@apollo-annotation/jbrowse-plugin-apollo 0.3.13 → 1.0.0

package/dist/jbrowse-plugin-apollo.cjs.production.min.js

@@ -1,2 +1,2 @@
-"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var e=require("@apollo-annotation/common"),t=require("@apollo-annotation/shared"),n=require("@jbrowse/core/Plugin"),o=require("@jbrowse/core/configuration"),a=require("@jbrowse/core/pluggableElementTypes"),s=require("@jbrowse/core/util"),r=require("@mui/icons-material/Add"),i=require("@mui/material"),l=require("@jbrowse/mobx-state-tree"),c=require("mobx"),d=require("socket.io-client"),u=require("@mui/icons-material/AdminPanelSettings"),f=require("@mui/icons-material/Delete"),g=require("@mui/icons-material/Input"),h=require("@mui/icons-material/Person"),p=require("@mui/icons-material/Rule"),m=require("react/jsx-runtime"),y=require("@jbrowse/core/util/tss-react"),b=require("@mui/icons-material/Info"),x=require("@mui/icons-material/Link"),S=require("@mui/icons-material/RadioButtonChecked"),w=require("@mui/icons-material/RadioButtonUnchecked"),C=require("bson-objectid"),v=require("react"),j=require("@gmod/gff"),T=require("@mui/icons-material/SkipNextRounded"),A=require("@mui/icons-material/SkipPreviousRounded"),F=require("@mui/x-data-grid"),D=require("@jbrowse/core/ui"),k=require("@mui/icons-material/Close"),N=require("mobx-react"),R=require("@jbrowse/core/util/types/mst"),I=require("idb/with-async-ittr"),M=require("@jbrowse/core/util/aborting"),L=require("jsonpath"),E=require("@jbrowse/core/util/io"),q=require("fast-deep-equal/es6"),P=require("file-saver"),O=require("nanoid"),_=require("@mui/icons-material/AccountCircle"),B=require("@jbrowse/core/pluggableElementTypes/AdapterType"),U=require("@jbrowse/core/data_adapters/BaseAdapter"),$=require("@jbrowse/core/util/rxjs"),G=require("@jbrowse/core/util/simpleFeature"),W=require("@jbrowse/core/TextSearch/BaseResults"),z=require("@mui/icons-material/ExpandMore"),H=require("@mui/icons-material/Edit"),V=require("@mui/icons-material/MoreHoriz"),J=require("@mui/icons-material/AddBox"),X=require("@apollo-annotation/mst"),K=require("@emotion/styled"),Z=require("@mui/icons-material/ContentCopy"),Y=require("@mui/icons-material/ContentCut"),Q=require("@mui/icons-material/Remove"),ee=require("@mui/icons-material/Clear"),te=require("@mui/icons-material/UnfoldLess"),ne=require("@jbrowse/core/util/tracks"),oe=require("@mui/icons-material/ExpandLess"),ae=require("@mui/icons-material/Lock"),se=require("@mui/icons-material/Error"),re=require("@mui/icons-material/Download"),ie=require("@mui/icons-material/FactCheck"),le=require("@mui/icons-material/FileOpen"),ce=require("@mui/icons-material/Logout"),de=require("@mui/icons-material/Redo"),ue=require("@mui/icons-material/TrackChanges"),fe=require("@mui/icons-material/Undo"),ge=require("@mui/icons-material/Save");const he=o.ConfigurationSchema("ApolloInternetAccount",{baseURL:{description:"Location of Apollo server",type:"string",defaultValue:""},tokenType:{description:"A custom name for a token to include in the header",type:"string",defaultValue:"Bearer"}},{baseConfiguration:a.BaseInternetAccountConfig,explicitlyTyped:!0});async function pe(e,n,o){const a=j.parseStringSync(n,{parseSequences:!0,parseComments:!0,parseDirectives:!1,parseFeatures:!0});if(0===a.length)throw new Error("No features found in GFF3 file");let s=0,r=o.assemblies.get(e);r||(r=o.addAssembly(e,"InMemoryFileDriver"));for(const e of a)if(Array.isArray(e)){const n=t.gff3ToAnnotationFeature(e),o=r.refSeqs.get(n.refSeq)??r.addRefSeq(n.refSeq,n.refSeq);o.features.has(n._id)||o.addFeature(n)}else if("comment"in e)r.addComment(e.comment);else{s++;let t=r.refSeqs.get(e.id);t||(t=r.addRefSeq(e.id,e.id,e.description)),e.description&&!t.description&&t.setDescription(e.description),t.addSequence({start:0,stop:e.sequence.length,sequence:e.sequence})}if(0===s)throw new Error("No embedded FASTA section found in GFF3");const i=await me(r);return o.addCheckResults(i),r}async function me(t){const n=[];for(const o of t.refSeqs.values())for(const t of o.features.values())for(const a of e.checkRegistry.getChecks().values()){const e=await a.checkFeature(l.getSnapshot(t),((e,t)=>Promise.resolve(o.getSequence(e,t))));n.push(...e)}return n}function ye(e){const{attributes:t}=e,n=t.get("gff_name");return n?n[0]:""}function be(e){const{attributes:t}=e,n=t.get("gff_id"),o=t.get("transcript_id"),a=t.get("exon_id"),s=t.get("protein_id");return n?n[0]:o?o[0]:a?a[0]:s?s[0]:""}function xe(e){const t=ye(e),n=be(e);return t?`: ${t}`:n?`: ${n}`:""}function Se(e,t,n=!1){const o=[];o.push(e);for(const t of function(e){const t=[];let{parent:n}=e;for(;n;)t.push(n),({parent:n}=n);return t}(e))o.push(t);const a=function(e){const t=[];if(e.children)for(const[,n]of e.children)t.push(n);return t}(e);for(const e of a)e.min<t&&e.max>=t&&o.push(e);if(!n)return o;if(e.parent){const n=e.parent.children;if(n)for(const[,a]of n)a._id!=e._id&&a.min<t&&a.max>=t&&o.push(a)}return o}function we(e,t){if(e.apolloDragging)return;e.setSelectedFeature(t);const{session:n}=e,{apolloDataStore:o}=n,{featureTypeOntology:a}=o.ontologyManager;if(!a)throw new Error("featureTypeOntology is undefined");let s=!1;for(const[,e]of t.children??[])if(a.isTypeOf(e.type,"CDS")||a.isTypeOf(e.type,"exon")){s=!0;break}(a.isTypeOf(t.type,"transcript")||a.isTypeOf(t.type,"pseudogenic_transcript"))&&s?e.showFeatureDetailsWidget(t,["ApolloTranscriptDetails","apolloTranscriptDetails"]):e.showFeatureDetailsWidget(t)}function Ce(e,t){const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is 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d)if(e.min>i){u.downstream=e;break}d=d.sort(((e,t)=>e.min>t.min?-1:1));for(const e of d)if(e.max<r){u.upstream=e;break}if(-1===l.strand){const e=u.downstream;u.downstream=u.upstream,u.upstream=e}return u}function Ae(e,t,n){let o=T;return-1===e&&(o=A),t&&(o=o===A?T:A),n&&(o=o===A?T:A),o}function Fe(e,t,n,o){const a=o.bpToPx({refName:t,coord:e.min,regionNumber:n}),s=o.bpToPx({refName:t,coord:e.max,regionNumber:n});if(void 0===a||void 0===s)return;const{offsetPx:r}=o;return[a.offsetPx-r,s.offsetPx-r]}function De(e,t,n){const[o,a]=n;if(!(Math.abs(a-o)<8))return Math.abs(o-t)<4?{feature:e,edge:"min"}:Math.abs(a-t)<4?{feature:e,edge:"max"}:void 0}function ke(e,t){return Boolean(t&&e._id===t._id)}function Ne(e,t){return!!t&&(e._id===t._id||e.hasDescendant(t._id))}function Re(e){let t;t=e.attributes.get("gff_name")?e.attributes.get("gff_name")?.join(","):e.attributes.get("gff_id")?e.attributes.get("gff_id")?.join(","):e._id;const 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Be=y.makeStyles()((e=>({dialogTitle:{background:e.palette.primary.main,color:e.palette.primary.contrastText,padding:e.spacing(2)},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1.5),color:e.palette.primary.contrastText}}))),Ue=N.observer((function(e){const{classes:t}=Be(),{handleClose:n,title:o,...a}=e;return m.jsx(D.Dialog,{...a,header:m.jsxs(m.Fragment,{children:[m.jsx(i.DialogTitle,{className:t.dialogTitle,children:o}),m.jsx(i.IconButton,{"aria-label":"close",onClick:n,className:t.closeButton,children:m.jsx(k,{})})]})})}));var $e;!function(e){e.GFF3="text/x-gff3",e.FASTA="text/x-fasta",e.BGZIP_FASTA="application/x-bgzip-fasta",e.FAI="text/x-fai",e.GZI="application/x-gzi",e.EXTERNAL="text/x-external"}($e||($e={}));const Ge=y.makeStyles()((e=>({accordion:{border:`1px solid ${e.palette.divider}`,"&:not(:last-child)":{borderBottom:0}},accordionSummary:{flexDirection:"row-reverse"},accordionDetails:{padding:e.spacing(2),borderTop:"1px solid rgba(0, 0, 0, .125)"},radioIcon:{color:e.palette.tertiary.contrastText},dialog:{minWidth:550,maxWidth:800}})));function We(e,t,n,o,a,s,r,i,l){return!(!e||!(t&&o||n===$e.GFF3&&o||o&&a&&s||r&&i&&l))}function ze({changeManager:e,handleClose:n,session:a}){const{classes:s}=Ge(),{internetAccounts:r}=l.getRoot(a),{notify:c}=a,d=r.filter((e=>"ApolloInternetAccount"===e.type));if(0===d.length)throw new Error("No Apollo internet account found");const[u,f]=v.useState(""),[g,h]=v.useState(""),[p,y]=v.useState(!1),[j,T]=v.useState($e.BGZIP_FASTA),[A,F]=v.useState(!0),[D,k]=v.useState(!1),[N,R]=v.useState(!1),[I,M]=v.useState(!0),[L,E]=v.useState(null),[q,P]=v.useState(null),[O,_]=v.useState(null),[B,U]=v.useState(""),[$,G]=v.useState(""),[W,z]=v.useState(""),[H,V]=v.useState(!1),[J,X]=v.useState(!1),[K,Z]=v.useState(!1);async function Y(e,t){const{jobsManager:n}=a,o=new AbortController,[{baseURL:s,getFetcher:r}]=d,i=new URL("files",s);i.searchParams.set("type",t);const l=i.href,c=new FormData;let f=e.name;const g=t===$e.BGZIP_FASTA||t===$e.FASTA&&(!D||J)||t===$e.GFF3&&K;g&&!e.name.toLocaleLowerCase().endsWith(".gz")?f=`${f}.gz`:!g&&e.name.toLocaleLowerCase().endsWith(".gz")&&(f=`${f}.txt`),c.append("file",e,f),c.append("type",t);const p=r({locationType:"UriLocation",uri:l}),m={name:`UploadAssemblyFile for ${u}`,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{o.abort(new DOMException(`Canceling adding of assembly "${u}"`,"AbortError")),n.abortJob(m.name)}};n.runJob(m),n.update(m.name,`Uploading ${e.name}, this may take awhile`);const{signal:y}=o,b=await p(l,{method:"POST",body:c,signal:y});if(!b.ok){const e=await _e(b,"Error when inserting new assembly (while uploading file)");return n.abortJob(m.name,e),h(e),""}const x=(await b.json())._id;return n.done(m),x}let Q=!1;try{const e=new URL(B);"http:"!==e.protocol&&"https:"!==e.protocol||(Q=!0)}catch{}let ee=!1;try{const e=new URL($);"http:"!==e.protocol&&"https:"!==e.protocol||(ee=!0)}catch{}let te=!1;try{const e=new URL(W);"http:"!==e.protocol&&"https:"!==e.protocol||(te=!0)}catch{}const[ne,oe]=v.useState("panelFastaInput"),ae=e=>(t,n)=>{n&&oe(e)};return m.jsxs(Ue,{open:!0,handleClose:n,"data-testid":"add-assembly-dialog",title:"Add new assembly",maxWidth:!1,children:[m.jsxs("form",{onSubmit:async function(o){let a;if(o.preventDefault(),h(""),R(!0),V(!0),c(`Assembly "${u}" is being added`,"info"),n(),o.preventDefault(),j===$e.EXTERNAL)a=new t.AddAssemblyFromExternalChange({typeName:"AddAssemblyFromExternalChange",assembly:(new C).toHexString(),assemblyName:u,externalLocation:{fa:B,fai:$,gzi:W}});else{if(!L)throw new Error("Missing fasta file");if(j===$e.GFF3&&A){const e=await Y(L,$e.GFF3);a=new t.AddAssemblyAndFeaturesFromFileChange({typeName:"AddAssemblyAndFeaturesFromFileChange",assembly:(new C).toHexString(),assemblyName:u,fileIds:{fa:e},parseOptions:{strict:I}})}else if(j===$e.GFF3){const e=await Y(L,$e.GFF3);a=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new C).toHexString(),assemblyName:u,fileIds:{fa:e}})}else if(D){const e=await Y(L,$e.FASTA);a=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new C).toHexString(),assemblyName:u,fileIds:{fa:e}})}else{if(!q||!O)throw new Error("Missing fasta index files");const e=await Y(L,$e.BGZIP_FASTA),n=await Y(q,$e.FAI),o=await Y(O,$e.GZI);a=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new C).toHexString(),assemblyName:u,fileIds:{fa:e,fai:n,gzi:o}})}}const[{internetAccountId:s}]=d;await e.submit(a,{internetAccountId:s,updateJobsManager:!0}),R(!1),V(!1)},"data-testid":"submit-form",children:[m.jsxs(i.DialogContent,{className:s.dialog,children:[H?m.jsx(i.LinearProgress,{}):null,m.jsx(i.TextField,{margin:"dense",id:"name",label:"Assembly name",type:"TextField",fullWidth:!0,variant:"outlined",onChange:e=>{R(!1),f(e.target.value),function(e){const{assemblies:t}=a;t.find((t=>o.readConfObject(t,"displayName")===e))?(y(!1),h(`Assembly ${e} 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URLs",m.jsx(i.Tooltip,{title:"Use external URLs to provide FASTA and index files. 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o.readConfObject(t.ApolloPlugin,"featureTypeOntologyName")}}))).views((e=>({get featureTypeOntology(){return this.findOntology(e.featureTypeOntologyName)},findOntology:(t,n)=>e.ontologies.find((e=>e.name===t&&(void 0===n||e.version===n))),openOntology(e,t){return this.findOntology(e,t)?.dataStore},applyPrefixes:t=>Xe(t,e.prefixes),expandPrefixes:t=>function(e,t){for(const[n,o]of t.entries())if(e.startsWith(String(n)))return e.replace(String(n),o);return e}(t,e.prefixes)}))).actions((e=>({addOntology(t,n,o,a){const s=e.ontologies.push({name:t,version:n,source:o,options:{prefixes:new Map(e.prefixes.entries()),...a}});e.ontologies[s-1].ping()}}))),pt=[{displayName:"Label",jsonPath:"$.lbl"},{displayName:"Synonym",jsonPath:"$.meta.synonyms[*].val"},{displayName:"Definition",jsonPath:"$.meta.definition.val"}],mt=o.ConfigurationSchema("OntologyRecord",{name:{type:"string",description:'the full name of the ontology, e.g. "Gene Ontology"',defaultValue:"My Ontology"},version:{type:"string",description:"the ontology's version string",defaultValue:"unversioned"},source:{type:"fileLocation",description:"the download location for the ontology's source file",defaultValue:{locationType:"UriLocation",uri:"http://example.com/myontology.json"}},textIndexFields:{type:"frozen",description:"JSON paths for text fields that will be indexed for text searching",defaultValue:pt}});function yt(e){return"CLASS"===e.type}function bt(e){return"PROPERTY"===e.type}async function xt(e,t,n){if(!e)return;const o=await t.getTermsWithLabelOrSynonym(e.type,{includeSubclasses:!1}),a=o.filter(yt);if(0===o.length)return;const s=await t.getClassesThat("part_of",a);return 0!==s.length?s:void 0}function St({fetchValidTerms:e,filterTerms:t,includeDeprecated:n,onChange:o,ontologyName:a,ontologyVersion:s,renderInput:r,session:l,style:c,value:d}){const[u,f]=v.useState(!1),[g,h]=v.useState(),[p,y]=v.useState(""),[b,x]=v.useState(),{ontologyManager:S}=l.apolloDataStore,w=S.findOntology(a,s)?.dataStore,C=w&&u&&!g,j=w&&!b,T=v.useCallback((e=>(n||!rt(e))&&(!t||t(e))),[t,n]);v.useEffect((()=>{const e=new AbortController,{signal:t}=e;return j&&async function(e,t,n,o){if(!t)return;const a=(await e.getTermsWithLabelOrSynonym(t,{includeSubclasses:!1})).find((e=>(n??(()=>!0))(e)));if(!a)throw new Error(`not a valid ${e.ontologyName} term`);return a}(w,d,T).then((e=>{y(""),t.aborted||x(e)}),(e=>{t.aborted||M.isAbortException(e)||y(String(e))})),()=>{e.abort(new DOMException("Cancel getting current term from ontology store","AbortError"))}}),[l,d,T,w,j]),v.useEffect((()=>{const t=new AbortController,{signal:n}=t;return C&&async function(e,t,n,o){let a;if(t){const n=await t(e,o);n&&(a=n)}return a||(a=await e.getAllTerms()),n?a.filter((e=>n(e))):a}(w,e,T,n).then((e=>{e&&!n.aborted&&h(e)}),(e=>{n.aborted||M.isAbortException(e)||l.notify(e instanceof Error?e.message:String(e),"error")})),()=>{t.abort(new DOMException("Canceling getting valid terms from ontology store","AbortError"))}}),[C,T,w,l,e]);const A={};return p&&(A.error=!0,A.helperText=p),m.jsx(i.Autocomplete,{style:c,autoComplete:!0,filterSelectedOptions:!0,disableClearable:!0,selectOnFocus:!0,clearOnBlur:!0,handleHomeEndKeys:!0,freeSolo:!0,value:d,options:g??[],onOpen:()=>{f(!0)},onClose:()=>{f(!1)},loading:C,renderInput:r??(e=>m.jsx(i.TextField,{...e,...A})),getOptionLabel:e=>"string"==typeof e?e:e.lbl??"",isOptionEqualToValue:(e,t)=>e.lbl===t.lbl,onChange:(e,t)=>{t&&("string"==typeof t?(x(void 0),o(d,t)):t.lbl!==d&&(y(""),x(t),o(d,t.lbl)))}})}function wt({changeManager:e,handleClose:n,session:o,sourceAssemblyId:a,sourceFeature:s}){const[r,l]=v.useState(String(s.max)),[c,d]=v.useState(String(s.min+1)),[u,f]=v.useState(""),[g,h]=v.useState(""),[p,y]=v.useState(""),b=Number(r)<=Number(c);return m.jsxs(Ue,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog",children:[m.jsxs("form",{onSubmit:function(i){i.preventDefault(),h("");const l=(new C).toHexString(),d=new t.AddFeatureChange({changedIds:[s._id],typeName:"AddFeatureChange",assembly:a,addedFeature:{_id:l,refSeq:s.refSeq,min:Number(c)-1,max:Number(r),type:u},parentFeatureId:s._id});e.submit(d).then((()=>{o.apolloSetSelectedFeature(l)})),n(),i.preventDefault()},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsx(i.