await e.submit(h),r.apolloSetSelectedFeature(i),t()}catch(e){y(e instanceof Error?e.message:"An unknown error occurred")}}(i)},children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[i.jsx(s.FormControl,{children:i.jsxs(s.RadioGroup,{value:c,onChange:e=>{d(e.target.value)},children:[i.jsx(s.FormControlLabel,{value:"longest-orf",control:i.jsx(s.Radio,{}),label:"Calculate longest open reading frame"}),i.jsx(s.FormControlLabel,{value:"manual",control:i.jsx(s.Radio,{}),label:"Manual"})]})}),"manual"===c?i.jsxs(i.Fragment,{children:[i.jsx(s.TextField,{margin:"dense",id:"cds-min",label:"Min",type:"number",fullWidth:!0,variant:"outlined",value:f,onChange:e=>{h(e.target.value)}}),i.jsx(s.TextField,{margin:"dense",id:"cds-max",label:"Max",type:"number",fullWidth:!0,variant:"outlined",value:p,onChange:e=>{g(e.target.value)},error:_,helperText:_?'"Max" must be greater than "Min"':null})]}):null]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{variant:"contained",type:"submit",disabled:v,children:"Submit"}),i.jsx(s.Button,{variant:"outlined",type:"button",onClick:t,children:"Cancel"})]})]}),m?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:m})}):null]})}class xl{clientStore;constructor(e){this.clientStore=e}}async function wl(e,t){return qa(`Apollo-${e}`,1,{upgrade(e){const n="changes";e.objectStoreNames.contains(n)||e.createObjectStore(n,{autoIncrement:!0});for(const n of t){const t=`features-${n}`;if(!e.objectStoreNames.contains(t)){const n=e.createObjectStore(t);n.createIndex("min","min",{unique:!1}),n.createIndex("max","max",{unique:!1})}const r=`checkresults-${n}`;if(!e.objectStoreNames.contains(r)){const t=e.createObjectStore(r,{keyPath:"_id"});t.createIndex("min","start",{unique:!1}),t.createIndex("max","end",{unique:!1}),t.createIndex("featureId","featureId",{unique:!1})}}}})}class Sl extends xl{async getFeatures(e){const{assemblyName:t,end:n,refName:r,start:o}=e,i=(await this.getRegions(t)).map((e=>e.refName)),a=`features-${r}`,s=`checkresults-${r}`,l=[],c=[],u=(await wl(t,i)).transaction([a,s]);for await(const e of u.objectStore(a).index("min").iterate(IDBKeyRange.upperBound(n,!0)))e.value.max>o&&l.push(e.value);for await(const e of u.objectStore(s).index("min").iterate(IDBKeyRange.upperBound(n,!0)))e.value.end>o&&c.push(e.value);return[l,c]}async getSequence(e){const t=o.getSession(this.clientStore),{assemblyManager:n}=t,r=await n.waitForAssembly(e.assemblyName);if(!r)throw new Error(`Assembly not found: "${e.assemblyName}"`);const{configuration:i}=r,{adapter:a}=i.sequence,{pluginManager:s}=o.getEnv(this.clientStore),l=s.getAdapterType(a.type);if(!l)throw new Error(`No adapter found for "${a.type}"`);const c=new(await l.getAdapterClass())(a,void 0,s),u=await c.getSequence({...e,refName:r.getSeqAdapterRefName(e.refName)});if(!u)throw new Error(`Sequence not found: ${JSON.stringify(e)}`);return{seq:u,refSeq:e.refName}}async getRegions(e){const t=o.getSession(this.clientStore),{assemblyManager:n}=t,r=await n.waitForAssembly(e);if(!r)throw new Error(`Assembly not found: "${e}"`);const{regions:i}=r;if(!i)throw new Error(`Assembly not found: "${e}"`);return i}getAssemblies(e){return[]}async getRefNameAliases(e){const t=o.getSession(this.clientStore),{assemblyManager:n}=t,r=await n.waitForAssembly(e);if(!r)throw new Error(`Assembly not found: "${e}"`);const{configuration:i}=r,{refNameAliases:a}=i;if(!a)return[];const{pluginManager:s}=o.getEnv(this.clientStore),l=s.getAdapterType(a.adapter.type);if(!l)throw new Error(`No adapter found for "${a.adapter.type}"`);return new(await l.getAdapterClass())(a.adapter,void 0,s).getRefNameAliases({})}async submitChange(e,t){if(!st(e))return new Wt;const{assembly:n,changedIds:r}=e,o=(await this.getRegions(n)).map((e=>e.refName)),i=await wl(n,o),a=new Set,s=[],c=new Set;if(function(e){return"DeleteFeatureChange"===e.typeName}(e))for(const t of e.changes)if(t.parentFeatureId){const e=this.clientStore.getFeature(t.parentFeatureId);e&&(a.add(e.topLevelFeature),c.add(e.topLevelFeature.refSeq))}else{const{refSeq:e,_id:n}=t.deletedFeature;s.push({refSeq:e,featureId:n}),c.add(e)}else for(const e of r){const t=this.clientStore.getFeature(e);t&&(a.add(t.topLevelFeature),c.add(t.refSeq))}const u=[...c].flatMap((e=>[`features-${e}`,`checkresults-${e}`]));u.push("changes");const d=i.transaction(u,"readwrite");for(const{refSeq:e,featureId:t}of s)d.objectStore(`features-${e}`).delete(t);for(const e of a){const t=l.getSnapshot(e);d.objectStore(`features-${e.refSeq}`).put(t,e._id)}for(const{featureId:e,refSeq:t}of s){const n=d.objectStore(`checkresults-${t}`);for await(const t of n.index("featureId").iterate(e))this.clientStore.deleteCheckResult(t.value._id),t.delete()}for(const e of a){const t=d.objectStore(`checkresults-${e.refSeq}`);for await(const n of t.index("featureId").iterate(e._id))this.clientStore.deleteCheckResult(n.value._id),n.delete()}if(d.objectStore("changes").put({...e.toJSON(),createdAt:new Date}),await d.done,a.size>0){const e=[...ne.getChecks().values()],t=[];for(const r of a){const o=l.getSnapshot(r),i=async(e,t)=>(await this.getSequence({assemblyName:n,refName:r.refSeq,start:e,end:t})).seq;for(const n of e){const e=await n.checkFeature(o,i);for(const n of e)t.push({refSeq:r.refSeq,result:n,topLevelFeatureId:r._id})}}if(t.length>0){const e=o.map((e=>`checkresults-${e}`)),n=i.transaction(e,"readwrite");for(const{refSeq:e,result:r,topLevelFeatureId:o}of t)n.objectStore(`checkresults-${e}`).put({...r,featureId:o});await n.done;for(const{result:e}of t)this.clientStore.addCheckResult(e)}}return new Wt}async searchFeatures(e,t){return[]}async getCheckResults(e){const t=(await this.getRegions(e)).map((e=>e.refName)),n=await wl(e,t),r=[],o=t.map((e=>`checkresults-${e}`)),i=n.transaction(o);for(const e of o)for await(const t of i.objectStore(e).iterate())r.push(t.value);return r}async getChanges(e,t={}){const n=(await this.getRegions(e)).map((e=>e.refName)),r=await wl(e,n);let o=[];for await(const e of r.transaction("changes").store.iterate())o.push({sequence:e.key,...e.value});const{filters:i}=t;if(i?.user){const e=new RegExp(i.user,"i");o=o.filter((t=>void 0!==t.user&&e.test(t.user)))}if(i?.typeName&&(o=o.filter((e=>e.typeName===i.typeName))),i?.startTime){const e=new Date(i.startTime).getTime();o=o.filter((t=>new Date(t.createdAt).getTime()>=e))}if(i?.endTime){const e=new Date(i.endTime).getTime();o=o.filter((t=>new Date(t.createdAt).getTime()<=e))}const a=o.length,s=t.sortField??"sequence",l="asc"===(t.sortOrder??"desc")?1:-1;if(o.sort(((e,t)=>{const n=e[s],r=t[s];return n===r?0:void 0===n?1:void 0===r?-1:n<r?-l:l})),void 0!==t.page&&void 0!==t.pageSize){const e=t.page*t.pageSize;o=o.slice(e,e+t.pageSize)}return{changes:o,totalCount:a}}}const Cl={async AddFeatureChange(e,t){const{assembly:n,changes:r}=t;for(const t of r){const{addedFeature:r,parentFeatureId:o}=t;if(o){let t=e.getFeature(o);if(!t&&(await e.loadFeatures([{assemblyName:n,refName:r.refSeq,start:r.min,end:r.max}]),t=e.getFeature(o),!t))throw new Error(`Could not find parent feature "${o}"`);t.attributes.get("_id")||t.setAttribute("_id",[t._id]),t.addChild(r)}else e.addFeature(n,r)}},async DeleteFeatureChange(e,t){for(const n of t.changes){const{deletedFeature:t,parentFeatureId:r}=n;if(r){const n=e.getFeature(r);if(!n)throw new Error(`Could not find parent feature "${r}"`);n.deleteChild(t._id)}else e.getFeature(t._id)&&e.deleteFeature(t._id)}},async FeatureAttributeChange(e,t){for(const[n,r]of t.changedIds.entries()){const o=e.getFeature(r);if(!o)throw new Error(`Could not find feature with identifier "${r}"`);o.setAttributes(new Map(Object.entries(t.changes[n].newAttributes)))}},async LocationEndChange(e,t){for(const n of t.changes){const{featureId:t,newEnd:r}=n,o=e.getFeature(t);if(!o)throw new Error(`Could not find feature with identifier "${t}"`);o.setMax(r)}},async LocationStartChange(e,t){for(const n of t.changes){const{featureId:t,newStart:r}=n,o=e.getFeature(t);if(!o)throw new Error(`Could not find feature with identifier "${t}"`);o.setMin(r)}},async MergeExonsChange(e,t){for(const n of t.changes){const{firstExon:t,secondExon:r}=n,o=e.getFeature(t._id);if(!o)throw new Error(`Could not find feature with identifier "${t._id}"`);o.setMin(Math.min(t.min,r.min)),o.setMax(Math.max(t.max,r.max));const i=o.attributes.get("merged_with")?.slice()??[],a=Lt(Mt(r.attributes));i.includes(a)||i.push(a),o.setAttribute("merged_with",i),o.parent?.deleteChild(r._id)}},async SplitExonChange(e,t){for(const[n]of t.changedIds.entries()){const{exonToBeSplit:r,parentFeatureId:o,upstreamCut:i,downstreamCut:a,leftExonId:s,rightExonId:l}=t.changes[n];if(!o)throw new Error("TODO: Split exon without parent");const[c,u]=t.makeSplitExons(r,i,a,s,l),d=e.getFeature(o);if(!d)throw new Error(`Could not find parent feature "${o}"`);d.addChild(c),d.addChild(u),e.getFeature(r._id)&&e.deleteFeature(r._id)}},async MergeTranscriptsChange(e,t){for(const[n,r]of t.changedIds.entries()){const{firstTranscript:o,secondTranscript:i}=t.changes[n],a=e.getFeature(o._id);if(!a)throw new Error(`Could not find feature with identifier "${r}"`);t.mergeTranscriptsOnClient(a,i),a.parent?.deleteChild(i._id)}},async UndoMergeExonsChange(e,t){for(const n of t.changes){const{exonsToRestore:t,parentFeatureId:r}=n;if(!r)throw new Error("Parent ID is missing");const o=e.getFeature(r);if(!o)throw new Error(`Could not find parent feature "${r}"`);o.attributes.get("_id")||o.setAttribute("_id",[o._id]);for(const e of t)o.addChild(e)}},async UndoSplitExonChange(e,t){for(const n of t.changes){const{exonToRestore:t,parentFeatureId:r,idsToDelete:o}=n;if(!r)throw new Error("Parent ID is missing");const i=e.getFeature(r);if(!i)throw new Error(`Could not find parent feature "${r}"`);i.attributes.get("_id")||i.setAttribute("_id",[i._id]),i.addChild(t),o.map((e=>{i.deleteChild(e)}))}},async UndoMergeTranscriptsChange(e,t){for(const n of t.changes){const{transcriptsToRestore:t,parentFeatureId:r}=n;if(!r)throw new Error("Parent ID is missing");const o=e.getFeature(r);if(!o)throw new Error(`Could not find parent feature "${r}"`);o.attributes.get("_id")||o.setAttribute("_id",[o._id]);for(const e of t)o.addChild(e)}},async StrandChange(e,t){for(const[n,r]of t.changedIds.entries()){const o=e.getFeature(r);if(!o)throw new Error(`Could not find feature with identifier "${r}"`);o.setStrand(t.changes[n].newStrand)}},async TypeChange(e,t){for(const[n,r]of t.changedIds.entries()){const o=e.getFeature(r);if(!o)throw new Error(`Could not find feature with identifier "${r}"`);o.setType(t.changes[n].newType)}}};class Al{dataStore;constructor(e){this.dataStore=e}recentChanges=[];undoneChanges=[];async submit(e,t={}){const{addToRecents:n=!0,submitToBackend:r=!0,updateJobsManager:i=!1}=t,a=o.getSession(this.dataStore),s=new AbortController,{jobsManager:l,isLocked:c,changeInProgress:u,setChangeInProgress:d}=o.getSession(this.dataStore);if(c)return a.notify("Cannot submit changes in locked mode"),void d(!1);if(u)return void a.notify("Could not submit change, there is another change still in progress");d(!0);const f={name:e.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{s.abort(new DOMException(`Cancelling change "${e.typeName}"`,"AbortError"))}};i&&l.runJob(f);const h=await Kt.frontendPreValidate(e);if(!h.ok){const e=`Pre-validation failed: "${h.resultsMessages}"`;return i&&l.abortJob(f.name,e),a.notify(e,"error"),void d(!1)}const p=e.typeName,g=function(e){return e in Cl}(p)?Cl[p]:void 0;if(g)try{await g(this.dataStore,e)}catch(e){return i&&l.abortJob(f.name,String(e)),console.error(e),a.notify(`Error encountered in client: ${String(e)}. Data may be out of sync, please refresh the page`,"error"),void d(!1)}if((await Kt.frontendPostValidate(e)).ok||await this.undo(e),r){i&&l.update(f.name,"Submitting to driver");const{collaborationServerDriver:r,getBackendDriver:o}=this.dataStore,s=te(e)?o(e.assembly)??r:r;let c;try{c=await s.submitChange(e,t)}catch(t){return i&&l.abortJob(f.name,String(t)),console.error(t),a.notify(String(t),"error"),d(!1),void await this.undo(e,!1)}if(!c.ok){const t=`Post-validation failed: "${h.resultsMessages}"`;return i&&l.abortJob(f.name,t),a.notify(t,"error"),d(!1),void await this.undo(e,!1)}e.notification&&a.notify(e.notification,"success"),n&&(this.recentChanges.push(e),this.undoneChanges=[])}i&&l.done(f),d(!1)}async undo(e,t=!0){const n=e.getInverse();return this.submit(n,{submitToBackend:t,addToRecents:!1})}async redo(e,t=!0){return this.submit(e,{submitToBackend:t,addToRecents:!1})}async undoLastChange(){const e=o.getSession(this.dataStore),t=this.recentChanges.pop();if(t)return this.undoneChanges.push(t),this.undo(t);e.notify("No changes to undo!","info")}async redoLastChange(){const e=o.getSession(this.dataStore),t=this.undoneChanges.pop();if(t)return this.recentChanges.push(t),this.redo(t);e.notify("No changes to redo!","info")}}class kl extends xl{inFlight=new Map;refSeqMaps=new Map;async fetch(e,t,n){return e.getFetcher({locationType:"UriLocation",uri:t.toString()})(t,n)}async searchFeatures(e,t){const n=this.clientStore.getInternetAccount(t[0]),{baseURL:r}=n,o=new URL("features/searchFeatures",r),i=new URLSearchParams({assemblies:t.join(","),term:e});o.search=i.toString();const a=o.toString(),s=await this.fetch(n,a);if(!s.ok){const e=await dl(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:r,start:i}=e,{assemblyManager:a}=o.getSession(this.clientStore);if(!a.get(t))throw new Error(`Could not find assembly with name "${t}"`);const s=(await this.getRefSeqMapping(t)).get(r);if(!s)throw new Error(`Could not find refSeq "${r}"`);const l=s.id,c=this.clientStore.getInternetAccount(t),{baseURL:u}=c,d=new URL("features/getFeatures",u),f=new URLSearchParams({refSeq:l,start:String(i),end:String(n)});d.search=f.toString();const h=d.toString(),p=await this.fetch(c,h);if(!p.ok){const e=await dl(p,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,r,c),p.json()}checkSocket(e,t,n){const{socket:r}=n,o=`${e}-${t}`;r.hasListeners(o)||r.on(o,(async e=>{const t=n.retrieveToken();if(!t)return;const r=sn(t),o=new Al(this.clientStore);if(n.setLastChangeSequenceNumber(e.changeSequence),e.userSessionId===r)return;const i=ee.fromJSON(e.changeInfo);st(i)&&this.haveDataForChange(i)&&await o.submit(i,{submitToBackend:!1})}))}haveDataForChange(e){const{assembly:t,changedIds:n}=e;if(!this.clientStore.assemblies.get(t))return!1;for(const e of n)if(this.clientStore.getFeature(e))return!0;return!1}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,n=this.inFlight.get(t),{assemblyName:r,end:i,refName:a,start:s}=e,{assemblyManager:l}=o.getSession(this.clientStore);if(!l.get(r))throw new Error(`Could not find assembly with name "${r}"`);const c=(await this.getRefSeqMapping(r)).get(a);if(!c)throw new Error(`Could not find refSeq "${a}"`);const u=c.id;if(n)return{seq:await n,refSeq:u};const d=this.clientStore.assemblies.get(r)??this.clientStore.addAssembly(r),f=d.refSeqs.get(u)??d.addRefSeq(u,a),h=f.getSequence(s,i);if(h.length===i-s)return{seq:h,refSeq:u};const p=this.clientStore.getInternetAccount(r),{baseURL:g}=p,m=new URL("sequence",g),y=new URLSearchParams({refSeq:u,start:String(s),end:String(i)});m.search=y.toString();const _=m.toString(),v=this.getSeqFromServer(p,_,f,s,i);this.inFlight.set(t,v);const b=await v;return this.checkSocket(r,a,p),this.inFlight.delete(t),{seq:b,refSeq:u}}async getSeqFromServer(e,t,n,r,o){const i=await this.fetch(e,t);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getSequence failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}const a=await i.text();return n.addSequence({sequence:a,start:r,stop:o}),a}async getRefSeqMapping(e){const t=this.refSeqMaps.get(e);if(t)return t;const{assemblyManager:n}=o.getSession(this.clientStore);if(!n.get(e))throw new Error(`Could not find assembly with name "${e}"`);const r=this.clientStore.getInternetAccount(e),{baseURL:i}=r,a=new URL("refSeqs",i),s=new URLSearchParams({assembly:e});a.search=s.toString();const l=a.toString(),c=await this.fetch(r,l);if(!c.ok){let e;try{e=await c.text()}catch{e=""}throw new Error(`getRefNameAliases failed: ${c.status} (${c.statusText})${e?` (${e})`:""}`)}const u=await c.json(),d=new Map(u.map((e=>[e.name,{refName:e.name,id:e._id,aliases:e.aliases}])));return this.refSeqMaps.set(e,d),d}async getRefNameAliases(e){return[...(await this.getRefSeqMapping(e)).values()].map((e=>({refName:e.refName,aliases:[...new Set([e.id,...e.aliases])],uniqueId:`alias-${e.id}`})))}async getRefSeqId(e,t){const n=await this.getRefSeqMapping(e);if(!n)return;const r=n.get(t);return r?.id}async getRegions(e){const{assemblyManager:t}=o.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:r}=n,i=new URL("refSeqs",r),a=new URLSearchParams({assembly:e});i.search=a.toString();const s=i.toString(),l=await this.fetch(n,s);if(!l.ok){let e;try{e=await l.text()}catch{e=""}throw new Error(`getRegions failed: ${l.status} (${l.statusText})${e?` (${e})`:""}`)}return(await l.json()).map((e=>({refName:e.name,start:0,end:e.length})))}getAssemblies(e){const{assemblyManager:t}=o.getSession(this.clientStore);return t.assemblies.filter((t=>{const r=n.getConf(t,["sequence","metadata"]);return!(!(r&&r.apollo&&r.internetAccountConfigId)||e&&r.internetAccountConfigId!==e)}))}async getChanges(e,t={}){const n=this.clientStore.getInternetAccount(e),{baseURL:r}=n,o=new URL("changes",r),i={assembly:e};void 0!==t.page&&(i.page=String(t.page)),void 0!==t.pageSize&&(i.pageSize=String(t.pageSize)),t.sortField&&(i.sortField=t.sortField),t.sortOrder&&(i.sortOrder=t.sortOrder),t.filters?.user&&(i.user=t.filters.user),t.filters?.typeName&&(i.typeName=t.filters.typeName),t.filters?.startTime&&(i.startTime=t.filters.startTime),t.filters?.endTime&&(i.endTime=t.filters.endTime),o.search=new URLSearchParams(i).toString();const a=await this.fetch(n,o.toString());if(!a.ok){const e=await dl(a,"getChanges failed");throw new Error(e)}return a.json()}async getCheckResults(e){const t=this.clientStore.getInternetAccount(e),{baseURL:n}=t,r=new URL("checks",n);r.search=new URLSearchParams({assembly:e}).toString();const o=await this.fetch(t,r.toString());if(!o.ok){const e=await dl(o,"getCheckResults failed");throw new Error(e)}return o.json()}async submitChange(e,t={}){const{internetAccountId:n}=t,r=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,n),{baseURL:o}=r,i=new URL("changes",o).href,a=await this.fetch(r,i,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!a.ok){const e=await dl(a,"submitChange failed");throw new Error(e)}const s=new Wt;return a.ok||(s.ok=!1),s}}var Nl;function Tl(e,t,n,r){const o={_id:(new at).toHexString(),refSeq:e,type:"CDS",min:n,max:r,strand:t},i={_id:(new at).toHexString(),refSeq:e,type:"exon",min:n,max:r,strand:t},a={};return a[o._id]=o,a[i._id]=i,{_id:(new at).toHexString(),refSeq:e,type:"mRNA",min:n,max:r,strand:t,children:a}}function Rl({changeManager:e,handleClose:t,region:n,session:r}){const[o,a]=u.useState(String(n.end)),[l,c]=u.useState(String(n.start+1)),[d,f]=u.useState(Nl.GENE_AND_SUBFEATURES),[h,p]=u.useState(""),[g,m]=u.useState(),[y,_]=u.useState(""),v=Number(o)<=Number(l);let b=v||!(l&&o&&d);return(d===Nl.CUSTOM&&!h||!g&&d===Nl.GENE_AND_SUBFEATURES||!g&&d===Nl.TRANSCRIPT_AND_SUBFEATURES)&&(b=!0),i.jsxs(Bs,{open:!0,title:"Add new feature",handleClose:t,maxWidth:!1,"data-testid":"add-feature-dialog",children:[i.jsxs("form",{onSubmit:async function(i){i.preventDefault(),_("");const a=r.apolloDataStore.getBackendDriver(n.assemblyName);if(!a)return void _("No backend driver found");let s=n.refName;if(a instanceof kl){const e=await a.getRefSeqId(n.assemblyName,n.refName);if(!e)return void _(`Could not find refSeq for "${n.refName}"`);s=e}if(d===Nl.GENE_AND_SUBFEATURES){const i=Tl(s,g,Number(l)-1,Number(o)),a={};a[i._id]=i;const c=(new at).toHexString(),u=new ht({changedIds:[c],typeName:"AddFeatureChange",assembly:n.assemblyName,addedFeature:{_id:c,refSeq:s,min:Number(l)-1,max:Number(o),type:"gene",strand:g,children:a}});return e.submit(u).then((()=>{r.apolloSetSelectedFeature(c)})),void t()}if(d===Nl.TRANSCRIPT_AND_SUBFEATURES){const i=Tl(s,g,Number(l)-1,Number(o)),a=new ht({changedIds:[i._id],typeName:"AddFeatureChange",assembly:n.assemblyName,addedFeature:i});return e.submit(a).then((()=>{r.apolloSetSelectedFeature(i._id)})),void t()}if(!h)return void _("No type selected");const c=(new at).toHexString(),u=new ht({changedIds:[c],typeName:"AddFeatureChange",assembly:n.assemblyName,addedFeature:{_id:c,refSeq:s,min:Number(l)-1,max:Number(o),type:h,strand:g}});e.submit(u).then((()=>{r.apolloSetSelectedFeature(c)})),t()},"data-testid":"submit-form",children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[i.jsx(s.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(l),onChange:e=>{c(e.target.value)}}),i.jsx(s.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:o,onChange:e=>{a(e.target.value)},error:v,helperText:v?'"End" must be greater than "Start"':null}),i.jsxs(s.FormControl,{children:[i.jsx(s.InputLabel,{id:"demo-simple-select-label",children:"Strand"}),i.jsxs(s.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Strand",value:g?.toString(),onChange:function(e){switch(_(""),Number(e.target.value)){case 1:m(1);break;case-1:m(-1);break;default:m(void 0)}},children:[i.jsx(s.MenuItem,{value:void 0}),i.jsx(s.MenuItem,{value:1,children:"+"}),i.jsx(s.MenuItem,{value:-1,children:"-"})]})]}),i.jsx(s.FormControl,{style:{marginTop:20},children:i.jsxs(s.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:Nl.GENE_AND_SUBFEATURES,name:"radio-buttons-group",value:d,onChange:e=>{_("");const{value:t}=e.target;Object.keys(Nl).includes(t)&&f(Nl[t])},children:[i.jsx(s.FormControlLabel,{value:Nl.GENE_AND_SUBFEATURES,control:i.jsx(s.Radio,{}),label:i.jsxs(s.Box,{display:"flex",alignItems:"center",children:["Add gene and sub-features",i.jsx(s.Tooltip,{title:"This is a shortcut to create a gene with a single mRNA, exon, and CDS",children:i.jsx(s.IconButton,{size:"small",children:i.jsx(ya,{sx:{fontSize:18}})})})]})}),i.jsx(s.FormControlLabel,{value:Nl.TRANSCRIPT_AND_SUBFEATURES,control:i.jsx(s.Radio,{}),label:i.jsxs(s.Box,{display:"flex",alignItems:"center",children:["Add transcript and sub-features",i.jsx(s.Tooltip,{title:"This is a shortcut to create a single mRNA with exon and CDS, but without a parent gene",children:i.jsx(s.IconButton,{size:"small",children:i.jsx(ya,{sx:{fontSize:18}})})})]})}),i.jsx(s.FormControlLabel,{value:Nl.CUSTOM,checked:d!==Nl.GENE_AND_SUBFEATURES&&d!==Nl.TRANSCRIPT_AND_SUBFEATURES,control:i.jsx(s.Radio,{}),label:"Add feature with a sequence ontology type"})]})}),d===Nl.CUSTOM?i.jsx(qs,{session:r,ontologyName:"Sequence Ontology",style:{width:170},value:h,filterTerms:Cs,renderInput:e=>i.jsx(s.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0}),onChange:(e,t)=>{var n;t&&(n=t,_(""),p(n))}}):null]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{variant:"contained",type:"submit",disabled:b,children:"Submit"}),i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:t,children:"Cancel"})]})]}),y?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:y})}):null]})}function El({changeManager:e,handleClose:t,session:n}){const{internetAccounts:r}=l.getRoot(n),[o,a]=u.useState(""),[c,d]=u.useState(!1),[f,h]=u.useState(!1),p=r.filter((e=>"ApolloInternetAccount"===e.type));if(0===p.length)throw new Error("No Apollo internet account found");const[g,m]=u.useState(p[0]),{collaborationServerDriver:y}=n.apolloDataStore,_=y.getAssemblies(),[v,b]=u.useState(_.at(0));return i.jsxs(Bs,{open:!0,title:"Delete Assembly",handleClose:t,maxWidth:!1,"data-testid":"delete-assembly",children:[i.jsxs("form",{onSubmit:async function(n){if(n.preventDefault(),h(!0),a(""),!v)return void a("Must select assembly!");const r=new xt({typeName:"DeleteAssemblyChange",assembly:v.name});await e.submit(r,{internetAccountId:g.internetAccountId}),t(),n.preventDefault()},children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[p.length>1?i.jsxs(i.Fragment,{children:[i.jsx(s.DialogContentText,{children:"Select account"}),i.jsx(s.Select,{value:g.internetAccountId,onChange:function(e){h(!1);const t=p.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID "${e.target.value}"`);m(t)},disabled:f&&!o,children:r.map((e=>i.jsx(s.MenuItem,{value:e.internetAccountId,children:e.name},e.id)))})]}):null,i.jsx(s.DialogContentText,{children:"Select assembly"}),i.jsx(s.Select,{labelId:"label",value:v?.name??"",onChange:function(e){const t=_.find((t=>t.name===e.target.value));b(t)},disabled:0===_.length,children:_.map((e=>i.jsx(s.MenuItem,{value:e.name,children:e.displayName},e.name)))}),i.jsx(s.DialogContentText,{children:i.jsx("strong",{style:{color:"red"},children:"NOTE: All assembly data will be deleted and this operation cannot be undone!"