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:c,onChange:e=>{d(e.target.value)}}),m.jsx(i.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:r,onChange:e=>{l(e.target.value)},error:b,helperText:b?'"End" must be greater than "Start"':null}),m.jsx(St,{session:o,ontologyName:"Sequence Ontology",style:{width:170},value:u,filterTerms:yt,fetchValidTerms:async function(e,t,n){const o=await xt(e,t);if(o)return o;y(`Type "${e?.type}" does not have any children in the ontology`)}.bind(null,s),renderInput:e=>m.jsx(i.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0,error:Boolean(p),helperText:p}),onChange:(e,t)=>{var n;t&&(n=t,h(""),f(n))}})]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{variant:"contained",type:"submit",disabled:b||!(c&&r&&u),children:"Submit"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:n,children:"Cancel"})]})]}),g?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:g})}):null]})}class Ct{clientStore;constructor(e){this.clientStore=e}}class vt{dataStore;constructor(e){this.dataStore=e}recentChanges=[];undoneChanges=[];async submit(n,o={}){const{addToRecents:a=!0,submitToBackend:r=!0,updateJobsManager:i=!1}=o,l=s.getSession(this.dataStore),c=new AbortController,{jobsManager:d,isLocked:u,changeInProgress:f,setChangeInProgress:g}=s.getSession(this.dataStore);if(u)return l.notify("Cannot submit changes in locked mode"),void g(!1);if(f)return void l.notify("Could not submit change, there is another change still in progress");g(!0);const h={name:n.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{c.abort(new DOMException(`Cancelling change "${n.typeName}"`,"AbortError"))}};i&&d.runJob(h);const p=await t.validationRegistry.frontendPreValidate(n);if(!p.ok){const e=`Pre-validation failed: "${p.resultsMessages}"`;return i&&d.abortJob(h.name,e),l.notify(e,"error"),void g(!1)}try{await n.execute(this.dataStore)}catch(e){return i&&d.abortJob(h.name,String(e)),console.error(e),l.notify(`Error encountered in client: ${String(e)}. Data may be out of sync, please refresh the page`,"error"),void g(!1)}if((await t.validationRegistry.frontendPostValidate(n,this.dataStore)).ok||await this.undo(n),r){i&&d.update(h.name,"Submitting to driver");const{collaborationServerDriver:t,getBackendDriver:s}=this.dataStore,r=e.isAssemblySpecificChange(n)?s(n.assembly)??t:t;let c;try{c=await r.submitChange(n,o)}catch(e){return i&&d.abortJob(h.name,String(e)),console.error(e),l.notify(String(e),"error"),await this.undo(n,!1),void g(!1)}if(!c.ok){const e=`Post-validation failed: "${p.resultsMessages}"`;return i&&d.abortJob(h.name,e),l.notify(e,"error"),await this.undo(n,!1),void g(!1)}n.notification&&l.notify(n.notification,"success"),a&&(this.recentChanges.push(n),this.undoneChanges=[])}i&&d.done(h),g(!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=s.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=s.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 jt extends Ct{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:o}=n,a=new URL("features/searchFeatures",o),s=new URLSearchParams({assemblies:t.join(","),term:e});a.search=s.toString();const r=a.toString(),i=await this.fetch(n,r);if(!i.ok){const e=await _e(i,"searchFeatures failed");throw new Error(e)}return i.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:o,start:a}=e,{assemblyManager:r}=s.getSession(this.clientStore);if(!r.get(t))throw new Error(`Could not find assembly with name "${t}"`);const i=(await this.getRefSeqMapping(t)).get(o);if(!i)throw new Error(`Could not find refSeq "${o}"`);const l=i.id,c=this.clientStore.getInternetAccount(t),{baseURL:d}=c,u=new URL("features/getFeatures",d),f=new URLSearchParams({refSeq:l,start:String(a),end:String(n)});u.search=f.toString();const g=u.toString(),h=await this.fetch(c,g);if(!h.ok){const e=await _e(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,c),h.json()}checkSocket(n,o,a){const{socket:s}=a,r=a.retrieveToken();if(!r)return;const i=t.makeUserSessionId(r),l=`${n}-${o}`,c=new vt(this.clientStore);s.hasListeners(l)||s.on(l,(async t=>{if(a.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId===i)return;const n=e.Change.fromJSON(t.changeInfo);e.isFeatureChange(n)&&this.haveDataForChange(n)&&await c.submit(n,{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}-${e.end}`,n=this.inFlight.get(t),{assemblyName:o,end:a,refName:r,start:i}=e,{assemblyManager:l}=s.getSession(this.clientStore);if(!l.get(o))throw new Error(`Could not find assembly with name "${o}"`);const c=(await this.getRefSeqMapping(o)).get(r);if(!c)throw new Error(`Could not find refSeq "${r}"`);const d=c.id;if(n)return{seq:await n,refSeq:d};let u=this.clientStore.assemblies.get(o);u||(u=this.clientStore.addAssembly(o));let f=u.refSeqs.get(d);f||(f=u.addRefSeq(d,r));const g=f.getSequence(i,a);if(g.length===a-i)return{seq:g,refSeq:d};const h=this.clientStore.getInternetAccount(o),{baseURL:p}=h,m=new URL("sequence",p),y=new URLSearchParams({refSeq:d,start:String(i),end:String(a)});m.search=y.toString();const b=m.toString(),x=this.getSeqFromServer(h,b,f,i,a);this.inFlight.set(t,x);const S=await x;return this.checkSocket(o,r,h),this.inFlight.delete(t),{seq:S,refSeq:d}}async getSeqFromServer(e,t,n,o,a){const s=await this.fetch(e,t);if(!s.ok){let e;try{e=await s.text()}catch{e=""}throw new Error(`getSequence failed: ${s.status} (${s.statusText})${e?` (${e})`:""}`)}const r=await s.text();return n.addSequence({sequence:r,start:o,stop:a}),r}async getRefSeqMapping(e){const t=this.refSeqMaps.get(e);if(t)return t;const{assemblyManager:n}=s.getSession(this.clientStore);if(!n.get(e))throw new Error(`Could not find assembly with name "${e}"`);const o=this.clientStore.getInternetAccount(e),{baseURL:a}=o,r=new URL("refSeqs",a),i=new URLSearchParams({assembly:e});r.search=i.toString();const l=r.toString(),c=await this.fetch(o,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 d=await c.json(),u=new Map(d.map((e=>[e.name,{refName:e.name,id:e._id,aliases:e.aliases}])));return this.refSeqMaps.set(e,u),u}async getRefNameAliases(e){return[...(await this.getRefSeqMapping(e)).values()].map((e=>({refName:e.refName,aliases:[...new Set([e.id,...e.aliases])],uniqueId:`alias-${e.id}`})))}async getRefSeqId(e,t){const n=await this.getRefSeqMapping(e);if(!n)return;const o=n.get(t);return o?.id}async getRegions(e){const{assemblyManager:t}=s.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:o}=n,a=new URL("refSeqs",o),r=new URLSearchParams({assembly:e});a.search=r.toString();const i=a.toString(),l=await this.fetch(n,i);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}=s.getSession(this.clientStore);return t.assemblies.filter((t=>{const n=o.getConf(t,["sequence","metadata"]);return!(!(n&&n.apollo&&n.internetAccountConfigId)||e&&n.internetAccountConfigId!==e)}))}async submitChange(e,n={}){const{internetAccountId:o}=n,a=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,o),{baseURL:s}=a,r=new URL("changes",s).href,i=await this.fetch(a,r,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!i.ok){const e=await _e(i,"submitChange failed");throw new Error(e)}const l=new t.ValidationResultSet;return i.ok||(l.ok=!1),l}}class Tt extends Ct{async getFeatures(){return[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:o,start:a}=e,s=this.clientStore.assemblies.get(t);if(!s)return{seq:"",refSeq:o};const r=s.refSeqs.get(o);return r?{seq:r.getSequence(a,n),refSeq:o}:{seq:"",refSeq:o}}async getRefNameAliases(e){const t=this.clientStore.assemblies.get(e),n=[];if(!t)return n;for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getRegions(e){const t=this.clientStore.assemblies.get(e);if(!t)return[];const n=[];for(const[,o]of t.refSeqs)n.push({assemblyName:e,refName:o.name,start:o.sequence[0].start,end:o.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=s.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=o.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.file&&!t.internetAccountConfigId)}))}async submitChange(e,n={}){const{clientStore:o}=this,{assemblies:a}=o;o.clearCheckResults();for(const[,e]of a)if("InMemoryFileDriver"===e.backendDriverType){const t=await me(e);o.addCheckResults(t)}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class At extends Ct{async loadAssembly(e){const{assemblyManager:t}=s.getSession(this.clientStore),n=t.get(e);if(!n)throw new Error(`Assembly ${e} not found`);const{file:a}=o.getConf(n,["sequence","metadata"]),r=require("node:fs");return pe(e,await r.promises.readFile(a,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getFeatures(e){return await this.getAssembly(e.assemblyName),[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:o,start:a}=e,s=(await this.getAssembly(t)).refSeqs.get(o);if(!s)throw new Error(`refSeq ${o} not found in client data store`);return{seq:s.getSequence(a,n),refSeq:o}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,o]of t.refSeqs)n.push({assemblyName:e,refName:o.name,start:o.sequence[0].start,end:o.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=s.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=o.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.internetAccountConfigId&&t.file)}))}async submitChange(n){if(!e.isAssemblySpecificChange(n))throw new Error(`Cannot use this type of change with local file: "${n.typeName}"`);const{assemblyManager:a}=s.getSession(this.clientStore),r=a.get(n.assembly);if(!r)throw new Error(`Could not find assembly with name "${n.assembly}"`);const{file:i}=o.getConf(r,["sequence","metadata"]),c=this.clientStore.assemblies.get(n.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${n.assembly}"`);const d=new Set(...c.refSeqs.keys()),{checkResults:u}=this.clientStore;for(const e of u.values())d.has(e.refSeq)&&u.delete(e._id);const f=await me(c);this.clientStore.addCheckResults(f);const g=[{directive:"gff-version",value:"3"}];for(const[,e]of c.refSeqs)g.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of c.comments)g.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)g.push(t.annotationFeatureToGFF3(l.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,o=t.splitStringIntoChunks(n.sequence,80).join("\n");g.push({id:e.name,description:e.description,sequence:o})}const h=j.formatSync(g),p=require("node:fs");return await p.promises.writeFile(i,h,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}var Ft;function Dt(e,t,n,o){const a={_id:(new C).toHexString(),refSeq:e,type:"CDS",min:n,max:o,strand:t},s={_id:(new C).toHexString(),refSeq:e,type:"exon",min:n,max:o,strand:t},r={};return r[a._id]=a,r[s._id]=s,{_id:(new C).toHexString(),refSeq:e,type:"mRNA",min:n,max:o,strand:t,children:r}}function kt({changeManager:e,handleClose:n,region:o,session:a}){const[s,r]=v.useState(String(o.end)),[l,c]=v.useState(String(o.start+1)),[d,u]=v.useState(Ft.GENE_AND_SUBFEATURES),[f,g]=v.useState(""),[h,p]=v.useState(),[y,x]=v.useState(""),S=Number(s)<=Number(l);let w=Boolean(S)||!(l&&s&&d);return(d===Ft.CUSTOM&&!f||!h&&d===Ft.GENE_AND_SUBFEATURES||!h&&d===Ft.TRANSCRIPT_AND_SUBFEATURES)&&(w=!0),m.jsxs(Ue,{open:!0,title:"Add new feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog",children:[m.jsxs("form",{onSubmit:async function(r){r.preventDefault(),x("");const i=a.apolloDataStore.getBackendDriver(o.assemblyName);if(!i)return void x("No backend driver found");let c=o.refName;if(i instanceof jt){const e=await i.getRefSeqId(o.assemblyName,o.refName);if(!e)return void x(`Could not find refSeq for "${o.refName}"`);c=e}if(d===Ft.GENE_AND_SUBFEATURES){const r=Dt(c,h,Number(l)-1,Number(s)),i={};i[r._id]=r;const d=(new C).toHexString(),u=new t.AddFeatureChange({changedIds:[d],typeName:"AddFeatureChange",assembly:o.assemblyName,addedFeature:{_id:d,refSeq:c,min:Number(l)-1,max:Number(s),type:"gene",strand:h,children:i}});return e.submit(u).then((()=>{a.apolloSetSelectedFeature(d)})),void n()}if(d===Ft.TRANSCRIPT_AND_SUBFEATURES){const r=Dt(c,h,Number(l)-1,Number(s)),i=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o.assemblyName,addedFeature:r});return e.submit(i).then((()=>{a.apolloSetSelectedFeature(r._id)})),void n()}if(!f)return void x("No type selected");const u=(new C).toHexString(),g=new t.AddFeatureChange({changedIds:[u],typeName:"AddFeatureChange",assembly:o.assemblyName,addedFeature:{_id:u,refSeq:c,min:Number(l)-1,max:Number(s),type:f,strand:h}});e.submit(g).then((()=>{a.apolloSetSelectedFeature(u)})),n()},"data-testid":"submit-form",children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsx(i.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(l),onChange:e=>{c(e.target.value)}}),m.jsx(i.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:s,onChange:e=>{r(e.target.value)},error:S,helperText:S?'"End" must be greater than "Start"':null}),m.jsxs(i.FormControl,{children:[m.jsx(i.InputLabel,{id:"demo-simple-select-label",children:"Strand"}),m.jsxs(i.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Strand",value:h?.toString(),onChange:function(e){switch(x(""),Number(e.target.value)){case 1:p(1);break;case-1:p(-1);break;default:p(void 0)}},children:[m.jsx(i.MenuItem,{value:void 0}),m.jsx(i.MenuItem,{value:1,children:"+"}),m.jsx(i.MenuItem,{value:-1,children:"-"})]})]}),m.jsx(i.FormControl,{style:{marginTop:20},children:m.jsxs(i.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:Ft.GENE_AND_SUBFEATURES,name:"radio-buttons-group",value:d,onChange:e=>{x("");const{value:t}=e.target;Object.keys(Ft).includes(t)&&u(Ft[t])},children:[m.jsx(i.FormControlLabel,{value:Ft.GENE_AND_SUBFEATURES,control:m.jsx(i.Radio,{}),label:m.jsxs(i.Box,{display:"flex",alignItems:"center",children:["Add gene and sub-features",m.jsx(i.Tooltip,{title:"This is a shortcut to create a gene with a single mRNA, exon, and CDS",children:m.jsx(i.IconButton,{size:"small",children:m.jsx(b,{sx:{fontSize:18}})})})]})}),m.jsx(i.FormControlLabel,{value:Ft.TRANSCRIPT_AND_SUBFEATURES,control:m.jsx(i.Radio,{}),label:m.jsxs(i.Box,{display:"flex",alignItems:"center",children:["Add transcript 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C).toHexString();t.push(n);const o={};if(e.children)for(const n of Object.values(e.children)){const e=Nt(n,t);o[e._id]=e}const a="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString();return{...e,refSeq:a,children:e.children&&o,_id:n}}function Rt({changeManager:e,handleClose:n,session:a,sourceAssemblyId:s,sourceFeature:r}){const{assemblyManager:c}=a,d=c.assemblyList,[u,f]=v.useState(d.find((e=>e.name!==s))?.name),[g,h]=v.useState([]),[p,y]=v.useState(""),[b,x]=v.useState(r.min),[S,w]=v.useState("");function C(e,t){const n={};if(e.children)for(const o of Object.values(e.children)){const e=C(o,t);e.refSeq=p,e.min=e.min+t,e.max=e.max+t,n[e._id]=e}const o="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString(),a="string"==typeof e._id?e._id:e._id.toHexString();return{...e,refSeq:o,children:e.children&&n,_id:a}}return v.useEffect((()=>{(async function(){if(y(""),!u)return void w("No assemblies to copy to");const e=await c.waitForAssembly(u);if(!e)return;const{refNameAliases:t}=e;if(!t)return;const n=[...Object.entries(t)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t})));h(n),y(n[0]?._id||"")})().catch((e=>{w(String(e))}))}),[u,c]),m.jsxs(Ue,{open:!0,title:"Copy features and annotations",handleClose:n,maxWidth:!1,"data-testid":"copy-feature",children:[m.jsxs("form",{onSubmit:async function(o){if(!u)return;o.preventDefault(),w("");const s=r.length,i=await c.waitForAssembly(u);if(!i)return void w(`Assembly not found: ${u}.`);const d=i.getCanonicalRefName(p),f=i.regions?.find((e=>e.refName===d));if(!f)return void w(`RefSeq not found: ${p}.`);const g=b+s;if(g>f.end)return void w(`Feature would extend beyond the bounds of the selected reference sequence. (Feature would end at ${g}, but reference sequence ends at ${f.end})`);if(b<f.start)return void w(`Reference sequence starts at ${f.start}, feature cannot start before that.`);const h=[],m=Nt(l.getSnapshot(r),h),y={...m.attributes};"Parent"in y&&delete y.Parent,m.refSeq=p;const x=b-m.min;m.min=b,m.max=b+s;const S=C(m,x),v=new t.AddFeatureChange({changedIds:[m._id],typeName:"AddFeatureChange",assembly:u,addedFeature:{_id:m._id,refSeq:m.refSeq,min:m.min,max:m.max,type:m.type,children:S.children,attributes:y,strand:m.strand},copyFeature:!0,allIds:h});e.submit(v).then((()=>{a.apolloSetSelectedFeature(m._id)})),n(),o.preventDefault()},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsx(i.DialogContentText,{children:"Target 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It({changeManager:e,handleClose:n,session:o}){const{internetAccounts:a}=l.getRoot(o),[s,r]=v.useState(""),[c,d]=v.useState(!1),[u,f]=v.useState(!1),g=a.filter((e=>"ApolloInternetAccount"===e.type));if(0===g.length)throw new Error("No Apollo internet account found");const[h,p]=v.useState(g[0]),{collaborationServerDriver:y}=o.apolloDataStore,b=y.getAssemblies(),[x,S]=v.useState(b.at(0));return m.jsxs(Ue,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly",children:[m.jsxs("form",{onSubmit:async function(o){if(o.preventDefault(),f(!0),r(""),!x)return void r("Must select assembly!");const a=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:x.name});await e.submit(a,{internetAccountId:h.internetAccountId}),n(),o.preventDefault()},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[g.length>1?m.jsxs(m.Fragment,{children:[m.jsx(i.DialogContentText,{children:"Select 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t)if(o._id!==e._id&&o.min>=e.min){n=o.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 o of n)if(o._id!=e._id&&o.max<=e.max){t=o.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 m.jsxs(Ue,{open:!0,title:"Delete feature",handleClose:n,maxWidth:!1,"data-testid":"delete-feature",children:[m.jsxs("form",{onSubmit:a=>{!async function(a){a.preventDefault(),u(""),o?._id===c._id&&s();const i=[],d=new t.DeleteFeatureChange({changedIds:[c._id],typeName:"DeleteFeatureChange",assembly:r,changes:[{deletedFeature:l.getSnapshot(c),parentFeatureId:c.parent?._id}]});if(g&&(g.isTypeOf(c.type,"transcript")||g.isTypeOf(c.type,"pseudogenic_transcript"))){const e=h(c);e&&i.push(e)}if(g&&g.isTypeOf(c.type,"exon")){const e=function(e){if(!g)return;if(!g.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 n=(e.parent.cdsLocations.at(0)??[]).sort((({min:e},{min:t})=>e-t));let o;for(const t of e.parent.children.values())if(t.type===n[0].type){o=t;break}if(!o)throw new Error("Unable to find CDS");const a=n[0].min,s=n[n.length-1].max;if(!(e.min>a&&e.max<s||e.max<a||e.min>s)){if(e.min<=a&&e.max>=s)return new t.DeleteFeatureChange({changedIds:[o._id],typeName:"DeleteFeatureChange",assembly:r,changes:[{deletedFeature:l.getSnapshot(o),parentFeatureId:o.parent?._id}]});if(e.min<=a&&e.max>a){let t;for(const o of n)if(o.min>e.max){t=o.min;break}if(!t)throw new Error("Error setting new CDS start");return{typeName:"LocationStartChange",changedId:o._id,featureId:o._id,oldLocation:o.min,newLocation:t}}if(e.min<s&&e.max>=s){let t;for(const o of n.reverse())if(o.max<e.min){t=o.max;break}if(!t)throw new Error("Error setting new CDS end");return{typeName:"LocationEndChange",changedId:o._id,featureId:o._id,oldLocation:o.max,newLocation:t}}throw new Error("Unexpected relationship between exon and CDS")}}(c);e&&("DeleteFeatureChange"===e.typeName?(d.changedIds.push(...e.changedIds),d.changes.push(...e.changes)):i.push(e));const n=h(c);if(n){i.push(n);const e=c.parent?.parent;if(e?.children)if("LocationStartChange"===n.typeName){let t=n.newLocation;for(const[,o]of e.children)o._id!=n.featureId&&o.min<t&&(t=o.min);t!=e.min&&i.push({typeName:n.typeName,changedId:e._id,featureId:e._id,oldLocation:e.min,newLocation:t})}else{let t=n.newLocation;for(const[,o]of e.children)o._id!=n.featureId&&o.max>t&&(t=o.max);t!=e.max&&i.push({typeName:n.typeName,changedId:e._id,featureId:e._id,oldLocation:e.max,newLocation:t})}}}const f=function(e,n){if(0===e.length)return;const o=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[],changes:[],assembly:n}),a=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[],changes:[],assembly:n});for(const t of e)"LocationStartChange"===t.typeName&&(o.changedIds.push(t.changedId),o.changes.push({featureId:t.featureId,oldStart:t.oldLocation,newStart:t.newLocation})),"LocationEndChange"===t.typeName&&(a.changedIds.push(t.changedId),a.changes.push({featureId:t.featureId,oldEnd:t.oldLocation,newEnd:t.newLocation}));if(o.changedIds.length>0&&0===a.changedIds.length)return o;if(a.changedIds.length>0&&0===o.changedIds.length)return a;throw new Error("Unexpected list of changes")}(i,r);await e.submit(d),f&&await e.submit(f),n(),a.preventDefault()}(a)},children:[m.jsx(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:m.jsx(i.DialogContentText,{children:"Are you sure you want to delete the selected feature?"})}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{variant:"contained",type:"submit",children:"Yes"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:n,children:"Cancel"})]})]}),d?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:d})}):null]})}function Lt({handleClose:e,session:n}){const[a,s]=v.useState(!1),[r,c]=v.useState(),[d,u]=v.useState(""),{collaborationServerDriver:f,getInternetAccount:g,inMemoryFileDriver:h}=n.apolloDataStore,p=[...f.getAssemblies(),...h.getAssemblies()];return m.jsxs(Ue,{open:!0,title:"Export GFF3",handleClose:e,maxWidth:!1,"data-testid":"download-gff3",children:[m.jsxs("form",{onSubmit:async function(s){if(s.preventDefault(),u(""),!r)return void u("Must select assembly to download");const{internetAccountConfigId:i}=o.getConf(r,["sequence","metadata"]);i?await async function(e){if(!r)return void u("Must select assembly to download");const t=g(r.configuration.name,e),n=new URL("export/getID",t.baseURL),o=new URLSearchParams({assembly:r.name});n.search=o.toString();const s=n.toString(),i=t.getFetcher({locationType:"UriLocation",uri:s}),l=await i(s,{method:"GET"});if(!l.ok){const e=await _e(l,"Error when exporting ID");return void u(e)}const{exportID:c}=await l.json(),d=new URL("export",t.baseURL),f=new URLSearchParams({exportID:c,includeFASTA:a?"true":"false"});d.search=f.toString();const h=d.toString();window.open(h,"_blank")}(i):function(e){if(!r)return void u("Must select assembly to download");const{assemblies:n}=e.apolloDataStore,a=n.get(r.name),s=a?.refSeqs;if(!s)return void u(`No refSeqs found for assembly "${r.name}"`);const i=[{directive:"gff-version",value:"3"}],c=o.getConf(r,["sequence","adapter","features"]);for(const e of c){const{end:t,refName:n,start:o}=e;i.push({directive:"sequence-region",value:`${n} ${o+1} ${t}`})}for(const[,e]of s){const{features:n}=e;if(n)for(const[,e]of n)i.push(t.annotationFeatureToGFF3(l.getSnapshot(e)))}for(const e of c){const{refName:t,seq:n}=e;i.push({id:t,description:"",sequence:n})}const d=j.formatSync(i),f=new Blob([d],{type:"text/plain;charset=utf-8"});P.saveAs(f,`${r.displayName??r.name}.gff3`)}(n),e()},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsx(i.DialogContentText,{children:"Select assembly"}),m.jsx(i.Select,{labelId:"label",value:r?.name??"",onChange:function(e){const t=p.find((t=>t.name===e.target.value));c(t)},disabled:0===p.length,children:p.map((e=>m.jsx(i.MenuItem,{value:e.name,children:e.displayName??e.name},e.name)))}),m.jsx(i.DialogContentText,{children:"Select assembly to export to GFF3"}),m.jsx(i.FormGroup,{children:m.jsx(i.FormControlLabel,{"data-testid":"include-fasta-checkbox",control:m.jsx(i.Checkbox,{checked:a,onChange:()=>{s(!a)}}),label:"Include fasta sequence in GFF output"})})]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{disabled:!r,variant:"contained",type:"submit",children:"Download"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:e,children:"Cancel"})]})]}),d?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:d})}):null]})}function Et({changeManager:e,handleClose:n,session:a}){const{apolloDataStore:s}=a,[r,l]=v.useState(),[c,d]=v.useState(),[u,f]=v.useState(""),[g,h]=v.useState(!1),[p,y]=v.useState(),[b,x]=v.useState(!1),[S,w]=v.useState(!0),[C,j]=v.useState(!1),{collaborationServerDriver:T,getInternetAccount:A}=s,F=T.getAssemblies();return v.useEffect((()=>{c&&(async()=>{const{internetAccountConfigId:e}=o.getConf(c,["sequence","metadata"]),t=A(c.name,e);if(!t)throw new Error("No Apollo internet account found");const{baseURL:n}=t,a=new URL("features/count",n),s=new URLSearchParams({assemblyId:c.name});a.search=s.toString();const r=t.getFetcher({locationType:"UriLocation",uri:a.toString()});j(!0);const i=await r(a.toString(),{method:"GET"});if(!i.ok)throw new Error(await _e(i));{const e=await i.json();y(e.count)}j(!1)})().catch((e=>{console.error(e),f(e.message??e)}))}),[A,a,c]),m.jsxs(Ue,{open:!0,title:"Import Features from GFF3 file",handleClose:n,maxWidth:!1,"data-testid":"import-features-dialog",children:[C?m.jsx(i.LinearProgress,{}):null,m.jsxs("form",{onSubmit:async function(s){s.preventDefault(),f(""),j(!0),h(!0);let i="";if(!r)return void f("must select a file");if(!c)return void f("Must select assembly to download");const{internetAccountConfigId:l}=o.getConf(c,["sequence","metadata"]),d=A(c.name,l),{baseURL:u}=d,g=new URL("files",u);g.searchParams.set("type","text/x-gff3");const p=g.href,m=new FormData;m.append("file",r),m.append("fileName",r.name),m.append("type","text/x-gff3");const y=d.getFetcher({locationType:"UriLocation",uri:p});n();const{jobsManager:x}=a,w=new AbortController,C={name:`Importing features for ${c.displayName}`,statusMessage:"Uploading file, this may take awhile",progressPct:0,cancelCallback:()=>{w.abort(new DOMException(`Canceling importing of features to ${c.displayName}`,"AbortError")),x.abortJob(C.name)}};if(x.runJob(C),y){const{signal:e}=w,t=await y(p,{method:"POST",body:m,signal:e});if(!t.ok){const e=await _e(t,"Error when inserting new features (while uploading file)");return x.abortJob(C.name,e),void f(e)}i=(await t.json())._id}const v=new t.AddFeaturesFromFileChange({typeName:"AddFeaturesFromFileChange",assembly:c.name,fileId:i,parseOptions:{strict:S},deleteExistingFeatures:b});x.done(C),await e.submit(v,{updateJobsManager:!0})},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsx(i.DialogContentText,{children:"Select assembly"}),m.jsx(i.Select,{labelId:"label",value:c?.name??"",onChange:function(e){const t=F.find((t=>t.name===e.target.value));d(t),h(!1)},disabled:g&&!u,children:F.map((e=>m.jsx(i.MenuItem,{value:e.name,children:e.displayName??e.name},e.name)))}),m.jsx(i.DialogContentText,{children:"Upload GFF3 to load features"}),m.jsx("input",{type:"file",onChange:function(e){h(!1),e.target.files&&l(e.target.files[0])},disabled:g&&!u}),m.jsx(i.FormControlLabel,{label:"Strict parsing",disabled:g&&!u,control:m.jsx(i.Checkbox,{checked:S,onChange:function(e){w(e.target.checked)}})}),m.jsx(i.FormHelperText,{children:"Don't import any features if any lines in the GFF3 are unable to be processed"}),p&&p>0?m.jsxs(m.Fragment,{children:[m.jsx(i.FormControlLabel,{label:"Delete existing 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l=`JBrowseAuthWindow-${e.internetAccountId}`;if(s.isElectron){const{ipcRenderer:t}=globalThis.require("electron"),s=await t.invoke("openAuthWindow",{internetAccountId:e.internetAccountId,data:{redirect_uri:a},url:r.toString()}),i=new MessageEvent("message",{data:{name:l,redirectUri:s}});this.finishOAuthWindow(i,n,o)}else this.addMessageChannel(n,o),window.open(r,l,"width=500,height=600")}}})).actions((e=>({async getTokenFromUser(t,n){const{baseURL:o}=e,a=await new Promise(((t,n)=>{const{session:o}=l.getRoot(e),{baseURL:a,name:s}=e;o.queueDialog((e=>[ln,{name:s,handleClose:o=>{o?o instanceof Error?n(o):t(o):n(new Error("user cancelled entry")),e()},baseURL:a}]))}));if("guest"!==a)return void e.openAuthWindow(a,t,n);const s=new URL("auth/login",o),r=new URLSearchParams({type:a});s.search=r.toString();const i=s.toString(),c=await fetch(i,{signal:e.controller.signal});if(!c.ok){const e=await _e(c,"Error when logging in");return void n(new Error(e))}const{token:d}=await c.json();t(d)}}))).volatile((()=>({lastChangeSequenceNumber:void 0}))).actions((e=>({setLastChangeSequenceNumber(t){e.lastChangeSequenceNumber=t}}))).actions((t=>({updateLastChangeSequenceNumber:l.flow((function*(){const{baseURL:e}=t,n=new URL("changes",e),o=new URLSearchParams({limit:"1"});n.search=o.toString();const a=n.toString(),s=t.getFetcher({locationType:"UriLocation",uri:a});let r;try{r=yield s(a,{method:"GET",signal:t.controller.signal})}catch(e){return void(t.controller.signal.aborted||console.error(e))}if(!r.ok){const e=yield _e(r,"Error when fetching server LastChangeSequence");throw new Error(e)}const i=yield r.json();t.setLastChangeSequenceNumber(i.length>0?i[0].sequence:0)})),getMissingChanges:l.flow((function*(){const{session:n}=l.getRoot(t),{changeManager:o}=n.apolloDataStore;if(!t.lastChangeSequenceNumber)throw new Error("No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server");const{baseURL:a,lastChangeSequenceNumber:s}=t,r=new URL("changes",a),i=new URLSearchParams({since:String(s),sort:"1"});r.search=i.toString();const c=r.toString(),d=t.getFetcher({locationType:"UriLocation",uri:c});let u;try{u=yield d(c,{method:"GET",signal:t.controller.signal})}catch(e){return void(t.controller.signal.aborted||console.error(e))}if(!u.ok)return void console.error(`Error when fetching the last updates to recover socket connection — ${u.status}`);const f=yield u.json();for(const t of f){const n=e.Change.fromJSON(t);o.submit(n,{submitToBackend:!1})}}))}))).volatile((e=>{const{origin:t,pathname:n}=new URL("socket.io/",e.baseURL);return{socket:d.io(t,{path:n})}})).actions((n=>({addSocketListeners(){const{session:o}=l.getRoot(n),{notify:a}=o,s=n.retrieveToken();if(!s)throw new Error("No Token found");const r=t.getDecodedToken(s),i=t.makeUserSessionId(r),{socket:c}=n,{addCheckResult:d,changeManager:u,deleteCheckResult:f}=o.apolloDataStore;c.on("connect",(()=>{n.getMissingChanges()})),c.on("connect_error",(e=>{console.error(e),a("Could not connect to the Apollo server.","error")})),c.on("COMMON",(t=>{if("checkResult"in t)return void(t.deleted?f(t.checkResult._id.toString()):d(t.checkResult));if(sessionStorage.setItem("LastChangeSequence",String(t.changeSequence)),t.userSessionId===i)return;const n=e.Change.fromJSON(t.changeInfo);u.submit(n,{submitToBackend:!1})})),c.on("USER_LOCATION",(e=>{const{channel:t,locations:n,userName:a,userSessionId:s}=e;"USER_LOCATION"===t&&s!==i&&o.addOrUpdateCollaborator({name:a,id:s,locations:n})})),c.on("REQUEST_INFORMATION",(e=>{const{channel:t,userSessionId:n}=e;"REQUEST_INFORMATION"===t&&n!==s&&o.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:o}=e,a=new URL("users/userLocation",n).href,s=new URLSearchParams(JSON.stringify(t)),r=e.getFetcher({locationType:"UriLocation",uri:a});try{if(!