})}),i.jsx(s.FormGroup,{children:i.jsx(s.FormControlLabel,{control:i.jsx(s.Checkbox,{checked:c,onChange:()=>{d(!c)}}),label:"I understand that all assembly data will be deleted"})})]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{disabled:!v||!c,variant:"contained",type:"submit",children:"Delete"}),i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:t,children:"Cancel"})]})]}),o?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:o})}):null]})}!function(e){e.GENE_AND_SUBFEATURES="GENE_AND_SUBFEATURES",e.TRANSCRIPT_AND_SUBFEATURES="TRANSCRIPT_AND_SUBFEATURES",e.CUSTOM="CUSTOM"}(Nl||(Nl={}));var Il,jl,Dl,Ol,Fl={},Ml={},Ll={},Pl={};function Bl(){if(Il)return Pl;function e(e){return decodeURIComponent(e)}function t(e,t){return String(t).replaceAll(e,(function(e){return encodeURIComponent(e).toUpperCase()}))}function n(e){return t(/[\n;\r\t=%&,\u0000-\u001f\u007f]/g,e)}function r(e){return t(/[\n\r\t%\u0000-\u001f\u007f]/g,e)}function o(t){if(null==t||!t.length||"."===t)return{};var n={};return t.replace(/\r\n|[\r\n]$/,"").split(";").forEach((function(t){var r,o,i=t.split("=",2);if(null!==(r=i[1])&&void 0!==r&&r.length){i[0]=i[0].trim();var a=n[i[0].trim()];a||(n[i[0]]=a=[]),(o=a).push.apply(o,W(i[1].split(",").map((function(e){return e.trim()})).map(e)))}})),n}function i(e){var t=[];return Object.entries(e).forEach((function(e){var r=G(e,2),o=r[0],i=r[1].map(n).join(",");t.push("".concat(n(o),"=").concat(i))})),t.length?t.join(";"):"."}function a(e,t){var n=null==e.attributes?".":i(e.attributes),o=[null===e.seq_id?".":r(e.seq_id),null===e.source?".":r(e.source),null===e.type?".":r(e.type),null===e.start?".":r(e.start),null===e.end?".":r(e.end),null===e.score?".":r(e.score),null===e.strand?".":r(e.strand),null===e.phase?".":r(e.phase),n],a="".concat(o.join("\t"),"\n");return t[a]?"":(t[a]=!0,a)}function s(e,t){if(Array.isArray(e))return e.map((function(e){return s(e,t)})).join("");var n,r=[a(e,t)];return void 0!==(n=e).child_features&&void 0!==n.derived_features&&r.push.apply(r,W(e.child_features.map((function(e){return s(e,t)}))).concat(W(e.derived_features.map((function(e){return s(e,t)}))))),r.join("")}function l(e){return s(e,{})}function c(e){var t="##".concat(e.directive);return e.value&&(t+=" ".concat(e.value)),t+"\n"}function u(e){return"# ".concat(e.comment,"\n")}function d(e){for(var t=">".concat(e.id).concat(e.description?" 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URL("auth/types",e).href,r=await fetch(t,{method:"GET",signal:n});if(!r.ok){const e=await dl(r,"Error when retrieving auth types from server");return void a(e)}const o=await r.json();c(o),0===o.length&&a("No login types configured")}().catch((e=>{ts(e)||a(String(e))})),()=>{t.abort(new DOMException("Error retrieving valid authentication types","AbortError"))}}),[e]),null===l)return"Loading…";const f=l.at(0);return f&&1===l.length&&!f.needsPopup&&d(f),i.jsxs(Bs,{open:!0,title:`Log in to ${n}`,handleClose:t,maxWidth:!1,"data-testid":"login-apollo",children:[i.jsx(s.DialogContent,{style:{display:"flex",flexDirection:"column",paddingTop:8},children:l.map((e=>"google"===e.name?i.jsx(vc,{message:e.message,onClick:()=>{d(e)}},e.name):"microsoft"===e.name?i.jsx(bc,{message:e.message,onClick:()=>{d(e)}},e.name):"guest"===e.name?i.jsxs(u.Fragment,{children:[i.jsx(s.Divider,{className:r.divider}),i.jsx(xc,{message:e.message,onClick:()=>{d(e)}})]},e.name):i.jsx(wc,{message:e.message,onClick:()=>{d(e)}},e.name)))}),i.jsx(s.DialogActions,{children:i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:()=>{t()},children:"Cancel"})}),o?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:o})}):null]})},Ac="undefined"==typeof sessionStorage,kc=e=>r.InternetAccount.named("ApolloInternetAccount").props({type:l.types.literal("ApolloInternetAccount"),configuration:n.ConfigurationReference(e)}).views((e=>({get baseURL(){return n.getConf(e,"baseURL")},getUserId(){const t=e.retrieveToken();if(t)return ln(t).id}}))).volatile((()=>({role:void 0,controller:new AbortController,tokenPromise:void 0}))).actions((e=>({setRole(){const t=e.retrieveToken();if(!t)return void(e.role=void 0);const n=ln(t),{role:r,exp:o}=n;if(o<Date.now()/1e3)return e.role=void 0,void e.removeToken();e.role!==r&&(e.role=r)}}))).actions((e=>{const t=e.getFetcher;return{getFetcher(n){const r=t(n);return async(t,n)=>{const o=await r(t,n);return 403===o.status?(e.removeToken(),e.setRole(),r(t,n)):o}}}})).actions((e=>({removeToken(){sessionStorage.removeItem(e.tokenKey),e.tokenPromise=void 0}}))).actions((e=>({async getToken(t){if(e.tokenPromise)return e.tokenPromise;let n=t?.internetAccountPreAuthorization?.authInfo?.token;if(n)return e.tokenPromise=Promise.resolve(n),e.tokenPromise;if(Ac)throw new Error("Did not get internet account pre-authorization info in worker");return n=e.retrieveToken(),n?(e.tokenPromise=Promise.resolve(n),e.tokenPromise):(e.tokenPromise=new Promise(((t,n)=>{e.getTokenFromUser((n=>{e.storeToken(n),t(n)}),(t=>{e.removeToken(),n(t)}))})),e.tokenPromise)}}))).actions((e=>{let t;return{addMessageChannel(e,n){t=t=>{this.finishOAuthWindow(t,e,n)},window.addEventListener("message",t)},deleteMessageChannel(){window.removeEventListener("message",t)},finishOAuthWindow(t,n,r){if(t.data.name!==`JBrowseAuthWindow-${e.internetAccountId}`)return;const o=t.data.redirectUri.replace("#","?"),i=new URL(o),a=new URLSearchParams(i.search).get("access_token");this.deleteMessageChannel(),a?(e.storeToken(a),e.setRole(),n(a)):r(new Error("Error with token endpoint"))},async openAuthWindow(t,n,r){const i=o.isElectron?"http://localhost/auth":globalThis.location.origin+globalThis.location.pathname,a=new URL("auth/login",e.baseURL),s=new URLSearchParams({type:t,redirect_uri:i});a.search=s.toString();const l=`JBrowseAuthWindow-${e.internetAccountId}`;if(o.isElectron){const{ipcRenderer:t}=globalThis.require("electron"),o=await t.invoke("openAuthWindow",{internetAccountId:e.internetAccountId,data:{redirect_uri:i},url:a.toString()}),s=new MessageEvent("message",{data:{name:l,redirectUri:o}});this.finishOAuthWindow(s,n,r)}else this.addMessageChannel(n,r),window.open(a,l,"width=500,height=600")}}})).actions((e=>({async getTokenFromUser(t,n){const{baseURL:r}=e,o=await new Promise(((t,n)=>{const{session:r}=l.getRoot(e),{baseURL:o,name:i}=e;r.queueDialog((e=>[Cc,{name:i,handleClose:r=>{r?r instanceof Error?n(r):t(r):n(new Error("user cancelled entry")),e()},baseURL:o}]))}));if(o.needsPopup)return void e.openAuthWindow(o.name,t,n);const i=new URL("auth/login",r),a=new URLSearchParams({type:o.name});i.search=a.toString();const s=i.toString(),c=await fetch(s,{signal:e.controller.signal});if(!c.ok){const e=await dl(c,"Error when logging in");return void n(new Error(e))}const{token:u}=await c.json();t(u)}}))).volatile((()=>({lastChangeSequenceNumber:void 0}))).actions((e=>({setLastChangeSequenceNumber(t){e.lastChangeSequenceNumber=t}}))).actions((e=>({updateLastChangeSequenceNumber:l.flow((function*(){const{baseURL:t}=e,n=new URL("changes",t),r=new URLSearchParams({limit:"1"});n.search=r.toString();const o=n.toString(),i=e.getFetcher({locationType:"UriLocation",uri:o});let a;try{a=yield i(o,{method:"GET",signal:e.controller.signal})}catch(t){return void(e.controller.signal.aborted||console.error(t))}if(!a.ok){const e=yield dl(a,"Error when fetching server LastChangeSequence");throw new Error(e)}const{changes:s}=yield a.json();e.setLastChangeSequenceNumber(s.length>0?s[0].sequence:0)})),getMissingChanges:l.flow((function*(){const{session:t}=l.getRoot(e),{changeManager:n}=t.apolloDataStore;if(!e.lastChangeSequenceNumber)throw new Error("No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server");const{baseURL:r,lastChangeSequenceNumber:o}=e,i=new URL("changes",r),a=new URLSearchParams({since:String(o),sort:"1"});i.search=a.toString();const s=i.toString(),c=e.getFetcher({locationType:"UriLocation",uri:s});let u;try{u=yield c(s,{method:"GET",signal:e.controller.signal})}catch(t){return void(e.controller.signal.aborted||console.error(t))}if(!u.ok)return void console.error(`Error when fetching the last updates to recover socket connection — ${u.status}`);const{changes:d}=yield u.json();for(const e of d){const t=ee.fromJSON(e);n.submit(t,{submitToBackend:!1})}}))}))).volatile((e=>{const{origin:t,pathname:n}=new URL("socket.io/",e.baseURL);return{socket:so(t,{path:n})}})).actions((e=>({addSocketListeners(){const{session:t}=l.getRoot(e),{notify:n}=t,r=e.retrieveToken();if(!r)throw new Error("No Token found");const o=sn(ln(r)),{socket:i}=e,{addCheckResult:a,changeManager:s,deleteCheckResult:c}=t.apolloDataStore;i.on("connect",(()=>{e.getMissingChanges()})),i.on("connect_error",(e=>{console.error(e),n("Could not connect to the Apollo server.","error")})),i.on("COMMON",(e=>{if("checkResult"in e)return void(e.deleted?c(e.checkResult._id):a(e.checkResult));if(sessionStorage.setItem("LastChangeSequence",String(e.changeSequence)),e.userSessionId===o)return;const t=ee.fromJSON(e.changeInfo);s.submit(t,{submitToBackend:!1})})),i.on("USER_LOCATION",(e=>{const{channel:n,locations:r,userName:i,userSessionId:a}=e;"USER_LOCATION"===n&&a!==o&&t.addOrUpdateCollaborator({name:i,id:a,locations:r})})),i.on("REQUEST_INFORMATION",(e=>{const{channel:n,userSessionId:o}=e;"REQUEST_INFORMATION"===n&&o!==r&&t.broadcastLocations()}))}}))).actions((e=>({postUserLocation:(t=>{let n;return t=>{clearTimeout(n),n=setTimeout((()=>{!async function(t){if(!l.isAlive(e)||"none"===e.role)return;const{baseURL:n,controller:r}=e,o=new URL("users/userLocation",n).href,i=new URLSearchParams(JSON.stringify(t)),a=e.getFetcher({locationType:"UriLocation",uri:o});try{if(!(await a(o,{method:"POST",body:i,signal:r.signal})).ok)throw new Error("ignore")}catch{console.error("Broadcasting user location failed")}}(t)}),300)}})()}))).volatile((()=>({roleNotificationSent:!1}))).actions((e=>{function t(){e.postUserLocation([])}function n(){if("hidden"===document.visibilityState&&e.postUserLocation([]),"visible"===document.visibilityState){const{session:t}=l.getRoot(e);t.broadcastLocations()}}return{initialize:l.flow((function*(r){if("none"===r){if(!e.roleNotificationSent){const{session:t}=l.getRoot(e);t.notify("You have registered as an Apollo user but have not been given access. Ask your administrator to enable access for your account.","warning"),e.roleNotificationSent=!0}return}if("admin"===r){const t=l.getRoot(e);o.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Admin",type:"subMenu",icon:lo,subMenu:[{label:"Add Assembly",icon:Ln,onClick:e=>{e.queueDialog((t=>[gl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Delete Assembly",icon:co,onClick:e=>{e.queueDialog((t=>[El,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Import Features",icon:uo,onClick:e=>{e.queueDialog((t=>[Jl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[lc,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add Assembly aliases",onClick:e=>{e.queueDialog((t=>[yl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Users",icon:fo,onClick:e=>{e.queueDialog((t=>[Zl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Checks",icon:ho,onClick:e=>{e.queueDialog((t=>[Yl,{session:e,handleClose:()=>{t()}}]))}}]})}(t)}yield e.updateLastChangeSequenceNumber(),e.addSocketListeners();const{baseURL:i}=e,a=new URL("users/locations",i).href,s=e.getFetcher({locationType:"UriLocation",uri:a});yield s(a,{method:"GET",signal:e.controller.signal}),window.addEventListener("beforeunload",t),document.addEventListener("visibilitychange",n)})),removeBeforeUnloadListener(){window.removeEventListener("beforeunload",t)},removeVisibilityChangeListener(){document.removeEventListener("visibilitychange",n)}}})).actions((e=>({afterAttach(){e.setRole(),c.autorun((async t=>{if(Ac)return;const{session:n}=l.getRoot(e);if(n&&e.role)try{await e.initialize(e.role),t.dispose()}catch{}}),{name:"ApolloInternetAccount"})},beforeDestroy(){e.removeBeforeUnloadListener(),e.removeVisibilityChangeListener(),e.controller.abort(new DOMException("Cleaning up Apollo connection","AbortError")),e.socket.close()}})));var Nc=function(){return crypto.getRandomValues(new Uint8Array(arguments.length>0&&void 0!==arguments[0]?arguments[0]:21)).reduce((function(e,t){return e+((t&=63)<36?t.toString(36):t<62?(t-26).toString(36).toUpperCase():t>62?"-":"_")}),"")};const Tc="undefined"==typeof sessionStorage;class Rc extends _.BaseAdapter{refNameAliasesP;async getRefNameAliases(){if(this.refNameAliasesP)return this.refNameAliasesP;const e=n.readConfObject(this.config,"assemblyId");if(!Tc){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e);if(!n)throw new Error("No backend driver found");return await n.getRefNameAliases(e)}const t=new Promise(((t,n)=>{const r=setTimeout((()=>{n(new Error("timeout"))}),2e4),o=Nc(),i=e=>{const n=e.data;(function(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo&&"refNameAliases"in e})(n)&&n.messageId===o&&(clearTimeout(r),removeEventListener("message",i),t(n.refNameAliases))};addEventListener("message",i),rpcServer.emit("apollo",{apollo:!0,method:"getRefNameAliases",assembly:e,messageId:o})}));return this.refNameAliasesP=t,t}freeResources(){}}var Ec=n.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function Ic(e){return"uniqueId"in e&&"object"!==K(e.data)}var jc=function(){function e(t){var n=this;R(this,e),D(this,"data",void 0),D(this,"subfeatures",void 0),D(this,"parentHandle",void 0),D(this,"uniqueId",void 0),Ic(t)?this.data=t:(this.data=t.data,this.parentHandle=t.parent);var r,o=Ic(t)?t.uniqueId:t.id;if(null==o)throw new Error("SimpleFeature requires a unique `id` or `data.uniqueId` attribute");if(this.uniqueId=String(o),!(this.data.aliases||this.data.end-this.data.start>=0))throw new Error("invalid feature data, end less than start. end: ".concat(this.data.end," start: ").concat(this.data.start));this.data.subfeatures&&(this.subfeatures=null===(r=this.data.subfeatures)||void 0===r?void 0:r.map((function(t,r){return"function"!=typeof t.get?new e({id:t.uniqueId||"".concat(o,"-").concat(r),data:B({strand:n.data.strand},t),parent:n}):t})))}return I(e,[{key:"get",value:function(e){return"subfeatures"===e?this.subfeatures:"parent"===e?this.parent():this.data[e]}},{key:"set",value:function(e,t){this.data[e]=t}},{key:"tags",value:function(){return Object.keys(this.data)}},{key:"id",value:function(){return this.uniqueId}},{key:"parent",value:function(){return this.parentHandle}},{key:"children",value:function(){return this.get("subfeatures")}},{key:"toJSON",value:function(){var e=B(B({},this.data),{},{uniqueId:this.id()}),t=this.parent();t&&(e.parentId=t.id());var n=this.children();return n&&(e.subfeatures=n.map((function(e){return e.toJSON()}))),e}}],[{key:"fromJSON",value:function(t){return new e(B({},t))}}])}();function Dc(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo}const Oc="undefined"==typeof sessionStorage;class Fc extends _.BaseSequenceAdapter{regions;async getRefNames(){return(await this.getRegions()).map((e=>e.refName))}async getRegions(){if(this.regions)return this.regions;const e=n.readConfObject(this.config,"assemblyId");if(!Oc){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e);if(!n)throw new Error("No backend driver found");const r=await n.getRegions(e);return this.regions=r,r}const t=await new Promise(((t,n)=>{const r=setTimeout((()=>{n("timeout")}),2e4),o=Nc(),i=e=>{const{data:n}=e;Dc(n)&&n.messageId===o&&(clearTimeout(r),removeEventListener("message",i),t(n.regions))};addEventListener("message",i),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getRegions",assembly:e,messageId:o})}));return this.regions=t,t}getFeatures(e){const{end:t,refName:r,start:o}=e,i=n.readConfObject(this.config,"assemblyId"),a={...e,assemblyName:i};return v.ObservableCreate((async e=>{if(!Oc){const n=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!n)return void e.error("No Apollo data store found");const s=n.getBackendDriver(i);if(!s)return void e.error("No backend driver found");const l=(await s.getRegions(a.assemblyName)).find((e=>e.refName===a.refName));if(!l)return void e.error("Cannot get region");a.end>l.end&&(a.end=l.end);const{seq:c}=await s.getSequence(a);return e.next(new jc({id:`${r} ${o}-${t}`,data:{refName:r,start:o,end:t,seq:c}})),void e.complete()}const n=await new Promise(((e,t)=>{const n=setTimeout((()=>{t("timeout")}),2e4),r=Nc(),o=t=>{const{data:i}=t;Dc(i)&&i.messageId===r&&(clearTimeout(n),removeEventListener("message",o),e(i.sequence))};addEventListener("message",o),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getSequence",region:a,messageId:r})}));e.next(new jc({id:`${r} ${o}-${t}`,data:{refName:r,start:o,end:t,seq:n}})),e.complete()}))}freeResources(){}}var Mc=n.ConfigurationSchema("ApolloSequenceAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0}),Lc=function(){return I((function e(t){R(this,e),D(this,"label",void 0),D(this,"renderingComponent",void 0),D(this,"displayString",void 0),D(this,"matchedAttribute",void 0),D(this,"matchedObject",void 0),D(this,"textSearchAdapter",void 0),D(this,"relevance",void 0),D(this,"trackId",void 0),D(this,"score",void 0),D(this,"locString",void 0),D(this,"results",void 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r.BaseDisplay.named("BaseLinearApolloReferenceSequenceDisplay").props({type:l.types.literal("LinearApolloReferenceSequenceDisplay"),configuration:n.ConfigurationReference(t),showStartCodons:!1,showStopCodons:!0,highContrast:!1,heightPreConfig:l.types.maybe(l.types.refinement("displayHeight",l.types.number,(e=>e>=20))),sequenceRowHeight:15}).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...b.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get lgv(){return o.getContainingView(e)}}))).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get session(){return o.getSession(e)},get regions(){return e.lgv.dynamicBlocks.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:r})=>({assemblyName:e,refName:n,start:Math.round(r),end:Math.round(t)})))},regionCannotBeRendered(){if(e.lgv&&e.lgv.bpPerPx>3)return"Zoom in to see sequence"}}))).views((e=>({get expandedRegions(){return 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e.lgv.bpPerPx<=1?8*t:6*t}}))).volatile((()=>({scrollTop:0}))).actions((e=>({setScrollTop(t){e.scrollTop=t},setHeight:t=>(e.heightPreConfig=Math.max(t,20),e.height),resizeHeight(t){const n=e.height;return this.setHeight(e.height+t)-n},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleHighContrast(){e.highContrast=!e.highContrast}}))).views((e=>{const{trackMenuItems:t}=e;return{trackMenuItems(){const{showStartCodons:n,showStopCodons:r,highContrast:o}=e;return[...t(),{type:"subMenu",label:"Appearance",subMenu:[{label:"Show start codons",type:"checkbox",checked:n,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:r,onClick:()=>{e.toggleShowStopCodons()}},{label:"Use high contrast 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d=e.getContext("2d");if(!d)return;d.clearRect(0,0,e.width,e.height);const{apolloDataStore:f}=u;for(const e of i.contentBlocks){const i=e.offsetPx-r;tf(d,n,t,a,i,e.widthPx,c,e.reversed);const u=f.assemblies.get(e.assemblyName),h=u?.getByRefName(e.refName),p=Math.floor(e.start),g=Math.ceil(e.end);let m=h?.getSequence(p,g);if(!m)return;m=m.toUpperCase(),e.reversed&&(m=o.revcom(m));const y=i-(e.reversed?g-e.end:e.start-p)/n;for(let r=0;r<m.length;r++){const o=e.reversed?g-r:p+r,i=m.slice(r,r+3);nf(d,m[r],r,y,n,c,t),3===i.length&&rf(d,i,y,r,t,a,n,o,c,s,l)}}}(n,r,u,d,f,i,a,s,l,c)}),{name:"LinearApolloReferenceSequenceDisplayRenderSequence"})),l.addDisposer(e,c.autorun((()=>{const{seqTrackOverlayCanvas:t}=e;if(!e.lgv.initialized||e.regionCannotBeRendered()||!t)return;const n=t.getContext("2d");if(!n)return;n.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.height);const{hoveredFeature:r,selectedFeature:o,lgv:i,sequenceRowHeight:a,session:s,theme:l}=e;if(!r&&!o)return;const{bpPerPx:c,dynamicBlocks:u,offsetPx:d}=i;!function(e,t,n,r,o,i,a,s,l,c){const{featureTypeOntology:u}=a.apolloDataStore.ontologyManager;if(!u)throw new Error("featureTypeOntology is undefined");for(const a of c.contentBlocks){t.save(),t.beginPath(),t.rect(a.offsetPx-l,0,a.widthPx,e.height),t.clip();for(const e of[r,n?.feature].filter((e=>void 0!==e)))u.isTypeOf(e.type,"CDS")?Qd(t,e,s,l,o,a,i,e._id===r?._id):Zd(t,e,s,l,o,a,i,e._id===r?._id);t.restore()}}(t,n,r,o,a,l,s,c,d,u)}),{name:"LinearApolloReferenceSequenceDisplayRenderSequenceHighlight"}))}})))}(0,t).named("LinearApolloReferenceSequenceDisplay")}const af=p.observer((function(e){const t=s.useTheme(),{model:n}=e,{height:r,regionCannotBeRendered:a,setSeqTrackCanvas:l,setSeqTrackOverlayCanvas:c,setTheme:d}=n,{classes:f}=$d();u.useEffect((()=>{d(t)}),[t,d]);const h=o.getContainingView(n),p=a();return p?i.jsx(s.Alert,{severity:"warning",classes:{message:f.ellipses},slotProps:{root:{className:f.center}},children:i.jsx(s.Tooltip,{title:p,children:i.jsx("div",{children:p})})}):i.jsx(i.Fragment,{children:3/h.bpPerPx>=1?i.jsxs("div",{className:f.canvasContainer,style:{width:h.dynamicBlocks.totalWidthPx,height:r},children:[i.jsx("canvas",{ref:async e=>{await Promise.resolve(),l(e)},width:h.dynamicBlocks.totalWidthPx,height:r,className:f.canvas,"data-testid":"seqTrackCanvas"}),i.jsx("canvas",{ref:async e=>{await Promise.resolve(),c(e)},width:h.dynamicBlocks.totalWidthPx,height:r,className:f.canvas,"data-testid":"seqTrackOverlayCanvas"})]}):null})})),sf=n.ConfigurationSchema("LinearApolloSixFrameDisplay",{},{explicitIdentifier:"displayId",explicitlyTyped:!0}),lf=p.observer((function({sourceFeature:e,filteredTranscripts:t,handleClose:n,onUpdate:r}){const o=[];if(e.children)for(const[,t]of e.children){const e=t.attributes.get("gff_id")?.toString();e&&o.push(e)}const[a,l]=u.useState(t);return i.jsx(Bs,{open:!0,maxWidth:!1,"data-testid":"filter-transcripts-dialog",title:"Filter transcripts by ID",handleClose:n,children:i.jsxs(s.DialogContent,{children:[i.jsx(s.DialogContentText,{children:"Select the alternate transcripts you want to display in the apollo track"}),i.jsx(s.Grid,{container:!0,spacing:2,children:i.jsx(s.Grid,{size:8,children:i.jsx(s.FormGroup,{children:o.map((e=>i.jsx(s.FormControlLabel,{control:i.jsx(s.Checkbox,{checked:!a.includes(e),onChange:()=>{(e=>{const 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n=o.getSession(e);o.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.addJob(t))},done(t){const n=o.getSession(e);o.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.removeJob(t.name),e.jobStatusWidget.addFinishedJob({name:t.name,statusMessage:"All operations successful",progressPct:100,cancelCallback:t.cancelCallback}))}})));function eh(e){const t={};if(e.children)for(const n of Object.values(e.children)){const e=eh(n);t[e._id]=e}return{...e,_id:(new at).toHexString(),children:e.children?t:void 0}}function th({assemblyName:e,changeManager:t,existingFeature:n,featureSnapshot:r,handleClose:o}){const[a,l]=u.useState("keepExisting"),[c,d]=u.useState(""),[f,h]=u.useState(!1);return i.jsxs(Bs,{open:!0,title:"Duplicate Feature Detected",handleClose:o,maxWidth:"sm",fullWidth:!0,children:[i.jsxs(s.DialogContent,{children:[i.jsxs(s.DialogContentText,{children:["A feature with ID “",r._id,"” already exists. How would you like to resolve this conflict?"]}),i.jsxs(s.FormControl,{component:"fieldset",sx:{mt:2},children:[i.jsx(s.FormLabel,{component:"legend",children:"Resolution"}),i.jsxs(s.RadioGroup,{value:a,onChange:e=>{l(e.target.value)},children:[i.jsx(s.FormControlLabel,{value:"keepExisting",control:i.jsx(s.Radio,{}),label:"Keep the existing feature"}),i.jsx(s.FormControlLabel,{value:"useNew",control:i.jsx(s.Radio,{}),label:"Replace with the new feature"}),i.jsx(s.FormControlLabel,{value:"keepBoth",control:i.jsx(s.Radio,{}),label:"Keep both (assign new IDs to the incoming feature)"})]})]}),c?i.jsx(s.DialogContentText,{color:"error",sx:{mt:1},children:c}):null]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{variant:"contained",onClick:async()=>{d(""),h(!0);try{if("useNew"===a){const o=new pt({typeName:"DeleteFeatureChange",assembly:e,changedIds:[n._id],deletedFeature:n});await t.submit(o);const i=new ht({typeName:"AddFeatureChange",assembly:e,changedIds:[r._id],addedFeature:r});await t.submit(i)}else if("keepBoth"===a){const n=eh(r),o=new ht({typeName:"AddFeatureChange",assembly:e,changedIds:[n._id],addedFeature:n});await t.submit(o)}o()}catch(e){d(String(e)),h(!1)}},disabled:f,children:"Confirm"}),i.jsx(s.Button,{onClick:o,disabled:f,children:"Cancel"})]})]})}function nh(e,t){const r=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",cu),i=function(e){return l.types.model("ClientDataStore",{typeName:l.types.optional(l.types.literal("Client"),"Client"),assemblies:l.types.map(fu),checkResults:l.types.map(hu),ontologyManager:l.types.optional(Os,{})}).views((t=>({get internetAccounts(){return l.getRoot(t).internetAccounts},get pluginConfiguration(){return l.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>l.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const r={_id:t,refSeqs:{}};return n&&(r.backendDriverType=n),e.assemblies.put(r)}}))).actions((e=>({addFeature(t,n){const r=o.getSession(e),{assemblyManager:i}=r;let a=e.assemblies.get(t);if(!a){if(!i.get(t))throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);a=e.addAssembly(t)}let s=a.refSeqs.get(n.refSeq);if(!s){const e=i.get(t);if(!e)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const r=e.getCanonicalRefName(n.refSeq);if(!r)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);s=a.addRefSeq(n.refSeq,r)}s.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:r,parent:o}=n;o?o.deleteChild(t):l.getParentOfType(n,du).deleteFeature(r)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)},clearCheckResults(){e.checkResults.clear()}}))).volatile((e=>({changeManager:new Al(e),collaborationServerDriver:new kl(e),localDriver:new Sl(e)}))).actions((e=>({afterCreate(){l.addDisposer(e,c.autorun((()=>{const{ontologyManager:t,pluginConfiguration:r}=e,i=r.ontologies;for(const r of i||[]){const[i,a,s,l]=[n.readConfObject(r,"name"),n.readConfObject(r,"version"),n.readConfObject(r,"source"),n.readConfObject(r,"textIndexFields")];if(!t.findOntology(i)){const n=o.getSession(e),{jobsManager:r}=n,c=new AbortController,u=`Loading ontology "${i}"`,d={name:u,statusMessage:`Loading ontology "${i}", version "${a}", this may take a while`,progressPct:0,cancelCallback:()=>{c.abort(new DOMException(`Canceling loading of ontology "${i}"`,"AbortError")),r.abortJob(d.name)}};t.addOntology(i,a,s,{textIndexing:{indexFields:l},update:(e,t)=>{0!==t?100!==t?r.update(u,e,t):r.done(d):r.runJob(d)}})}}})))}}))).views((e=>({getBackendDriver(t){const r=o.getSession(e),{assemblyManager:i}=r,a=i.get(t);if(!a)return;const{internetAccountConfigId:s}=n.getConf(a,["sequence","metadata"]);return s?e.collaborationServerDriver:e.localDriver},getInternetAccount(t,r){if(!(t??r))throw new Error("Must provide either assemblyName or internetAccountId");let i=r;if(t&&!i){const{assemblyManager:r}=o.getSession(e),a=r.get(t);if(!a)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:i}=n.getConf(a,["sequence","metadata"]))}const{internetAccounts:a}=e,s=a.find((e=>e.internetAccountId===i));if(!s)throw new Error(`No InternetAccount found with config id ${r}`);return s}}))).actions((e=>({loadFeatures:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[r,o]=yield t.getFeatures(n);if(0===r.length)continue;const{assemblyName:i,refName:a}=n,s=e.assemblies.get(i)??e.assemblies.put({_id:i,refSeqs:{}}),[l]=r,c=s.refSeqs.get(l.refSeq)??s.refSeqs.put({_id:l.refSeq,name:a,features:{}});for(const e of r)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:r,seq:o}=yield t.getSequence(n),{assemblyName:i,end:a,refName:s,start:l}=n,c=e.assemblies.get(i)??e.assemblies.put({_id:i,refSeqs:{}});(c.refSeqs.get(r)??c.refSeqs.put({_id:r,name:s,sequence:[]})).addSequence({start:l,stop:a,sequence:o})}}))})))}(r),a=t.props({apolloDataStore:l.types.optional(i,{typeName:"Client"}),apolloSelectedFeature:l.types.safeReference(r),jobsManager:l.types.optional(Qf,{}),isLocked:l.types.optional(l.types.boolean,!1),changeInProgress:l.types.optional(l.types.boolean,!1)}).volatile((()=>({apolloHoveredFeature:void 0,abortController:new AbortController}))).extend((()=>{const e=c.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},apolloSetHoveredFeature(t){e.apolloHoveredFeature=t},addApolloLocalTrackConfig(t){const n=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===n))||l.getRoot(e).jbrowse.addTrackConf({type:"ApolloTrack",trackId:n,name:`Annotations (${t.displayName})`,assemblyNames:[t.name],category:["Apollo"]})},toggleLocked(){e.isLocked=!e.isLocked},setChangeInProgress(t){e.changeInProgress=t},getPluginConfiguration(){const{jbrowse:t}=l.getRoot(e);return t.configuration.ApolloPlugin},broadcastLocations(){const{internetAccounts:t}=l.getRoot(e),n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const r=t;if(r.initialized){const{dynamicBlocks:t}=r;for(const r of t.contentBlocks){const{assemblyName:t,end:o,refName:i,start:a}=r,s=e.apolloDataStore.assemblies.get(t);"CollaborationServerDriver"===s?.backendDriverType&&n.push({assemblyName:t,refName:i,start:a,end:o})}}}if(0===n.length){for(const e of t)Xl(e)&&e.postUserLocation([]);return}const r=[];for(const e of t)if(Xl(e)){for(const e of n)r.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(r)}}}))).actions((e=>({apolloSetEventualSelectedFeature:c.flow((function*(t){yield c.when((()=>Boolean(e.apolloDataStore.getFeature(t)))),e.apolloSetSelectedFeature(t)}))}))).volatile((e=>({previousSnapshot:l.getSnapshot(e)}))).actions((e=>({afterCreate(){l.applySnapshot(e,{name:e.name,id:e.id});const{internetAccounts:t,jbrowse:r,reloadPluginManagerCallback:o}=l.getRoot(e);l.addDisposer(e,c.autorun((()=>{const n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const r=t;if(r.initialized){const{dynamicBlocks:t}=r;for(const r of t.contentBlocks){const{assemblyName:t,end:o,refName:i,start:a}=r,s=e.apolloDataStore.assemblies.get(t);"CollaborationServerDriver"===s?.backendDriverType&&n.push({assemblyName:t,refName:i,start:a,end:o})}}}if(0===n.length){for(const e of t)Xl(e)&&e.postUserLocation([]);return}const r=[];for(const e of t)if(Xl(e)){for(const e of n)r.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(r)}}),{name:"ApolloSessionBroadcastLocations"})),l.addDisposer(e,c.autorun((async i=>{const a=r.configuration.ApolloPlugin,s=n.readConfObject(a,"hasRole"),c=n.readConfObject(a,"featureTypeOntologyName"),u=t.some((e=>Xl(e))),d=e.assemblyManager.assemblies.filter((e=>!n.getConf(e,["sequence","metadata"]).apollo));if(!u||s){const{assemblies:t}=e.assemblyManager;if(0===t.length)return;const{pluginConfiguration:r}=e.apolloDataStore;r.ontologies.find((e=>n.readConfObject(e,"name")===c))||r.addOntology({name:"Sequence Ontology",version:"01c33c6d9b6c8dca12e7d3e37b49ee113093c2fa",source:{uri:"https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/01c33c6d9b6c8dca12e7d3e37b49ee113093c2fa/Ontology_Files/so.json",locationType:"UriLocation"}});for(const t of d)e.addApolloLocalTrackConfig(t);return l.applySnapshot(e,e.previousSnapshot),void i.dispose()}const{signal:f}=e.abortController;for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:t}=n,r=new URL("jbrowse/config.json",t).href,a=n.getFetcher({locationType:"UriLocation",uri:r});let s,l;try{s=await a(r,{signal:f})}catch(t){e.abortController.signal.aborted||console.error(t);continue}if(s.ok){try{l=await s.json()}catch(e){console.error(e);continue}l.configuration.ApolloPlugin.hasRole&&(o(l,e.previousSnapshot),i.dispose())}else{const e=await dl(s,"Failed to fetch assemblies");console.error(e)}}}),{name:"ApolloSessionLoadConfig"}))},beforeDestroy(){e.abortController.abort(new DOMException("Clean up Apollo session","AbortError"))}}))).actions((e=>({async afterCreate(){if(o.isElectron)return;const t=new URL(globalThis.location.href).searchParams.get("apolloFeatures");if(!t)return;const{assemblyManager:n}=e;await async function(e,t,n,r){const o=function(e){let t=e.replaceAll("-","+").replaceAll("_","/");const n=t.length%4;return n&&(t+="=".repeat(4-n)),t}(e),i=await async function(e){const t=atob(e),n=Uint8Array.from(t,(e=>e.charCodeAt(0))),r=new Blob([n]).stream(),o=new DecompressionStream("gzip"),i=r.pipeThrough(o),a=new Response(i),s=await a.arrayBuffer();return JSON.parse((new TextDecoder).decode(s))}(o);for(const[e,o]of Object.entries(i)){if(!(t.getBackendDriver(e)instanceof Sl))continue;const i=await n.waitForAssembly(e);if(!i)throw new Error(`Assembly not found: "${e}"`);const{regions:a}=i;if(!a)throw new Error(`Assembly not found: "${e}"`);const s=a.map((e=>e.refName)),l=await wl(e,s);for(const n of o){const o=`features-${n.refSeq}`,i=await l.get(o,n._id);if(void 0===i){const r=new ht({typeName:"AddFeatureChange",assembly:e,changedIds:[n._id],addedFeature:n});await t.changeManager.submit(r)}else{const o=JSON.parse(JSON.stringify(i));Ss(n,o)||await new Promise((i=>{r.queueDialog((r=>[th,{featureSnapshot:n,existingFeature:o,assemblyName:e,changeManager:t.changeManager,handleClose:()=>{r(),i()}}]))}))}}}}(t,e.apolloDataStore,n,e),await new Promise((e=>setTimeout(e,2e3)));const r=new URL(globalThis.location.href);r.searchParams.delete("apolloFeatures"),globalThis.history.replaceState(null,"",r.toString())},afterAttach(){l.addDisposer(e,c.autorun((t=>{const{focusedViewId:n,activeWidgets:r}=e;if(!n||!r)return;const o=r.get("hierarchicalTrackSelector");o?.setView(n),t.dispose()})))}}))).views((e=>{const t=e.getTrackActions;return{getTrackActions(r){if("ApolloTrack"===r.type||"ReferenceSequenceTrack"===r.type)return t?.(r);const o=n.readConfObject(r,"trackId");return o.endsWith("-sessionTrack")?[...t?.(r)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:t,jbrowse:n}=l.getRoot(e);let i;i=kt(l.getSnapshot(n)),0===Object.keys(i).length&&(i=void 0);const a={...l.getSnapshot(r),trackId:o.slice(0,o.length-13)};for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const t=new Nt({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:i?.tracks&&[...i.tracks,a]}}),{internetAccountId:r}=n;await e.apolloDataStore.changeManager.submit(t,{internetAccountId:r});const{notify:o}=e;o("Track added","success")}e.deleteTrackConf(r),n.addTrackConf(a)},icon:Zf}]:[...t?.(r)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:t,jbrowse:n}=l.getRoot(e);let i;i=kt(l.getSnapshot(n)),0===Object.keys(i).length&&(i=void 0);const a=i?.tracks?.filter((e=>e.trackId!==o));for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const t=new Nt({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:a}}),{internetAccountId:r}=n;await e.apolloDataStore.changeManager.submit(t,{internetAccountId:r});const{notify:o}=e;o("Track removed","success")}e.deleteTrackConf(r),n.deleteTrackConf(r)},icon:Zf}]}}}));return l.types.snapshotProcessor(a,{postProcessor(e,t){if(e.apolloSelectedFeature=void 0,e.apolloDataStore={typeName:"Client",checkResults:{}},!t)return e;const{apolloDataStore:n}=t,{checkResults:r}=n;for(const[,e]of r){const[t]=e.ids}return e}})}const rh="WorkerGlobalScope"in globalThis;for(const[e,t]of Object.entries(Gt))Q.registerChange(e,t);const oh=new Sn;ne.registerCheck(oh.name,oh);const ih=new Rn;ne.registerCheck(ih.name,ih),Kt.registerValidation(new Xt),Kt.registerValidation(new Zt),e.default=class extends t{name="ApolloPlugin";version="1.1.0";configurationSchema=vf;install(e){!function(e){e.addAdapterType((()=>new y({name:"ApolloSequenceAdapter",configSchema:Mc,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Fc})))}(e),function(e){e.addAdapterType((()=>new y({name:"ApolloRefNameAliasAdapter",configSchema:Ec,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Rc})))}(e),function(e){e.addTextSearchAdapterType((()=>new r.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:qc,AdapterClass:Bc,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new r.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:pu,ReactComponent:su})})),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloTranscriptDetails",{});return new r.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:gu,ReactComponent:Hu})})),e.addTrackType((()=>{const t=n.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:r.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new r.TrackType({name:"ApolloTrack",configSchema:t,stateModel:r.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new r.InternetAccountType({name:"ApolloInternetAccount",configSchema:Pn,stateModel:kc(Pn)}))),e.addDisplayType((()=>new r.DisplayType({name:"LinearApolloDisplay",configSchema:Gu,stateModel:Wd(0,Gu),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Wf}))),e.addDisplayType((()=>new r.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:sf,stateModel:_f(0,sf),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Jf}))),e.addDisplayType((()=>new r.DisplayType({name:"LinearApolloReferenceSequenceDisplay",configSchema:Jd,stateModel:of(0,Jd),displayName:"Apollo reference sequence display",trackType:"ReferenceSequenceTrack",viewType:"LinearGenomeView",ReactComponent:af}))),e.addToExtensionPoint("Core-extendSession",nh.bind(this,e)),e.addToExtensionPoint("Core-extendPluggableElement",(e=>{if("LinearGenomeView"===e.name){const{stateModel:t}=e,n=t.views((e=>{const t=e.rubberBandMenuItems;return{rubberBandMenuItems:()=>[...t(),{label:"Add new feature",icon:Ln,onClick:()=>{const t=o.getSession(e),{leftOffset:n,rightOffset:r}=e,i=e.getSelectedRegions(n,r);t.queueDialog((e=>[Rl,{session:t,handleClose:()=>{e()},region:i[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Nf),e.addToExtensionPoint("Core-extendPluggableElement",Df),e.addToExtensionPoint("Core-preProcessTrackConfig",(e=>{if("ReferenceSequenceTrack"!==e.type)return e;const t=e.displays??[],n=t.findIndex((e=>"LinearApolloReferenceSequenceDisplay"===e.type));if(0===n)return e;if(-1===n)return{...e,displays:[{type:"LinearApolloReferenceSequenceDisplay",displayId:`${e.trackId}-LinearApolloReferenceSequenceDisplay`},...t]};const r=t.toSpliced(n,1);return r.unshift({type:"LinearApolloReferenceSequenceDisplay",displayId:`${e.trackId}-LinearApolloReferenceSequenceDisplay`}),{...e,displays:r}})),e.addToExtensionPoint("LinearGenomeView-searchResultSelected",((e,t)=>{const{session:n,result:r}=t,o=r.getTrackId(),i=r.matchedObject;return o?.startsWith("apollo_track_")&&i&&n.apolloSetEventualSelectedFeature(i._id),e})),rh||e.addToExtensionPoint("Core-extendWorker",(t=>"on"in t.client&&t.client.on?(t.client.on("apollo",(async n=>{if("object"!=typeof(r=n)||null===r||!("apollo"in r)||!0!==r.apollo)return;var r;const{apollo:o,messageId:i,method:a}=n;switch(a){case"getSequence":{const{region:r}=n,{assemblyName:a}=r,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const l=s.getBackendDriver(a);if(!l)break;const{seq:c}=await l.getSequence(r);t.worker.postMessage({apollo:o,messageId:i,sequence:c});break}case"getRegions":{const{assembly:r}=n,a=e.rootModel?.session?.apolloDataStore;if(!a)break;const s=a.getBackendDriver(r);if(!s)break;const l=await s.getRegions(r);t.worker.postMessage({apollo:o,messageId:i,regions:l});break}case"getRefNameAliases":{const{assembly:r}=n,a=e.rootModel?.session?.apolloDataStore;if(!a)break;const s=a.getBackendDriver(r);if(!s)break;const l=await s.getRefNameAliases(r);t.worker.postMessage({apollo:o,messageId:i,refNameAliases:l});break}}})),t):t))}configure(e){o.isAbstractMenuManager(e.rootModel)&&(e.jexl.addFunction("geneBackgroundColor",(e=>"pseudogene"===e?s.alpha("rgb(148, 203, 236)",.6):"ncRNA_gene"===e?s.alpha("rgb(194, 106, 119)",.6):void 0)),function(e){e.insertInMenu("Apollo",{label:"Redo",icon:Yf,onClick(e){const{apolloDataStore:t}=e;t.changeManager.redoLastChange()}},0),e.insertInMenu("Apollo",{label:"Undo",icon:Xf,onClick(e){const{apolloDataStore:t}=e;t.changeManager.undoLastChange()}},0),e.appendToMenu("Apollo",{label:"Lock/Unlock session",onClick:e=>{e.toggleLocked()}});const{internetAccounts:t}=e;t.some((e=>Xl(e)))&&e.appendToMenu("Apollo",{label:"Log out",icon:Kf,onClick:e=>{e.queueDialog((t=>[Kl,{session:e,handleClose:()=>{t()}}]))}})}(e.rootModel))}},Object.defineProperty(e,"__esModule",{value:!0})}));
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports,require("@jbrowse/core/Plugin"),require("@jbrowse/core/configuration"),require("@jbrowse/core/pluggableElementTypes"),require("@jbrowse/core/util"),require("react/jsx-runtime"),require("@mui/material/utils"),require("@mui/material"),require("@jbrowse/mobx-state-tree"),require("mobx"),require("react"),require("@jbrowse/core/util/types/mst"),require("@jbrowse/core/util/io"),require("@jbrowse/core/ui"),require("mobx-react"),require("@mui/material/styles"),require("@mui/x-data-grid"),require("@jbrowse/core/pluggableElementTypes/AdapterType"),require("@jbrowse/core/data_adapters/BaseAdapter"),require("@jbrowse/core/util/rxjs"),require("@jbrowse/core/util/tracks")):"function"==typeof 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R(this,t),D(r=T(this,t,[e,n]),"typeName","FeatureAttributeChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldAttributes:o.oldAttributes,newAttributes:o.newAttributes}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger;return new t({changedIds:W(this.changedIds).reverse(),typeName:"FeatureAttributeChange",changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldAttributes:e.newAttributes,newAttributes:e.oldAttributes}})),assembly:e},{logger:r})}}])}(ft),Ct=["__v","_id","assemblies","configuration","internetAccounts","plugins","tracks"],At=["hasRole"];function kt(e){var t,n=e.assemblies,r=e.configuration,o=e.internetAccounts,i=e.plugins,a=e.tracks,s=q(e,Ct);if(n&&(s.assemblies=n.filter((function(e){return"ApolloSequenceAdapter"!==e.sequence.adapter.type}))),null!=r&&null!==(t=r.ApolloPlugin)&&void 0!==t&&t.hasRole){var l=q(r.ApolloPlugin,At);s.configuration=B(B({},r),{},{ApolloPlugin:l})}return o&&(s.internetAccounts=o.filter((function(e){return"ApolloInternetAccount"!==e.type}))),i&&(s.plugins=i.filter((function(e){return"Apollo"!==e.name}))),a&&(s.tracks=a.filter((function(e){return"ApolloTrack"!==e.type}))),s}var Nt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","ImportJBrowseConfigChange"),D(r,"oldJBrowseConfig",void 0),D(r,"newJBrowseConfig",void 0),r.oldJBrowseConfig=e.oldJBrowseConfig,r.newJBrowseConfig=e.newJBrowseConfig,r}return M(t,e),I(t,[{key:"toJSON",value:function(){return{typeName:this.typeName,oldJBrowseConfig:this.oldJBrowseConfig,newJBrowseConfig:this.newJBrowseConfig}}},{key:"getInverse",value:function(){return new t({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:this.newJBrowseConfig,newJBrowseConfig:this.oldJBrowseConfig},{logger:this.logger})}}])}(ct),Tt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","LocationEndChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldEnd:o.oldEnd,newEnd:o.newEnd}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldEnd:e.newEnd,newEnd:e.oldEnd}})),assembly:e},{logger:r})}}])}(ft);function Rt(e){return"LocationEndChange"===e.typeName}var Et=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","LocationStartChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldStart:o.oldStart,newStart:o.newStart}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldStart:e.newStart,newStart:e.oldStart}})),assembly:e},{logger:r})}}])}(ft);function It(e){return"LocationStartChange"===e.typeName}var jt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","MergeExonsChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"notification",get:function(){return"Exons successfully merged"}},{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,firstExon:o.firstExon,secondExon:o.secondExon,parentFeatureId:o.parentFeatureId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e,t=this.assembly,n=this.changes,r=this.logger,o=W(this.changedIds).reverse(),i=W(n).reverse().map((function(e){return{exonsToRestore:[e.firstExon,e.secondExon],parentFeatureId:e.parentFeatureId}}));return null===(e=r.debug)||void 0===e||e.call(r,"INVERSE CHANGE '".concat(JSON.stringify(i),"'")),new Dt({changedIds:o,typeName:"UndoMergeExonsChange",changes:i,assembly:t},{logger:r})}}])}(ft),Dt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","UndoMergeExonsChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,exonsToRestore:o.exonsToRestore,parentFeatureId:o.parentFeatureId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,t=this.changes,n=this.logger,r=W(this.changedIds).reverse(),o=W(t).reverse().map((function(e){return{firstExon:e.exonsToRestore[0],secondExon:e.exonsToRestore[1],parentFeatureId:e.parentFeatureId}}));return new jt({changedIds:r,typeName:"MergeExonsChange",changes:o,assembly:e},{logger:n})}}])}(ft);function Ot(e,t){for(var n=[],r=0;r<e.length;r+=t){var o=e.slice(r,r+t);n.push(o)}return n}function Ft(e){var t,n,r=e,o=null===(t=r.attributes.get("gff_id"))||void 0===t?void 0:t.join(",");if(o)return"ID=".concat(o," (_id: ").concat(e._id.toString(),")");var i=null===(n=r.attributes.get("gff_name"))||void 0===n?void 0:n.join(",");return i?"Name=".concat(i," (_id: ").concat(e._id.toString(),")"):"_id: ".concat(e._id.toString())}function Mt(e){var t={};if(!e)return t;for(var n=0,r=Object.entries(e);n<r.length;n++){var o=G(r[n],2),i=o[1];t[o[0]]=null==i?void 0:i.slice()}return t}function Lt(e){if(!e)return"";for(var t=[],n=0,r=Object.entries(e);n<r.length;n++){var o=G(r[n],2),i=o[1],a=o[0];a.startsWith("gff_")&&(a=(a=a.slice(4)).charAt(0).toUpperCase()+a.slice(1)),t.push(i?"".concat(a,"=").concat(i.join(",")):a)}return encodeURIComponent(t.join(";"))}var Pt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","MergeTranscriptsChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"notification",get:function(){return"Transcripts successfully merged"}},{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,firstTranscript:o.firstTranscript,secondTranscript:o.secondTranscript,parentFeatureId:o.parentFeatureId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"mergeTranscriptsOnServer",value:function(e,t){e.min=Math.min(e.min,t.min),e.max=Math.max(e.max,t.max);var n=e.attributes?JSON.parse(JSON.stringify(e.attributes)):{};if(t.attributes&&(Object.keys(n).includes("merged_with")||(n.merged_with=[]),n.merged_with.push(Lt(Mt(t.attributes)))),e.attributes=n,t.children)for(var r=0,o=Object.entries(t.children);r<o.length;r++){var i=G(o[r],2);this.mergeFeatureIntoTranscriptOnServer(i[1],e)}}},{key:"mergeFeatureIntoTranscriptOnServer",value:function(e,t){var n,r=this;null!==(n=t.children)&&void 0!==n||(t.children=new Map);var i,a,s,l=!1,c=j(t.children);try{for(c.s();!(s=c.n()).done;){var u=G(s.value,2)[1];if(l&&i?a=!0:(a=!1,i=u),i.type===e.type&&i.type===u.type&&o.doesIntersect2(e.min,e.max,i.min,i.max)&&o.doesIntersect2(u.min,u.max,i.min,i.max)){var d,f;i.min=Math.min(e.min,i.min,u.min),i.max=Math.max(e.max,i.max,u.max),null!==(f=(d=i).attributes)&&void 0!==f||(d.attributes={});var h=JSON.parse(JSON.stringify(i.attributes));Object.keys(h).includes("merged_with")||(h.merged_with=[]);var p=h.merged_with;if(p.push(Lt(Mt(e.attributes))),a){var g=u.attributes?JSON.parse(JSON.stringify(u.attributes)):void 0;p.push(Lt(g)),t.children.delete(u._id.toString())}h.merged_with=W(new Set(p)),i.attributes=h,l=!0}}}catch(e){c.e(e)}finally{c.f()}l&&i&&e.children&&Object.entries(e.children).map((function(e){var t=G(e,2);r.addChild(i,t[1])})),this.addChild(t,l&&i?i:e)}},{key:"mergeTranscriptsOnClient",value:function(e,t){var n,r;e.setMin(Math.min(e.min,t.min)),e.setMax(Math.max(e.max,t.max));var o=null!==(n=null===(r=e.attributes.get("merged_with"))||void 0===r?void 0:r.slice())&&void 0!==n?n:[],i=Lt(Mt(t.attributes));if(o.includes(i)||o.push(i),e.setAttribute("merged_with",o),t.children)for(var a=0,s=Object.entries(t.children);a<s.length;a++){var l=G(s[a],2);this.mergeFeatureIntoTranscriptOnClient(l[1],e)}}},{key:"mergeFeatureIntoTranscriptOnClient",value:function(e,t){var n;null!==(n=t.children)&&void 0!==n||(t.children=new Map);var r,i,a,s=!1,c=j(t.children);try{for(c.s();!(a=c.n()).done;){var u=G(a.value,2)[1];if(s&&r?i=!0:(i=!1,r=u),r.type===e.type&&r.type===u.type&&o.doesIntersect2(e.min,e.max,r.min,r.max)&&o.doesIntersect2(u.min,u.max,r.min,r.max)){var d,f;r.setMin(Math.min(e.min,r.min,u.min)),r.setMax(Math.max(e.max,r.max,u.max));var h=null!==(d=null===(f=r.attributes.get("merged_with"))||void 0===f?void 0:f.slice())&&void 0!