(await r(a,{method:"POST",body:s,signal:o.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*(o){if("none"===o){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"===o){const t=l.getRoot(e);s.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Admin",type:"subMenu",icon:u,subMenu:[{label:"Add Assembly",icon:r,onClick:e=>{e.queueDialog((t=>[ze,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Delete Assembly",icon:f,onClick:e=>{e.queueDialog((t=>[It,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Import Features",icon:g,onClick:e=>{e.queueDialog((t=>[Et,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[Jt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add Assembly aliases",onClick:e=>{e.queueDialog((t=>[Ve,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Users",icon:h,onClick:e=>{e.queueDialog((t=>[Ot,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Checks",icon:p,onClick:e=>{e.queueDialog((t=>[Pt,{session:e,handleClose:()=>{t()}}]))}}]})}(t)}yield e.updateLastChangeSequenceNumber(),e.addSocketListeners();const{baseURL:a}=e,i=new URL("users/locations",a).href,c=e.getFetcher({locationType:"UriLocation",uri:i});yield c(i,{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(cn)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()}}))),un="undefined"==typeof sessionStorage;class fn extends U.BaseAdapter{refNameAliases;async getRefNameAliases(){const e=o.readConfObject(this.config,"assemblyId");if(!un){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=await new Promise(((t,n)=>{const o=setTimeout((()=>{n(new Error("timeout"))}),2e4),a=O.nanoid(),s=e=>{const n=e.data;(function(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo&&"refNameAliases"in 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n.named("LinearApolloReferenceSequenceDisplayRendering").volatile((()=>({seqTrackCanvas:null,seqTrackOverlayCanvas:null,theme:i.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:o,highContrast:a,showStartCodons:r,showStopCodons:i,sequenceRowHeight:l,session:c}=e;if(!t.initialized||e.regionCannotBeRendered()||!n)return;if(3/t.bpPerPx<1)return;const{bpPerPx:d,offsetPx:u,dynamicBlocks:f}=t;!function(e,t,n,o,a,r,i,l,c,d){const u=e.getContext("2d");if(!u)return;u.clearRect(0,0,e.width,e.height);const{apolloDataStore:f}=d;for(const e of a.contentBlocks){const a=e.offsetPx-o;ya(u,n,t,r,a,e.widthPx,c,e.reversed);const d=f.assemblies.get(e.assemblyName),g=d?.getByRefName(e.refName),h=Math.floor(e.start),p=Math.ceil(e.end);let m=g?.getSequence(h,p);if(!m)return;m=m.toUpperCase(),e.reversed&&(m=s.revcom(m));const 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o=s.getFrame(n.min,n.max,a??1,n.phase),i=(e.showFeatureLabels?[0,5,3,1,15,13,11]:[0,2,1,0,8,7,6]).at(o);if(!i)continue;r.get(i)||r.set(i,[]);const l=r.get(i);l?.push({rowNum:i,feature:t})}}}}return r}))},getFeatureLayoutPosition(e){const{featureLayouts:t}=this;for(const[n,o]of t.entries())for(const[,t]of o)for(const{feature:o}of t)if(e._id===o._id)return{layoutIndex:n,layoutRow:0,featureRow:0}}}))).views((e=>({get highestRow(){return 5}}))).actions((e=>({afterAttach(){l.addDisposer(e,c.autorun((()=>{if(e.lgv.initialized&&!e.regionCannotBeRendered())for(const t of e.regions){const n=e.session.apolloDataStore.assemblies.get(t.assemblyName),o=n?.getByRefName(t.refName),a=o?.features;if(a)for(const[,n]of a)s.doesIntersect2(t.start,t.end,n.min,n.max)&&!e.seenFeatures.has(n._id)&&e.addSeenFeature(n)}}),{name:"LinearApolloSixFrameDisplaySetSeenFeatures",delay:1e3}))}})))}(0,t).named("LinearApolloSixFrameDisplayRendering").props({apolloRowHeight:20,detailsMinHeight:200,detailsHeight:200,lastRowTooltipBufferHeight:120,isShown:!0,filteredTranscripts:l.types.array(l.types.string)}).volatile((()=>({canvas:null,overlayCanvas:null,collaboratorCanvas:null,theme:i.createTheme()}))).views((e=>({get featuresHeight(){return(e.highestRow+1)*e.apolloRowHeight*(e.showFeatureLabels?2:1)+e.lastRowTooltipBufferHeight}}))).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);for(const n of e.session.collaborators){const{locations:o}=n;if(0===o.length)continue;let a=0;for(const s of e.lgv.displayedRegions){for(const r of o){if(r.refSeq!==s.refName)continue;const{end:o,refSeq:i,start:l}=r,c=e.lgv.bpToPx({refName:i,coord:l,regionNumber:a});if(!c)continue;const d=c.offsetPx-e.lgv.offsetPx,u=(o-l)/e.lgv.bpPerPx;t.fillStyle="rgba(0,255,0,.2)",t.fillRect(d,1,u,100),t.fillStyle="black",t.fillText(n.name,d+1,11,u-2)}a++}}}}),{name:"LinearApolloSixFrameDisplayRenderCollaborators"})),l.addDisposer(e,c.autorun((()=>{const{apolloRowHeight:t,canvas:n,featureLayouts:o,featuresHeight:a,lgv:r,session:i,theme:l,showFeatureLabels:c,showStartCodons:d,showStopCodons:u}=e;if(!r.initialized||e.regionCannotBeRendered())return;const{bpPerPx:f,offsetPx:g,displayedRegions:h,dynamicBlocks:p}=r,m=n?.getContext("2d");if(m){m.clearRect(0,0,p.totalWidthPx,a);for(const[t,n]of o.entries()){const o=h[t];for(const[a,r]of n.entries())for(const{feature:n}of r){if(!n.looksLikeGene)continue;if(!s.doesIntersect2(o.start,o.end,n.min,n.max))continue;const{topLevelFeature:r}=n,i=e.getGlyph(r);void 0!==i&&i.draw(m,r,a,e,t)}}if(d||u){const{apolloDataStore:e}=i;for(const n of p.contentBlocks){const o=e.assemblies.get(n.assemblyName),a=o?.getByRefName(n.refName),s=Math.floor(n.start),r=Math.ceil(n.end);let i=a?.getSequence(s,r);if(!i)break;i=i.toUpperCase();const h=Math.round(n.offsetPx-g-(n.start-s)/f);for(let e=0;e<i.length;e++){const n=s+e;Ia(m,i.slice(e,e+3),h,e,l,!0,f,n,t,c,d,u)}}}}}),{name:"LinearApolloSixFrameDisplayRenderFeatures"}))}})))}(0,t);return n.named("LinearApolloSixFrameDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0}))).views((e=>({getMousePosition(t){const n=Oe(t,e.lgv),{bp:o,regionNumber:a,y:r}=n,i=Math.floor(r/e.apolloRowHeight)+1,l=e.featureLayouts[a].get(i);if(!l)return n;const{featureTypeOntology:c}=e.session.apolloDataStore.ontologyManager;if(!c)throw new Error("featureTypeOntology is undefined");let d;if(e.geneTrackRowNums.includes(i)?(d=l.find((e=>"exon"==e.feature.type&&o>=e.feature.min&&o<=e.feature.max)),d||(d=l.find((e=>o>=e.feature.min&&o<=e.feature.max)))):d=l.find((t=>{const{feature:n}=t,a=n.attributes.get("gff_id")?.toString();if(!c.isTypeOf(n.type,"transcript"))return!1;for(const t of n.cdsLocations)for(const r of t){const t=s.getFrame(r.min,r.max,n.strand??1,r.phase),l=(e.showFeatureLabels?[0,5,3,1,15,13,11]:[0,2,1,0,8,7,6]).at(t);if(i===l&&o>=r.min&&o<=r.max)return void 0===a||!e.filteredTranscripts.includes(a)}return!1})),!d)return n;const{feature:u}=d;return{...n,feature:u}}}))).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(t){e.filteredTranscripts=l.cast(t)}}))).actions((()=>({onClick(){}})))}(0,n).views((e=>({contextMenuItems(t){const{hoveredFeature:n}=e;if(!n)return[];const o=e.getMousePosition(t),{topLevelFeature:a}=n.feature,s=e.getGlyph(a);return Pe(o)?s.getContextMenuItems(e,o):[]}}))).actions((e=>({startDrag(t,n,o,a=!1){e.apolloDragging={start:t,current:t,feature:n,edge:o,shrinkParent:a}},endDrag(){if(!e.apolloDragging)throw new Error("endDrag() called with no current drag in progress");const{current:n,edge:o,feature:a,start:s,shrinkParent:r}=e.apolloDragging;if(Math.abs(n.x-s.x)<=4)return e.setDragging(),void e.setCursor();const{displayedRegions:i}=e.lgv,l=e.getAssemblyId(i[s.regionNumber].assemblyName),c=qe(a,n.bp,o,r),d="max"===o?new t.LocationEndChange({typeName:"LocationEndChange",changedIds:c.map((e=>e.featureId)),changes:c.map((e=>({featureId:e.featureId,oldEnd:e.oldLocation,newEnd:e.newLocation}))),assembly:l}):new t.LocationStartChange({typeName:"LocationStartChange",changedIds:c.map((e=>e.featureId)),changes:c.map((e=>({featureId:e.featureId,oldStart:e.oldLocation,newStart:e.newLocation}))),assembly:l});e.changeManager.submit(d),e.setDragging(),e.setCursor()}}))).actions((e=>({onMouseDown(t){const n=e.getMousePosition(t);Pe(n)&&e.getGlyph(n.feature).onMouseDown(e,n,t)},onMouseMove(t){const n=e.getMousePosition(t);if(e.apolloDragging)return e.setCursor("col-resize"),void e.continueDrag(n,t);Pe(n)?e.getGlyph(n.feature).onMouseMove(e,n,t):(e.setHoveredFeature(),e.setCursor())},onMouseLeave(t){e.setDragging(),e.setHoveredFeature();const n=e.getMousePosition(t);Pe(n)&&e.getGlyph(n.feature).onMouseLeave(e,n,t)},onMouseUp(t){const n=e.getMousePosition(t);Pe(n)?e.getGlyph(n.feature).onMouseUp(e,n,t):e.setSelectedFeature(),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){l.addDisposer(e,c.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.overlayCanvas?.getContext("2d");if(!t)return;t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.featuresHeight);const{apolloDragging:n,hoveredFeature:o}=e;if(!o)return;const a=e.getGlyph(o.feature);a.drawHover(e,t),a.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloSixFrameDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:l.types.optional(xo,{})}).named("LinearApolloSixFrameDisplay")}const La=o.ConfigurationSchema("ApolloPlugin",{ontologies:l.types.array(mt),featureTypeOntologyName:{description:"Name of the feature type ontology",type:"string",defaultValue:"Sequence Ontology"},hasRole:{description:"Flag used internally by jbrowse-plugin-apollo",type:"boolean",defaultValue:!1},geneBackgroundColor:{description:"Color for feature background",type:"string",defaultValue:"jexl:geneBackgroundColor(featureType)",contextVariable:["featureType"]}}),Ea=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"gene")||n.isTypeOf(e.type,"transcript")||n.isTypeOf(e.type,"pseudogene")||n.isTypeOf(e.type,"pseudogenic_transcript")},qa=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"gene")||n.isTypeOf(e.type,"pseudogene")},Pa=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"transcript")||n.isTypeOf(e.type,"pseudogenic_transcript")};function Oa(e){const{attributes:t}=e,n=["gene_name","gene_id","gene_stable_id"];for(const e of n){const n=t?.[e];if(n?.[0])return n[0]}return""}const _a=e=>{const t=function(e){const{attributes:t}=e,n=["name","gff_name","transcript_name","gene_name"];for(const e of n){const n=t?.[e];if(n?.[0])return n[0]}return""}(e),n=function(e){const{attributes:t}=e,n=["id","gff_id","transcript_id","gene_id","gene_stable_id","stable_id"];for(const e of n){const n=t?.[e];if(n?.[0])return n[0]}return""}(e);return t?`${e.type} - ${t}`:n?`${e.type} - ${n}`:e.type};function Ba({annotationFeature:e,assembly:n,handleClose:o,refSeqId:a,session:s,region:r}){const c=s,{featureTypeOntology:d}=c.apolloDataStore.ontologyManager,u=v.useMemo((()=>Object.keys(e.children??{})),[e]),[f,g]=v.useState(!0),[h,p]=v.useState(u),[y,b]=v.useState(""),[x,S]=v.useState([]),[w,j]=v.useState(!1),[T,A]=v.useState(),F=c.apolloDataStore.assemblies.get(n.name),D=F?.refSeqs.get(a),k=D?.getFeatures(r.start,r.end),N=()=>{const e=[];for(const t of k??[])if(!(t.min>r.end||t.max<r.start)&&d?.isTypeOf(t.type,"gene")){const n=l.getSnapshot(t);e.push(n)}return e};v.useEffect((()=>{b("");const e=N();S(e),A(e[0])}),[h,f,r]);const R=async e=>{if(T)for(const o of Object.keys(e)){const a=e[o];if(a.strand=T.strand,a.children)for(const e of Object.keys(a.children))a.children[e].strand=T.strand;const s=new t.AddFeatureChange({parentFeatureId:T._id,changedIds:[T._id],typeName:"AddFeatureChange",assembly:n.name,addedFeature:a});await L(s,o)}},I=async o=>{const s=(new C).toHexString(),r=Math.min(...Object.values(o).map((e=>e.min))),i=Math.max(...Object.values(o).map((e=>e.max))),l=new t.AddFeatureChange({changedIds:[s],typeName:"AddFeatureChange",assembly:n.name,addedFeature:{_id:s,refSeq:a,min:r,max:i,strand:e.strand,type:"gene",children:o,attributes:{name:[Oa(e)],gene_name:[Oa(e)]}}});await L(l,s)},M=async(e,o)=>{if(!T)return;const a=[];e!==T.min&&a.push(new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[T._id],featureId:T._id,assembly:n.name,oldStart:T.min,newStart:e})),o!==T.max&&a.push(new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[T._id],featureId:T._id,assembly:n.name,oldEnd:T.max,newEnd:o}));for(const e of a)await L(e)},L=async(e,t)=>{await c.apolloDataStore.changeManager.submit(e).then((()=>{c.apolloSetSelectedFeature(t)}))};return m.jsxs(Ue,{open:!0,title:"Create Apollo Annotation",handleClose:o,fullWidth:!0,maxWidth:"sm",children:[m.jsx(i.DialogTitle,{fontSize:15,children:"Select the feature to be copied to apollo track"}),m.jsxs(i.DialogContent,{children:[m.jsxs(i.Box,{sx:{ml:3},children:[Ea(e,c)&&m.jsx(i.FormControlLabel,{control:m.jsx(i.Checkbox,{size:"small",checked:f,onChange:e=>{const t=e.target.checked;g(t),p(t?u:[])}}),label:`${_a(e)} (${e.min+1}..${e.max})`}),e.children&&m.jsx(i.Box,{sx:{display:"flex",flexDirection:"column",ml:3},children:Object.values(e.children).filter((e=>Pa(e,c))).map((e=>m.jsx(i.FormControlLabel,{control:m.jsx(i.Checkbox,{size:"small",checked:h.includes(e._id),onChange:t=>{((e,t)=>{p((n=>e.target.checked?[...n,t._id]:n.filter((e=>e!==t._id))))})(t,e)}}),label:`${_a(e)} (${e.min+1}..${e.max})`},e._id)))})]}),x.length>0&&(!f&&h.length>0||f&&Pa(e,c))&&m.jsxs("div",{style:{border:"1px solid #ccc",marginTop:20,padding:10,borderRadius:5},children:[m.jsxs(i.Box,{sx:{ml:3},children:[m.jsx(i.Typography,{variant:"caption",fontSize:12,children:"Select the destination feature to copy the selected features"}),m.jsx(i.Box,{sx:{mt:1},children:m.jsx(i.Select,{labelId:"label",style:{width:"100%"},value:T?._id??"",onChange:e=>{const t=x.find((t=>t._id===e.target.value));A(t)},disabled:w,children:x.map((e=>m.jsx(i.MenuItem,{value:e._id,children:`${_a(e)} (${e.min+1}..${e.max})`},e._id)))})})]}),m.jsx(i.Box,{sx:{ml:3},children:m.jsx(i.FormGroup,{children:m.jsx(i.FormControlLabel,{control:m.jsx(i.Checkbox,{checked:w,onChange:e=>{j(e.target.checked)}}),label:"Create new gene"})})})]})]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{variant:"contained",type:"submit",disabled:0===h.length||!f&&h.length>0&&!T,onClick:async()=>{if(f){if(qa(e,c)&&(await(async()=>{let o;if(e.children&&h.length!==Object.values(e.children).length){const a={};for(const t of h)a[t]=e.children[t];o=new t.AddFeatureChange({changedIds:[e._id],typeName:"AddFeatureChange",assembly:n.name,addedFeature:{...e,children:a}})}else o=new t.AddFeatureChange({changedIds:[e._id],typeName:"AddFeatureChange",assembly:n.name,addedFeature:e});await L(o,e._id)})(),s.notify("Successfully copied selected gene and transcript(s)","success")),Pa(e,c))if(T&&!w){const t={};if(t[e._id]=e,T.max<e.max||T.min>e.min){const n=Math.min(T.min,e.min),o=Math.max(T.max,e.max);await M(n,o),await R(t)}else await R(t);s.notify("Successfully copied selected transcripts to destination gene","success")}else{const t={};t[e._id]=e,await I(t),s.notify("Successfully created a new gene with selected transcripts","success")}}else{if(!e.children)return;if(T&&!w){const t={};for(const n of h)t[n]=e.children[n];const n=Math.min(...Object.values(t).map((e=>e.min))),o=Math.max(...Object.values(t).map((e=>e.max)));if(T.min>n||T.max<o){const e=Math.min(T.min,n),a=Math.max(T.max,o);await M(e,a),await R(t)}else await R(t);s.notify("Successfully copied transcript to destination gene","success")}else{const t={};for(const n of h)t[n]=e.children[n];await I(t),s.notify("Successfully created a new gene with selected transcript","success")}}o()},children:"Create"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:o,children:"Cancel"})]}),y?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:y})}):null]})}function Ua(e){if("LinearPileupDisplay"!