==d?d:[];h.push(Lt(Mt(e.attributes))),i&&(h.push(Lt(l.getSnapshot(u).attributes)),t.deleteChild(u._id)),r.setAttribute("merged_with",W(new Set(h))),s=!0}}}catch(e){c.e(e)}finally{c.f()}s&&r&&e.children&&Object.entries(e.children).map((function(e){var t=G(e,2);r.addChild(t[1])})),t.addChild(s&&r?l.getSnapshot(r):e)}},{key:"getInverse",value:function(){var e,t=this.assembly,n=this.changes,r=this.logger,o=W(this.changedIds).reverse(),i=W(n).reverse().map((function(e){return{transcriptsToRestore:[e.firstTranscript,e.secondTranscript],parentFeatureId:e.parentFeatureId}}));return null===(e=r.debug)||void 0===e||e.call(r,"INVERSE CHANGE 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Pt({changedIds:r,typeName:"MergeTranscriptsChange",changes:o,assembly:e},{logger:n})}}])}(ft),qt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","SplitExonChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"notification",get:function(){return"Exon successfully split"}},{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,exonToBeSplit:o.exonToBeSplit,parentFeatureId:o.parentFeatureId,upstreamCut:o.upstreamCut,downstreamCut:o.downstreamCut,leftExonId:o.leftExonId,rightExonId:o.rightExonId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e,t=this.assembly,n=this.changes,r=this.logger,o=W(this.changedIds).reverse(),i=W(n).reverse().map((function(e){return{exonToRestore:e.exonToBeSplit,parentFeatureId:e.parentFeatureId,idsToDelete:[e.leftExonId,e.rightExonId],upstreamCut:e.upstreamCut,downstreamCut:e.downstreamCut,leftExonId:e.leftExonId,rightExonId:e.rightExonId}}));return null===(e=r.debug)||void 0===e||e.call(r,"INVERSE CHANGE '".concat(JSON.stringify(i),"'")),new Ut({changedIds:o,typeName:"UndoSplitExonChange",changes:i,assembly:t},{logger:r})}},{key:"makeSplitExons",value:function(e,t,n,r,o){var i=JSON.parse(JSON.stringify(e));delete i.attributes._id,delete i.attributes.gff_id;var a=structuredClone(i);a._id=r,a.max=t;var s=structuredClone(i);return s.min=n,s._id=o,[a,s]}}])}(ft),Ut=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","UndoSplitExonChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,exonToRestore:o.exonToRestore,parentFeatureId:o.parentFeatureId,idsToDelete:o.idsToDelete,upstreamCut:o.upstreamCut,downstreamCut:o.downstreamCut,leftExonId:o.leftExonId,rightExonId:o.rightExonId}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,t=this.changes,n=this.logger,r=W(this.changedIds).reverse(),o=W(t).reverse().map((function(e){return{parentFeatureId:e.parentFeatureId,exonToBeSplit:e.exonToRestore,upstreamCut:e.upstreamCut,downstreamCut:e.downstreamCut,leftExonId:e.leftExonId,rightExonId:e.rightExonId}}));return new qt({changedIds:r,typeName:"SplitExonChange",changes:o,assembly:e},{logger:n})}}])}(ft),zt=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","StrandChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldStrand:o.oldStrand,newStrand:o.newStrand}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldStrand:e.newStrand,newStrand:e.oldStrand}})),assembly:e},{logger:r})}}])}(ft),$t=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","TypeChange"),D(r,"changes",void 0),r.changes="changes"in e?e.changes:[e],r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.assembly,t=this.changedIds,n=this.changes,r=this.typeName;if(1===n.length){var o=G(n,1)[0];return{typeName:r,changedIds:t,assembly:e,featureId:o.featureId,oldType:o.oldType,newType:o.newType}}return{typeName:r,changedIds:t,assembly:e,changes:n}}},{key:"getInverse",value:function(){var e=this.assembly,n=this.changes,r=this.logger,o=this.typeName;return new t({changedIds:W(this.changedIds).reverse(),typeName:o,changes:W(n).reverse().map((function(e){return{featureId:e.featureId,oldType:e.newType,newType:e.oldType}})),assembly:e},{logger:r})}}])}(ft),Ht=function(e){function t(e,n){var r;return R(this,t),D(r=T(this,t,[e,n]),"typeName","UserChange"),D(r,"changes",void 0),D(r,"userId",void 0),r.changes="changes"in e?e.changes:[e],r.userId=e.userId,r}return M(t,e),I(t,[{key:"toJSON",value:function(){var e=this.changes,t=this.typeName,n=this.userId;return 1===e.length?{typeName:t,userId:n,role:G(e,1)[0].role}:{typeName:t,userId:n,changes:e}}},{key:"getInverse",value:function(){return new t({typeName:this.typeName,changes:this.changes,userId:this.userId},{logger:this.logger})}}])}(ct),Gt=B(B({},{AddFeatureChange:ht,DeleteFeatureChange:pt,FeatureAttributeChange:St,LocationEndChange:Tt,LocationStartChange:Et,MergeExonsChange:jt,SplitExonChange:qt,MergeTranscriptsChange:Pt,UndoMergeExonsChange:Dt,UndoSplitExonChange:Ut,UndoMergeTranscriptsChange:Bt,StrandChange:zt,TypeChange:$t}),{},{AddAssemblyAndFeaturesFromFileChange:mt,AddAssemblyFromFileChange:_t,AddAssemblyFromExternalChange:yt,AddFeaturesFromFileChange:vt,DeleteAssemblyChange:xt,DeleteUserChange:wt,ImportJBrowseConfigChange:Nt,UserChange:Ht,AddRefSeqAliasesChange:bt,AddAssemblyAliasesChange:gt}),Vt=function(){return I((function e(){R(this,e)}),[{key:"frontendPreValidate",value:(o=k(U().m((function e(t){return U().w((function(e){for(;;)if(0===e.n)return e.a(2,{validationName:this.name})}),e,this)}))),function(e){return o.apply(this,arguments)})},{key:"frontendPostValidate",value:(r=k(U().m((function e(t){return 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location&&"https:"===location.protocol,r.hostname&&!r.port&&(r.port=n.secure?"443":"80"),n.hostname=r.hostname||("undefined"!=typeof location?location.hostname:"localhost"),n.port=r.port||("undefined"!=typeof location&&location.port?location.port:n.secure?"443":"80"),n.transports=r.transports||["polling","websocket","webtransport"],n.writeBuffer=[],n.prevBufferLen=0,n.opts=Object.assign({path:"/engine.io",agent:!1,withCredentials:!1,upgrade:!0,timestampParam:"t",rememberUpgrade:!1,addTrailingSlash:!0,rejectUnauthorized:!0,perMessageDeflate:{threshold:1024},transportOptions:{},closeOnBeforeunload:!1},r),n.opts.path=n.opts.path.replace(/\/$/,"")+(n.opts.addTrailingSlash?"/":""),"string"==typeof n.opts.query&&(n.opts.query=function(e){for(var t={},n=e.split("&"),r=0,o=n.length;r<o;r++){var i=n[r].split("=");t[decodeURIComponent(i[0])]=decodeURIComponent(i[1])}return t}(n.opts.query)),n.id=null,n.upgrades=null,n.pingInterval=null,n.pingTimeout=null,n.pingTimeoutTimer=null,"function"==typeof addEventListener&&(n.opts.closeOnBeforeunload&&(n.beforeunloadEventListener=function(){n.transport&&(n.transport.removeAllListeners(),n.transport.close())},addEventListener("beforeunload",n.beforeunloadEventListener,!1)),"localhost"!==n.hostname&&(n.offlineEventListener=function(){n.onClose("transport close",{description:"network connection lost"})},addEventListener("offline",n.offlineEventListener,!1))),n.open(),n}return M(t,e),I(t,[{key:"createTransport",value:function(e){var t=Object.assign({},this.opts.query);t.EIO=4,t.transport=e,this.id&&(t.sid=this.id);var n=Object.assign({},this.opts,{query:t,socket:this,hostname:this.hostname,secure:this.secure,port:this.port},this.opts.transportOptions[e]);return new jr[e](n)}},{key:"open",value:function(){var e,n=this;if(this.opts.rememberUpgrade&&t.priorWebsocketSuccess&&-1!==this.transports.indexOf("websocket"))e="websocket";else{if(0===this.transports.length)return void this.setTimeoutFn((function(){n.emitReserved("error","No transports available")}),0);e=this.transports[0]}this.readyState="opening";try{e=this.createTransport(e)}catch(e){return this.transports.shift(),void this.open()}e.open(),this.setTransport(e)}},{key:"setTransport",value:function(e){var t=this;this.transport&&this.transport.removeAllListeners(),this.transport=e,e.on("drain",this.onDrain.bind(this)).on("packet",this.onPacket.bind(this)).on("error",this.onError.bind(this)).on("close",(function(e){return t.onClose("transport close",e)}))}},{key:"probe",value:function(e){var n=this,r=this.createTransport(e),o=!1;t.priorWebsocketSuccess=!1;var i=function(){o||(r.send([{type:"ping",data:"probe"}]),r.once("packet",(function(e){if(!o)if("pong"===e.type&&"probe"===e.data){if(n.upgrading=!0,n.emitReserved("upgrading",r),!r)return;t.priorWebsocketSuccess="websocket"===r.name,n.transport.pause((function(){o||"closed"!==n.readyState&&(d(),n.setTransport(r),r.send([{type:"upgrade"}]),n.emitReserved("upgrade",r),r=null,n.upgrading=!1,n.flush())}))}else{var i=new Error("probe error");i.transport=r.name,n.emitReserved("upgradeError",i)}})))};function a(){o||(o=!0,d(),r.close(),r=null)}var s=function(e){var t=new Error("probe error: "+e);t.transport=r.name,a(),n.emitReserved("upgradeError",t)};function l(){s("transport closed")}function c(){s("socket closed")}function u(e){r&&e.name!==r.name&&a()}var d=function(){r.removeListener("open",i),r.removeListener("error",s),r.removeListener("close",l),n.off("close",c),n.off("upgrading",u)};r.once("open",i),r.once("error",s),r.once("close",l),this.once("close",c),this.once("upgrading",u),-1!==this.upgrades.indexOf("webtransport")&&"webtransport"!==e?this.setTimeoutFn((function(){o||r.open()}),200):r.open()}},{key:"onOpen",value:function(){if(this.readyState="open",t.priorWebsocketSuccess="websocket"===this.transport.name,this.emitReserved("open"),this.flush(),"open"===this.readyState&&this.opts.upgrade)for(var e=0,n=this.upgrades.length;e<n;e++)this.probe(this.upgrades[e])}},{key:"onPacket",value:function(e){if("opening"===this.readyState||"open"===this.readyState||"closing"===this.readyState)switch(this.emitReserved("packet",e),this.emitReserved("heartbeat"),this.resetPingTimeout(),e.type){case"open":this.onHandshake(JSON.parse(e.data));break;case"ping":this.sendPacket("pong"),this.emitReserved("ping"),this.emitReserved("pong");break;case"error":var t=new Error("server error");t.code=e.data,this.onError(t);break;case"message":this.emitReserved("data",e.data),this.emitReserved("message",e.data)}}},{key:"onHandshake",value:function(e){this.emitReserved("handshake",e),this.id=e.sid,this.transport.query.sid=e.sid,this.upgrades=this.filterUpgrades(e.upgrades),this.pingInterval=e.pingInterval,this.pingTimeout=e.pingTimeout,this.maxPayload=e.maxPayload,this.onOpen(),"closed"!==this.readyState&&this.resetPingTimeout()}},{key:"resetPingTimeout",value:function(){var e=this;this.clearTimeoutFn(this.pingTimeoutTimer),this.pingTimeoutTimer=this.setTimeoutFn((function(){e.onClose("ping timeout")}),this.pingInterval+this.pingTimeout),this.opts.autoUnref&&this.pingTimeoutTimer.unref()}},{key:"onDrain",value:function(){this.writeBuffer.splice(0,this.prevBufferLen),this.prevBufferLen=0,0===this.writeBuffer.length?this.emitReserved("drain"):this.flush()}},{key:"flush",value:function(){if("closed"!==this.readyState&&this.transport.writable&&!this.upgrading&&this.writeBuffer.length){var e=this.getWritablePackets();this.transport.send(e),this.prevBufferLen=e.length,this.emitReserved("flush")}}},{key:"getWritablePackets",value:function(){if(!(this.maxPayload&&"polling"===this.transport.name&&this.writeBuffer.length>1))return this.writeBuffer;for(var e,t=1,n=0;n<this.writeBuffer.length;n++){var r=this.writeBuffer[n].data;if(r&&(t+="string"==typeof(e=r)?function(e){for(var t=0,n=0,r=0,o=e.length;r<o;r++)(t=e.charCodeAt(r))<128?n+=1:t<2048?n+=2:t<55296||t>=57344?n+=3:(r++,n+=4);return n}(e):Math.ceil(1.33*(e.byteLength||e.size))),n>0&&t>this.maxPayload)return this.writeBuffer.slice(0,n);t+=2}return this.writeBuffer}},{key:"write",value:function(e,t,n){return this.sendPacket("message",e,t,n),this}},{key:"send",value:function(e,t,n){return this.sendPacket("message",e,t,n),this}},{key:"sendPacket",value:function(e,t,n,r){if("function"==typeof t&&(r=t,t=void 0),"function"==typeof n&&(r=n,n=null),"closing"!==this.readyState&&"closed"!==this.readyState){(n=n||{}).compress=!1!==n.compress;var o={type:e,data:t,options:n};this.emitReserved("packetCreate",o),this.writeBuffer.push(o),r&&this.once("flush",r),this.flush()}}},{key:"close",value:function(){var e=this,t=function(){e.onClose("forced close"),e.transport.close()},n=function(){e.off("upgrade",n),e.off("upgradeError",n),t()},r=function(){e.once("upgrade",n),e.once("upgradeError",n)};return"opening"!==this.readyState&&"open"!==this.readyState||(this.readyState="closing",this.writeBuffer.length?this.once("drain",(function(){e.upgrading?r():t()})):this.upgrading?r():t()),this}},{key:"onError",value:function(e){t.priorWebsocketSuccess=!1,this.emitReserved("error",e),this.onClose("transport error",e)}},{key:"onClose",value:function(e,t){"opening"!==this.readyState&&"open"!==this.readyState&&"closing"!==this.readyState||(this.clearTimeoutFn(this.pingTimeoutTimer),this.transport.removeAllListeners("close"),this.transport.close(),this.transport.removeAllListeners(),"function"==typeof removeEventListener&&(removeEventListener("beforeunload",this.beforeunloadEventListener,!1),removeEventListener("offline",this.offlineEventListener,!1)),this.readyState="closed",this.id=null,this.emitReserved("close",e,t),this.writeBuffer=[],this.prevBufferLen=0)}},{key:"filterUpgrades",value:function(e){for(var t=[],n=0,r=e.length;n<r;n++)~this.transports.indexOf(e[n])&&t.push(e[n]);return t}}])}(ir);Mr.protocol=4;var Lr="function"==typeof ArrayBuffer,Pr=function(e){return"function"==typeof ArrayBuffer.isView?ArrayBuffer.isView(e):e.buffer instanceof ArrayBuffer},Br=Object.prototype.toString,qr="function"==typeof Blob||"undefined"!=typeof Blob&&"[object BlobConstructor]"===Br.call(Blob),Ur="function"==typeof File||"undefined"!=typeof File&&"[object FileConstructor]"===Br.call(File);function zr(e){return Lr&&(e instanceof ArrayBuffer||Pr(e))||qr&&e instanceof Blob||Ur&&e instanceof File}function $r(e,t){if(!e||"object"!==K(e))return!1;if(Array.isArray(e)){for(var n=0,r=e.length;n<r;n++)if($r(e[n]))return!0;return!1}if(zr(e))return!0;if(e.toJSON&&"function"==typeof e.toJSON&&1===arguments.length)return $r(e.toJSON(),!0);for(var o in e)if(Object.prototype.hasOwnProperty.call(e,o)&&$r(e[o]))return!0;return!1}function Hr(e){var t=[],n=e;return n.data=Gr(e.data,t),n.attachments=t.length,{packet:n,buffers:t}}function Gr(e,t){if(!e)return e;if(zr(e)){var n={_placeholder:!0,num:t.length};return t.push(e),n}if(Array.isArray(e)){for(var r=new Array(e.length),o=0;o<e.length;o++)r[o]=Gr(e[o],t);return r}if("object"===K(e)&&!(e instanceof Date)){var i={};for(var a in e)Object.prototype.hasOwnProperty.call(e,a)&&(i[a]=Gr(e[a],t));return i}return e}function Vr(e,t){return e.data=Wr(e.data,t),delete e.attachments,e}function Wr(e,t){if(!e)return e;if(e&&!0===e._placeholder){if("number"==typeof e.num&&e.num>=0&&e.num<t.length)return t[e.num];throw new Error("illegal attachments")}if(Array.isArray(e))for(var n=0;n<e.length;n++)e[n]=Wr(e[n],t);else if("object"===K(e))for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&(e[r]=Wr(e[r],t));return e}var Jr,Kr=["connect","connect_error","disconnect","disconnecting","newListener","removeListener"];!function(e){e[e.CONNECT=0]="CONNECT",e[e.DISCONNECT=1]="DISCONNECT",e[e.EVENT=2]="EVENT",e[e.ACK=3]="ACK",e[e.CONNECT_ERROR=4]="CONNECT_ERROR",e[e.BINARY_EVENT=5]="BINARY_EVENT",e[e.BINARY_ACK=6]="BINARY_ACK"}(Jr||(Jr={}));var Yr=function(){return I((function e(t){R(this,e),this.replacer=t}),[{key:"encode",value:function(e){return e.type!==Jr.EVENT&&e.type!==Jr.ACK||!$r(e)?[this.encodeAsString(e)]:this.encodeAsBinary({type:e.type===Jr.EVENT?Jr.BINARY_EVENT:Jr.BINARY_ACK,nsp:e.nsp,data:e.data,id:e.id})}},{key:"encodeAsString",value:function(e){var t=""+e.type;return e.type!==Jr.BINARY_EVENT&&e.type!==Jr.BINARY_ACK||(t+=e.attachments+"-"),e.nsp&&"/"!==e.nsp&&(t+=e.nsp+","),null!=e.id&&(t+=e.id),null!=e.data&&(t+=JSON.stringify(e.data,this.replacer)),t}},{key:"encodeAsBinary",value:function(e){var t=Hr(e),n=this.encodeAsString(t.packet),r=t.buffers;return r.unshift(n),r}}])}();function Xr(e){return"[object Object]"===Object.prototype.toString.call(e)}var Zr=function(e){function t(e){var n;return R(this,t),(n=T(this,t)).reviver=e,n}return M(t,e),I(t,[{key:"add",value:function(e){var n;if("string"==typeof e){if(this.reconstructor)throw new Error("got plaintext data when reconstructing a packet");var r=(n=this.decodeString(e)).type===Jr.BINARY_EVENT;r||n.type===Jr.BINARY_ACK?(n.type=r?Jr.EVENT:Jr.ACK,this.reconstructor=new Qr(n),0===n.attachments&&V(t,"emitReserved",this,3)(["decoded",n])):V(t,"emitReserved",this,3)(["decoded",n])}else{if(!zr(e)&&!e.base64)throw new Error("Unknown type: "+e);if(!this.reconstructor)throw new Error("got binary data when not reconstructing a packet");(n=this.reconstructor.takeBinaryData(e))&&(this.reconstructor=null,V(t,"emitReserved",this,3)(["decoded",n]))}}},{key:"decodeString",value:function(e){var n=0,r={type:Number(e.charAt(0))};if(void 0===Jr[r.type])throw new Error("unknown packet type "+r.type);if(r.type===Jr.BINARY_EVENT||r.type===Jr.BINARY_ACK){for(var o=n+1;"-"!==e.charAt(++n)&&n!=e.length;);var i=e.substring(o,n);if(i!=Number(i)||"-"!==e.charAt(n))throw new Error("Illegal attachments");r.attachments=Number(i)}if("/"===e.charAt(n+1)){for(var a=n+1;++n&&","!==e.charAt(n)&&n!==e.length;);r.nsp=e.substring(a,n)}else r.nsp="/";var s=e.charAt(n+1);if(""!==s&&Number(s)==s){for(var l=n+1;++n;){var c=e.charAt(n);if(null==c||Number(c)!=c){--n;break}if(n===e.length)break}r.id=Number(e.substring(l,n+1))}if(e.charAt(++n)){var u=this.tryParse(e.substr(n));if(!t.isPayloadValid(r.type,u))throw new Error("invalid payload");r.data=u}return r}},{key:"tryParse",value:function(e){try{return JSON.parse(e,this.reviver)}catch(e){return!1}}},{key:"destroy",value:function(){this.reconstructor&&(this.reconstructor.finishedReconstruction(),this.reconstructor=null)}}],[{key:"isPayloadValid",value:function(e,t){switch(e){case Jr.CONNECT:return Xr(t);case Jr.DISCONNECT:return void 0===t;case Jr.CONNECT_ERROR:return"string"==typeof t||Xr(t);case Jr.EVENT:case Jr.BINARY_EVENT:return Array.isArray(t)&&("number"==typeof t[0]||"string"==typeof t[0]&&-1===Kr.indexOf(t[0]));case Jr.ACK:case Jr.BINARY_ACK:return Array.isArray(t)}}}])}(ir),Qr=function(){return I((function e(t){R(this,e),this.packet=t,this.buffers=[],this.reconPack=t}),[{key:"takeBinaryData",value:function(e){if(this.buffers.push(e),this.buffers.length===this.reconPack.attachments){var t=Vr(this.reconPack,this.buffers);return this.finishedReconstruction(),t}return null}},{key:"finishedReconstruction",value:function(){this.reconPack=null,this.buffers=[]}}])}(),eo={__proto__:null,Decoder:Zr,Encoder:Yr,get PacketType(){return Jr}};function to(e,t,n){return e.on(t,n),function(){e.off(t,n)}}var no=Object.freeze({connect:1,connect_error:1,disconnect:1,disconnecting:1,newListener:1,removeListener:1}),ro=function(e){function t(e,n,r){var o;return R(this,t),(o=T(this,t)).connected=!1,o.recovered=!1,o.receiveBuffer=[],o.sendBuffer=[],o._queue=[],o._queueSeq=0,o.ids=0,o.acks={},o.flags={},o.io=e,o.nsp=n,r&&r.auth&&(o.auth=r.auth),o._opts=Object.assign({},r),o.io._autoConnect&&o.open(),o}return M(t,e),I(t,[{key:"disconnected",get:function(){return!this.connected}},{key:"subEvents",value:function(){if(!this.subs){var e=this.io;this.subs=[to(e,"open",this.onopen.bind(this)),to(e,"packet",this.onpacket.bind(this)),to(e,"error",this.onerror.bind(this)),to(e,"close",this.onclose.bind(this))]}}},{key:"active",get:function(){return!!this.subs}},{key:"connect",value:function(){return this.connected||(this.subEvents(),this.io._reconnecting||this.io.open(),"open"===this.io._readyState&&this.onopen()),this}},{key:"open",value:function(){return this.connect()}},{key:"send",value:function(){for(var e=arguments.length,t=new Array(e),n=0;n<e;n++)t[n]=arguments[n];return t.unshift("message"),this.emit.apply(this,t),this}},{key:"emit",value:function(e){if(no.hasOwnProperty(e))throw new Error('"'+e.toString()+'" is a reserved event name');for(var t=arguments.length,n=new Array(t>1?t-1:0),r=1;r<t;r++)n[r-1]=arguments[r];if(n.unshift(e),this._opts.retries&&!this.flags.fromQueue&&!this.flags.volatile)return this._addToQueue(n),this;var o={type:Jr.EVENT,data:n,options:{}};if(o.options.compress=!1!==this.flags.compress,"function"==typeof n[n.length-1]){var i=this.ids++,a=n.pop();this._registerAckCallback(i,a),o.id=i}return this.flags.volatile&&(!(this.io.engine&&this.io.engine.transport&&this.io.engine.transport.writable)||!this.connected)||(this.connected?(this.notifyOutgoingListeners(o),this.packet(o)):this.sendBuffer.push(o)),this.flags={},this}},{key:"_registerAckCallback",value:function(e,t){var n,r=this,o=null!==(n=this.flags.timeout)&&void 0!==n?n:this._opts.ackTimeout;if(void 0!==o){var i=this.io.setTimeoutFn((function(){delete r.acks[e];for(var n=0;n<r.sendBuffer.length;n++)r.sendBuffer[n].id===e&&r.sendBuffer.splice(n,1);t.call(r,new Error("operation has timed out"))}),o);this.acks[e]=function(){r.io.clearTimeoutFn(i);for(var e=arguments.length,n=new Array(e),o=0;o<e;o++)n[o]=arguments[o];t.apply(r,[null].concat(n))}}else this.acks[e]=t}},{key:"emitWithAck",value:function(e){for(var t=this,n=arguments.length,r=new Array(n>1?n-1:0),o=1;o<n;o++)r[o-1]=arguments[o];var i=void 0!==this.flags.timeout||void 0!==this._opts.ackTimeout;return new Promise((function(n,o){r.push((function(e,t){return i?e?o(e):n(t):n(e)})),t.emit.apply(t,[e].concat(r))}))}},{key:"_addToQueue",value:function(e){var t,n=this;"function"==typeof e[e.length-1]&&(t=e.pop());var r={id:this._queueSeq++,tryCount:0,pending:!1,args:e,flags:Object.assign({fromQueue:!0},this.flags)};e.push((function(e){if(r===n._queue[0]){if(null!==e)r.tryCount>n._opts.retries&&(n._queue.shift(),t&&t(e));else if(n._queue.shift(),t){for(var o=arguments.length,i=new Array(o>1?o-1:0),a=1;a<o;a++)i[a-1]=arguments[a];t.apply(void 0,[null].concat(i))}return r.pending=!1,n._drainQueue()}})),this._queue.push(r),this._drainQueue()}},{key:"_drainQueue",value:function(){if(this.connected&&0!==this._queue.length){var e=this._queue[0];e.pending&&!(arguments.length>0&&void 0!==arguments[0]&&arguments[0])||(e.pending=!0,e.tryCount++,this.flags=e.flags,this.emit.apply(this,e.args))}}},{key:"packet",value:function(e){e.nsp=this.nsp,this.io._packet(e)}},{key:"onopen",value:function(){var e=this;"function"==typeof this.auth?this.auth((function(t){e._sendConnectPacket(t)})):this._sendConnectPacket(this.auth)}},{key:"_sendConnectPacket",value:function(e){this.packet({type:Jr.CONNECT,data:this._pid?Object.assign({pid:this._pid,offset:this._lastOffset},e):e})}},{key:"onerror",value:function(e){this.connected||this.emitReserved("connect_error",e)}},{key:"onclose",value:function(e,t){this.connected=!1,delete this.id,this.emitReserved("disconnect",e,t)}},{key:"onpacket",value:function(e){if(e.nsp===this.nsp)switch(e.type){case Jr.CONNECT:e.data&&e.data.sid?this.onconnect(e.data.sid,e.data.pid):this.emitReserved("connect_error",new Error("It seems you are trying to reach a Socket.IO server in v2.x with a v3.x client, but they are not compatible (more information here: https://socket.io/docs/v3/migrating-from-2-x-to-3-0/)"));break;case Jr.EVENT:case Jr.BINARY_EVENT:this.onevent(e);break;case Jr.ACK:case Jr.BINARY_ACK:this.onack(e);break;case Jr.DISCONNECT:this.ondisconnect();break;case Jr.CONNECT_ERROR:this.destroy();var t=new Error(e.data.message);t.data=e.data.data,this.emitReserved("connect_error",t)}}},{key:"onevent",value:function(e){var t=e.data||[];null!=e.id&&t.push(this.ack(e.id)),this.connected?this.emitEvent(t):this.receiveBuffer.push(Object.freeze(t))}},{key:"emitEvent",value:function(e){if(this._anyListeners&&this._anyListeners.length){var n,r=j(this._anyListeners.slice());try{for(r.s();!(n=r.n()).done;)n.value.apply(this,e)}catch(e){r.e(e)}finally{r.f()}}V(t,"emit",this,1).apply(this,e),this._pid&&e.length&&"string"==typeof e[e.length-1]&&(this._lastOffset=e[e.length-1])}},{key:"ack",value:function(e){var t=this,n=!1;return function(){if(!n){n=!0;for(var r=arguments.length,o=new Array(r),i=0;i<r;i++)o[i]=arguments[i];t.packet({type:Jr.ACK,id:e,data:o})}}}},{key:"onack",value:function(e){var t=this.acks[e.id];"function"==typeof t&&(t.apply(this,e.data),delete this.acks[e.id])}},{key:"onconnect",value:function(e,t){this.id=e,this.recovered=t&&this._pid===t,this._pid=t,this.connected=!0,this.emitBuffered(),this.emitReserved("connect"),this._drainQueue(!0)}},{key:"emitBuffered",value:function(){var e=this;this.receiveBuffer.forEach((function(t){return e.emitEvent(t)})),this.receiveBuffer=[],this.sendBuffer.forEach((function(t){e.notifyOutgoingListeners(t),e.packet(t)})),this.sendBuffer=[]}},{key:"ondisconnect",value:function(){this.destroy(),this.onclose("io server disconnect")}},{key:"destroy",value:function(){this.subs&&(this.subs.forEach((function(e){return e()})),this.subs=void 0),this.io._destroy(this)}},{key:"disconnect",value:function(){return this.connected&&this.packet({type:Jr.DISCONNECT}),this.destroy(),this.connected&&this.onclose("io client disconnect"),this}},{key:"close",value:function(){return this.disconnect()}},{key:"compress",value:function(e){return this.flags.compress=e,this}},{key:"volatile",get:function(){return this.flags.volatile=!0,this}},{key:"timeout",value:function(e){return this.flags.timeout=e,this}},{key:"onAny",value:function(e){return this._anyListeners=this._anyListeners||[],this._anyListeners.push(e),this}},{key:"prependAny",value:function(e){return this._anyListeners=this._anyListeners||[],this._anyListeners.unshift(e),this}},{key:"offAny",value:function(e){if(!this._anyListeners)return this;if(e){for(var t=this._anyListeners,n=0;n<t.length;n++)if(e===t[n])return t.splice(n,1),this}else this._anyListeners=[];return this}},{key:"listenersAny",value:function(){return this._anyListeners||[]}},{key:"onAnyOutgoing",value:function(e){return this._anyOutgoingListeners=this._anyOutgoingListeners||[],this._anyOutgoingListeners.push(e),this}},{key:"prependAnyOutgoing",value:function(e){return this._anyOutgoingListeners=this._anyOutgoingListeners||[],this._anyOutgoingListeners.unshift(e),this}},{key:"offAnyOutgoing",value:function(e){if(!this._anyOutgoingListeners)return this;if(e){for(var 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34:this.$=a[l]}},table:[{3:1,4:[1,2],6:3,13:4,15:[1,5],16:[1,6],17:[1,7],18:[1,8],19:[1,9]},{1:[3]},{1:[2,1],5:10,7:11,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,3],5:21,7:11,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,12],12:[2,12],14:[2,12],22:[2,12]},{1:[2,14],12:[2,14],14:[2,14],22:[2,14]},{1:[2,15],12:[2,15],14:[2,15],22:[2,15]},{1:[2,16],12:[2,16],14:[2,16],22:[2,16]},{1:[2,17],12:[2,17],14:[2,17],22:[2,17]},{1:[2,18],12:[2,18],14:[2,18],22:[2,18]},{1:[2,2],7:22,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,5],12:[2,5],14:[2,5],22:[2,5]},{1:[2,7],12:[2,7],14:[2,7],22:[2,7]},{1:[2,8],12:[2,8],14:[2,8],22:[2,8]},{1:[2,9],12:[2,9],14:[2,9],22:[2,9]},{1:[2,10],12:[2,10],14:[2,10],22:[2,10]},{1:[2,19],12:[2,19],14:[2,19],22:[2,19]},{1:[2,20],12:[2,20],14:[2,20],22:[2,20]},{13:23,15:[1,5],16:[1,6],17:[1,7],18:[1,8],19:[1,9]},{13:24,15:[1,5],16:[1,6],17:[1,7],18:[1,8],19:[1,9],22:[1,25]},{15:[1,29],17:[1,30],18:[1,33],23:26,25:27,26:28,27:32,29:34,30:[1,35],31:[1,31],32:[1,36],33:[1,37]},{1:[2,4],7:22,8:12,9:13,10:14,11:15,12:[1,18],14:[1,19],20:16,21:17,22:[1,20]},{1:[2,6],12:[2,6],14:[2,6],22:[2,6]},{1:[2,11],12:[2,11],14:[2,11],22:[2,11]},{1:[2,13],12:[2,13],14:[2,13],22:[2,13]},{15:[1,29],17:[1,30],18:[1,33],23:38,25:27,26:28,27:32,29:34,30:[1,35],31:[1,31],32:[1,36],33:[1,37]},{24:[1,39]},{24:[2,23]},{24:[2,24],28:[1,40]},{24:[2,30]},{24:[2,31]},{24:[2,32]},{24:[2,25],28:[2,25]},{24:[2,27],28:[2,27]},{24:[2,28],28:[2,28]},{24:[2,29],28:[2,29]},{24:[2,33],28:[2,33]},{24:[2,34],28:[2,34]},{24:[1,41]},{1:[2,21],12:[2,21],14:[2,21],22:[2,21]},{18:[1,33],27:42,29:34,30:[1,35],32:[1,36],33:[1,37]},{1:[2,22],12:[2,22],14:[2,22],22:[2,22]},{24:[2,26],28:[2,26]}],defaultActions:{27:[2,23],29:[2,30],30:[2,31],31:[2,32]},parseError:function(e,t){if(!t.recoverable)throw new Error(e);this.trace(e)},parse:function(e){var t=this,n=[0],r=[null],o=[],i=this.table,a="",s=0,l=0,c=o.slice.call(arguments,1);this.lexer.setInput(e),this.lexer.yy=this.yy,this.yy.lexer=this.lexer,this.yy.parser=this,void 0===this.lexer.yylloc&&(this.lexer.yylloc={});var u=this.lexer.yylloc;o.push(u);var d=this.lexer.options&&this.lexer.options.ranges;function f(){var e;return"number"!=typeof(e=t.lexer.lex()||1)&&(e=t.symbols_[e]||e),e}this.parseError="function"==typeof this.yy.parseError?this.yy.parseError:Object.getPrototypeOf(this).parseError;for(var h,p,g,m,y,_,v,b={};;){if(this.defaultActions[p=n[n.length-1]]?g=this.defaultActions[p]:(null==h&&(h=f()),g=i[p]&&i[p][h]),void 0===g||!g.length||!g[0]){var x;for(y in v=[],i[p])this.terminals_[y]&&y>2&&v.push("'"+this.terminals_[y]+"'");x=this.lexer.showPosition?"Parse error on line "+(s+1)+":\n"+this.lexer.showPosition()+"\nExpecting "+v.join(", ")+", got '"+(this.terminals_[h]||h)+"'":"Parse error on line "+(s+1)+": Unexpected "+(1==h?"end of input":"'"+(this.terminals_[h]||h)+"'"),this.parseError(x,{text:this.lexer.match,token:this.terminals_[h]||h,line:this.lexer.yylineno,loc:u,expected:v})}if(g[0]instanceof Array&&g.length>1)throw new Error("Parse Error: multiple actions possible at state: "+p+", token: "+h);switch(g[0]){case 1:n.push(h),r.push(this.lexer.yytext),o.push(this.lexer.yylloc),n.push(g[1]),h=null,l=this.lexer.yyleng,a=this.lexer.yytext,s=this.lexer.yylineno,u=this.lexer.yylloc;break;case 2:if(b.$=r[r.length-(_=this.productions_[g[1]][1])],b._$={first_line:o[o.length-(_||1)].first_line,last_line:o[o.length-1].last_line,first_column:o[o.length-(_||1)].first_column,last_column:o[o.length-1].last_column},d&&(b._$.range=[o[o.length-(_||1)].range[0],o[o.length-1].range[1]]),void 0!==(m=this.performAction.apply(b,[a,l,s,this.yy,g[1],r,o].concat(c))))return m;_&&(n=n.slice(0,-1*_*2),r=r.slice(0,-1*_),o=o.slice(0,-1*_)),n.push(this.productions_[g[1]][0]),r.push(b.$),o.push(b._$),n.push(i[n[n.length-2]][n[n.length-1]]);break;case 3:return!0}}return!0}},t={initialize:function(){this._nodes=[],this._node={},this._stash=[]},set:function(e){for(var t in e)this._node[t]=e[t];return this._node},node:function(e){return arguments.length&&(this._node=e),this._node},push:function(){this._nodes.push(this._node),this._node={}},unshift:function(){this._nodes.unshift(this._node),this._node={}},yield:function(){var e=this._nodes;return this.initialize(),e}},n=function(){var e={EOF:1,parseError:function(e,t){if(!this.yy.parser)throw new Error(e);this.yy.parser.parseError(e,t)},setInput:function(e){return this._input=e,this._more=this._backtrack=this.done=!1,this.yylineno=this.yyleng=0,this.yytext=this.matched=this.match="",this.conditionStack=["INITIAL"],this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0},this.options.ranges&&(this.yylloc.range=[0,0]),this.offset=0,this},input:function(){var e=this._input[0];return this.yytext+=e,this.yyleng++,this.offset++,this.match+=e,this.matched+=e,e.match(/(?:\r\n?|\n).*/g)?(this.yylineno++,this.yylloc.last_line++):this.yylloc.last_column++,this.options.ranges&&this.yylloc.range[1]++,this._input=this._input.slice(1),e},unput:function(e){var t=e.length,n=e.split(/(?:\r\n?|\n)/g);this._input=e+this._input,this.yytext=this.yytext.substr(0,this.yytext.length-t-1),this.offset-=t;var r=this.match.split(/(?:\r\n?|\n)/g);this.match=this.match.substr(0,this.match.length-1),this.matched=this.matched.substr(0,this.matched.length-1),n.length-1&&(this.yylineno-=n.length-1);var o=this.yylloc.range;return this.yylloc={first_line:this.yylloc.first_line,last_line:this.yylineno+1,first_column:this.yylloc.first_column,last_column:n?(n.length===r.length?this.yylloc.first_column:0)+r[r.length-n.length].length-n[0].length:this.yylloc.first_column-t},this.options.ranges&&(this.yylloc.range=[o[0],o[0]+this.yyleng-t]),this.yyleng=this.yytext.length,this},more:function(){return this._more=!0,this},reject:function(){return this.options.backtrack_lexer?(this._backtrack=!0,this):this.parseError("Lexical error on line "+(this.yylineno+1)+". You can only invoke reject() in the lexer when the lexer is of the backtracking persuasion (options.backtrack_lexer = true).\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},less:function(e){this.unput(this.match.slice(e))},pastInput:function(){var e=this.matched.substr(0,this.matched.length-this.match.length);return(e.length>20?"...":"")+e.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var e=this.match;return e.length<20&&(e+=this._input.substr(0,20-e.length)),(e.substr(0,20)+(e.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var e=this.pastInput(),t=new Array(e.length+1).join("-");return e+this.upcomingInput()+"\n"+t+"^"},test_match:function(e,t){var n,r,o;if(this.options.backtrack_lexer&&(o={yylineno:this.yylineno,yylloc:{first_line:this.yylloc.first_line,last_line:this.last_line,first_column:this.yylloc.first_column,last_column:this.yylloc.last_column},yytext:this.yytext,match:this.match,matches:this.matches,matched:this.matched,yyleng:this.yyleng,offset:this.offset,_more:this._more,_input:this._input,yy:this.yy,conditionStack:this.conditionStack.slice(0),done:this.done},this.options.ranges&&(o.yylloc.range=this.yylloc.range.slice(0))),(r=e[0].match(/(?:\r\n?|\n).*/g))&&(this.yylineno+=r.length),this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:r?r[r.length-1].length-r[r.length-1].match(/\r?\n?/)[0].length:this.yylloc.last_column+e[0].length},this.yytext+=e[0],this.match+=e[0],this.matches=e,this.yyleng=this.yytext.length,this.options.ranges&&(this.yylloc.range=[this.offset,this.offset+=this.yyleng]),this._more=!1,this._backtrack=!1,this._input=this._input.slice(e[0].length),this.matched+=e[0],n=this.performAction.call(this,this.yy,this,t,this.conditionStack[this.conditionStack.length-1]),this.done&&this._input&&(this.done=!1),n)return n;if(this._backtrack){for(var i in o)this[i]=o[i];return!1}return!1},next:function(){if(this.done)return this.EOF;var e,t,n,r;this._input||(this.done=!0),this._more||(this.yytext="",this.match="");for(var o=this._currentRules(),i=0;i<o.length;i++)if((n=this._input.match(this.rules[o[i]]))&&(!t||n[0].length>t[0].length)){if(t=n,r=i,this.options.backtrack_lexer){if(!1!==(e=this.test_match(n,o[i])))return e;if(this._backtrack){t=!1;continue}return!1}if(!this.options.flex)break}return t?!1!==(e=this.test_match(t,o[r]))&&e:""===this._input?this.EOF:this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})},lex:function(){return this.next()||this.lex()},begin:function(e){this.conditionStack.push(e)},popState:function(){return this.conditionStack.length-1>0?this.conditionStack.pop():this.conditionStack[0]},_currentRules:function(){return this.conditionStack.length&&this.conditionStack[this.conditionStack.length-1]?this.conditions[this.conditionStack[this.conditionStack.length-1]].rules:this.conditions.INITIAL.rules},topState:function(e){return(e=this.conditionStack.length-1-Math.abs(e||0))>=0?this.conditionStack[e]:"INITIAL"},pushState:function(e){this.begin(e)},stateStackSize:function(){return this.conditionStack.length},options:{},performAction:function(e,t,n,r){switch(n){case 0:return 4;case 1:return 14;case 2:return 12;case 3:return 15;case 4:return 16;case 5:return 22;case 6:return 24;case 7:return 28;case 8:return 30;case 9:return 18;case 10:return t.yytext=t.yytext.substr(1,t.yyleng-2),32;case 11:return t.yytext=t.yytext.substr(1,t.yyleng-2),33;case 12:return 17;case 13:return 31}},rules:[/^(?:\$)/,/^(?:\.\.)/,/^(?:\.)/,/^(?:\*)/,/^(?:[a-zA-Z_]+[a-zA-Z0-9_]*)/,/^(?:\[)/,/^(?:\])/,/^(?:,)/,/^(?:((-?(?:0|[1-9][0-9]*)))?\:((-?(?:0|[1-9][0-9]*)))?(\:((-?(?:0|[1-9][0-9]*)))?)?)/,/^(?:(-?(?:0|[1-9][0-9]*)))/,/^(?:"(?:\\["bfnrt/\\]|\\u[a-fA-F0-9]{4}|[^"\\])*")/,/^(?:'(?:\\['bfnrt/\\]|\\u[a-fA-F0-9]{4}|[^'\\])*')/,/^(?:\(.+?\)(?=\]))/,/^(?:\?\(.+?\)(?=\]))/],conditions:{INITIAL:{rules:[0,1,2,3,4,5,6,7,8,9,10,11,12,13],inclusive:!0}}};return e}();function r(){this.yy={}}return e.lexer=n,r.prototype=e,e.Parser=r,new r}();void 0!==e&&void 0!==n&&(n.parser=o,n.Parser=o.Parser,n.parse=function(){return o.parse.apply(o,arguments)},n.main=function(t){t[1]||(console.log("Usage: "+t[0]+" FILE"),r.exit(1));var o=e("fs").readFileSync(e("path").normalize(t[1]),"utf8");return n.parser.parse(o)},void 0!==t&&e.main===t&&n.main(r.argv.slice(1)))}).call(this,e("_process"))},{_process:14,fs:12,path:13}],2:[function(e,t,n){t.exports={identifier:"[a-zA-Z_]+[a-zA-Z0-9_]*",integer:"-?(?:0|[1-9][0-9]*)",qq_string:'"(?:\\\\["bfnrt/\\\\]|\\\\u[a-fA-F0-9]{4}|[^"\\\\])*"',q_string:"'(?:\\\\['bfnrt/\\\\]|\\\\u[a-fA-F0-9]{4}|[^'\\\\])*'"}},{}],3:[function(e,t,n){var r=e("./dict"),o=e("fs"),i={lex:{macros:{esc:"\\\\",int:r.integer},rules:[["\\$","return 'DOLLAR'"],["\\.\\.","return 'DOT_DOT'"],["\\.","return 'DOT'"],["\\*","return 'STAR'"],[r.identifier,"return 'IDENTIFIER'"],["\\[","return '['"],["\\]","return ']'"],[",","return ','"],["({int})?\\:({int})?(\\:({int})?)?","return 'ARRAY_SLICE'"],["{int}","return 'INTEGER'"],[r.qq_string,"yytext = yytext.substr(1,yyleng-2); return 'QQ_STRING';"],[r.q_string,"yytext = yytext.substr(1,yyleng-2); return 'Q_STRING';"],["\\(.+?\\)(?=\\])","return 'SCRIPT_EXPRESSION'"],["\\?\\(.+?\\)(?=\\])","return 'FILTER_EXPRESSION'"]]},start:"JSON_PATH",bnf:{JSON_PATH:[["DOLLAR",'yy.ast.set({ expression: { type: "root", value: $1 } }); yy.ast.unshift(); return yy.ast.yield()'],["DOLLAR PATH_COMPONENTS",'yy.ast.set({ expression: { type: "root", value: $1 } }); yy.ast.unshift(); return yy.ast.yield()'],["LEADING_CHILD_MEMBER_EXPRESSION","yy.ast.unshift(); return yy.ast.yield()"],["LEADING_CHILD_MEMBER_EXPRESSION PATH_COMPONENTS",'yy.ast.set({ operation: "member", scope: "child", expression: { type: "identifier", value: $1 }}); yy.ast.unshift(); return yy.ast.yield()']],PATH_COMPONENTS:[["PATH_COMPONENT",""],["PATH_COMPONENTS PATH_COMPONENT",""]],PATH_COMPONENT:[["MEMBER_COMPONENT",'yy.ast.set({ operation: "member" }); yy.ast.push()'],["SUBSCRIPT_COMPONENT",'yy.ast.set({ operation: "subscript" }); yy.ast.push() ']],MEMBER_COMPONENT:[["CHILD_MEMBER_COMPONENT",'yy.ast.set({ scope: "child" })'],["DESCENDANT_MEMBER_COMPONENT",'yy.ast.set({ scope: "descendant" })']],CHILD_MEMBER_COMPONENT:[["DOT MEMBER_EXPRESSION",""]],LEADING_CHILD_MEMBER_EXPRESSION:[["MEMBER_EXPRESSION",'yy.ast.set({ scope: "child", operation: "member" })']],DESCENDANT_MEMBER_COMPONENT:[["DOT_DOT MEMBER_EXPRESSION",""]],MEMBER_EXPRESSION:[["STAR",'yy.ast.set({ expression: { type: "wildcard", value: $1 } })'],["IDENTIFIER",'yy.ast.set({ expression: { type: "identifier", value: $1 } })'],["SCRIPT_EXPRESSION",'yy.ast.set({ expression: { type: "script_expression", value: $1 } })'],["INTEGER",'yy.ast.set({ expression: { type: "numeric_literal", value: parseInt($1) } })'],["END",""]],SUBSCRIPT_COMPONENT:[["CHILD_SUBSCRIPT_COMPONENT",'yy.ast.set({ scope: "child" })'],["DESCENDANT_SUBSCRIPT_COMPONENT",'yy.ast.set({ scope: "descendant" })']],CHILD_SUBSCRIPT_COMPONENT:[["[ SUBSCRIPT ]",""]],DESCENDANT_SUBSCRIPT_COMPONENT:[["DOT_DOT [ SUBSCRIPT ]",""]],SUBSCRIPT:[["SUBSCRIPT_EXPRESSION",""],["SUBSCRIPT_EXPRESSION_LIST",'$1.length > 1? yy.ast.set({ expression: { type: "union", value: $1 } }) : $$ = $1']],SUBSCRIPT_EXPRESSION_LIST:[["SUBSCRIPT_EXPRESSION_LISTABLE","$$ = [$1]"],["SUBSCRIPT_EXPRESSION_LIST , SUBSCRIPT_EXPRESSION_LISTABLE","$$ = $1.concat($3)"]],SUBSCRIPT_EXPRESSION_LISTABLE:[["INTEGER",'$$ = { expression: { type: "numeric_literal", value: parseInt($1) } }; yy.ast.set($$)'],["STRING_LITERAL",'$$ = { expression: { type: "string_literal", value: $1 } }; yy.ast.set($$)'],["ARRAY_SLICE",'$$ = { expression: { type: "slice", value: $1 } }; yy.ast.set($$)']],SUBSCRIPT_EXPRESSION:[["STAR",'$$ = { expression: { type: "wildcard", value: $1 } }; yy.ast.set($$)'],["SCRIPT_EXPRESSION",'$$ = { expression: { type: "script_expression", value: $1 } }; yy.ast.set($$)'],["FILTER_EXPRESSION",'$$ = { expression: { type: "filter_expression", value: $1 } }; yy.ast.set($$)']],STRING_LITERAL:[["QQ_STRING","$$ = $1"],["Q_STRING","$$ = $1"]]}};o.readFileSync&&(i.moduleInclude=o.readFileSync(e.resolve("../include/module.js")),i.actionInclude=o.readFileSync(e.resolve("../include/action.js"))),t.exports=i},{"./dict":2,fs:12}],4:[function(e,t,n){var r=e("./aesprim"),o=e("./slice"),i=e("static-eval"),a=e("underscore").uniq,s=function(){return this.initialize.apply(this,arguments)};function l(t,n,o){var i=e("./index"),a=h(r.parse(n).body[0].expression,{"@":t.value}),s=o.replace(/\{\{\s*value\s*\}\}/g,a),l=i.nodes(t.value,s);return l.forEach((function(e){e.path=t.path.concat(e.path.slice(1))})),l}function c(e){return Array.isArray(e)}function u(e){return function(t,n,r,o){var i=t.value,a=t.path,s=[],l=function(t,i){var a;c(t)?(t.forEach((function(e,t){s.length>=o||r(t,e,n)&&s.push({path:i.concat(t),value:e})})),t.forEach((function(t,n){s.length>=o||e&&l(t,i.concat(n))}))):(a=t)&&!(a instanceof Array)&&a instanceof 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Function)throw new Error("handler must be a function");this._fns[e]=t},s.prototype._fns={"member-child-identifier":function(e,t){var n=e.expression.value,r=t.value;if(r instanceof Object&&n in r)return[{value:r[n],path:t.path.concat(n)}]},"member-descendant-identifier":f((function(e,t,n){return e==n})),"subscript-child-numeric_literal":d((function(e,t,n){return e===n})),"member-child-numeric_literal":d((function(e,t,n){return String(e)===String(n)})),"subscript-descendant-numeric_literal":f((function(e,t,n){return e===n})),"member-child-wildcard":d((function(){return!0})),"member-descendant-wildcard":f((function(){return!0})),"subscript-descendant-wildcard":f((function(){return!0})),"subscript-child-wildcard":d((function(){return!0})),"subscript-child-slice":function(e,t){if(c(t.value)){var n=e.expression.value.split(":").map(g),r=t.value.map((function(e,n){return{value:e,path:t.path.concat(n)}}));return o.apply(null,[r].concat(n))}},"subscript-child-union":function(e,t){var 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t(e.oldVersion,e)})),Pa(n).then((function(){}))}(this.dbName),e}}async termCount(e){const t=await this.db;return(e??t.transaction("nodes")).objectStore("nodes").count()}unique(e){const t=new Map,n=[];for(const r of e)t.has(r.id)||(t.set(r.id,!0),n.push(r));return n}async getTermsWithLabelOrSynonym(e,t,n){const r=t?.includeSubclasses??!0,o=await this.db,i=n??o.transaction(["nodes","edges"]),a=i.objectStore("nodes"),s=[...await a.index("by-label").getAll(e),...await a.index("by-synonym").getAll(e)];if(r){const e=await this.recurseEdges("by-object",s.map((e=>e.id)),(e=>"is_a"===e.pred),"sub",i);for(const t of e){const e=await a.get(t);e&&s.push(e)}}return s}async getPropertiesByLabel(e,t,n){const r=t?.includeSubProperties??!0,o=await this.db,i=n??o.transaction(["nodes","edges"]),a=(await this.getTermsWithLabelOrSynonym(e,{includeSubclasses:!1},i)).filter((e=>As(e)));if(r){const e=await 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at).toHexString(),l={_id:s,refSeq:o.refSeq,min:Number(c)-1,max:Number(a),type:f};o.strand&&(l.strand=o.strand);const u=new ht({changedIds:[o._id],typeName:"AddFeatureChange",assembly:r,addedFeature:l,parentFeatureId:o._id});e.submit(u).then((()=>{n.apolloSetSelectedFeature(s)})),t(),i.preventDefault()},children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[i.jsx(s.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:c,onChange:e=>{d(e.target.value)}}),i.jsx(s.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:a,onChange:e=>{l(e.target.value)},error:_,helperText:_?'"End" must be greater than "Start"':null}),i.jsx(qs,{session:n,ontologyName:"Sequence Ontology",style:{width:170},value:f,filterTerms:Cs,fetchValidTerms:async function(e,t,n){const r=await Ms(e,t);if(r)return r;y(`Type "${e?.type}" does not have any children in the 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Vs({changeManager:e,handleClose:t,selectedFeature:n,session:r,setSelectedFeature:o,sourceAssemblyId:a,sourceFeature:c}){const[d,f]=u.useState(""),{ontologyManager:h}=r.apolloDataStore,{featureTypeOntology:p}=h;function g(e){if(!e.parent?.children||1===e.parent.children.size)return;const t=[];for(const n of e.parent.children.values())p?.isTypeOf(n.type,"CDS")||t.push(n);t.sort(((e,t)=>e.min-t.min));const n=[];for(const t of e.parent.children.values())p?.isTypeOf(t.type,"CDS")||n.push(t);if(n.sort(((e,t)=>t.max-e.max)),e.min===t[0].min){let n;for(const r of t)if(r._id!==e._id&&r.min>=e.min){n=r.min;break}if(n&&n!=e.parent.min)return{typeName:"LocationStartChange",changedId:e.parent._id,featureId:e.parent._id,oldLocation:e.parent.min,newLocation:n}}if(e.max===n[0].max){let t;for(const r of n)if(r._id!=e._id&&r.max<=e.max){t=r.max;break}if(t&&t!=e.parent.max)return{typeName:"LocationEndChange",changedId:e.parent._id,featureId:e.parent._id,oldLocation:e.parent.max,newLocation:t}}}return i.jsxs(Bs,{open:!0,title:"Delete feature",handleClose:t,maxWidth:!1,"data-testid":"delete-feature",children:[i.jsxs("form",{onSubmit:r=>{!async function(r){r.preventDefault(),f(""),n?._id===c._id&&o();const i=[],s=new pt({changedIds:[c._id],typeName:"DeleteFeatureChange",assembly:a,changes:[{deletedFeature:l.getSnapshot(c),parentFeatureId:c.parent?._id}]});if(p&&(p.isTypeOf(c.type,"transcript")||p.isTypeOf(c.type,"pseudogenic_transcript"))){const e=g(c);e&&i.push(e)}if(p?.isTypeOf(c.type,"exon")){const e=function(e){if(!p)return;if(!p.isTypeOf(e.type,"exon"))return;if(!e.parent?.cdsLocations||0===e.parent.cdsLocations.length||0===e.parent.cdsLocations[0].length)return;if(!e.parent.children)throw new Error("Unable to find parent of CDS");if(1!=e.parent.cdsLocations.length)throw new Error("Unable to handle a transcript with multiple CDSs");const t=(e.parent.cdsLocations.at(0)??[]).sort((({min:e},{min:t})=>e-t));let n;for(const r of e.parent.children.values())if(r.type===t[0].type){n=r;break}if(!n)throw new Error("Unable to find CDS");const r=t[0].min,o=t[t.length-1].max;if(!(e.min>r&&e.max<o||e.max<r||e.min>o)){if(e.min<=r&&e.max>=o)return new pt({changedIds:[n._id],typeName:"DeleteFeatureChange",assembly:a,changes:[{deletedFeature:l.getSnapshot(n),parentFeatureId:n.parent?._id}]});if(e.min<=r&&e.max>r){let r;for(const n of t)if(n.min>e.max){r=n.min;break}if(!r)throw new Error("Error setting new CDS start");return{typeName:"LocationStartChange",changedId:n._id,featureId:n._id,oldLocation:n.min,newLocation:r}}if(e.min<o&&e.max>=o){let r;for(const n of t.reverse())if(n.max<e.min){r=n.max;break}if(!r)throw new Error("Error setting new CDS end");return{typeName:"LocationEndChange",changedId:n._id,featureId:n._id,oldLocation:n.max,newLocation:r}}throw new Error("Unexpected relationship between exon and 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File can be gzip compressed.",children:i.jsx(ya,{className:o.radioIcon,sx:{fontSize:18}})})]})}),i.jsx(s.AccordionDetails,{className:o.accordionDetails,children:i.jsxs(s.Box,{style:{marginTop:20},children:[i.jsx("input",{"data-testid":"gff3-input-file",type:"file",disabled:C&&!p,onChange:e=>{const t=e.target.files?.item(0);t&&(R(t),v(fl.GFF3),t.name.endsWith(".gz")&&G(!0))}}),i.jsxs(s.FormGroup,{style:{display:"grid"},children:[i.jsx(s.FormControlLabel,{control:i.jsx(s.Checkbox,{checked:b,onChange:()=>{x(!b)},disabled:C&&!p}),label:"Load features from GFF3 file"}),i.jsx(s.FormControlLabel,{label:"Strict parsing",disabled:!b||C&&!p,control:i.jsx(s.Checkbox,{checked:k,onChange:e=>{N(e.target.checked)}})}),i.jsx(s.FormHelperText,{children:"Don't import any features if any lines in the GFF3 are unable to be processed"}),i.jsx(s.FormControlLabel,{"data-testid":"gff3-is-gzip-checkbox",control:i.jsx(s.Checkbox,{checked:H,onChange:()=>{G(!H)},disabled:C&&!p}),label:"GFF3 is gzip compressed"})]})]})})]})]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{disabled:!pl(m,w,_,T,E,j,W,J,K)||C,variant:"contained",type:"submit","data-testid":"submit-button",children:C?"Submitting...":"Submit"}),i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:t,children:"Cancel"})]})]}),p?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:p})}):null]})}const ml=[{field:"name",headerName:"Assembly Name",width:150,editable:!1},{field:"aliases",headerName:"Aliases",width:300,editable:!0}];function yl({changeManager:e,handleClose:t,session:n}){const{apolloDataStore:r}=n,{collaborationServerDriver:o}=r,a=o.getAssemblies().map((e=>({id:e.name,name:e.displayName,aliases:e.aliases.join(", ")}))),[l,c]=u.useState("");return i.jsxs(Bs,{open:!0,title:"Add assembly aliases",handleClose:t,maxWidth:"sm","data-testid":"add-assembly-alias",fullWidth:!0,children:[i.jsx(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:i.jsx(s.Box,{sx:{height:400,width:"100%"},children:i.jsx(m.DataGrid,{rows:a,columns:ml,initialState:{pagination:{paginationModel:{pageSize:5}}},pageSizeOptions:[5],processRowUpdate:(n,r)=>{const o=new gt({typeName:"AddAssemblyAliasesChange",assembly:n.id,aliases:n.aliases.split(",")});return e.submit(o).catch((()=>{c("Error submitting change")})),t(),n},disableRowSelectionOnClick:!0})})}),l?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:l})}):null]})}const _l=new Set(["TAA","TAG","TGA"]);function vl(e,t,n){let r=0;for(const o of t){const t=o.max-o.min;if(e<=r+t){const t=e-r;return 1===n?o.min+t:o.max-t}r+=t}const o=t.at(-1);if(!o)throw new Error("No exons found");return 1===n?o.max:o.min}function bl({changeManager:e,handleClose:t,refName:n,session:r,sourceAssemblyId:a,sourceFeature:l}){const[c,d]=u.useState("longest-orf"),[f,h]=u.useState(""),[p,g]=u.useState(""),[m,y]=u.useState(""),_="manual"===c&&Boolean(f)&&Boolean(p)&&Number(p)<=Number(f),v="manual"===c&&(!