==e.name)return e;const{stateModel:t}=e,n=t.views((e=>({getFirstRegion:()=>s.getContainingView(e).dynamicBlocks.contentBlocks[0],getAssembly(){const t=e.getFirstRegion(),n=s.getSession(e),{assemblyManager:o}=n,{assemblyName:a}=t,r=o.get(a);if(!r)throw new Error(`Could not find assembly named ${a}`);return r},getRefSeqId(t){const n=e.getFirstRegion(),{refName:o}=n,{refNameAliases:a}=t;if(!a)throw new Error(`Could not find aliases for ${t.name}`);const s=[...Object.entries(a)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t}))),r=s.find((e=>e.name===o))?._id;if(!r)throw new Error(`Could not find refSeqId named ${o}`);return r},getAnnotationFeature(){const t=e.contextMenuFeature,n=e.getAssembly(),o=e.getRefSeqId(n),a=t.get("start"),s=t.get("end"),r=t.get("strand"),i=t.get("name"),l=function(e){const t=/(\d+)([MIDNSHPX=])/g,n=[];let o;for(;null!==(o=t.exec(e));)n.push([o[2],Number.parseInt(o[1],10)]);return n}(t.get("CIGAR"));let c,d=a;const u=[];for(const[e,t]of l)switch(e){case"M":case"=":case"X":void 0===c&&(c=d),d+=t;break;case"N":void 0!==c&&(u.push({start:c,end:d}),c=void 0),d+=t;break;case"D":d+=t;break;case"I":case"S":case"H":case"P":break;default:throw new Error(`Unknown CIGAR operation: ${e}`)}void 0!==c&&u.push({start:c,end:d});const f={_id:C().toHexString(),refSeq:o,min:a,max:s,type:"mRNA",strand:r,attributes:{name:[i]}};if(0===u.length)return f;f.children={};for(const e of u){const t={_id:C().toHexString(),refSeq:o,min:e.start,max:e.end,type:"exon",strand:r};f.children[t._id]=t}return f}}))).views((e=>{const t=e.contextMenuItems;return{contextMenuItems(){const n=s.getSession(e),o=e.getAssembly(),a=e.getFirstRegion();return e.contextMenuFeature?[...t(),{label:"Create Apollo annotation",icon:r,onClick:()=>{n.queueDialog((t=>[Ba,{session:n,handleClose:()=>{t()},annotationFeature:e.getAnnotationFeature(o),assembly:o,refSeqId:e.getRefSeqId(o),region:a}]))}}]:t()}}}));return e.stateModel=n,e}function $a(e,t){const 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n)o.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(o)}}),{name:"ApolloSessionBroadcastLocations"})),l.addDisposer(e,c.autorun((async s=>{if(o.readConfObject(n.configuration.ApolloPlugin,"hasRole"))return l.applySnapshot(e,e.previousSnapshot),void s.dispose();const{signal:r}=e.abortController;for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:t}=n,o=new URL("jbrowse/config.json",t).href,i=n.getFetcher({locationType:"UriLocation",uri:o});let l,c;try{l=await i(o,{signal:r})}catch(t){e.abortController.signal.aborted||console.error(t);continue}if(l.ok){try{c=await l.json()}catch(e){console.error(e);continue}c.configuration.ApolloPlugin.hasRole&&(a(c,e.previousSnapshot),s.dispose())}else{const e=await _e(l,"Failed to fetch assemblies");console.error(e)}}}),{name:"ApolloSessionLoadConfig"}))},beforeDestroy(){e.abortController.abort(new DOMException("Clean up Apollo session","AbortError"))}}))).views((e=>{const n=e.getTrackActionMenuItems;return{getTrackActionMenuItems(a){if("ApolloTrack"===a.type||"ReferenceSequenceTrack"===a.type)return n?.(a);const s=o.readConfObject(a,"trackId");return s.endsWith("-sessionTrack")?[...n?.(a)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:o}=l.getRoot(e),r=l.getSnapshot(o);let i;i=t.filterJBrowseConfig(r),0===Object.keys(i).length&&(i=void 0);const c={...l.getSnapshot(a),trackId:s.slice(0,s.length-13)};for(const o of n){if("ApolloInternetAccount"!==o.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:i?.tracks&&[...i.tracks,c]}}),{internetAccountId:a}=o;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:a});const{notify:s}=e;s("Track added","success")}e.deleteTrackConf(a),o.addTrackConf(c)},icon:ge}]:[...n?.(a)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:o}=l.getRoot(e),r=l.getSnapshot(o);let i;i=t.filterJBrowseConfig(r),0===Object.keys(i).length&&(i=void 0);const c=i?.tracks?.filter((e=>e.trackId!==s));for(const o of n){if("ApolloInternetAccount"!==o.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:c}}),{internetAccountId:a}=o;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:a});const{notify:s}=e;s("Track removed","success")}e.deleteTrackConf(a),o.deleteTrackConf(a)},icon:ge}]}}}));return l.types.snapshotProcessor(i,{postProcessor(e,t){e.apolloSelectedFeature=void 0;const n=Object.fromEntries(Object.entries(e.apolloDataStore.assemblies).filter((([,e])=>"InMemoryFileDriver"===e.backendDriverType)));if(e.apolloDataStore={typeName:"Client",assemblies:n,checkResults:{}},!t)return e;const{apolloDataStore:o}=t,{checkResults:a}=o;for(const[,t]of a){const[n]=t.ids;if(!n)continue;const a=o.assemblies.get(n.assemblyId);a&&"InMemoryFileDriver"===a.backendDriverType&&(e.apolloDataStore.checkResults[t._id]=l.getSnapshot(t))}return e}})}const as="WorkerGlobalScope"in globalThis;for(const[n,o]of Object.entries(t.changes))e.changeRegistry.registerChange(n,o);const ss=new t.CDSCheck;e.checkRegistry.registerCheck(ss.name,ss);const rs=new t.TranscriptCheck;e.checkRegistry.registerCheck(rs.name,rs),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends n{name="ApolloPlugin";version="0.3.13";configurationSchema=La;install(e){!function(e){e.addAdapterType((()=>new B({name:"ApolloSequenceAdapter",configSchema:yn,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:mn})))}(e),function(e){e.addAdapterType((()=>new B({name:"ApolloRefNameAliasAdapter",configSchema:gn,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:fn})))}(e),function(e){e.addTextSearchAdapterType((()=>new a.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:Sn,AdapterClass:xn,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=o.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new a.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:On,ReactComponent:Pn})})),e.addWidgetType((()=>{const e=o.ConfigurationSchema("ApolloTranscriptDetails",{});return new a.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:_n,ReactComponent:to})})),e.addTrackType((()=>{const t=o.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:a.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new a.TrackType({name:"ApolloTrack",configSchema:t,stateModel:a.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new a.InternetAccountType({name:"ApolloInternetAccount",configSchema:he,stateModel:dn(he)}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloDisplay",configSchema:no,stateModel:la(0,no),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:es}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:Ca,stateModel:Ma(0,Ca),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:ts}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloReferenceSequenceDisplay",configSchema:ca,stateModel:Sa(0,ca),displayName:"Apollo reference sequence display",trackType:"ReferenceSequenceTrack",viewType:"LinearGenomeView",ReactComponent:wa}))),e.addToExtensionPoint("Core-extendSession",os.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:r,onClick:()=>{const t=s.getSession(e),{leftOffset:n,rightOffset:o}=e,a=e.getSelectedRegions(n,o);t.queueDialog((e=>[kt,{session:t,handleClose:()=>{e()},region:a[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Ua),e.addToExtensionPoint("Core-extendPluggableElement",za),e.addToExtensionPoint("LinearGenomeView-searchResultSelected",((e,t)=>{const{session:n,result:o}=t,a=o.getTrackId(),s=o.matchedObject;return a?.startsWith("apollo_track_")&&s&&n.apolloSetEventualSelectedFeature(s._id),e})),as||e.addToExtensionPoint("Core-extendWorker",(t=>"on"in t&&t.on?(t.on("apollo",(async n=>{if("object"!=typeof(o=n)||null===o||!("apollo"in o)||!0!==o.apollo)return;var o;const{apollo:a,messageId:s,method:r}=n;switch(r){case"getSequence":{const{region:o}=n,{assemblyName:r}=o,i=e.rootModel?.session?.apolloDataStore;if(!i)break;const l=i.getBackendDriver(r);if(!l)break;const{seq:c}=await l.getSequence(o);t.workers[0].postMessage({apollo:a,messageId:s,sequence:c});break}case"getRegions":{const{assembly:o}=n,r=e.rootModel?.session?.apolloDataStore;if(!r)break;const i=r.getBackendDriver(o);if(!i)break;const l=await i.getRegions(o);t.workers[0].postMessage({apollo:a,messageId:s,regions:l});break}case"getRefNameAliases":{const{assembly:o}=n,r=e.rootModel?.session?.apolloDataStore;if(!r)break;const i=r.getBackendDriver(o);if(!i)break;const l=await i.getRefNameAliases(o);t.workers[0].postMessage({apollo:a,messageId:s,refNameAliases:l});break}}})),t):t))}configure(e){var t;s.isAbstractMenuManager(e.rootModel)&&(e.jexl.addFunction("geneBackgroundColor",(e=>"pseudogene"===e?i.alpha("rgb(148, 203, 236)",.6):"ncRNA_gene"===e?i.alpha("rgb(194, 106, 119)",.6):void 0)),(t=e.rootModel).insertInMenu("Apollo",{label:"Redo",icon:de,onClick(e){const{apolloDataStore:t}=e;t.changeManager.redoLastChange()}},0),t.insertInMenu("Apollo",{label:"Undo",icon:fe,onClick(e){const{apolloDataStore:t}=e;t.changeManager.undoLastChange()}},0),t.appendToMenu("Apollo",{label:"Download GFF3",icon:re,onClick:e=>{e.queueDialog((t=>[Lt,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"View Change Log",icon:ue,onClick:e=>{e.queueDialog((t=>[zt,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"Open local GFF3 file",icon:le,onClick:e=>{e.queueDialog((t=>[Gt,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),t.appendToMenu("Apollo",{label:"View check results",icon:ie,onClick:e=>{e.queueDialog((t=>[Xt,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"Lock/Unlock session",onClick:e=>{e.toggleLocked()}}),t.appendToMenu("Apollo",{label:"Log out",icon:ce,onClick:e=>{e.queueDialog((t=>[qt,{session:e,handleClose:()=>{t()}}]))}}))}};
+"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var e=require("@apollo-annotation/common"),t=require("@apollo-annotation/shared"),n=require("@jbrowse/core/Plugin"),o=require("@jbrowse/core/configuration"),a=require("@jbrowse/core/pluggableElementTypes"),s=require("@jbrowse/core/util"),r=require("@mui/icons-material/Add"),i=require("@mui/material"),l=require("@jbrowse/mobx-state-tree"),c=require("mobx"),d=require("socket.io-client"),u=require("@mui/icons-material/AdminPanelSettings"),g=require("@mui/icons-material/Delete"),f=require("@mui/icons-material/Input"),h=require("@mui/icons-material/Person"),p=require("@mui/icons-material/Rule"),m=require("react/jsx-runtime"),y=require("@jbrowse/core/util/tss-react"),b=require("@mui/icons-material/Info"),x=require("@mui/icons-material/Link"),w=require("@mui/icons-material/RadioButtonChecked"),S=require("@mui/icons-material/RadioButtonUnchecked"),C=require("bson-objectid"),v=require("react"),j=require("@mui/icons-material/SkipNextRounded"),T=require("@mui/icons-material/SkipPreviousRounded"),A=require("@jbrowse/core/util/types/mst"),F=require("idb/with-async-ittr"),k=require("@jbrowse/core/util/aborting"),D=require("jsonpath"),N=require("@jbrowse/core/util/io"),I=require("fast-deep-equal/es6"),R=require("@jbrowse/core/ui"),M=require("@mui/icons-material/Close"),E=require("mobx-react"),L=require("@mui/x-data-grid"),q=require("@gmod/gff"),P=require("file-saver"),_=require("@mui/icons-material/AccountCircle"),O=require("@jbrowse/core/pluggableElementTypes/AdapterType"),B=require("@jbrowse/core/data_adapters/BaseAdapter"),U=require("nanoid"),$=require("@jbrowse/core/util/rxjs"),z=require("@jbrowse/core/util/simpleFeature"),W=require("@jbrowse/core/TextSearch/BaseResults"),G=require("@mui/icons-material/ExpandMore"),H=require("@mui/icons-material/Edit"),V=require("@mui/icons-material/MoreHoriz"),J=require("@mui/icons-material/AddBox"),X=require("@apollo-annotation/mst"),K=require("@emotion/styled"),Z=require("@mui/icons-material/ContentCopy"),Y=require("@mui/icons-material/ContentCut"),Q=require("@mui/icons-material/Remove"),ee=require("@mui/icons-material/Clear"),te=require("@mui/icons-material/UnfoldLess"),ne=require("@jbrowse/core/util/tracks"),oe=require("@mui/icons-material/FactCheck"),ae=require("@mui/icons-material/TrackChanges"),se=require("@mui/icons-material/ExpandLess"),re=require("@mui/icons-material/Lock"),ie=require("@mui/icons-material/Error"),le=require("@mui/icons-material/Logout"),ce=require("@mui/icons-material/Redo"),de=require("@mui/icons-material/Undo"),ue=require("@mui/icons-material/Save");const ge=o.ConfigurationSchema("ApolloInternetAccount",{baseURL:{description:"Location of Apollo server",type:"string",defaultValue:""},tokenType:{description:"A custom name for a token to include in the header",type:"string",defaultValue:"Bearer"}},{baseConfiguration:a.BaseInternetAccountConfig,explicitlyTyped:!0});function fe(e){const{attributes:t}=e,n=t.get("gff_name");return n?n[0]:""}function he(e){const{attributes:t}=e,n=t.get("gff_id"),o=t.get("transcript_id"),a=t.get("exon_id"),s=t.get("protein_id");return n?n[0]:o?o[0]:a?a[0]:s?s[0]:""}function pe(e){const t=fe(e),n=he(e);return t?`: ${t}`:n?`: ${n}`:""}function me(e,t,n=!1){const o=[];o.push(e);for(const t of function(e){const t=[];let{parent:n}=e;for(;n;)t.push(n),({parent:n}=n);return t}(e))o.push(t);const a=function(e){const t=[];if(e.children)for(const[,n]of e.children)t.push(n);return t}(e);for(const e of a)e.min<t&&e.max>=t&&o.push(e);if(!n)return o;if(e.parent){const n=e.parent.children;if(n)for(const[,a]of n)a._id!=e._id&&a.min<t&&a.max>=t&&o.push(a)}return o}function ye(e,t){if(e.attributes){const n={};for(const[o,a]of Object.entries(e.attributes))t.has(o)||(n[o]=a);e.attributes=0===Object.keys(n).length?void 0:n}if(e.children){const n={};for(const[o,a]of Object.entries(e.children)){const e={...a};ye(e,t),n[o]=e}e.children=n}}const be=new Set(["i","me","my","myself","we","our","ours","ourselves","you","your","yours","yourself","yourselves","he","him","his","himself","she","her","hers","herself","it","its","itself","they","them","their","theirs","themselves","what","which","who","whom","this","that","these","those","am","is","are","was","were","be","been","being","have","has","had","having","do","does","did","doing","a","an","the","and","but","if","or","because","as","until","while","of","at","by","for","with","about","against","between","into","through","during","before","after","above","below","to","from","up","down","in","out","on","off","over","under","again","further","then","once","here","there","when","where","why","how","all","any","both","each","few","more","most","other","some","such","no","nor","not","only","own","same","so","than","too","very","s","t","can","will","just","don","should","now","0","1","2","3","4","5","6","7","8","9"]);function xe(e,t){for(const[n,o]of t.entries())if(e.startsWith(o))return e.replace(o,String(n));return e}const we="$PREFIXED_ID";function Se(e,t,n){if(t===we)return[xe(e.id,n)];let o;try{o=D.query(e,t)}catch{o=D.query(JSON.parse(JSON.stringify(e)),t)}return o}function Ce(e){return e.toLowerCase().split(/[^\d:A-Za-z]+/).filter((e=>e&&!be.has(e)))}function*ve(e){for(const t of e)yield*Ce(t)}function*je(e){for(const t of e)if("string"==typeof t)yield t;else if("object"==typeof t){const e=D.query(t,"$..*");yield*je(e)}}function*Te(e,t,n){for(const o of t){const t=Se(e,o,n);if(t.length>0)for(const e of ve(je(t)))yield[o,e]}}async function Ae(e,t,n){const o=await this.db,a=t??o.transaction(["nodes"]);k.checkAbortSignal(n);const s=[...Ce(e)],r=[],i=new Map;r.push(...s.map((async(e,t)=>{k.checkAbortSignal(n);const o=a.objectStore("nodes").index("full-text-words");for await(const a of o.iterate(IDBKeyRange.bound(e,`${e}￿`,!1,!1))){k.checkAbortSignal(n);const e=a.value,o=i.get(e.id)??