(f&&p)||_);return i.jsxs(Bs,{open:!0,title:"Add coding sequence",handleClose:t,maxWidth:!1,"data-testid":"add-coding-sequence",children:[i.jsxs("form",{onSubmit:i=>{!async function(i){let s,u;i.preventDefault(),y("");try{if("longest-orf"===c){const e=l.transcriptExonParts.filter((e=>"exon"===e.type));if(0===e.length)return void y("No exons found in this transcript");const i=r.apolloDataStore.getBackendDriver(a);if(!i)return void y("No backend driver found for this assembly");let c="";for(const t of e){const{seq:e}=await i.getSequence({assemblyName:a,refName:n,start:t.min,end:t.max});c+=-1===l.strand?o.revcom(e):e}const d=function(e){const t=[null,null,null];let n;for(let r=0;r<e.length-2;r++){const o=e.slice(r,r+3).toUpperCase(),i=r%3;if("ATG"===o&&null===t[i])t[i]=r;else if(_l.has(o)){const e=t[i];if(null===e)continue;(!n||n[1]-n[0]<r-e)&&(n=[e,r]),t[i]=null}}return n}(c);if(!d)return r.notify("No open reading frame found in this transcript","error"),void t();1===(l.strand??1)?(s=vl(d[0],e,1),u=vl(d[1]+3,e,1)):(u=vl(d[0],e,-1),s=vl(d[1]+3,e,-1))}else s=Number(f)-1,u=Number(p);const i=(new at).toHexString(),d={_id:i,refSeq:l.refSeq,min:s,max:u,type:"CDS"};l.strand&&(d.strand=l.strand);const h=new ht({changedIds:[l._id],typeName:"AddFeatureChange",assembly:a,addedFeature:d,parentFeatureId:l._id});await e.submit(h),r.apolloSetSelectedFeature(i),t()}catch(e){y(e instanceof Error?e.message:"An unknown error occurred")}}(i)},children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[i.jsx(s.FormControl,{children:i.jsxs(s.RadioGroup,{value:c,onChange:e=>{d(e.target.value)},children:[i.jsx(s.FormControlLabel,{value:"longest-orf",control:i.jsx(s.Radio,{}),label:"Calculate longest open reading frame"}),i.jsx(s.FormControlLabel,{value:"manual",control:i.jsx(s.Radio,{}),label:"Manual"})]})}),"manual"===c?i.jsxs(i.Fragment,{children:[i.jsx(s.TextField,{margin:"dense",id:"cds-min",label:"Min",type:"number",fullWidth:!0,variant:"outlined",value:f,onChange:e=>{h(e.target.value)}}),i.jsx(s.TextField,{margin:"dense",id:"cds-max",label:"Max",type:"number",fullWidth:!0,variant:"outlined",value:p,onChange:e=>{g(e.target.value)},error:_,helperText:_?'"Max" must be greater than "Min"':null})]}):null]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{variant:"contained",type:"submit",disabled:v,children:"Submit"}),i.jsx(s.Button,{variant:"outlined",type:"button",onClick:t,children:"Cancel"})]})]}),m?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:m})}):null]})}class xl{clientStore;constructor(e){this.clientStore=e}}async function wl(e,t){return qa(`Apollo-${e}`,1,{upgrade(e){const n="changes";e.objectStoreNames.contains(n)||e.createObjectStore(n,{autoIncrement:!0});for(const n of t){const t=`features-${n}`;if(!e.objectStoreNames.contains(t)){const n=e.createObjectStore(t);n.createIndex("min","min",{unique:!1}),n.createIndex("max","max",{unique:!1})}const r=`checkresults-${n}`;if(!e.objectStoreNames.contains(r)){const t=e.createObjectStore(r,{keyPath:"_id"});t.createIndex("min","start",{unique:!1}),t.createIndex("max","end",{unique:!1}),t.createIndex("featureId","featureId",{unique:!1})}}}})}class Sl extends xl{async getFeatures(e){const{assemblyName:t,end:n,refName:r,start:o}=e,i=(await this.getRegions(t)).map((e=>e.refName)),a=`features-${r}`,s=`checkresults-${r}`,l=[],c=[],u=(await wl(t,i)).transaction([a,s]);for await(const e of u.objectStore(a).index("min").iterate(IDBKeyRange.upperBound(n,!0)))e.value.max>o&&l.push(e.value);for await(const e of u.objectStore(s).index("min").iterate(IDBKeyRange.upperBound(n,!0)))e.value.end>o&&c.push(e.value);return[l,c]}async getSequence(e){const t=o.getSession(this.clientStore),{assemblyManager:n}=t,r=await n.waitForAssembly(e.assemblyName);if(!r)throw new Error(`Assembly not found: "${e.assemblyName}"`);const{configuration:i}=r,{adapter:a}=i.sequence,{pluginManager:s}=o.getEnv(this.clientStore),l=s.getAdapterType(a.type);if(!l)throw new Error(`No adapter found for "${a.type}"`);const c=new(await l.getAdapterClass())(a,void 0,s),u=await c.getSequence({...e,refName:r.getSeqAdapterRefName(e.refName)});if(!u)throw new Error(`Sequence not found: ${JSON.stringify(e)}`);return{seq:u,refSeq:e.refName}}async getRegions(e){const t=o.getSession(this.clientStore),{assemblyManager:n}=t,r=await n.waitForAssembly(e);if(!r)throw new Error(`Assembly not found: "${e}"`);const{regions:i}=r;if(!i)throw new Error(`Assembly not found: "${e}"`);return i}getAssemblies(e){return[]}async getRefNameAliases(e){const t=o.getSession(this.clientStore),{assemblyManager:n}=t,r=await n.waitForAssembly(e);if(!r)throw new Error(`Assembly not found: "${e}"`);const{configuration:i}=r,{refNameAliases:a}=i;if(!a)return[];const{pluginManager:s}=o.getEnv(this.clientStore),l=s.getAdapterType(a.adapter.type);if(!l)throw new Error(`No adapter found for "${a.adapter.type}"`);return new(await l.getAdapterClass())(a.adapter,void 0,s).getRefNameAliases({})}async submitChange(e,t){if(!st(e))return new Wt;const{assembly:n,changedIds:r}=e,o=(await this.getRegions(n)).map((e=>e.refName)),i=await wl(n,o),a=new Set,s=[],c=new Set;if(function(e){return"DeleteFeatureChange"===e.typeName}(e))for(const t of e.changes)if(t.parentFeatureId){const e=this.clientStore.getFeature(t.parentFeatureId);e&&(a.add(e.topLevelFeature),c.add(e.topLevelFeature.refSeq))}else{const{refSeq:e,_id:n}=t.deletedFeature;s.push({refSeq:e,featureId:n}),c.add(e)}else for(const e of r){const t=this.clientStore.getFeature(e);t&&(a.add(t.topLevelFeature),c.add(t.refSeq))}const u=[...c].flatMap((e=>[`features-${e}`,`checkresults-${e}`]));u.push("changes");const d=i.transaction(u,"readwrite");for(const{refSeq:e,featureId:t}of s)d.objectStore(`features-${e}`).delete(t);for(const e of a){const t=l.getSnapshot(e);d.objectStore(`features-${e.refSeq}`).put(t,e._id)}for(const{featureId:e,refSeq:t}of s){const n=d.objectStore(`checkresults-${t}`);for await(const t of n.index("featureId").iterate(e))this.clientStore.deleteCheckResult(t.value._id),t.delete()}for(const e of a){const t=d.objectStore(`checkresults-${e.refSeq}`);for await(const n of t.index("featureId").iterate(e._id))this.clientStore.deleteCheckResult(n.value._id),n.delete()}if(d.objectStore("changes").put({...e.toJSON(),createdAt:new Date}),await d.done,a.size>0){const e=[...ne.getChecks().values()],t=[];for(const r of a){const o=l.getSnapshot(r),i=async(e,t)=>(await this.getSequence({assemblyName:n,refName:r.refSeq,start:e,end:t})).seq;for(const n of e){const e=await n.checkFeature(o,i);for(const n of e)t.push({refSeq:r.refSeq,result:n,topLevelFeatureId:r._id})}}if(t.length>0){const e=o.map((e=>`checkresults-${e}`)),n=i.transaction(e,"readwrite");for(const{refSeq:e,result:r,topLevelFeatureId:o}of t)n.objectStore(`checkresults-${e}`).put({...r,featureId:o});await n.done;for(const{result:e}of t)this.clientStore.addCheckResult(e)}}return new Wt}async searchFeatures(e,t){return[]}async getCheckResults(e){const t=(await this.getRegions(e)).map((e=>e.refName)),n=await wl(e,t),r=[],o=t.map((e=>`checkresults-${e}`)),i=n.transaction(o);for(const e of o)for await(const t of i.objectStore(e).iterate())r.push(t.value);return r}async getChanges(e,t={}){const n=(await this.getRegions(e)).map((e=>e.refName)),r=await wl(e,n);let o=[];for await(const e of r.transaction("changes").store.iterate())o.push({sequence:e.key,...e.value});const{filters:i}=t;if(i?.user){const e=new RegExp(i.user,"i");o=o.filter((t=>void 0!==t.user&&e.test(t.user)))}if(i?.typeName&&(o=o.filter((e=>e.typeName===i.typeName))),i?.startTime){const e=new Date(i.startTime).getTime();o=o.filter((t=>new Date(t.createdAt).getTime()>=e))}if(i?.endTime){const e=new Date(i.endTime).getTime();o=o.filter((t=>new Date(t.createdAt).getTime()<=e))}const a=o.length,s=t.sortField??"sequence",l="asc"===(t.sortOrder??"desc")?1:-1;if(o.sort(((e,t)=>{const n=e[s],r=t[s];return n===r?0:void 0===n?1:void 0===r?-1:n<r?-l:l})),void 0!==t.page&&void 0!==t.pageSize){const e=t.page*t.pageSize;o=o.slice(e,e+t.pageSize)}return{changes:o,totalCount:a}}}const Cl={async AddFeatureChange(e,t){const{assembly:n,changes:r}=t;for(const t of r){const{addedFeature:r,parentFeatureId:o}=t;if(o){let t=e.getFeature(o);if(!t&&(await e.loadFeatures([{assemblyName:n,refName:r.refSeq,start:r.min,end:r.max}]),t=e.getFeature(o),!t))throw new Error(`Could not find parent feature "${o}"`);t.attributes.get("_id")||t.setAttribute("_id",[t._id]),t.addChild(r)}else e.addFeature(n,r)}},async DeleteFeatureChange(e,t){for(const n of t.changes){const{deletedFeature:t,parentFeatureId:r}=n;if(r){const n=e.getFeature(r);if(!n)throw new Error(`Could not find parent feature "${r}"`);n.deleteChild(t._id)}else e.getFeature(t._id)&&e.deleteFeature(t._id)}},async FeatureAttributeChange(e,t){for(const[n,r]of t.changedIds.entries()){const o=e.getFeature(r);if(!o)throw new Error(`Could not find feature with identifier "${r}"`);o.setAttributes(new Map(Object.entries(t.changes[n].newAttributes)))}},async LocationEndChange(e,t){for(const n of t.changes){const{featureId:t,newEnd:r}=n,o=e.getFeature(t);if(!o)throw new Error(`Could not find feature with identifier "${t}"`);o.setMax(r)}},async LocationStartChange(e,t){for(const n of t.changes){const{featureId:t,newStart:r}=n,o=e.getFeature(t);if(!o)throw new Error(`Could not find feature with identifier "${t}"`);o.setMin(r)}},async MergeExonsChange(e,t){for(const n of t.changes){const{firstExon:t,secondExon:r}=n,o=e.getFeature(t._id);if(!o)throw new Error(`Could not find feature with identifier "${t._id}"`);o.setMin(Math.min(t.min,r.min)),o.setMax(Math.max(t.max,r.max));const i=o.attributes.get("merged_with")?.slice()??[],a=Lt(Mt(r.attributes));i.includes(a)||i.push(a),o.setAttribute("merged_with",i),o.parent?.deleteChild(r._id)}},async SplitExonChange(e,t){for(const[n]of t.changedIds.entries()){const{exonToBeSplit:r,parentFeatureId:o,upstreamCut:i,downstreamCut:a,leftExonId:s,rightExonId:l}=t.changes[n];if(!o)throw new Error("TODO: Split exon without parent");const[c,u]=t.makeSplitExons(r,i,a,s,l),d=e.getFeature(o);if(!d)throw new Error(`Could not find parent feature "${o}"`);d.addChild(c),d.addChild(u),e.getFeature(r._id)&&e.deleteFeature(r._id)}},async MergeTranscriptsChange(e,t){for(const[n,r]of t.changedIds.entries()){const{firstTranscript:o,secondTranscript:i}=t.changes[n],a=e.getFeature(o._id);if(!a)throw new Error(`Could not find feature with identifier "${r}"`);t.mergeTranscriptsOnClient(a,i),a.parent?.deleteChild(i._id)}},async UndoMergeExonsChange(e,t){for(const n of t.changes){const{exonsToRestore:t,parentFeatureId:r}=n;if(!r)throw new Error("Parent ID is missing");const o=e.getFeature(r);if(!o)throw new Error(`Could not find parent feature "${r}"`);o.attributes.get("_id")||o.setAttribute("_id",[o._id]);for(const e of t)o.addChild(e)}},async UndoSplitExonChange(e,t){for(const n of t.changes){const{exonToRestore:t,parentFeatureId:r,idsToDelete:o}=n;if(!r)throw new Error("Parent ID is missing");const i=e.getFeature(r);if(!i)throw new Error(`Could not find parent feature "${r}"`);i.attributes.get("_id")||i.setAttribute("_id",[i._id]),i.addChild(t),o.map((e=>{i.deleteChild(e)}))}},async UndoMergeTranscriptsChange(e,t){for(const n of t.changes){const{transcriptsToRestore:t,parentFeatureId:r}=n;if(!r)throw new Error("Parent ID is missing");const o=e.getFeature(r);if(!o)throw new Error(`Could not find parent feature "${r}"`);o.attributes.get("_id")||o.setAttribute("_id",[o._id]);for(const e of t)o.addChild(e)}},async StrandChange(e,t){for(const[n,r]of t.changedIds.entries()){const o=e.getFeature(r);if(!o)throw new Error(`Could not find feature with identifier "${r}"`);o.setStrand(t.changes[n].newStrand)}},async TypeChange(e,t){for(const[n,r]of t.changedIds.entries()){const o=e.getFeature(r);if(!o)throw new Error(`Could not find feature with identifier "${r}"`);o.setType(t.changes[n].newType)}}};class Al{dataStore;constructor(e){this.dataStore=e}recentChanges=[];undoneChanges=[];async submit(e,t={}){const{addToRecents:n=!0,submitToBackend:r=!0,updateJobsManager:i=!1}=t,a=o.getSession(this.dataStore),s=new AbortController,{jobsManager:l,isLocked:c,changeInProgress:u,setChangeInProgress:d}=o.getSession(this.dataStore);if(c)return a.notify("Cannot submit changes in locked mode"),void d(!1);if(u)return void a.notify("Could not submit change, there is another change still in progress");d(!0);const f={name:e.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{s.abort(new DOMException(`Cancelling change "${e.typeName}"`,"AbortError"))}};i&&l.runJob(f);const h=await Kt.frontendPreValidate(e);if(!h.ok){const e=`Pre-validation failed: "${h.resultsMessages}"`;return i&&l.abortJob(f.name,e),a.notify(e,"error"),void d(!1)}const p=e.typeName,g=function(e){return e in Cl}(p)?Cl[p]:void 0;if(g)try{await g(this.dataStore,e)}catch(e){return i&&l.abortJob(f.name,String(e)),console.error(e),a.notify(`Error encountered in client: ${String(e)}. Data may be out of sync, please refresh the page`,"error"),void d(!1)}if((await Kt.frontendPostValidate(e)).ok||await this.undo(e),r){i&&l.update(f.name,"Submitting to driver");const{collaborationServerDriver:r,getBackendDriver:o}=this.dataStore,s=te(e)?o(e.assembly)??r:r;let c;try{c=await s.submitChange(e,t)}catch(t){return i&&l.abortJob(f.name,String(t)),console.error(t),a.notify(String(t),"error"),d(!1),void await this.undo(e,!1)}if(!c.ok){const t=`Post-validation failed: "${h.resultsMessages}"`;return i&&l.abortJob(f.name,t),a.notify(t,"error"),d(!1),void await this.undo(e,!1)}e.notification&&a.notify(e.notification,"success"),n&&(this.recentChanges.push(e),this.undoneChanges=[])}i&&l.done(f),d(!1)}async undo(e,t=!0){const n=e.getInverse();return this.submit(n,{submitToBackend:t,addToRecents:!1})}async redo(e,t=!0){return this.submit(e,{submitToBackend:t,addToRecents:!1})}async undoLastChange(){const e=o.getSession(this.dataStore),t=this.recentChanges.pop();if(t)return this.undoneChanges.push(t),this.undo(t);e.notify("No changes to undo!","info")}async redoLastChange(){const e=o.getSession(this.dataStore),t=this.undoneChanges.pop();if(t)return this.recentChanges.push(t),this.redo(t);e.notify("No changes to redo!","info")}}class kl extends xl{inFlight=new Map;refSeqMaps=new Map;async fetch(e,t,n){return e.getFetcher({locationType:"UriLocation",uri:t.toString()})(t,n)}async searchFeatures(e,t){const n=this.clientStore.getInternetAccount(t[0]),{baseURL:r}=n,o=new URL("features/searchFeatures",r),i=new URLSearchParams({assemblies:t.join(","),term:e});o.search=i.toString();const a=o.toString(),s=await this.fetch(n,a);if(!s.ok){const e=await dl(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:r,start:i}=e,{assemblyManager:a}=o.getSession(this.clientStore);if(!a.get(t))throw new Error(`Could not find assembly with name "${t}"`);const s=(await this.getRefSeqMapping(t)).get(r);if(!s)throw new Error(`Could not find refSeq "${r}"`);const l=s.id,c=this.clientStore.getInternetAccount(t),{baseURL:u}=c,d=new URL("features/getFeatures",u),f=new URLSearchParams({refSeq:l,start:String(i),end:String(n)});d.search=f.toString();const h=d.toString(),p=await this.fetch(c,h);if(!p.ok){const e=await dl(p,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,r,c),p.json()}checkSocket(e,t,n){const{socket:r}=n,o=`${e}-${t}`;r.hasListeners(o)||r.on(o,(async e=>{const t=n.retrieveToken();if(!t)return;const r=sn(t),o=new Al(this.clientStore);if(n.setLastChangeSequenceNumber(e.changeSequence),e.userSessionId===r)return;const i=ee.fromJSON(e.changeInfo);st(i)&&this.haveDataForChange(i)&&await o.submit(i,{submitToBackend:!1})}))}haveDataForChange(e){const{assembly:t,changedIds:n}=e;if(!this.clientStore.assemblies.get(t))return!1;for(const e of n)if(this.clientStore.getFeature(e))return!0;return!1}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,n=this.inFlight.get(t),{assemblyName:r,end:i,refName:a,start:s}=e,{assemblyManager:l}=o.getSession(this.clientStore);if(!l.get(r))throw new Error(`Could not find assembly with name "${r}"`);const c=(await this.getRefSeqMapping(r)).get(a);if(!c)throw new Error(`Could not find refSeq "${a}"`);const u=c.id;if(n)return{seq:await n,refSeq:u};const d=this.clientStore.assemblies.get(r)??this.clientStore.addAssembly(r),f=d.refSeqs.get(u)??d.addRefSeq(u,a),h=f.getSequence(s,i);if(h.length===i-s)return{seq:h,refSeq:u};const p=this.clientStore.getInternetAccount(r),{baseURL:g}=p,m=new URL("sequence",g),y=new URLSearchParams({refSeq:u,start:String(s),end:String(i)});m.search=y.toString();const _=m.toString(),v=this.getSeqFromServer(p,_,f,s,i);this.inFlight.set(t,v);const b=await v;return this.checkSocket(r,a,p),this.inFlight.delete(t),{seq:b,refSeq:u}}async getSeqFromServer(e,t,n,r,o){const i=await this.fetch(e,t);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getSequence failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}const a=await i.text();return n.addSequence({sequence:a,start:r,stop:o}),a}async getRefSeqMapping(e){const t=this.refSeqMaps.get(e);if(t)return t;const{assemblyManager:n}=o.getSession(this.clientStore);if(!n.get(e))throw new Error(`Could not find assembly with name "${e}"`);const r=this.clientStore.getInternetAccount(e),{baseURL:i}=r,a=new URL("refSeqs",i),s=new URLSearchParams({assembly:e});a.search=s.toString();const l=a.toString(),c=await this.fetch(r,l);if(!c.ok){let e;try{e=await c.text()}catch{e=""}throw new Error(`getRefNameAliases failed: ${c.status} (${c.statusText})${e?` (${e})`:""}`)}const u=await c.json(),d=new Map(u.map((e=>[e.name,{refName:e.name,id:e._id,aliases:e.aliases}])));return this.refSeqMaps.set(e,d),d}async getRefNameAliases(e){return[...(await this.getRefSeqMapping(e)).values()].map((e=>({refName:e.refName,aliases:[...new Set([e.id,...e.aliases])],uniqueId:`alias-${e.id}`})))}async getRefSeqId(e,t){const n=await this.getRefSeqMapping(e);if(!n)return;const r=n.get(t);return r?.id}async getRegions(e){const{assemblyManager:t}=o.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:r}=n,i=new URL("refSeqs",r),a=new URLSearchParams({assembly:e});i.search=a.toString();const s=i.toString(),l=await this.fetch(n,s);if(!l.ok){let e;try{e=await l.text()}catch{e=""}throw new Error(`getRegions failed: ${l.status} (${l.statusText})${e?` (${e})`:""}`)}return(await l.json()).map((e=>({refName:e.name,start:0,end:e.length})))}getAssemblies(e){const{assemblyManager:t}=o.getSession(this.clientStore);return t.assemblies.filter((t=>{const r=n.getConf(t,["sequence","metadata"]);return!(!(r&&r.apollo&&r.internetAccountConfigId)||e&&r.internetAccountConfigId!==e)}))}async getChanges(e,t={}){const n=this.clientStore.getInternetAccount(e),{baseURL:r}=n,o=new URL("changes",r),i={assembly:e};void 0!==t.page&&(i.page=String(t.page)),void 0!==t.pageSize&&(i.pageSize=String(t.pageSize)),t.sortField&&(i.sortField=t.sortField),t.sortOrder&&(i.sortOrder=t.sortOrder),t.filters?.user&&(i.user=t.filters.user),t.filters?.typeName&&(i.typeName=t.filters.typeName),t.filters?.startTime&&(i.startTime=t.filters.startTime),t.filters?.endTime&&(i.endTime=t.filters.endTime),o.search=new URLSearchParams(i).toString();const a=await this.fetch(n,o.toString());if(!a.ok){const e=await dl(a,"getChanges failed");throw new Error(e)}return a.json()}async getCheckResults(e){const t=this.clientStore.getInternetAccount(e),{baseURL:n}=t,r=new URL("checks",n);r.search=new URLSearchParams({assembly:e}).toString();const o=await this.fetch(t,r.toString());if(!o.ok){const e=await dl(o,"getCheckResults failed");throw new Error(e)}return o.json()}async submitChange(e,t={}){const{internetAccountId:n}=t,r=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,n),{baseURL:o}=r,i=new URL("changes",o).href,a=await this.fetch(r,i,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!a.ok){const e=await dl(a,"submitChange failed");throw new Error(e)}const s=new Wt;return a.ok||(s.ok=!1),s}}var Nl;function Tl(e,t,n,r){const o={_id:(new at).toHexString(),refSeq:e,type:"CDS",min:n,max:r,strand:t},i={_id:(new at).toHexString(),refSeq:e,type:"exon",min:n,max:r,strand:t},a={};return a[o._id]=o,a[i._id]=i,{_id:(new at).toHexString(),refSeq:e,type:"mRNA",min:n,max:r,strand:t,children:a}}function Rl({changeManager:e,handleClose:t,region:n,session:r}){const[o,a]=u.useState(String(n.end)),[l,c]=u.useState(String(n.start+1)),[d,f]=u.useState(Nl.GENE_AND_SUBFEATURES),[h,p]=u.useState(""),[g,m]=u.useState(),[y,_]=u.useState(""),v=Number(o)<=Number(l);let b=v||!(l&&o&&d);return(d===Nl.CUSTOM&&!h||!g&&d===Nl.GENE_AND_SUBFEATURES||!g&&d===Nl.TRANSCRIPT_AND_SUBFEATURES)&&(b=!0),i.jsxs(Bs,{open:!0,title:"Add new feature",handleClose:t,maxWidth:!1,"data-testid":"add-feature-dialog",children:[i.jsxs("form",{onSubmit:async function(i){i.preventDefault(),_("");const a=r.apolloDataStore.getBackendDriver(n.assemblyName);if(!a)return void _("No backend driver found");let s=n.refName;if(a instanceof kl){const e=await a.getRefSeqId(n.assemblyName,n.refName);if(!e)return void _(`Could not find refSeq for "${n.refName}"`);s=e}if(d===Nl.GENE_AND_SUBFEATURES){const i=Tl(s,g,Number(l)-1,Number(o)),a={};a[i._id]=i;const c=(new at).toHexString(),u=new ht({changedIds:[c],typeName:"AddFeatureChange",assembly:n.assemblyName,addedFeature:{_id:c,refSeq:s,min:Number(l)-1,max:Number(o),type:"gene",strand:g,children:a}});return e.submit(u).then((()=>{r.apolloSetSelectedFeature(c)})),void t()}if(d===Nl.TRANSCRIPT_AND_SUBFEATURES){const i=Tl(s,g,Number(l)-1,Number(o)),a=new ht({changedIds:[i._id],typeName:"AddFeatureChange",assembly:n.assemblyName,addedFeature:i});return e.submit(a).then((()=>{r.apolloSetSelectedFeature(i._id)})),void t()}if(!h)return void _("No type selected");const c=(new at).toHexString(),u=new ht({changedIds:[c],typeName:"AddFeatureChange",assembly:n.assemblyName,addedFeature:{_id:c,refSeq:s,min:Number(l)-1,max:Number(o),type:h,strand:g}});e.submit(u).then((()=>{r.apolloSetSelectedFeature(c)})),t()},"data-testid":"submit-form",children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[i.jsx(s.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(l),onChange:e=>{c(e.target.value)}}),i.jsx(s.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:o,onChange:e=>{a(e.target.value)},error:v,helperText:v?'"End" must be greater than "Start"':null}),i.jsxs(s.FormControl,{children:[i.jsx(s.InputLabel,{id:"demo-simple-select-label",children:"Strand"}),i.jsxs(s.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Strand",value:g?.toString(),onChange:function(e){switch(_(""),Number(e.target.value)){case 1:m(1);break;case-1:m(-1);break;default:m(void 0)}},children:[i.jsx(s.MenuItem,{value:void 0}),i.jsx(s.MenuItem,{value:1,children:"+"}),i.jsx(s.MenuItem,{value:-1,children:"-"})]})]}),i.jsx(s.FormControl,{style:{marginTop:20},children:i.jsxs(s.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:Nl.GENE_AND_SUBFEATURES,name:"radio-buttons-group",value:d,onChange:e=>{_("");const{value:t}=e.target;Object.keys(Nl).includes(t)&&f(Nl[t])},children:[i.jsx(s.FormControlLabel,{value:Nl.GENE_AND_SUBFEATURES,control:i.jsx(s.Radio,{}),label:i.jsxs(s.Box,{display:"flex",alignItems:"center",children:["Add gene and sub-features",i.jsx(s.Tooltip,{title:"This is a shortcut to create a gene with a single mRNA, exon, and CDS",children:i.jsx(s.IconButton,{size:"small",children:i.jsx(ya,{sx:{fontSize:18}})})})]})}),i.jsx(s.FormControlLabel,{value:Nl.TRANSCRIPT_AND_SUBFEATURES,control:i.jsx(s.Radio,{}),label:i.jsxs(s.Box,{display:"flex",alignItems:"center",children:["Add transcript and sub-features",i.jsx(s.Tooltip,{title:"This is a shortcut to create a single mRNA with exon and CDS, but without a parent gene",children:i.jsx(s.IconButton,{size:"small",children:i.jsx(ya,{sx:{fontSize:18}})})})]})}),i.jsx(s.FormControlLabel,{value:Nl.CUSTOM,checked:d!==Nl.GENE_AND_SUBFEATURES&&d!==Nl.TRANSCRIPT_AND_SUBFEATURES,control:i.jsx(s.Radio,{}),label:"Add feature with a sequence ontology type"})]})}),d===Nl.CUSTOM?i.jsx(qs,{session:r,ontologyName:"Sequence Ontology",style:{width:170},value:h,filterTerms:Cs,renderInput:e=>i.jsx(s.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0}),onChange:(e,t)=>{var n;t&&(n=t,_(""),p(n))}}):null]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{variant:"contained",type:"submit",disabled:b,children:"Submit"}),i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:t,children:"Cancel"})]})]}),y?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:y})}):null]})}function El({changeManager:e,handleClose:t,session:n}){const{internetAccounts:r}=l.getRoot(n),[o,a]=u.useState(""),[c,d]=u.useState(!1),[f,h]=u.useState(!1),p=r.filter((e=>"ApolloInternetAccount"===e.type));if(0===p.length)throw new Error("No Apollo internet account found");const[g,m]=u.useState(p[0]),{collaborationServerDriver:y}=n.apolloDataStore,_=y.getAssemblies(),[v,b]=u.useState(_.at(0));return i.jsxs(Bs,{open:!0,title:"Delete Assembly",handleClose:t,maxWidth:!1,"data-testid":"delete-assembly",children:[i.jsxs("form",{onSubmit:async function(n){if(n.preventDefault(),h(!0),a(""),!v)return void a("Must select assembly!");const r=new xt({typeName:"DeleteAssemblyChange",assembly:v.name});await e.submit(r,{internetAccountId:g.internetAccountId}),t(),n.preventDefault()},children:[i.jsxs(s.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[p.length>1?i.jsxs(i.Fragment,{children:[i.jsx(s.DialogContentText,{children:"Select account"}),i.jsx(s.Select,{value:g.internetAccountId,onChange:function(e){h(!1);const t=p.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID "${e.target.value}"`);m(t)},disabled:f&&!o,children:r.map((e=>i.jsx(s.MenuItem,{value:e.internetAccountId,children:e.name},e.id)))})]}):null,i.jsx(s.DialogContentText,{children:"Select assembly"}),i.jsx(s.Select,{labelId:"label",value:v?.name??"",onChange:function(e){const t=_.find((t=>t.name===e.target.value));b(t)},disabled:0===_.length,children:_.map((e=>i.jsx(s.MenuItem,{value:e.name,children:e.displayName},e.name)))}),i.jsx(s.DialogContentText,{children:i.jsx("strong",{style:{color:"red"},children:"NOTE: All assembly data will be deleted and this operation cannot be undone!"})}),i.jsx(s.FormGroup,{children:i.jsx(s.FormControlLabel,{control:i.jsx(s.Checkbox,{checked:c,onChange:()=>{d(!c)}}),label:"I understand that all assembly data will be deleted"})})]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{disabled:!v||!c,variant:"contained",type:"submit",children:"Delete"}),i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:t,children:"Cancel"})]})]}),o?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:o})}):null]})}!function(e){e.GENE_AND_SUBFEATURES="GENE_AND_SUBFEATURES",e.TRANSCRIPT_AND_SUBFEATURES="TRANSCRIPT_AND_SUBFEATURES",e.CUSTOM="CUSTOM"}(Nl||(Nl={}));var Il,jl,Dl,Ol,Fl={},Ml={},Ll={},Pl={};function Bl(){if(Il)return Pl;function e(e){return decodeURIComponent(e)}function t(e,t){return String(t).replaceAll(e,(function(e){return encodeURIComponent(e).toUpperCase()}))}function n(e){return t(/[\n;\r\t=%&,\u0000-\u001f\u007f]/g,e)}function r(e){return t(/[\n\r\t%\u0000-\u001f\u007f]/g,e)}function o(t){if(null==t||!t.length||"."===t)return{};var n={};return t.replace(/\r\n|[\r\n]$/,"").split(";").forEach((function(t){var r,o,i=t.split("=",2);if(null!==(r=i[1])&&void 0!==r&&r.length){i[0]=i[0].trim();var a=n[i[0].trim()];a||(n[i[0]]=a=[]),(o=a).push.apply(o,W(i[1].split(",").map((function(e){return e.trim()})).map(e)))}})),n}function i(e){var t=[];return Object.entries(e).forEach((function(e){var r=G(e,2),o=r[0],i=r[1].map(n).join(",");t.push("".concat(n(o),"=").concat(i))})),t.length?t.join(";"):"."}function a(e,t){var n=null==e.attributes?".":i(e.attributes),o=[null===e.seq_id?".":r(e.seq_id),null===e.source?".":r(e.source),null===e.type?".":r(e.type),null===e.start?".":r(e.start),null===e.end?".":r(e.end),null===e.score?".":r(e.score),null===e.strand?".":r(e.strand),null===e.phase?".":r(e.phase),n],a="".concat(o.join("\t"),"\n");return t[a]?"":(t[a]=!0,a)}function s(e,t){if(Array.isArray(e))return e.map((function(e){return s(e,t)})).join("");var n,r=[a(e,t)];return void 0!==(n=e).child_features&&void 0!==n.derived_features&&r.push.apply(r,W(e.child_features.map((function(e){return s(e,t)}))).concat(W(e.derived_features.map((function(e){return s(e,t)}))))),r.join("")}function l(e){return s(e,{})}function c(e){var t="##".concat(e.directive);return e.value&&(t+=" ".concat(e.value)),t+"\n"}function u(e){return"# ".concat(e.comment,"\n")}function d(e){for(var t=">".concat(e.id).concat(e.description?" 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URL("auth/types",e).href,r=await fetch(t,{method:"GET",signal:n});if(!r.ok){const e=await dl(r,"Error when retrieving auth types from server");return void a(e)}const o=await r.json();c(o),0===o.length&&a("No login types configured")}().catch((e=>{ts(e)||a(String(e))})),()=>{t.abort(new DOMException("Error retrieving valid authentication types","AbortError"))}}),[e]),null===l)return"Loading…";const f=l.at(0);return f&&1===l.length&&!f.needsPopup&&d(f),i.jsxs(Bs,{open:!0,title:`Log in to ${n}`,handleClose:t,maxWidth:!1,"data-testid":"login-apollo",children:[i.jsx(s.DialogContent,{style:{display:"flex",flexDirection:"column",paddingTop:8},children:l.map((e=>"google"===e.name?i.jsx(vc,{message:e.message,onClick:()=>{d(e)}},e.name):"microsoft"===e.name?i.jsx(bc,{message:e.message,onClick:()=>{d(e)}},e.name):"guest"===e.name?i.jsxs(u.Fragment,{children:[i.jsx(s.Divider,{className:r.divider}),i.jsx(xc,{message:e.message,onClick:()=>{d(e)}})]},e.name):i.jsx(wc,{message:e.message,onClick:()=>{d(e)}},e.name)))}),i.jsx(s.DialogActions,{children:i.jsx(s.Button,{variant:"outlined",type:"submit",onClick:()=>{t()},children:"Cancel"})}),o?i.jsx(s.DialogContent,{children:i.jsx(s.DialogContentText,{color:"error",children:o})}):null]})},Ac="undefined"==typeof sessionStorage,kc=e=>r.InternetAccount.named("ApolloInternetAccount").props({type:l.types.literal("ApolloInternetAccount"),configuration:n.ConfigurationReference(e)}).views((e=>({get baseURL(){return n.getConf(e,"baseURL")},getUserId(){const t=e.retrieveToken();if(t)return ln(t).id}}))).volatile((()=>({role:void 0,controller:new AbortController,tokenPromise:void 0}))).actions((e=>({setRole(){const t=e.retrieveToken();if(!t)return void(e.role=void 0);const n=ln(t),{role:r,exp:o}=n;if(o<Date.now()/1e3)return e.role=void 0,void e.removeToken();e.role!==r&&(e.role=r)}}))).actions((e=>{const t=e.getFetcher;return{getFetcher(n){const r=t(n);return async(t,n)=>{const o=await r(t,n);return 403===o.status?(e.removeToken(),e.setRole(),r(t,n)):o}}}})).actions((e=>({removeToken(){sessionStorage.removeItem(e.tokenKey),e.tokenPromise=void 0}}))).actions((e=>({async getToken(t){if(e.tokenPromise)return e.tokenPromise;let n=t?.internetAccountPreAuthorization?.authInfo?.token;if(n)return e.tokenPromise=Promise.resolve(n),e.tokenPromise;if(Ac)throw new Error("Did not get internet account pre-authorization info in worker");return n=e.retrieveToken(),n?(e.tokenPromise=Promise.resolve(n),e.tokenPromise):(e.tokenPromise=new Promise(((t,n)=>{e.getTokenFromUser((n=>{e.storeToken(n),t(n)}),(t=>{e.removeToken(),n(t)}))})),e.tokenPromise)}}))).actions((e=>{let t;return{addMessageChannel(e,n){t=t=>{this.finishOAuthWindow(t,e,n)},window.addEventListener("message",t)},deleteMessageChannel(){window.removeEventListener("message",t)},finishOAuthWindow(t,n,r){if(t.data.name!==`JBrowseAuthWindow-${e.internetAccountId}`)return;const o=t.data.redirectUri.replace("#","?"),i=new URL(o),a=new URLSearchParams(i.search).get("access_token");this.deleteMessageChannel(),a?(e.storeToken(a),e.setRole(),n(a)):r(new Error("Error with token endpoint"))},async openAuthWindow(t,n,r){const i=o.isElectron?"http://localhost/auth":globalThis.location.origin+globalThis.location.pathname,a=new URL("auth/login",e.baseURL),s=new URLSearchParams({type:t,redirect_uri:i});a.search=s.toString();const l=`JBrowseAuthWindow-${e.internetAccountId}`;if(o.isElectron){const{ipcRenderer:t}=globalThis.require("electron"),o=await t.invoke("openAuthWindow",{internetAccountId:e.internetAccountId,data:{redirect_uri:i},url:a.toString()}),s=new MessageEvent("message",{data:{name:l,redirectUri:o}});this.finishOAuthWindow(s,n,r)}else this.addMessageChannel(n,r),window.open(a,l,"width=500,height=600")}}})).actions((e=>({async getTokenFromUser(t,n){const{baseURL:r}=e,o=await new Promise(((t,n)=>{const{session:r}=l.getRoot(e),{baseURL:o,name:i}=e;r.queueDialog((e=>[Cc,{name:i,handleClose:r=>{r?r instanceof Error?n(r):t(r):n(new Error("user cancelled entry")),e()},baseURL:o}]))}));if(o.needsPopup)return void e.openAuthWindow(o.name,t,n);const i=new URL("auth/login",r),a=new URLSearchParams({type:o.name});i.search=a.toString();const s=i.toString(),c=await fetch(s,{signal:e.controller.signal});if(!c.ok){const e=await dl(c,"Error when logging in");return void n(new Error(e))}const{token:u}=await c.json();t(u)}}))).volatile((()=>({lastChangeSequenceNumber:void 0}))).actions((e=>({setLastChangeSequenceNumber(t){e.lastChangeSequenceNumber=t}}))).actions((e=>({updateLastChangeSequenceNumber:l.flow((function*(){const{baseURL:t}=e,n=new URL("changes",t),r=new URLSearchParams({limit:"1"});n.search=r.toString();const o=n.toString(),i=e.getFetcher({locationType:"UriLocation",uri:o});let a;try{a=yield i(o,{method:"GET",signal:e.controller.signal})}catch(t){return void(e.controller.signal.aborted||console.error(t))}if(!a.ok){const e=yield dl(a,"Error when fetching server LastChangeSequence");throw new Error(e)}const{changes:s}=yield a.json();e.setLastChangeSequenceNumber(s.length>0?s[0].sequence:0)})),getMissingChanges:l.flow((function*(){const{session:t}=l.getRoot(e),{changeManager:n}=t.apolloDataStore;if(!e.lastChangeSequenceNumber)throw new Error("No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server");const{baseURL:r,lastChangeSequenceNumber:o}=e,i=new URL("changes",r),a=new URLSearchParams({since:String(o),sort:"1"});i.search=a.toString();const s=i.toString(),c=e.getFetcher({locationType:"UriLocation",uri:s});let u;try{u=yield c(s,{method:"GET",signal:e.controller.signal})}catch(t){return void(e.controller.signal.aborted||console.error(t))}if(!u.ok)return void console.error(`Error when fetching the last updates to recover socket connection — ${u.status}`);const{changes:d}=yield u.json();for(const e of d){const t=ee.fromJSON(e);n.submit(t,{submitToBackend:!1})}}))}))).volatile((e=>{const{origin:t,pathname:n}=new URL("socket.io/",e.baseURL);return{socket:so(t,{path:n})}})).actions((e=>({addSocketListeners(){const{session:t}=l.getRoot(e),{notify:n}=t,r=e.retrieveToken();if(!r)throw new Error("No Token found");const o=sn(ln(r)),{socket:i}=e,{addCheckResult:a,changeManager:s,deleteCheckResult:c}=t.apolloDataStore;i.on("connect",(()=>{e.getMissingChanges()})),i.on("connect_error",(e=>{console.error(e),n("Could not connect to the Apollo server.","error")})),i.on("COMMON",(e=>{if("checkResult"in e)return void(e.deleted?c(e.checkResult._id):a(e.checkResult));if(sessionStorage.setItem("LastChangeSequence",String(e.changeSequence)),e.userSessionId===o)return;const t=ee.fromJSON(e.changeInfo);s.submit(t,{submitToBackend:!1})})),i.on("USER_LOCATION",(e=>{const{channel:n,locations:r,userName:i,userSessionId:a}=e;"USER_LOCATION"===n&&a!==o&&t.addOrUpdateCollaborator({name:i,id:a,locations:r})})),i.on("REQUEST_INFORMATION",(e=>{const{channel:n,userSessionId:o}=e;"REQUEST_INFORMATION"===n&&o!==r&&t.broadcastLocations()}))}}))).actions((e=>({postUserLocation:(t=>{let n;return t=>{clearTimeout(n),n=setTimeout((()=>{!async function(t){if(!l.isAlive(e)||"none"===e.role)return;const{baseURL:n,controller:r}=e,o=new URL("users/userLocation",n).href,i=new URLSearchParams(JSON.stringify(t)),a=e.getFetcher({locationType:"UriLocation",uri:o});try{if(!(await a(o,{method:"POST",body:i,signal:r.signal})).ok)throw new Error("ignore")}catch{console.error("Broadcasting user location failed")}}(t)}),300)}})()}))).volatile((()=>({roleNotificationSent:!1}))).actions((e=>{function t(){e.postUserLocation([])}function n(){if("hidden"===document.visibilityState&&e.postUserLocation([]),"visible"===document.visibilityState){const{session:t}=l.getRoot(e);t.broadcastLocations()}}return{initialize:l.flow((function*(r){if("none"===r){if(!e.roleNotificationSent){const{session:t}=l.getRoot(e);t.notify("You have registered as an Apollo user but have not been given access. Ask your administrator to enable access for your account.","warning"),e.roleNotificationSent=!0}return}if("admin"===r){const t=l.getRoot(e);o.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Admin",type:"subMenu",icon:lo,subMenu:[{label:"Add Assembly",icon:Ln,onClick:e=>{e.queueDialog((t=>[gl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Delete Assembly",icon:co,onClick:e=>{e.queueDialog((t=>[El,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Import Features",icon:uo,onClick:e=>{e.queueDialog((t=>[Jl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[lc,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add Assembly aliases",onClick:e=>{e.queueDialog((t=>[yl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Users",icon:fo,onClick:e=>{e.queueDialog((t=>[Zl,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Checks",icon:ho,onClick:e=>{e.queueDialog((t=>[Yl,{session:e,handleClose:()=>{t()}}]))}}]})}(t)}yield e.updateLastChangeSequenceNumber(),e.addSocketListeners();const{baseURL:i}=e,a=new URL("users/locations",i).href,s=e.getFetcher({locationType:"UriLocation",uri:a});yield s(a,{method:"GET",signal:e.controller.signal}),window.addEventListener("beforeunload",t),document.addEventListener("visibilitychange",n)})),removeBeforeUnloadListener(){window.removeEventListener("beforeunload",t)},removeVisibilityChangeListener(){document.removeEventListener("visibilitychange",n)}}})).actions((e=>({afterAttach(){e.setRole(),c.autorun((async t=>{if(Ac)return;const{session:n}=l.getRoot(e);if(n&&e.role)try{await e.initialize(e.role),t.dispose()}catch{}}),{name:"ApolloInternetAccount"})},beforeDestroy(){e.removeBeforeUnloadListener(),e.removeVisibilityChangeListener(),e.controller.abort(new DOMException("Cleaning up Apollo connection","AbortError")),e.socket.close()}})));var Nc=function(){return crypto.getRandomValues(new Uint8Array(arguments.length>0&&void 0!==arguments[0]?arguments[0]:21)).reduce((function(e,t){return e+((t&=63)<36?t.toString(36):t<62?(t-26).toString(36).toUpperCase():t>62?"-":"_")}),"")};const Tc="undefined"==typeof sessionStorage;class Rc extends _.BaseAdapter{refNameAliasesP;async getRefNameAliases(){if(this.refNameAliasesP)return this.refNameAliasesP;const e=n.readConfObject(this.config,"assemblyId");if(!Tc){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e);if(!n)throw new Error("No backend driver found");return await n.getRefNameAliases(e)}const t=new Promise(((t,n)=>{const r=setTimeout((()=>{n(new Error("timeout"))}),2e4),o=Nc(),i=e=>{const n=e.data;(function(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo&&"refNameAliases"in e})(n)&&n.messageId===o&&(clearTimeout(r),removeEventListener("message",i),t(n.refNameAliases))};addEventListener("message",i),rpcServer.emit("apollo",{apollo:!0,method:"getRefNameAliases",assembly:e,messageId:o})}));return this.refNameAliasesP=t,t}freeResources(){}}var Ec=n.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function Ic(e){return"uniqueId"in e&&"object"!==K(e.data)}var jc=function(){function e(t){var n=this;R(this,e),D(this,"data",void 0),D(this,"subfeatures",void 0),D(this,"parentHandle",void 0),D(this,"uniqueId",void 0),Ic(t)?this.data=t:(this.data=t.data,this.parentHandle=t.parent);var r,o=Ic(t)?t.uniqueId:t.id;if(null==o)throw new Error("SimpleFeature requires a unique `id` or `data.uniqueId` attribute");if(this.uniqueId=String(o),!(this.data.aliases||this.data.end-this.data.start>=0))throw new Error("invalid feature data, end less than start. end: ".concat(this.data.end," start: ").concat(this.data.start));this.data.subfeatures&&(this.subfeatures=null===(r=this.data.subfeatures)||void 0===r?void 0:r.map((function(t,r){return"function"!=typeof t.get?new e({id:t.uniqueId||"".concat(o,"-").concat(r),data:B({strand:n.data.strand},t),parent:n}):t})))}return I(e,[{key:"get",value:function(e){return"subfeatures"===e?this.subfeatures:"parent"===e?this.parent():this.data[e]}},{key:"set",value:function(e,t){this.data[e]=t}},{key:"tags",value:function(){return Object.keys(this.data)}},{key:"id",value:function(){return this.uniqueId}},{key:"parent",value:function(){return this.parentHandle}},{key:"children",value:function(){return this.get("subfeatures")}},{key:"toJSON",value:function(){var e=B(B({},this.data),{},{uniqueId:this.id()}),t=this.parent();t&&(e.parentId=t.id());var n=this.children();return n&&(e.subfeatures=n.map((function(e){return e.toJSON()}))),e}}],[{key:"fromJSON",value:function(t){return new e(B({},t))}}])}();function Dc(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo}const Oc="undefined"==typeof sessionStorage;class Fc extends _.BaseSequenceAdapter{regions;async getRefNames(){return(await this.getRegions()).map((e=>e.refName))}async getRegions(){if(this.regions)return this.regions;const e=n.readConfObject(this.config,"assemblyId");if(!Oc){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e);if(!n)throw new Error("No backend driver found");const r=await n.getRegions(e);return this.regions=r,r}const t=await new Promise(((t,n)=>{const r=setTimeout((()=>{n("timeout")}),2e4),o=Nc(),i=e=>{const{data:n}=e;Dc(n)&&n.messageId===o&&(clearTimeout(r),removeEventListener("message",i),t(n.regions))};addEventListener("message",i),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getRegions",assembly:e,messageId:o})}));return this.regions=t,t}getFeatures(e){const{end:t,refName:r,start:o}=e,i=n.readConfObject(this.config,"assemblyId"),a={...e,assemblyName:i};return v.ObservableCreate((async e=>{if(!Oc){const n=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!n)return void e.error("No Apollo data store found");const s=n.getBackendDriver(i);if(!s)return void e.error("No backend driver found");const l=(await s.getRegions(a.assemblyName)).find((e=>e.refName===a.refName));if(!l)return void e.error("Cannot get region");a.end>l.end&&(a.end=l.end);const{seq:c}=await s.getSequence(a);return e.next(new jc({id:`${r} ${o}-${t}`,data:{refName:r,start:o,end:t,seq:c}})),void e.complete()}const n=await new Promise(((e,t)=>{const n=setTimeout((()=>{t("timeout")}),2e4),r=Nc(),o=t=>{const{data:i}=t;Dc(i)&&i.messageId===r&&(clearTimeout(n),removeEventListener("message",o),e(i.sequence))};addEventListener("message",o),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getSequence",region:a,messageId:r})}));e.next(new jc({id:`${r} ${o}-${t}`,data:{refName:r,start:o,end:t,seq:n}})),e.complete()}))}freeResources(){}}var Mc=n.ConfigurationSchema("ApolloSequenceAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0}),Lc=function(){return I((function e(t){R(this,e),D(this,"label",void 0),D(this,"renderingComponent",void 0),D(this,"displayString",void 0),D(this,"matchedAttribute",void 0),D(this,"matchedObject",void 0),D(this,"textSearchAdapter",void 0),D(this,"relevance",void 0),D(this,"trackId",void 0),D(this,"score",void 0),D(this,"locString",void 0),D(this,"results",void 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i="forward"===e?r.createLinearGradient(0,o,o,0):r.createLinearGradient(0,0,o,o);i.addColorStop(0,a),i.addColorStop(.25,a),i.addColorStop(.25,s),i.addColorStop(.5,s),i.addColorStop(.5,a),i.addColorStop(.75,a),i.addColorStop(.75,s),i.addColorStop(1,s),r.fillStyle=i,r.clearRect(0,0,o,o),r.fillRect(0,0,o,o),t[e]=r.createPattern(n,"repeat")}return t}}))).actions((e=>({toggleShown(){e.isShown=!e.isShown},setDetailsHeight(t){e.detailsHeight=e.isShown?Math.max(Math.min(t,e.height-100),Math.min(e.height,e.detailsMinHeight)):t},setCanvas(t){e.canvas=t},setOverlayCanvas(t){e.overlayCanvas=t},setCollaboratorCanvas(t){e.collaboratorCanvas=t},setTheme(t){e.theme=t}}))).actions((e=>({afterAttach(){l.addDisposer(e,c.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.collaboratorCanvas?.getContext("2d");if(t){t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight(e.lgv.assemblyNames[0]));for(const n of e.session.collaborators){const{locations:r}=n;if(0===r.length)continue;let o=0;for(const i of e.lgv.displayedRegions){for(const a of r){if(a.refSeq!==i.refName)continue;const{end:r,refSeq:s,start:l}=a,c=e.lgv.bpToPx({refName:s,coord:l,regionNumber:o});if(!c)continue;const u=c.offsetPx-e.lgv.offsetPx,d=(r-l)/e.lgv.bpPerPx;t.fillStyle="rgba(0,255,0,.2)",t.fillRect(u,1,d,100),t.fillStyle="black",t.fillText(n.name,u+1,11,d-2)}o++}}}}),{name:"LinearApolloDisplayRenderCollaborators"})),l.addDisposer(e,c.autorun((()=>{const{canvas:t,layouts:n,lgv:r}=e;if(!r.initialized||e.regionCannotBeRendered()||!t)return;const{dynamicBlocks:i,offsetPx:a}=r,s=t.getContext("2d");if(!s)return;const l=n.get(r.assemblyNames[0]);if(l){s.clearRect(0,0,t.width,t.height);for(const n of i.contentBlocks){const r=n.offsetPx-a;s.save(),s.beginPath(),s.rect(r,0,n.widthPx,t.height),s.clip();const i=l.get(n.refName);if(!i)return;const{byRow:c}=i;for(const[t,r]of c.entries())for(const i of r){const{feature:r,rowInFeature:a}=i;o.doesIntersect2(n.start,n.end,r.min,r.max)&&e.getGlyph(r).draw(e,s,r,t,a,n)}for(const[t,r]of c.entries())for(const i of r){const{feature:r,rowInFeature:a}=i;o.doesIntersect2(n.start,n.end,r.min,r.max)&&e.getGlyph(r).drawOverlay(e,s,r,t,n,"highlight",a)}s.restore()}}}),{name:"LinearApolloDisplayRenderFeatures"}))}})))}(0,t);return i.named("LinearApolloDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0}))).views((e=>({getMousePosition:t=>function(e,t){const n=e.currentTarget,{clientX:r,clientY:o}=e,{left:i,top:a}=n.getBoundingClientRect(),s=r-i,l=o-a,{coord:c,index:u,assemblyName:d,refName:f}=t.pxToBp(s);return{x:s,y:l,assemblyName:d,refName:f,bp:c,regionNumber:u}}(t,e.lgv),getFeaturesAtMousePosition(t){const{bp:n,assemblyName:r,refName:o,y:i}=t,a=Math.floor(i/e.apolloRowHeight),s=e.layouts.get(r)?.get(o);return s?e.getFeaturesAtPosition(r,o,a,n):[]}}))).actions((e=>({continueDrag(t,n){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in progress");n.stopPropagation(),e.apolloDragging={...e.apolloDragging,current:t}},setDragging(t){e.apolloDragging=t??null}}))).actions((e=>({setCursor(t){e.cursor!==t&&(e.cursor=t)},updateFilteredTranscripts(e){}}))).actions((()=>({onClick(){}})))}(0,t).views((e=>({contextMenuItems(t){const n=e.getMousePosition(t),r=e.getFeaturesAtMousePosition(n);if(1===r.length)return il(e,r[0]);const o=[];for(const t of r){const n=e.getGlyph(t);o.push({label:t.type,subMenu:[...il(e,t),...n.getContextMenuItems(e,t)]})}return o}}))).actions((e=>{function t(t){"Escape"===t.key&&e.setDragging()}return{startDrag(n,r,o,i=!1){globalThis.addEventListener("keydown",t,!0),e.apolloDragging={start:n,current:n,feature:r,edge:o,shrinkParent:i}},endDrag(){if(globalThis.removeEventListener("keydown",t,!0),!e.apolloDragging)throw new Error("endDrag() called with no current drag in 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e.setCursor("col-resize"),void e.continueDrag(n,t);const r=e.getFeaturesAtMousePosition(n);let o=r.at(-1);if(o&&Xs(o,e.session)){const t=r.at(-2);t&&!Ys(t,e.session)&&(o=t)}o?e.setHoveredFeature({feature:o,bp:n.bp}):e.setHoveredFeature();for(const t of r.toReversed())if(e.getGlyph(t).isDraggable&&pd(n,t,e))return void e.setCursor("col-resize");e.setCursor()},onMouseLeave(t){e.setDragging(),e.setHoveredFeature()},onMouseUp(t){if(e.apolloDragging)return void e.endDrag();const n=e.getMousePosition(t),r=e.getFeaturesAtMousePosition(n);let o=r.at(-1);if(o&&Xs(o,e.session)){const t=r.at(-2);t&&!Ys(t,e.session)&&(o=t)}o?(Ws(e,o),e.setSelectedFeature(o)):e.setSelectedFeature()}}))).actions((e=>({afterAttach(){l.addDisposer(e,c.autorun((()=>{const{lgv:t,overlayCanvas:n}=e;if(!t.initialized||e.regionCannotBeRendered()||!n)return;const{dynamicBlocks:r,offsetPx:i}=t,a=n.getContext("2d");if(!a)return;a.clearRect(0,0,n.width,n.height);const{apolloDragging:s,hoveredFeature:l}=e;if(!l)return;const{feature:c}=l,u=e.getGlyph(c),d=e.getRowForFeature(c);if(void 0!==d)for(const t of r.contentBlocks){const r=t.offsetPx-i;if(a.save(),a.beginPath(),a.rect(r,0,t.widthPx,n.height),a.clip(),t.assemblyName===c.assemblyId&&o.doesIntersect2(t.start,t.end,c.min,c.max)&&u.drawOverlay(e,a,c,d,t,"hover"),s){const{current:n,start:r,feature:i}=s,l=Math.min(n.bp,r.bp),c=Math.max(n.bp,r.bp);if(o.doesIntersect2(t.start,t.end,l,c)){const n=e.getGlyph(i),r=e.getRowForFeature(i);void 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r=(1===n?3:4)*a,u=1===n?t:o.revcom(t);e.fillStyle=Vd(u,s),e.fillRect(l,r,c,a),1/i>=12&&(hd(e,l,r,c,a,s.palette.text.disabled),ef(e,l,r,c,u))}}function rf(e,t,n,r,i,a,s,l,c,u,d){const f=(s<=1?[0,2,1,0,7,6,5]:[0,2,1,0,5,4,3]).map((e=>e*c)),h=[-1,1];for(const p of h){const h=o.getFrame(l,l+3,p,0),g=f.at(h);if(void 0===g)continue;const m=Math.round(n+r/s),y=Math.round(n+(r+3)/s)-m,_=1===p?t:o.revcom(t),v=o.defaultCodonTable[_],b=Gd(v,i,a);b&&(d&&"*"==v||u&&"*"!=v)&&(e.fillStyle=b,e.fillRect(m,g,y,c)),1/s>=4&&(hd(e,m,g,y,c,i.palette.text.disabled),ef(e,m,g,y,v))}}function of(e,t){return function(e,t){const i=function(e,t){return r.BaseDisplay.named("BaseLinearApolloReferenceSequenceDisplay").props({type:l.types.literal("LinearApolloReferenceSequenceDisplay"),configuration:n.ConfigurationReference(t),showStartCodons:!1,showStopCodons:!0,highContrast:!1,heightPreConfig:l.types.maybe(l.types.refinement("displayHeight",l.types.number,(e=>e>=20))),sequenceRowHeight:15}).