[e,new Set];o[1].add(t),i.set(e.id,o)}}))),await Promise.all(r),k.checkAbortSignal(n);const l=[];for(const[,[e,t]]of i)k.checkAbortSignal(n),l.push(...Fe(this.textIndexFields,e,t,s,this.prefixes));return l.sort(((e,t)=>t.score-e.score)),l.slice(0,this.options.maxSearchResults??this.DEFAULT_MAX_SEARCH_RESULTS)}function Fe(e,t,n,o,a){const s=[...n].sort().map((e=>o[e])),r=s.map((e=>{const t=e.replaceAll(/[$()*+./?[\\\]^{|}-]/g,String.raw`\$&`);return new RegExp(`\\b${t}`,"gi")}));let i=[],l=0;for(const[n,s]of e.entries()){const c=new Set,d=e.length-n-1,u=[...je(Se(t,s.jsonPath,a))];for(const e of u){let n=0;const a=[];for(const[t,s]of r.entries())for(const r of e.matchAll(s)){n+=1+1*d,c.add(t);const s=r.index,i=o[t];void 0!==s&&(n+=.01*i.length,n+=i.length/e.length*100*.05,a.push({wordIndex:t,position:s}))}n+=100*c.size,l<n&&(l=n),a.sort(((e,t)=>e.position-t.position)),a.length>0&&i.push({term:t,field:s,str:e,score:n,wordMatches:a})}}i=i.filter((e=>e.score===l));for(const e of i){const{wordMatches:t}=e;for(let n=0;n<t.length-1;n++){const o=t[n],a=t[n+1],r=a.wordIndex-o.wordIndex;if(1===r||-1===r){e.score+=1,1===r&&(e.score+=1);const t=Math.abs(a.position-(o.position+s[o.wordIndex].length))-1;e.score-=.05*t}}}return i}function ke(e){return"string"==typeof e.id}function De(e){return"string"==typeof e.sub&&"string"==typeof e.pred&&"string"==typeof e.obj}function Ne(e){return Boolean(e.meta?.deprecated)}function Ie(e){return"CLASS"===e.type}function Re(e){return"PROPERTY"===e.type}const Me=[{displayName:"Label",jsonPath:"$.lbl"},{displayName:"Synonym",jsonPath:"$.meta.synonyms[*].val"},{displayName:"Definition",jsonPath:"$.meta.definition.val"}];async function Ee(e){return F.openDB(e,2,{upgrade(e,t,n,o,a){if(t<2&&(e.objectStoreNames.contains("meta")&&e.deleteObjectStore("meta"),e.objectStoreNames.contains("nodes")&&e.deleteObjectStore("nodes"),e.objectStoreNames.contains("edges")&&e.deleteObjectStore("edges")),e.objectStoreNames.contains("meta")||e.createObjectStore("meta"),!e.objectStoreNames.contains("nodes")){e.createObjectStore("nodes",{keyPath:"id"});const t=o.objectStore("nodes");t.createIndex("by-label","lbl"),t.createIndex("by-type","type"),t.createIndex("by-synonym",["meta","synonyms","val"]),t.createIndex("full-text-words","fullTextWords",{multiEntry:!0})}if(!e.objectStoreNames.contains("edges")){e.createObjectStore("edges",{autoIncrement:!0});const t=o.objectStore("edges");t.createIndex("by-subject","sub"),t.createIndex("by-object","obj"),t.createIndex("by-predicate","pred")}}})}function Le(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function qe(e){const t=Date.now();let n,o=1;this.options.update?.("Parsing JSON",o);try{n=JSON.parse(await N.openLocation(this.sourceLocation).readFile("utf8"))}catch{throw new Error("Error in loading ontology")}o+=5,this.options.update?.("Parsing JSON complete",o);const a=Date.now(),[s,...r]=n.graphs??[];if(s){if(r.length>0)throw new Error("multiple graphs not supported");try{const n=e.transaction(["meta","nodes","edges"],"readwrite");await n.objectStore("meta").clear(),await n.objectStore("nodes").clear(),await n.objectStore("edges").clear();const r=n.objectStore("nodes"),i=Pe.call(this).map((e=>e.jsonPath));if(s.nodes){let e=Math.round(o);for(const[,t]of s.nodes.entries())o+=1/s.nodes.length*64,Math.round(o)!=e&&o<100&&(this.options.update?.("Processing nodes",o),e=Math.round(o)),ke(t)&&await r.add({...t,fullTextWords:Le(Te(t,i,this.prefixes))})}const l=n.objectStore("edges");if(s.edges){let e=Math.round(o);for(const[,t]of s.edges.entries())o+=1/s.edges.length*30,Math.round(o)!=e&&o<100&&(this.options.update?.("Processing 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Set}))).actions((e=>({ping(){},initDataStore(){e.dataStore=new Oe(e.name,e.version,l.getSnapshot(e.source),e.options)},afterCreate(){l.addDisposer(e,c.autorun((()=>{this.initDataStore()})))},setEquivalentTypes(t,n){e.equivalentTypes.set(t,n)}}))).actions((e=>({loadEquivalentTypes:l.flow((function*(t){if(!e.dataStore)return;if(e.startedEquivalentTypeRequests.has(t))return;e.startedEquivalentTypeRequests.add(t);const n=(yield e.dataStore.getTermsWithLabelOrSynonym(t)).map((e=>e.lbl)).filter((e=>null!=e));l.isAlive(e)&&e.setEquivalentTypes(t,n)}))}))).actions((e=>({afterCreate(){c.autorun((t=>{e.dataStore&&(e.loadEquivalentTypes("gene"),e.loadEquivalentTypes("pseudogene"),e.loadEquivalentTypes("transcript"),e.loadEquivalentTypes("pseudogenic_transcript"),e.loadEquivalentTypes("CDS"),e.loadEquivalentTypes("mRNA"),t.dispose())}))},setEquivalentTypes(t,n){e.equivalentTypes.set(t,n)}}))).views((e=>({isTypeOf(t,n){if(t===n)return!0;if(!e.dataStore)return!1;const 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Ye({changeManager:e,handleClose:n,selectedFeature:o,session:a,setSelectedFeature:s,sourceAssemblyId:r,sourceFeature:c}){const[d,u]=v.useState(""),{ontologyManager:g}=a.apolloDataStore,{featureTypeOntology:f}=g;function h(e){if(!e.parent?.children||1===e.parent.children.size)return;const t=[];for(const n of e.parent.children.values())f?.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())f?.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 o of t)if(o._id!==e._id&&o.min>=e.min){n=o.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 o of n)if(o._id!=e._id&&o.max<=e.max){t=o.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 m.jsxs(Ge,{open:!0,title:"Delete feature",handleClose:n,maxWidth:!1,"data-testid":"delete-feature",children:[m.jsxs("form",{onSubmit:a=>{!async function(a){a.preventDefault(),u(""),o?._id===c._id&&s();const i=[],d=new t.DeleteFeatureChange({changedIds:[c._id],typeName:"DeleteFeatureChange",assembly:r,changes:[{deletedFeature:l.getSnapshot(c),parentFeatureId:c.parent?._id}]});if(f&&(f.isTypeOf(c.type,"transcript")||f.isTypeOf(c.type,"pseudogenic_transcript"))){const e=h(c);e&&i.push(e)}if(f&&f.isTypeOf(c.type,"exon")){const e=function(e){if(!f)return;if(!f.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 n=(e.parent.cdsLocations.at(0)??[]).sort((({min:e},{min:t})=>e-t));let o;for(const t of e.parent.children.values())if(t.type===n[0].type){o=t;break}if(!o)throw new Error("Unable to find CDS");const a=n[0].min,s=n[n.length-1].max;if(!(e.min>a&&e.max<s||e.max<a||e.min>s)){if(e.min<=a&&e.max>=s)return new t.DeleteFeatureChange({changedIds:[o._id],typeName:"DeleteFeatureChange",assembly:r,changes:[{deletedFeature:l.getSnapshot(o),parentFeatureId:o.parent?._id}]});if(e.min<=a&&e.max>a){let t;for(const o of n)if(o.min>e.max){t=o.min;break}if(!t)throw new Error("Error setting new CDS start");return{typeName:"LocationStartChange",changedId:o._id,featureId:o._id,oldLocation:o.min,newLocation:t}}if(e.min<s&&e.max>=s){let t;for(const o of n.reverse())if(o.max<e.min){t=o.max;break}if(!t)throw new Error("Error setting new CDS end");return{typeName:"LocationEndChange",changedId:o._id,featureId:o._id,oldLocation:o.max,newLocation:t}}throw new Error("Unexpected relationship between exon and 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t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new C).toHexString(),assemblyName:u,fileIds:{fa:e,fai:n,gzi:o}})}}const[{internetAccountId:s}]=d;await e.submit(a,{internetAccountId:s,updateJobsManager:!0}),I(!1),V(!1)},"data-testid":"submit-form",children:[m.jsxs(i.DialogContent,{className:s.dialog,children:[H?m.jsx(i.LinearProgress,{}):null,m.jsx(i.TextField,{margin:"dense",id:"name",label:"Assembly name",type:"TextField",fullWidth:!0,variant:"outlined",onChange:e=>{I(!1),g(e.target.value),function(e){const{assemblies:t}=a;t.find((t=>o.readConfObject(t,"displayName")===e))?(y(!1),h(`Assembly ${e} already 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Does not copy the files to the Apollo collaboration server, so ensure the URLs are stable.",placement:"top-start",children:m.jsx(i.IconButton,{size:"small",children:m.jsx(b,{sx:{fontSize:18}})})})]})}),m.jsx(i.FormControlLabel,{"data-testid":"sequence-is-editable-checkbox",control:m.jsx(i.Checkbox,{onChange:()=>{D(!k)}}),checked:k,disabled:j===bt.EXTERNAL,label:m.jsxs(i.Box,{display:"flex",alignItems:"center",children:["Store sequence in database",m.jsx(i.Tooltip,{title:"Enables users to edit the genomic sequence, but comes with performance impacts. Use with care.",placement:"top-start",children:m.jsx(i.IconButton,{size:"small",children:m.jsx(b,{sx:{fontSize:18}})})})]})}),m.jsx(i.FormControlLabel,{"data-testid":"fasta-is-gzip-checkbox",control:m.jsx(i.Checkbox,{checked:!k||J,onChange:()=>{X(!k||!J)},disabled:!k}),label:"FASTA is gzip compressed"}),m.jsx(i.Table,j===bt.BGZIP_FASTA||j===bt.GFF3?{size:"small",sx:{mt:2},children:m.jsxs(i.TableBody,{children:[m.jsxs(i.TableRow,{children:[m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsxs(i.Box,{display:"flex",alignItems:"center",children:[m.jsx("span",{children:"FASTA"}),m.jsx(i.Tooltip,{title:'Unless "Store sequence in database" enabled, FASTA input must be compressed with bgzip and indexed with samtools faidx (or equivalent). Compression is optional for sequences stored in the database.',children:m.jsx(i.IconButton,{size:"small",children:m.jsx(b,{sx:{fontSize:18}})})})]})}),m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsx("input",{"data-testid":"fasta-input-file",type:"file",onChange:e=>{const t=e.target.files?.item(0);t&&(L(t),t.name.endsWith(".gz")&&X(!0))},disabled:N&&!f})})]}),m.jsxs(i.TableRow,{children:[m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:"FASTA index (.fai)"}),m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsx("input",{"data-testid":"fai-input-file",type:"file",onChange:e=>{P(e.target.files?.item(0)??null)},disabled:N&&!f||k})})]}),m.jsxs(i.TableRow,{children:[m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:"FASTA binary index (.gzi)"}),m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsx("input",{"data-testid":"gzi-input-file",type:"file",onChange:e=>{O(e.target.files?.item(0)??null)},disabled:N&&!f||k})})]})]})}:{size:"small",sx:{mt:2},children:m.jsxs(i.TableBody,{children:[m.jsxs(i.TableRow,{children:[m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsxs(i.Box,{display:"flex",alignItems:"center",children:[m.jsx("span",{children:"FASTA"}),m.jsx(i.Tooltip,{title:"Remote FASTA input must be compressed with bgzip and indexed with samtools faidx (or equivalent)",children:m.jsx(i.IconButton,{size:"small",children:m.jsx(b,{sx:{fontSize:18}})})})]})}),m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsx(i.TextField,{"data-testid":"fasta-input-url",variant:"outlined",value:B,error:!Q,onChange:e=>{const{value:t}=e.target;U(t),z(t?`${t}.fai`:""),G(t?`${t}.gzi`:"")},disabled:N&&!f,slotProps:{input:{startAdornment:m.jsx(i.InputAdornment,{position:"start",children:m.jsx(x,{})})}}})})]}),m.jsxs(i.TableRow,{children:[m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:"FASTA index (.fai)"}),m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsx(i.TextField,{"data-testid":"fai-input-url",variant:"outlined",value:$,error:!ee,onChange:e=>{z(e.target.value)},disabled:N&&!f,slotProps:{input:{startAdornment:m.jsx(i.InputAdornment,{position:"start",children:m.jsx(x,{})})}}})})]}),m.jsxs(i.TableRow,{children:[m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:"FASTA binary index (.gzi)"}),m.jsx(i.TableCell,{style:{borderBottomWidth:0},children:m.jsx(i.TextField,{"data-testid":"gzi-input-url",variant:"outlined",value:W,error:!te,onChange:e=>{G(e.target.value)},disabled:N&&!f,slotProps:{input:{startAdornment:m.jsx(i.InputAdornment,{position:"start",children:m.jsx(x,{})})}}})})]})]})})]})})]}),m.jsxs(i.Accordion,{disableGutters:!0,elevation:0,square:!0,className:s.accordion,expanded:"panelGffInput"===ne,onChange:ae("panelGffInput"),children:[m.jsx(i.AccordionSummary,{className:s.accordionSummary,expandIcon:"panelGffInput"===ne?m.jsx(w,{className:s.radioIcon,sx:{fontSize:"1.2rem",ml:5}}):m.jsx(S,{className:s.radioIcon,sx:{fontSize:"1.2rem",mr:5}}),"aria-controls":"panelGffInputd-content",children:m.jsxs(i.Typography,{component:"span",children:["GFF3 input",m.jsx(i.Tooltip,{title:"GFF3 must includes FASTA sequences. File can be gzip compressed.",children:m.jsx(b,{className:s.radioIcon,sx:{fontSize:18}})})]})}),m.jsx(i.AccordionDetails,{className:s.accordionDetails,children:m.jsxs(i.Box,{style:{marginTop:20},children:[m.jsx("input",{"data-testid":"gff3-input-file",type:"file",disabled:N&&!f,onChange:e=>{const t=e.target.files?.item(0);t&&(L(t),T(bt.GFF3),t.name.endsWith(".gz")&&Z(!0))}}),m.jsxs(i.FormGroup,{style:{display:"grid"},children:[m.jsx(i.FormControlLabel,{control:m.jsx(i.Checkbox,{checked:A,onChange:()=>{F(!A)},disabled:N&&!f}),label:"Load features from GFF3 file"}),m.jsx(i.FormControlLabel,{label:"Strict parsing",disabled:!A||N&&!f,control:m.jsx(i.Checkbox,{checked:R,onChange:e=>{M(e.target.checked)}})}),m.jsx(i.FormHelperText,{children:"Don't import any features if any lines in the GFF3 are unable to be processed"}),m.jsx(i.FormControlLabel,{"data-testid":"gff3-is-gzip-checkbox",control:m.jsx(i.Checkbox,{checked:K,onChange:()=>{Z(!K)},disabled:N&&!f}),label:"GFF3 is gzip compressed"})]})]})})]})]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{disabled:!wt(p,k,j,E,q,_,Q,ee,te)||N,variant:"contained",type:"submit","data-testid":"submit-button",children:N?"Submitting...":"Submit"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:n,children:"Cancel"})]})]}),f?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:f})}):null]})}const Ct=[{field:"name",headerName:"Assembly Name",width:150,editable:!1},{field:"aliases",headerName:"Aliases",width:300,editable:!0}];function vt({changeManager:e,handleClose:n,session:o}){const{apolloDataStore:a}=o,{collaborationServerDriver:s}=a,r=s.getAssemblies().map((e=>({id:e.name,name:e.displayName,aliases:e.aliases.join(", ")}))),[l,c]=v.useState("");return m.jsxs(Ge,{open:!0,title:"Add assembly aliases",handleClose:n,maxWidth:"sm","data-testid":"add-assembly-alias",fullWidth:!0,children:[m.jsx(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:m.jsx(i.Box,{sx:{height:400,width:"100%"},children:m.jsx(L.DataGrid,{rows:r,columns:Ct,initialState:{pagination:{paginationModel:{pageSize:5}}},pageSizeOptions:[5],processRowUpdate:(o,a)=>{const s=new t.AddAssemblyAliasesChange({typeName:"AddAssemblyAliasesChange",assembly:o.id,aliases:o.aliases.split(",")});return e.submit(s).catch((()=>{c("Error submitting change")})),n(),o},disableRowSelectionOnClick:!0})})}),l?