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...b.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get lgv(){return o.getContainingView(e)}}))).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get session(){return o.getSession(e)},get regions(){return e.lgv.dynamicBlocks.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:r})=>({assemblyName:e,refName:n,start:Math.round(r),end:Math.round(t)})))},regionCannotBeRendered(){if(e.lgv&&e.lgv.bpPerPx>3)return"Zoom in to see sequence"}}))).views((e=>({get expandedRegions(){return e.lgv.dynamicBlocks.contentBlocks.map((e=>{const{assemblyName:t,end:n,refName:r,start:o}=e,{parentRegion:i}=e;return{assemblyName:t,refName:r,start:Math.round(Math.max(o-5,i.start)),end:Math.round(Math.min(n+5,i.end))}}))},get apolloInternetAccount(){const[t]=e.regions,{internetAccounts:r}=l.getRoot(e),{assemblyName:o}=t,{assemblyManager:i}=e.session,a=i.get(o);if(!a)throw new Error(`No assembly found with name ${o}`);const{internetAccountConfigId:s}=n.getConf(a,["sequence","metadata"]);return r.find((e=>n.getConf(e,"internetAccountId")===s))},get changeManager(){return e.session.apolloDataStore.changeManager},getAssemblyId(t){const{assemblyManager:n}=e.session,r=n.get(t);if(!r)throw new Error(`Could not find assembly named ${t}`);return r.name},get selectedFeature(){return e.session.apolloSelectedFeature},get hoveredFeature(){return e.session.apolloHoveredFeature},get height(){const{sequenceRowHeight:t}=e;return e.lgv.bpPerPx<=1?8*t:6*t}}))).volatile((()=>({scrollTop:0}))).actions((e=>({setScrollTop(t){e.scrollTop=t},setHeight:t=>(e.heightPreConfig=Math.max(t,20),e.height),resizeHeight(t){const n=e.height;return this.setHeight(e.height+t)-n},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleHighContrast(){e.highContrast=!e.highContrast}}))).views((e=>{const{trackMenuItems:t}=e;return{trackMenuItems(){const{showStartCodons:n,showStopCodons:r,highContrast:o}=e;return[...t(),{type:"subMenu",label:"Appearance",subMenu:[{label:"Show start codons",type:"checkbox",checked:n,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:r,onClick:()=>{e.toggleShowStopCodons()}},{label:"Use high contrast colors",type:"checkbox",checked:o,onClick:()=>{e.toggleHighContrast()}}]}]}}})).actions((e=>({afterAttach(){l.addDisposer(e,c.autorun((()=>{e.lgv.initialized&&!e.regionCannotBeRendered()&&e.lgv.bpPerPx<=3&&e.session.apolloDataStore.loadRefSeq(e.expandedRegions)}),{name:"LinearApolloReferenceSequenceDisplayLoadFeatures",delay:1e3}))}})))}(0,t);return i.named("LinearApolloReferenceSequenceDisplayRendering").volatile((()=>({seqTrackCanvas:null,seqTrackOverlayCanvas:null,theme:s.createTheme()}))).actions((e=>({setSeqTrackCanvas(t){e.seqTrackCanvas=t},setSeqTrackOverlayCanvas(t){e.seqTrackOverlayCanvas=t},setTheme(t){e.theme=t},afterAttach(){l.addDisposer(e,c.autorun((()=>{const{lgv:t,seqTrackCanvas:n,theme:r,highContrast:i,showStartCodons:a,showStopCodons:s,sequenceRowHeight:l,session:c}=e;if(!t.initialized||e.regionCannotBeRendered()||!n)return;if(3/t.bpPerPx<1)return;const{bpPerPx:u,offsetPx:d,dynamicBlocks:f}=t;!function(e,t,n,r,i,a,s,l,c,u){const d=e.getContext("2d");if(!d)return;d.clearRect(0,0,e.width,e.height);const{apolloDataStore:f}=u;for(const e of i.contentBlocks){const i=e.offsetPx-r;tf(d,n,t,a,i,e.widthPx,c,e.reversed);const u=f.assemblies.get(e.assemblyName),h=u?.getByRefName(e.refName),p=Math.floor(e.start),g=Math.ceil(e.end);let m=h?.getSequence(p,g);if(!m)return;m=m.toUpperCase(),e.reversed&&(m=o.revcom(m));const y=i-(e.reversed?g-e.end:e.start-p)/n;for(let r=0;r<m.length;r++){const o=e.reversed?g-r:p+r,i=m.slice(r,r+3);nf(d,m[r],r,y,n,c,t),3===i.length&&rf(d,i,y,r,t,a,n,o,c,s,l)}}}(n,r,u,d,f,i,a,s,l,c)}),{name:"LinearApolloReferenceSequenceDisplayRenderSequence"})),l.addDisposer(e,c.autorun((()=>{const{seqTrackOverlayCanvas:t}=e;if(!e.lgv.initialized||e.regionCannotBeRendered()||!t)return;const n=t.getContext("2d");if(!n)return;n.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.height);const{hoveredFeature:r,selectedFeature:o,lgv:i,sequenceRowHeight:a,session:s,theme:l}=e;if(!r&&!o)return;const{bpPerPx:c,dynamicBlocks:u,offsetPx:d}=i;!function(e,t,n,r,o,i,a,s,l,c){const{featureTypeOntology:u}=a.apolloDataStore.ontologyManager;if(!u)throw new Error("featureTypeOntology is undefined");for(const a of c.contentBlocks){t.save(),t.beginPath(),t.rect(a.offsetPx-l,0,a.widthPx,e.height),t.clip();for(const e of[r,n?.feature].filter((e=>void 0!==e)))u.isTypeOf(e.type,"CDS")?Qd(t,e,s,l,o,a,i,e._id===r?._id):Zd(t,e,s,l,o,a,i,e._id===r?._id);t.restore()}}(t,n,r,o,a,l,s,c,d,u)}),{name:"LinearApolloReferenceSequenceDisplayRenderSequenceHighlight"}))}})))}(0,t).named("LinearApolloReferenceSequenceDisplay")}const af=p.observer((function(e){const t=s.useTheme(),{model:n}=e,{height:r,regionCannotBeRendered:a,setSeqTrackCanvas:l,setSeqTrackOverlayCanvas:c,setTheme:d}=n,{classes:f}=$d();u.useEffect((()=>{d(t)}),[t,d]);const h=o.getContainingView(n),p=a();return p?i.jsx(s.Alert,{severity:"warning",classes:{message:f.ellipses},slotProps:{root:{className:f.center}},children:i.jsx(s.Tooltip,{title:p,children:i.jsx("div",{children:p})})}):i.jsx(i.Fragment,{children:3/h.bpPerPx>=1?i.jsxs("div",{className:f.canvasContainer,style:{width:h.dynamicBlocks.totalWidthPx,height:r},children:[i.jsx("canvas",{ref:async e=>{await Promise.resolve(),l(e)},width:h.dynamicBlocks.totalWidthPx,height:r,className:f.canvas,"data-testid":"seqTrackCanvas"}),i.jsx("canvas",{ref:async e=>{await 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i.jsxs("div",{style:{height:h},children:[i.jsx(Vf,{open:p,title:"Graphical",onClick:_}),i.jsx("div",{className:c.shading,ref:v,style:{height:r},children:i.jsx(zf,{model:e,...t})}),i.jsx(Vf,{title:"Table",open:y.isShown,onClick:y.togglePane,onResize:b}),i.jsx("div",{className:c.details,style:{height:n},children:i.jsx(ld,{model:e})})]})}return i.jsx("div",f?{className:c.shading,ref:v,style:{height:h},children:i.jsx(zf,{model:e,...t})}:{className:c.details,style:{height:h},children:i.jsx(ld,{model:e})})}));var Kf=a.createSvgIcon(i.jsx("path",{d:"m17 7-1.41 1.41L18.17 11H8v2h10.17l-2.58 2.58L17 17l5-5zM4 5h8V3H4c-1.1 0-2 .9-2 2v14c0 1.1.9 2 2 2h8v-2H4z"}),"Logout"),Yf=a.createSvgIcon(i.jsx("path",{d:"M18.4 10.6C16.55 8.99 14.15 8 11.5 8c-4.65 0-8.58 3.03-9.96 7.22L3.9 16c1.05-3.19 4.05-5.5 7.6-5.5 1.95 0 3.73.72 5.12 1.88L13 16h9V7z"}),"Redo"),Xf=a.createSvgIcon(i.jsx("path",{d:"M12.5 8c-2.65 0-5.05.99-6.9 2.6L2 7v9h9l-3.62-3.62c1.39-1.16 3.16-1.88 5.12-1.88 3.54 0 6.55 2.31 7.6 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n=o.getSession(e);o.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.addJob(t))},done(t){const n=o.getSession(e);o.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.removeJob(t.name),e.jobStatusWidget.addFinishedJob({name:t.name,statusMessage:"All operations successful",progressPct:100,cancelCallback:t.cancelCallback}))}})));function eh(e){const t={};if(e.children)for(const n of Object.values(e.children)){const e=eh(n);t[e._id]=e}return{...e,_id:(new at).toHexString(),children:e.children?t:void 0}}function th({assemblyName:e,changeManager:t,existingFeature:n,featureSnapshot:r,handleClose:o}){const[a,l]=u.useState("keepExisting"),[c,d]=u.useState(""),[f,h]=u.useState(!1);return i.jsxs(Bs,{open:!0,title:"Duplicate Feature Detected",handleClose:o,maxWidth:"sm",fullWidth:!0,children:[i.jsxs(s.DialogContent,{children:[i.jsxs(s.DialogContentText,{children:["A feature with ID “",r._id,"” already exists. How would you like to resolve this conflict?"]}),i.jsxs(s.FormControl,{component:"fieldset",sx:{mt:2},children:[i.jsx(s.FormLabel,{component:"legend",children:"Resolution"}),i.jsxs(s.RadioGroup,{value:a,onChange:e=>{l(e.target.value)},children:[i.jsx(s.FormControlLabel,{value:"keepExisting",control:i.jsx(s.Radio,{}),label:"Keep the existing feature"}),i.jsx(s.FormControlLabel,{value:"useNew",control:i.jsx(s.Radio,{}),label:"Replace with the new feature"}),i.jsx(s.FormControlLabel,{value:"keepBoth",control:i.jsx(s.Radio,{}),label:"Keep both (assign new IDs to the incoming feature)"})]})]}),c?i.jsx(s.DialogContentText,{color:"error",sx:{mt:1},children:c}):null]}),i.jsxs(s.DialogActions,{children:[i.jsx(s.Button,{variant:"contained",onClick:async()=>{d(""),h(!0);try{if("useNew"===a){const o=new pt({typeName:"DeleteFeatureChange",assembly:e,changedIds:[n._id],deletedFeature:n});await t.submit(o);const i=new ht({typeName:"AddFeatureChange",assembly:e,changedIds:[r._id],addedFeature:r});await t.submit(i)}else if("keepBoth"===a){const n=eh(r),o=new ht({typeName:"AddFeatureChange",assembly:e,changedIds:[n._id],addedFeature:n});await t.submit(o)}o()}catch(e){d(String(e)),h(!1)}},disabled:f,children:"Confirm"}),i.jsx(s.Button,{onClick:o,disabled:f,children:"Cancel"})]})]})}function nh(e,t){const r=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",cu),i=function(e){return l.types.model("ClientDataStore",{typeName:l.types.optional(l.types.literal("Client"),"Client"),assemblies:l.types.map(fu),checkResults:l.types.map(hu),ontologyManager:l.types.optional(Os,{})}).views((t=>({get internetAccounts(){return l.getRoot(t).internetAccounts},get pluginConfiguration(){return l.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>l.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const r={_id:t,refSeqs:{}};return n&&(r.backendDriverType=n),e.assemblies.put(r)}}))).actions((e=>({addFeature(t,n){const r=o.getSession(e),{assemblyManager:i}=r;let a=e.assemblies.get(t);if(!a){if(!i.get(t))throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);a=e.addAssembly(t)}let s=a.refSeqs.get(n.refSeq);if(!s){const e=i.get(t);if(!e)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const r=e.getCanonicalRefName(n.refSeq);if(!r)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);s=a.addRefSeq(n.refSeq,r)}s.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:r,parent:o}=n;o?o.deleteChild(t):l.getParentOfType(n,du).deleteFeature(r)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)},clearCheckResults(){e.checkResults.clear()}}))).volatile((e=>({changeManager:new Al(e),collaborationServerDriver:new kl(e),localDriver:new Sl(e)}))).actions((e=>({afterCreate(){l.addDisposer(e,c.autorun((()=>{const{ontologyManager:t,pluginConfiguration:r}=e,i=r.ontologies;for(const r of i||[]){const[i,a,s,l]=[n.readConfObject(r,"name"),n.readConfObject(r,"version"),n.readConfObject(r,"source"),n.readConfObject(r,"textIndexFields")];if(!t.findOntology(i)){const n=o.getSession(e),{jobsManager:r}=n,c=new AbortController,u=`Loading ontology "${i}"`,d={name:u,statusMessage:`Loading ontology "${i}", version "${a}", this may take a while`,progressPct:0,cancelCallback:()=>{c.abort(new DOMException(`Canceling loading of ontology "${i}"`,"AbortError")),r.abortJob(d.name)}};t.addOntology(i,a,s,{textIndexing:{indexFields:l},update:(e,t)=>{0!==t?100!==t?r.update(u,e,t):r.done(d):r.runJob(d)}})}}})))}}))).views((e=>({getBackendDriver(t){const r=o.getSession(e),{assemblyManager:i}=r,a=i.get(t);if(!a)return;const{internetAccountConfigId:s}=n.getConf(a,["sequence","metadata"]);return s?e.collaborationServerDriver:e.localDriver},getInternetAccount(t,r){if(!(t??r))throw new Error("Must provide either assemblyName or internetAccountId");let i=r;if(t&&!i){const{assemblyManager:r}=o.getSession(e),a=r.get(t);if(!a)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:i}=n.getConf(a,["sequence","metadata"]))}const{internetAccounts:a}=e,s=a.find((e=>e.internetAccountId===i));if(!s)throw new Error(`No InternetAccount found with config id ${r}`);return s}}))).actions((e=>({loadFeatures:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[r,o]=yield t.getFeatures(n);if(0===r.length)continue;const{assemblyName:i,refName:a}=n,s=e.assemblies.get(i)??e.assemblies.put({_id:i,refSeqs:{}}),[l]=r,c=s.refSeqs.get(l.refSeq)??s.refSeqs.put({_id:l.refSeq,name:a,features:{}});for(const e of r)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:r,seq:o}=yield t.getSequence(n),{assemblyName:i,end:a,refName:s,start:l}=n,c=e.assemblies.get(i)??e.assemblies.put({_id:i,refSeqs:{}});(c.refSeqs.get(r)??c.refSeqs.put({_id:r,name:s,sequence:[]})).addSequence({start:l,stop:a,sequence:o})}}))})))}(r),a=t.props({apolloDataStore:l.types.optional(i,{typeName:"Client"}),apolloSelectedFeature:l.types.safeReference(r),jobsManager:l.types.optional(Qf,{}),isLocked:l.types.optional(l.types.boolean,!1),changeInProgress:l.types.optional(l.types.boolean,!1)}).volatile((()=>({apolloHoveredFeature:void 0,abortController:new AbortController}))).extend((()=>{const e=c.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},apolloSetHoveredFeature(t){e.apolloHoveredFeature=t},addApolloLocalTrackConfig(t){const n=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===n))||l.getRoot(e).jbrowse.addTrackConf({type:"ApolloTrack",trackId:n,name:`Annotations (${t.displayName})`,assemblyNames:[t.name],category:["Apollo"]})},toggleLocked(){e.isLocked=!e.isLocked},setChangeInProgress(t){e.changeInProgress=t},getPluginConfiguration(){const{jbrowse:t}=l.getRoot(e);return t.configuration.ApolloPlugin},broadcastLocations(){const{internetAccounts:t}=l.getRoot(e),n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const r=t;if(r.initialized){const{dynamicBlocks:t}=r;for(const r of t.contentBlocks){const{assemblyName:t,end:o,refName:i,start:a}=r,s=e.apolloDataStore.assemblies.get(t);"CollaborationServerDriver"===s?.backendDriverType&&n.push({assemblyName:t,refName:i,start:a,end:o})}}}if(0===n.length){for(const e of t)Xl(e)&&e.postUserLocation([]);return}const r=[];for(const e of t)if(Xl(e)){for(const e of n)r.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(r)}}}))).actions((e=>({apolloSetEventualSelectedFeature:c.flow((function*(t){yield c.when((()=>Boolean(e.apolloDataStore.getFeature(t)))),e.apolloSetSelectedFeature(t)}))}))).volatile((e=>({previousSnapshot:l.getSnapshot(e)}))).actions((e=>({afterCreate(){l.applySnapshot(e,{name:e.name,id:e.id});const{internetAccounts:t,jbrowse:r,reloadPluginManagerCallback:o}=l.getRoot(e);l.addDisposer(e,c.autorun((()=>{const n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const r=t;if(r.initialized){const{dynamicBlocks:t}=r;for(const r of t.contentBlocks){const{assemblyName:t,end:o,refName:i,start:a}=r,s=e.apolloDataStore.assemblies.get(t);"CollaborationServerDriver"===s?.backendDriverType&&n.push({assemblyName:t,refName:i,start:a,end:o})}}}if(0===n.length){for(const e of t)Xl(e)&&e.postUserLocation([]);return}const r=[];for(const e of t)if(Xl(e)){for(const e of n)r.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(r)}}),{name:"ApolloSessionBroadcastLocations"})),l.addDisposer(e,c.autorun((async i=>{const a=r.configuration.ApolloPlugin,s=n.readConfObject(a,"hasRole"),c=n.readConfObject(a,"featureTypeOntologyName"),u=t.some((e=>Xl(e))),d=e.assemblyManager.assemblies.filter((e=>!n.getConf(e,["sequence","metadata"]).apollo));if(!u||s){const{assemblies:t}=e.assemblyManager;if(0===t.length)return;const{pluginConfiguration:r}=e.apolloDataStore;r.ontologies.find((e=>n.readConfObject(e,"name")===c))||r.addOntology({name:"Sequence Ontology",version:"01c33c6d9b6c8dca12e7d3e37b49ee113093c2fa",source:{uri:"https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/01c33c6d9b6c8dca12e7d3e37b49ee113093c2fa/Ontology_Files/so.json",locationType:"UriLocation"}});for(const t of d)e.addApolloLocalTrackConfig(t);return l.applySnapshot(e,e.previousSnapshot),void i.dispose()}const{signal:f}=e.abortController;for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:t}=n,r=new URL("jbrowse/config.json",t).href,a=n.getFetcher({locationType:"UriLocation",uri:r});let s,l;try{s=await a(r,{signal:f})}catch(t){e.abortController.signal.aborted||console.error(t);continue}if(s.ok){try{l=await s.json()}catch(e){console.error(e);continue}l.configuration.ApolloPlugin.hasRole&&(o(l,e.previousSnapshot),i.dispose())}else{const e=await dl(s,"Failed to fetch assemblies");console.error(e)}}}),{name:"ApolloSessionLoadConfig"}))},beforeDestroy(){e.abortController.abort(new DOMException("Clean up Apollo session","AbortError"))}}))).actions((e=>({async afterCreate(){if(o.isElectron)return;const t=new URL(globalThis.location.href).searchParams.get("apolloFeatures");if(!t)return;const{assemblyManager:n}=e;await async function(e,t,n,r){const o=function(e){let t=e.replaceAll("-","+").replaceAll("_","/");const n=t.length%4;return n&&(t+="=".repeat(4-n)),t}(e),i=await async function(e){const t=atob(e),n=Uint8Array.from(t,(e=>e.charCodeAt(0))),r=new Blob([n]).stream(),o=new DecompressionStream("gzip"),i=r.pipeThrough(o),a=new Response(i),s=await a.arrayBuffer();return JSON.parse((new TextDecoder).decode(s))}(o);for(const[e,o]of Object.entries(i)){if(!(t.getBackendDriver(e)instanceof Sl))continue;const i=await n.waitForAssembly(e);if(!i)throw new Error(`Assembly not found: "${e}"`);const{regions:a}=i;if(!a)throw new Error(`Assembly not found: "${e}"`);const s=a.map((e=>e.refName)),l=await wl(e,s);for(const n of o){const o=`features-${n.refSeq}`,i=await l.get(o,n._id);if(void 0===i){const r=new ht({typeName:"AddFeatureChange",assembly:e,changedIds:[n._id],addedFeature:n});await t.changeManager.submit(r)}else{const o=JSON.parse(JSON.stringify(i));Ss(n,o)||await new Promise((i=>{r.queueDialog((r=>[th,{featureSnapshot:n,existingFeature:o,assemblyName:e,changeManager:t.changeManager,handleClose:()=>{r(),i()}}]))}))}}}}(t,e.apolloDataStore,n,e),await new Promise((e=>setTimeout(e,2e3)));const r=new URL(globalThis.location.href);r.searchParams.delete("apolloFeatures"),globalThis.history.replaceState(null,"",r.toString())},afterAttach(){l.addDisposer(e,c.autorun((t=>{const{focusedViewId:n,activeWidgets:r}=e;if(!n||!r)return;const o=r.get("hierarchicalTrackSelector");o?.setView(n),t.dispose()})))}}))).views((e=>{const t=e.getTrackActions;return{getTrackActions(r){if("ApolloTrack"===r.type||"ReferenceSequenceTrack"===r.type)return t?.(r);const o=n.readConfObject(r,"trackId");return o.endsWith("-sessionTrack")?[...t?.(r)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:t,jbrowse:n}=l.getRoot(e);let i;i=kt(l.getSnapshot(n)),0===Object.keys(i).length&&(i=void 0);const a={...l.getSnapshot(r),trackId:o.slice(0,o.length-13)};for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const t=new Nt({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:i?.tracks&&[...i.tracks,a]}}),{internetAccountId:r}=n;await e.apolloDataStore.changeManager.submit(t,{internetAccountId:r});const{notify:o}=e;o("Track added","success")}e.deleteTrackConf(r),n.addTrackConf(a)},icon:Zf}]:[...t?.(r)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:t,jbrowse:n}=l.getRoot(e);let i;i=kt(l.getSnapshot(n)),0===Object.keys(i).length&&(i=void 0);const a=i?.tracks?.filter((e=>e.trackId!==o));for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const t=new Nt({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:a}}),{internetAccountId:r}=n;await e.apolloDataStore.changeManager.submit(t,{internetAccountId:r});const{notify:o}=e;o("Track removed","success")}e.deleteTrackConf(r),n.deleteTrackConf(r)},icon:Zf}]}}}));return l.types.snapshotProcessor(a,{postProcessor(e,t){if(e.apolloSelectedFeature=void 0,e.apolloDataStore={typeName:"Client",checkResults:{}},!t)return e;const{apolloDataStore:n}=t,{checkResults:r}=n;for(const[,e]of r){const[t]=e.ids}return e}})}const rh="WorkerGlobalScope"in globalThis;for(const[e,t]of Object.entries(Gt))Q.registerChange(e,t);const oh=new Sn;ne.registerCheck(oh.name,oh);const ih=new Rn;ne.registerCheck(ih.name,ih),Kt.registerValidation(new Xt),Kt.registerValidation(new Zt),e.default=class extends t{name="ApolloPlugin";version="1.1.2";configurationSchema=vf;install(e){!function(e){e.addAdapterType((()=>new y({name:"ApolloSequenceAdapter",configSchema:Mc,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Fc})))}(e),function(e){e.addAdapterType((()=>new y({name:"ApolloRefNameAliasAdapter",configSchema:Ec,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Rc})))}(e),function(e){e.addTextSearchAdapterType((()=>new r.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:qc,AdapterClass:Bc,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new r.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:pu,ReactComponent:su})})),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloTranscriptDetails",{});return new r.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:gu,ReactComponent:Hu})})),e.addTrackType((()=>{const t=n.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:r.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new r.TrackType({name:"ApolloTrack",configSchema:t,stateModel:r.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new r.InternetAccountType({name:"ApolloInternetAccount",configSchema:Pn,stateModel:kc(Pn)}))),e.addDisplayType((()=>new r.DisplayType({name:"LinearApolloDisplay",configSchema:Gu,stateModel:Wd(0,Gu),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Wf}))),e.addDisplayType((()=>new r.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:sf,stateModel:_f(0,sf),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Jf}))),e.addDisplayType((()=>new r.DisplayType({name:"LinearApolloReferenceSequenceDisplay",configSchema:Jd,stateModel:of(0,Jd),displayName:"Apollo reference sequence display",trackType:"ReferenceSequenceTrack",viewType:"LinearGenomeView",ReactComponent:af}))),e.addToExtensionPoint("Core-extendSession",nh.bind(this,e)),e.addToExtensionPoint("Core-extendPluggableElement",(e=>{if("LinearGenomeView"===e.name){const{stateModel:t}=e,n=t.views((e=>{const t=e.rubberBandMenuItems;return{rubberBandMenuItems:()=>[...t(),{label:"Add new feature",icon:Ln,onClick:()=>{const t=o.getSession(e),{leftOffset:n,rightOffset:r}=e,i=e.getSelectedRegions(n,r);t.queueDialog((e=>[Rl,{session:t,handleClose:()=>{e()},region:i[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Nf),e.addToExtensionPoint("Core-extendPluggableElement",Df),e.addToExtensionPoint("Core-preProcessTrackConfig",(e=>{if("ReferenceSequenceTrack"!==e.type)return e;const t=e.displays??[],n=t.findIndex((e=>"LinearApolloReferenceSequenceDisplay"===e.type));if(0===n)return e;if(-1===n)return{...e,displays:[{type:"LinearApolloReferenceSequenceDisplay",displayId:`${e.trackId}-LinearApolloReferenceSequenceDisplay`},...t]};const r=t.toSpliced(n,1);return r.unshift({type:"LinearApolloReferenceSequenceDisplay",displayId:`${e.trackId}-LinearApolloReferenceSequenceDisplay`}),{...e,displays:r}})),e.addToExtensionPoint("LinearGenomeView-searchResultSelected",((e,t)=>{const{session:n,result:r}=t,o=r.getTrackId(),i=r.matchedObject;return o?.startsWith("apollo_track_")&&i&&n.apolloSetEventualSelectedFeature(i._id),e})),rh||e.addToExtensionPoint("Core-extendWorker",(t=>"on"in t.client&&t.client.on?(t.client.on("apollo",(async n=>{if("object"!=typeof(r=n)||null===r||!("apollo"in r)||!0!==r.apollo)return;var r;const{apollo:o,messageId:i,method:a}=n;switch(a){case"getSequence":{const{region:r}=n,{assemblyName:a}=r,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const l=s.getBackendDriver(a);if(!l)break;const{seq:c}=await l.getSequence(r);t.worker.postMessage({apollo:o,messageId:i,sequence:c});break}case"getRegions":{const{assembly:r}=n,a=e.rootModel?.session?.apolloDataStore;if(!a)break;const s=a.getBackendDriver(r);if(!s)break;const l=await s.getRegions(r);t.worker.postMessage({apollo:o,messageId:i,regions:l});break}case"getRefNameAliases":{const{assembly:r}=n,a=e.rootModel?.session?.apolloDataStore;if(!a)break;const s=a.getBackendDriver(r);if(!s)break;const l=await s.getRefNameAliases(r);t.worker.postMessage({apollo:o,messageId:i,refNameAliases:l});break}}})),t):t))}configure(e){o.isAbstractMenuManager(e.rootModel)&&(e.jexl.addFunction("geneBackgroundColor",(e=>"pseudogene"===e?s.alpha("rgb(148, 203, 236)",.6):"ncRNA_gene"===e?s.alpha("rgb(194, 106, 119)",.6):void 0)),function(e){e.insertInMenu("Apollo",{label:"Redo",icon:Yf,onClick(e){const{apolloDataStore:t}=e;t.changeManager.redoLastChange()}},0),e.insertInMenu("Apollo",{label:"Undo",icon:Xf,onClick(e){const{apolloDataStore:t}=e;t.changeManager.undoLastChange()}},0),e.appendToMenu("Apollo",{label:"Lock/Unlock session",onClick:e=>{e.toggleLocked()}});const{internetAccounts:t}=e;t.some((e=>Xl(e)))&&e.appendToMenu("Apollo",{label:"Log out",icon:Kf,onClick:e=>{e.queueDialog((t=>[Kl,{session:e,handleClose:()=>{t()}}]))}})}(e.rootModel))}},Object.defineProperty(e,"__esModule",{value:!0})}));
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