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:l})}):null]})}class jt{clientStore;constructor(e){this.clientStore=e}}async function Tt(e,t){return F.openDB(`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 o=`checkresults-${n}`;if(!e.objectStoreNames.contains(o)){const t=e.createObjectStore(o,{keyPath:"_id"});t.createIndex("min","start",{unique:!1}),t.createIndex("max","end",{unique:!1}),t.createIndex("featureId","featureId",{unique:!1})}}}})}class At extends jt{async getFeatures(e){const{assemblyName:t,end:n,refName:o,start:a}=e,s=(await this.getRegions(t)).map((e=>e.refName)),r=`features-${o}`,i=`checkresults-${o}`,l=[],c=[],d=(await Tt(t,s)).transaction([r,i]);for await(const e of d.objectStore(r).index("min").iterate(IDBKeyRange.upperBound(n,!0)))e.value.max>a&&l.push(e.value);for await(const e of d.objectStore(i).index("min").iterate(IDBKeyRange.upperBound(n,!0)))e.value.end>a&&c.push(e.value);return[l,c]}async getSequence(e){const t=s.getSession(this.clientStore),{assemblyManager:n}=t,o=await n.waitForAssembly(e.assemblyName);if(!o)throw new Error(`Assembly not found: "${e.assemblyName}"`);const{configuration:a}=o,{adapter:r}=a.sequence,{pluginManager:i}=s.getEnv(this.clientStore),l=i.getAdapterType(r.type);if(!l)throw new Error(`No adapter found for "${r.type}"`);const c=new(await l.getAdapterClass())(r,void 0,i),d=await c.getSequence(e);if(!d)throw new Error(`Sequence not found: ${JSON.stringify(e)}`);return{seq:d,refSeq:e.refName}}async getRegions(e){const t=s.getSession(this.clientStore),{assemblyManager:n}=t,o=await n.waitForAssembly(e);if(!o)throw new Error(`Assembly not found: "${e}"`);const{regions:a}=o;if(!a)throw new Error(`Assembly not found: "${e}"`);return a}getAssemblies(e){return[]}async getRefNameAliases(e){const t=s.getSession(this.clientStore),{assemblyManager:n}=t,o=await n.waitForAssembly(e);if(!o)throw new Error(`Assembly not found: "${e}"`);const{configuration:a}=o,{refNameAliases:r}=a;if(!r)return[];const{pluginManager:i}=s.getEnv(this.clientStore),l=i.getAdapterType(r.adapter.type);if(!l)throw new Error(`No adapter found for "${r.adapter.type}"`);return new(await l.getAdapterClass())(r.adapter,void 0,i).getRefNameAliases({})}async submitChange(n,o){if(!e.isFeatureChange(n))return new t.ValidationResultSet;const{assembly:a,changedIds:s}=n,r=(await this.getRegions(a)).map((e=>e.refName)),i=await Tt(a,r),c=new Set,d=[],u=new Set;if(t.isDeleteFeatureChange(n))for(const e of n.changes)if(e.parentFeatureId){const t=this.clientStore.getFeature(e.parentFeatureId);t&&(c.add(t.topLevelFeature),u.add(t.topLevelFeature.refSeq))}else{const{refSeq:t,_id:n}=e.deletedFeature;d.push({refSeq:t,featureId:n}),u.add(t)}else for(const e of s){const t=this.clientStore.getFeature(e);t&&(c.add(t.topLevelFeature),u.add(t.refSeq))}const g=[...u].flatMap((e=>[`features-${e}`,`checkresults-${e}`]));g.push("changes");const f=i.transaction(g,"readwrite");for(const{refSeq:e,featureId:t}of d)f.objectStore(`features-${e}`).delete(t);for(const e of c){const t=l.getSnapshot(e);f.objectStore(`features-${e.refSeq}`).put(t,e._id)}for(const{featureId:e,refSeq:t}of d){const n=f.objectStore(`checkresults-${t}`);for await(const t of n.index("featureId").iterate(e))this.clientStore.deleteCheckResult(t.value._id),t.delete()}for(const e of c){const t=f.objectStore(`checkresults-${e.refSeq}`);for await(const n of t.index("featureId").iterate(e._id))this.clientStore.deleteCheckResult(n.value._id),n.delete()}if(f.objectStore("changes").put({...n.toJSON(),createdAt:new Date}),await f.done,c.size>0){const t=[...e.checkRegistry.getChecks().values()],n=[];for(const e of c){const o=l.getSnapshot(e),s=async(t,n)=>(await this.getSequence({assemblyName:a,refName:e.refSeq,start:t,end:n})).seq;for(const a of t){const t=await a.checkFeature(o,s);for(const o of t)n.push({refSeq:e.refSeq,result:o,topLevelFeatureId:e._id})}}if(n.length>0){const e=r.map((e=>`checkresults-${e}`)),t=i.transaction(e,"readwrite");for(const{refSeq:e,result:o,topLevelFeatureId:a}of n)t.objectStore(`checkresults-${e}`).put({...o,featureId:a});await t.done;for(const{result:e}of n)this.clientStore.addCheckResult(e)}}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}async getCheckResults(e){const t=(await this.getRegions(e)).map((e=>e.refName)),n=await Tt(e,t),o=[],a=t.map((e=>`checkresults-${e}`)),s=n.transaction(a);for(const e of a)for await(const t of s.objectStore(e).iterate())o.push(t.value);return o}async getChanges(e,t={}){const n=(await this.getRegions(e)).map((e=>e.refName)),o=await Tt(e,n);let a=[];for await(const e of o.transaction("changes").store.iterate())a.push({sequence:e.key,...e.value});const{filters:s}=t;if(s?.user){const e=new RegExp(s.user,"i");a=a.filter((t=>void 0!==t.user&&e.test(t.user)))}if(s?.typeName&&(a=a.filter((e=>e.typeName===s.typeName))),s?.startTime){const e=new Date(s.startTime).getTime();a=a.filter((t=>new Date(t.createdAt).getTime()>=e))}if(s?.endTime){const e=new Date(s.endTime).getTime();a=a.filter((t=>new Date(t.createdAt).getTime()<=e))}const r=a.length,i=t.sortField??"sequence",l="asc"===(t.sortOrder??"desc")?1:-1;if(a.sort(((e,t)=>{const n=e[i],o=t[i];return n===o?0:void 0===n?1:void 0===o?-1:n<o?-l:l})),void 0!==t.page&&void 0!==t.pageSize){const e=t.page*t.pageSize;a=a.slice(e,e+t.pageSize)}return{changes:a,totalCount:r}}}const Ft={async AddFeatureChange(e,t){const{assembly:n,changes:o}=t;for(const t of o){const{addedFeature:o,parentFeatureId:a}=t;if(a){let t=e.getFeature(a);if(!t&&(await e.loadFeatures([{assemblyName:n,refName:o.refSeq,start:o.min,end:o.max}]),t=e.getFeature(a),!t))throw new Error(`Could not find parent feature "${a}"`);t.attributes.get("_id")||t.setAttribute("_id",[t._id]),t.addChild(o)}else e.addFeature(n,o)}},async DeleteFeatureChange(e,t){for(const n of t.changes){const{deletedFeature:t,parentFeatureId:o}=n;if(o){const n=e.getFeature(o);if(!n)throw new Error(`Could not find parent feature "${o}"`);n.deleteChild(t._id)}else e.getFeature(t._id)&&e.deleteFeature(t._id)}},async FeatureAttributeChange(e,t){for(const[n,o]of t.changedIds.entries()){const a=e.getFeature(o);if(!a)throw new Error(`Could not find feature with identifier "${o}"`);a.setAttributes(new Map(Object.entries(t.changes[n].newAttributes)))}},async LocationEndChange(e,t){for(const n of t.changes){const{featureId:t,newEnd:o}=n,a=e.getFeature(t);if(!a)throw new Error(`Could not find feature with identifier "${t}"`);a.setMax(o)}},async LocationStartChange(e,t){for(const n of t.changes){const{featureId:t,newStart:o}=n,a=e.getFeature(t);if(!a)throw new Error(`Could not find feature with identifier "${t}"`);a.setMin(o)}},async MergeExonsChange(e,n){for(const o of n.changes){const{firstExon:n,secondExon:a}=o,s=e.getFeature(n._id);if(!s)throw new Error(`Could not find feature with identifier "${n._id}"`);s.setMin(Math.min(n.min,a.min)),s.setMax(Math.max(n.max,a.max));const r=s.attributes.get("merged_with")?.slice()??[],i=t.stringifyAttributes(t.attributesToRecords(a.attributes));r.includes(i)||r.push(i),s.setAttribute("merged_with",r),s.parent?.deleteChild(a._id)}},async SplitExonChange(e,t){for(const[n]of t.changedIds.entries()){const{exonToBeSplit:o,parentFeatureId:a,upstreamCut:s,downstreamCut:r,leftExonId:i,rightExonId:l}=t.changes[n];if(!a)throw new Error("TODO: Split exon without parent");const[c,d]=t.makeSplitExons(o,s,r,i,l),u=e.getFeature(a);if(!u)throw new Error(`Could not find parent feature "${a}"`);u.addChild(c),u.addChild(d),e.getFeature(o._id)&&e.deleteFeature(o._id)}},async MergeTranscriptsChange(e,t){for(const[n,o]of t.changedIds.entries()){const{firstTranscript:a,secondTranscript:s}=t.changes[n],r=e.getFeature(a._id);if(!r)throw new Error(`Could not find feature with identifier "${o}"`);t.mergeTranscriptsOnClient(r,s),r.parent?.deleteChild(s._id)}},async UndoMergeExonsChange(e,t){for(const n of t.changes){const{exonsToRestore:t,parentFeatureId:o}=n;if(!o)throw new Error("Parent ID is missing");const a=e.getFeature(o);if(!a)throw new Error(`Could not find parent feature "${o}"`);a.attributes.get("_id")||a.setAttribute("_id",[a._id]);for(const e of t)a.addChild(e)}},async UndoSplitExonChange(e,t){for(const n of t.changes){const{exonToRestore:t,parentFeatureId:o,idsToDelete:a}=n;if(!o)throw new Error("Parent ID is missing");const s=e.getFeature(o);if(!s)throw new Error(`Could not find parent feature "${o}"`);s.attributes.get("_id")||s.setAttribute("_id",[s._id]),s.addChild(t),a.map((e=>{s.deleteChild(e)}))}},async UndoMergeTranscriptsChange(e,t){for(const n of t.changes){const{transcriptsToRestore:t,parentFeatureId:o}=n;if(!o)throw new Error("Parent ID is missing");const a=e.getFeature(o);if(!a)throw new Error(`Could not find parent feature "${o}"`);a.attributes.get("_id")||a.setAttribute("_id",[a._id]);for(const e of t)a.addChild(e)}},async StrandChange(e,t){for(const[n,o]of t.changedIds.entries()){const a=e.getFeature(o);if(!a)throw new Error(`Could not find feature with identifier "${o}"`);a.setStrand(t.changes[n].newStrand)}},async TypeChange(e,t){for(const[n,o]of t.changedIds.entries()){const a=e.getFeature(o);if(!a)throw new Error(`Could not find feature with identifier "${o}"`);a.setType(t.changes[n].newType)}}};class kt{dataStore;constructor(e){this.dataStore=e}recentChanges=[];undoneChanges=[];async submit(n,o={}){const{addToRecents:a=!0,submitToBackend:r=!0,updateJobsManager:i=!1}=o,l=s.getSession(this.dataStore),c=new AbortController,{jobsManager:d,isLocked:u,changeInProgress:g,setChangeInProgress:f}=s.getSession(this.dataStore);if(u)return l.notify("Cannot submit changes in locked mode"),void f(!1);if(g)return void l.notify("Could not submit change, there is another change still in progress");f(!0);const h={name:n.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{c.abort(new DOMException(`Cancelling change "${n.typeName}"`,"AbortError"))}};i&&d.runJob(h);const p=await t.validationRegistry.frontendPreValidate(n);if(!p.ok){const e=`Pre-validation failed: "${p.resultsMessages}"`;return i&&d.abortJob(h.name,e),l.notify(e,"error"),void f(!1)}const m=n.typeName,y=function(e){return e in Ft}(m)?Ft[m]:void 0;if(y)try{await y(this.dataStore,n)}catch(e){return i&&d.abortJob(h.name,String(e)),console.error(e),l.notify(`Error encountered in client: ${String(e)}. Data may be out of sync, please refresh the page`,"error"),void f(!1)}if((await t.validationRegistry.frontendPostValidate(n)).ok||await this.undo(n),r){i&&d.update(h.name,"Submitting to driver");const{collaborationServerDriver:t,getBackendDriver:s}=this.dataStore,r=e.isAssemblySpecificChange(n)?s(n.assembly)??t:t;let c;try{c=await r.submitChange(n,o)}catch(e){return i&&d.abortJob(h.name,String(e)),console.error(e),l.notify(String(e),"error"),f(!1),void await this.undo(n,!1)}if(!c.ok){const e=`Post-validation failed: "${p.resultsMessages}"`;return i&&d.abortJob(h.name,e),l.notify(e,"error"),f(!1),void await this.undo(n,!1)}n.notification&&l.notify(n.notification,"success"),a&&(this.recentChanges.push(n),this.undoneChanges=[])}i&&d.done(h),f(!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=s.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=s.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 Dt extends jt{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:o}=n,a=new URL("features/searchFeatures",o),s=new URLSearchParams({assemblies:t.join(","),term:e});a.search=s.toString();const r=a.toString(),i=await this.fetch(n,r);if(!i.ok){const e=await yt(i,"searchFeatures failed");throw new Error(e)}return i.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:o,start:a}=e,{assemblyManager:r}=s.getSession(this.clientStore);if(!r.get(t))throw new Error(`Could not find assembly with name "${t}"`);const i=(await this.getRefSeqMapping(t)).get(o);if(!i)throw new Error(`Could not find refSeq "${o}"`);const l=i.id,c=this.clientStore.getInternetAccount(t),{baseURL:d}=c,u=new URL("features/getFeatures",d),g=new URLSearchParams({refSeq:l,start:String(a),end:String(n)});u.search=g.toString();const f=u.toString(),h=await this.fetch(c,f);if(!h.ok){const e=await yt(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,c),h.json()}checkSocket(n,o,a){const{socket:s}=a,r=`${n}-${o}`;s.hasListeners(r)||s.on(r,(async n=>{const o=a.retrieveToken();if(!o)return;const s=t.makeUserSessionId(o),r=new kt(this.clientStore);if(a.setLastChangeSequenceNumber(Number(n.changeSequence)),n.userSessionId===s)return;const i=e.Change.fromJSON(n.changeInfo);e.isFeatureChange(i)&&this.haveDataForChange(i)&&await r.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}-${e.end}`,n=this.inFlight.get(t),{assemblyName:o,end:a,refName:r,start:i}=e,{assemblyManager:l}=s.getSession(this.clientStore);if(!l.get(o))throw new Error(`Could not find assembly with name "${o}"`);const c=(await this.getRefSeqMapping(o)).get(r);if(!c)throw new Error(`Could not find refSeq "${r}"`);const d=c.id;if(n)return{seq:await n,refSeq:d};let u=this.clientStore.assemblies.get(o);u||(u=this.clientStore.addAssembly(o));let g=u.refSeqs.get(d);g||(g=u.addRefSeq(d,r));const f=g.getSequence(i,a);if(f.length===a-i)return{seq:f,refSeq:d};const h=this.clientStore.getInternetAccount(o),{baseURL:p}=h,m=new URL("sequence",p),y=new URLSearchParams({refSeq:d,start:String(i),end:String(a)});m.search=y.toString();const b=m.toString(),x=this.getSeqFromServer(h,b,g,i,a);this.inFlight.set(t,x);const w=await x;return this.checkSocket(o,r,h),this.inFlight.delete(t),{seq:w,refSeq:d}}async getSeqFromServer(e,t,n,o,a){const s=await this.fetch(e,t);if(!s.ok){let e;try{e=await s.text()}catch{e=""}throw new Error(`getSequence failed: ${s.status} (${s.statusText})${e?` (${e})`:""}`)}const r=await s.text();return n.addSequence({sequence:r,start:o,stop:a}),r}async getRefSeqMapping(e){const t=this.refSeqMaps.get(e);if(t)return t;const{assemblyManager:n}=s.getSession(this.clientStore);if(!n.get(e))throw new Error(`Could not find assembly with name "${e}"`);const o=this.clientStore.getInternetAccount(e),{baseURL:a}=o,r=new URL("refSeqs",a),i=new URLSearchParams({assembly:e});r.search=i.toString();const l=r.toString(),c=await this.fetch(o,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 d=await c.json(),u=new Map(d.map((e=>[e.name,{refName:e.name,id:e._id,aliases:e.aliases}])));return this.refSeqMaps.set(e,u),u}async getRefNameAliases(e){return[...(await this.getRefSeqMapping(e)).values()].map((e=>({refName:e.refName,aliases:[...new Set([e.id,...e.aliases])],uniqueId:`alias-${e.id}`})))}async getRefSeqId(e,t){const n=await this.getRefSeqMapping(e);if(!n)return;const o=n.get(t);return o?.id}async getRegions(e){const{assemblyManager:t}=s.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:o}=n,a=new URL("refSeqs",o),r=new URLSearchParams({assembly:e});a.search=r.toString();const i=a.toString(),l=await this.fetch(n,i);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}=s.getSession(this.clientStore);return t.assemblies.filter((t=>{const n=o.getConf(t,["sequence","metadata"]);return!(!(n&&n.apollo&&n.internetAccountConfigId)||e&&n.internetAccountConfigId!==e)}))}async getChanges(e,t={}){const n=this.clientStore.getInternetAccount(e),{baseURL:o}=n,a=new URL("changes",o),s={assembly:e};void 0!==t.page&&(s.page=String(t.page)),void 0!==t.pageSize&&(s.pageSize=String(t.pageSize)),t.sortField&&(s.sortField=t.sortField),t.sortOrder&&(s.sortOrder=t.sortOrder),t.filters?.user&&(s.user=t.filters.user),t.filters?.typeName&&(s.typeName=t.filters.typeName),t.filters?.startTime&&(s.startTime=t.filters.startTime),t.filters?.endTime&&(s.endTime=t.filters.endTime),a.search=new URLSearchParams(s).toString();const r=await this.fetch(n,a.toString());if(!r.ok){const e=await yt(r,"getChanges failed");throw new Error(e)}return r.json()}async getCheckResults(e){const t=this.clientStore.getInternetAccount(e),{baseURL:n}=t,o=new URL("checks",n);o.search=new URLSearchParams({assembly:e}).toString();const a=await this.fetch(t,o.toString());if(!a.ok){const e=await yt(a,"getCheckResults failed");throw new Error(e)}return a.json()}async submitChange(e,n={}){const{internetAccountId:o}=n,a=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,o),{baseURL:s}=a,r=new URL("changes",s).href,i=await this.fetch(a,r,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!i.ok){const e=await yt(i,"submitChange failed");throw new Error(e)}const l=new t.ValidationResultSet;return i.ok||(l.ok=!1),l}}var Nt;function It(e,t,n,o){const a={_id:(new C).toHexString(),refSeq:e,type:"CDS",min:n,max:o,strand:t},s={_id:(new C).toHexString(),refSeq:e,type:"exon",min:n,max:o,strand:t},r={};return r[a._id]=a,r[s._id]=s,{_id:(new C).toHexString(),refSeq:e,type:"mRNA",min:n,max:o,strand:t,children:r}}function Rt({changeManager:e,handleClose:n,region:o,session:a}){const[s,r]=v.useState(String(o.end)),[l,c]=v.useState(String(o.start+1)),[d,u]=v.useState(Nt.GENE_AND_SUBFEATURES),[g,f]=v.useState(""),[h,p]=v.useState(),[y,x]=v.useState(""),w=Number(s)<=Number(l);let S=Boolean(w)||!(l&&s&&d);return(d===Nt.CUSTOM&&!g||!h&&d===Nt.GENE_AND_SUBFEATURES||!h&&d===Nt.TRANSCRIPT_AND_SUBFEATURES)&&(S=!0),m.jsxs(Ge,{open:!0,title:"Add new feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog",children:[m.jsxs("form",{onSubmit:async function(r){r.preventDefault(),x("");const i=a.apolloDataStore.getBackendDriver(o.assemblyName);if(!i)return void x("No backend driver found");let c=o.refName;if(i instanceof Dt){const e=await i.getRefSeqId(o.assemblyName,o.refName);if(!e)return void x(`Could not find refSeq for "${o.refName}"`);c=e}if(d===Nt.GENE_AND_SUBFEATURES){const r=It(c,h,Number(l)-1,Number(s)),i={};i[r._id]=r;const d=(new C).toHexString(),u=new t.AddFeatureChange({changedIds:[d],typeName:"AddFeatureChange",assembly:o.assemblyName,addedFeature:{_id:d,refSeq:c,min:Number(l)-1,max:Number(s),type:"gene",strand:h,children:i}});return e.submit(u).then((()=>{a.apolloSetSelectedFeature(d)})),void n()}if(d===Nt.TRANSCRIPT_AND_SUBFEATURES){const r=It(c,h,Number(l)-1,Number(s)),i=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o.assemblyName,addedFeature:r});return e.submit(i).then((()=>{a.apolloSetSelectedFeature(r._id)})),void n()}if(!g)return void x("No type selected");const u=(new C).toHexString(),f=new t.AddFeatureChange({changedIds:[u],typeName:"AddFeatureChange",assembly:o.assemblyName,addedFeature:{_id:u,refSeq:c,min:Number(l)-1,max:Number(s),type:g,strand:h}});e.submit(f).then((()=>{a.apolloSetSelectedFeature(u)})),n()},"data-testid":"submit-form",children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsx(i.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(l),onChange:e=>{c(e.target.value)}}),m.jsx(i.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:s,onChange:e=>{r(e.target.value)},error:w,helperText:w?'"End" must be greater than "Start"':null}),m.jsxs(i.FormControl,{children:[m.jsx(i.InputLabel,{id:"demo-simple-select-label",children:"Strand"}),m.jsxs(i.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Strand",value:h?.toString(),onChange:function(e){switch(x(""),Number(e.target.value)){case 1:p(1);break;case-1:p(-1);break;default:p(void 0)}},children:[m.jsx(i.MenuItem,{value:void 0}),m.jsx(i.MenuItem,{value:1,children:"+"}),m.jsx(i.MenuItem,{value:-1,children:"-"})]})]}),m.jsx(i.FormControl,{style:{marginTop:20},children:m.jsxs(i.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:Nt.GENE_AND_SUBFEATURES,name:"radio-buttons-group",value:d,onChange:e=>{x("");const{value:t}=e.target;Object.keys(Nt).includes(t)&&u(Nt[t])},children:[m.jsx(i.FormControlLabel,{value:Nt.GENE_AND_SUBFEATURES,control:m.jsx(i.Radio,{}),label:m.jsxs(i.Box,{display:"flex",alignItems:"center",children:["Add gene and sub-features",m.jsx(i.Tooltip,{title:"This is a shortcut to create a gene with a single mRNA, exon, and CDS",children:m.jsx(i.IconButton,{size:"small",children:m.jsx(b,{sx:{fontSize:18}})})})]})}),m.jsx(i.FormControlLabel,{value:Nt.TRANSCRIPT_AND_SUBFEATURES,control:m.jsx(i.Radio,{}),label:m.jsxs(i.Box,{display:"flex",alignItems:"center",children:["Add transcript 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Mt({changeManager:e,handleClose:n,session:o}){const{internetAccounts:a}=l.getRoot(o),[s,r]=v.useState(""),[c,d]=v.useState(!1),[u,g]=v.useState(!1),f=a.filter((e=>"ApolloInternetAccount"===e.type));if(0===f.length)throw new Error("No Apollo internet account found");const[h,p]=v.useState(f[0]),{collaborationServerDriver:y}=o.apolloDataStore,b=y.getAssemblies(),[x,w]=v.useState(b.at(0));return m.jsxs(Ge,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly",children:[m.jsxs("form",{onSubmit:async function(o){if(o.preventDefault(),g(!0),r(""),!x)return void r("Must select assembly!");const a=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:x.name});await e.submit(a,{internetAccountId:h.internetAccountId}),n(),o.preventDefault()},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[f.length>1?m.jsxs(m.Fragment,{children:[m.jsx(i.DialogContentText,{children:"Select 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function(n){n.preventDefault(),c(""),await(f?async function(e){const t=d(a,e),n=new URL("export/getID",t.baseURL),o=new URLSearchParams({assembly:a});n.search=o.toString();const r=n.toString(),i=t.getFetcher({locationType:"UriLocation",uri:r}),l=await i(r,{method:"GET"});if(!l.ok){const e=await yt(l,"Error when exporting ID");return void c(e)}const{exportID:u}=await l.json(),g=new URL("export",t.baseURL),f=new URLSearchParams({exportID:u,includeFASTA:s?"true":"false"});g.search=f.toString();const h=g.toString();window.open(h,"_blank")}(f):async function(e){const n=function(e){const n=new ReadableStream({async start(n){for await(const o of async function*(e){const t=await Tt(e,[]);for(const e of t.objectStoreNames){const n=t.transaction(e);for await(const e of n.store.iterate())yield e.value}t.close()}(e)){const e=t.annotationFeatureToGFF3(o);n.enqueue(e)}n.close()}});return n.pipeThrough(new TransformStream(new q.GFFFormattingTransformer))}(e),o=`${e}.gff3`;try{const e=await globalThis.showSaveFilePicker({suggestedName:o}),t=await e.createWritable();await n.pipeTo(t)}catch{const e=await new Response(n).blob();P.saveAs(e,o)}}(a)),e()},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsxs(i.DialogContentText,{children:["Exporting annotations for ",a]}),m.jsx(i.FormGroup,{children:m.jsx(i.FormControlLabel,{"data-testid":"include-fasta-checkbox",control:m.jsx(i.Checkbox,{checked:s,onChange:()=>{r(!s)},disabled:!f}),label:"Include fasta sequence in GFF output"})})]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{variant:"contained",type:"submit",children:"Download"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:e,children:"Cancel"})]})]}),l?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:l})}):null]})}function qt({changeManager:e,handleClose:n,session:a}){const{apolloDataStore:s}=a,[r,l]=v.useState(),[c,d]=v.useState(),[u,g]=v.useState(""),[f,h]=v.useState(!1),[p,y]=v.useState(),[b,x]=v.useState(!1),[w,S]=v.useState(!0),[C,j]=v.useState(!1),{collaborationServerDriver:T,getInternetAccount:A}=s,F=T.getAssemblies();return v.useEffect((()=>{c&&(async()=>{const{internetAccountConfigId:e}=o.getConf(c,["sequence","metadata"]),t=A(c.name,e);if(!t)throw new Error("No Apollo internet account found");const{baseURL:n}=t,a=new URL("features/count",n),s=new URLSearchParams({assemblyId:c.name});a.search=s.toString();const r=t.getFetcher({locationType:"UriLocation",uri:a.toString()});j(!0);const i=await r(a.toString(),{method:"GET"});if(!i.ok)throw new Error(await yt(i));{const e=await i.json();y(e.count)}j(!1)})().catch((e=>{console.error(e),g(e.message??e)}))}),[A,a,c]),m.jsxs(Ge,{open:!0,title:"Import Features from GFF3 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y(p,{method:"POST",body:m,signal:e});if(!t.ok){const e=await yt(t,"Error when inserting new features (while uploading file)");return x.abortJob(C.name,e),void g(e)}i=(await t.json())._id}const v=new t.AddFeaturesFromFileChange({typeName:"AddFeaturesFromFileChange",assembly:c.name,fileId:i,parseOptions:{strict:w},deleteExistingFeatures:b});x.done(C),await e.submit(v,{updateJobsManager:!0})},children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column"},children:[m.jsx(i.DialogContentText,{children:"Select assembly"}),m.jsx(i.Select,{labelId:"label",value:c?.name??"",onChange:function(e){const t=F.find((t=>t.name===e.target.value));d(t),h(!1)},disabled:f&&!u,children:F.map((e=>m.jsx(i.MenuItem,{value:e.name,children:e.displayName??e.name},e.name)))}),m.jsx(i.DialogContentText,{children:"Upload GFF3 to load features"}),m.jsx("input",{type:"file",onChange:function(e){h(!1),e.target.files&&l(e.target.files[0])},disabled:f&&!u}),m.jsx(i.FormControlLabel,{label:"Strict 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21",style:{fontSize:21},...e,children:[m.jsx("rect",{x:"1",y:"1",width:"9",height:"9",fill:"disabled"===t?"#7B7B7B":"#F25022"}),m.jsx("rect",{x:"1",y:"11",width:"9",height:"9",fill:"disabled"===t?"#7B7B7B":"#00A4EF"}),m.jsx("rect",{x:"11",y:"1",width:"9",height:"9",fill:"disabled"===t?"#939393":"#7FBA00"}),m.jsx("rect",{x:"11",y:"11",width:"9",height:"9",fill:"disabled"===t?"#B9B9B9":"#FFB900"})]})}const an=y.makeStyles()((e=>({loginButton:{marginBottom:e.spacing(1),width:"220px",height:"40px",fontSize:"16px",textTransform:"none",justifyContent:"left",padding:"3px 12px"}})));function sn(e){const{classes:t}=an(),{disabled:n}=e;return m.jsx(i.Button,{className:t.loginButton,variant:"outlined",startIcon:m.jsx(nn,{color:n?"disabled":void 0}),...e,children:"Sign in with Google"})}function rn(e){const{classes:t}=an(),{disabled:n}=e;return m.jsx(i.Button,{className:t.loginButton,variant:"outlined",startIcon:m.jsx(on,{color:n?"disabled":void 0}),...e,children:"Sign in with Microsoft"})}function ln(e){const{classes:t}=an();return m.jsx(i.Button,{className:t.loginButton,variant:"outlined",startIcon:m.jsx(_,{fontSize:"small"}),...e,children:"Continue as Guest"})}const cn=y.makeStyles()((e=>({divider:{marginTop:e.spacing(4),marginBottom:e.spacing(5)}}))),dn=({baseURL:e,handleClose:t,name:n})=>{const{classes:o}=cn(),[a,s]=v.useState(""),[r,l]=v.useState([]);function c(e){t("google"===e?"google":"microsoft"===e?"microsoft":"guest")}v.useEffect((()=>{const t=new AbortController,{signal:n}=t;return async function(){const t=new URL("auth/types",e).href,o=await fetch(t,{method:"GET",signal:n});if(!o.ok){const e=await yt(o,"Error when retrieving auth types from server");return void s(e)}const a=await o.json();l(a)}().catch((e=>{k.isAbortException(e)||s(String(e))})),()=>{t.abort(new DOMException("Error retrieving valid authentication types","AbortError"))}}),[e]);const d=r.includes("google"),u=r.includes("microsoft"),g=r.includes("guest");return m.jsxs(Ge,{open:!0,title:`Log in to ${n}`,handleClose:t,maxWidth:!1,"data-testid":"login-apollo",children:[m.jsxs(i.DialogContent,{style:{display:"flex",flexDirection:"column",paddingTop:8},children:[d?m.jsx(sn,{disabled:!d,onClick:()=>{c("google")}}):null,u?m.jsx(rn,{disabled:!u,onClick:()=>{c("microsoft")}}):null,g?m.jsxs(m.Fragment,{children:[m.jsx(i.Divider,{className:o.divider}),m.jsx(ln,{onClick:()=>{c("guest")}})]}):null]}),m.jsx(i.DialogActions,{children:m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:()=>{t()},children:"Cancel"})}),a?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:a})}):null]})},un="undefined"==typeof sessionStorage,gn=n=>a.InternetAccount.named("ApolloInternetAccount").props({type:l.types.literal("ApolloInternetAccount"),configuration:o.ConfigurationReference(n)}).views((e=>({get baseURL(){return o.getConf(e,"baseURL")},getUserId(){const n=e.retrieveToken();if(n)return t.getDecodedToken(n).id}}))).volatile((()=>({role:void 0,controller:new AbortController,tokenPromise:void 0}))).actions((e=>({setRole(){const n=e.retrieveToken();if(!n)return void(e.role=void 0);const o=t.getDecodedToken(n),{role:a,exp:s}=o;if(s<Date.now()/1e3)return e.role=void 0,void e.removeToken();e.role!==a&&(e.role=a)}}))).actions((e=>{const t=e.getFetcher;return{getFetcher(n){const o=t(n);return async(t,n)=>{const a=await o(t,n);return 403===a.status?(e.removeToken(),e.setRole(),o(t,n)):a}}}})).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(un)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,o){if(t.data.name!==`JBrowseAuthWindow-${e.internetAccountId}`)return;const a=t.data.redirectUri.replace("#","?"),s=new URL(a),r=new URLSearchParams(s.search).get("access_token");this.deleteMessageChannel(),r?(e.storeToken(r),e.setRole(),n(r)):o(new Error("Error with token endpoint"))},async openAuthWindow(t,n,o){const a=s.isElectron?"http://localhost/auth":globalThis.location.origin+globalThis.location.pathname,r=new URL("auth/login",e.baseURL),i=new URLSearchParams({type:t,redirect_uri:a});r.search=i.toString();const l=`JBrowseAuthWindow-${e.internetAccountId}`;if(s.isElectron){const{ipcRenderer:t}=globalThis.require("electron"),s=await t.invoke("openAuthWindow",{internetAccountId:e.internetAccountId,data:{redirect_uri:a},url:r.toString()}),i=new MessageEvent("message",{data:{name:l,redirectUri:s}});this.finishOAuthWindow(i,n,o)}else this.addMessageChannel(n,o),window.open(r,l,"width=500,height=600")}}})).actions((e=>({async getTokenFromUser(t,n){const{baseURL:o}=e,a=await new Promise(((t,n)=>{const{session:o}=l.getRoot(e),{baseURL:a,name:s}=e;o.queueDialog((e=>[dn,{name:s,handleClose:o=>{o?o instanceof Error?n(o):t(o):n(new Error("user cancelled entry")),e()},baseURL:a}]))}));if("guest"!==a)return void e.openAuthWindow(a,t,n);const s=new URL("auth/login",o),r=new URLSearchParams({type:a});s.search=r.toString();const i=s.toString(),c=await fetch(i,{signal:e.controller.signal});if(!c.ok){const e=await yt(c,"Error when logging in");return void n(new Error(e))}const{token:d}=await c.json();t(d)}}))).volatile((()=>({lastChangeSequenceNumber:void 0}))).actions((e=>({setLastChangeSequenceNumber(t){e.lastChangeSequenceNumber=t}}))).actions((t=>({updateLastChangeSequenceNumber:l.flow((function*(){const{baseURL:e}=t,n=new URL("changes",e),o=new URLSearchParams({limit:"1"});n.search=o.toString();const a=n.toString(),s=t.getFetcher({locationType:"UriLocation",uri:a});let r;try{r=yield s(a,{method:"GET",signal:t.controller.signal})}catch(e){return void(t.controller.signal.aborted||console.error(e))}if(!r.ok){const e=yield yt(r,"Error when fetching server LastChangeSequence");throw new Error(e)}const{changes:i}=yield r.json();t.setLastChangeSequenceNumber(i.length>0?i[0].sequence:0)})),getMissingChanges:l.flow((function*(){const{session:n}=l.getRoot(t),{changeManager:o}=n.apolloDataStore;if(!t.lastChangeSequenceNumber)throw new Error("No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server");const{baseURL:a,lastChangeSequenceNumber:s}=t,r=new URL("changes",a),i=new URLSearchParams({since:String(s),sort:"1"});r.search=i.toString();const c=r.toString(),d=t.getFetcher({locationType:"UriLocation",uri:c});let u;try{u=yield d(c,{method:"GET",signal:t.controller.signal})}catch(e){return void(t.controller.signal.aborted||console.error(e))}if(!u.ok)return void console.error(`Error when fetching the last updates to recover socket connection — ${u.status}`);const{changes:g}=yield u.json();for(const t of g){const n=e.Change.fromJSON(t);o.submit(n,{submitToBackend:!1})}}))}))).volatile((e=>{const{origin:t,pathname:n}=new URL("socket.io/",e.baseURL);return{socket:d.io(t,{path:n})}})).actions((n=>({addSocketListeners(){const{session:o}=l.getRoot(n),{notify:a}=o,s=n.retrieveToken();if(!s)throw new Error("No Token found");const r=t.getDecodedToken(s),i=t.makeUserSessionId(r),{socket:c}=n,{addCheckResult:d,changeManager:u,deleteCheckResult:g}=o.apolloDataStore;c.on("connect",(()=>{n.getMissingChanges()})),c.on("connect_error",(e=>{console.error(e),a("Could not connect to the Apollo server.","error")})),c.on("COMMON",(t=>{if("checkResult"in t)return void(t.deleted?g(t.checkResult._id.toString()):d(t.checkResult));if(sessionStorage.setItem("LastChangeSequence",String(t.changeSequence)),t.userSessionId===i)return;const n=e.Change.fromJSON(t.changeInfo);u.submit(n,{submitToBackend:!1})})),c.on("USER_LOCATION",(e=>{const{channel:t,locations:n,userName:a,userSessionId:s}=e;"USER_LOCATION"===t&&s!==i&&o.addOrUpdateCollaborator({name:a,id:s,locations:n})})),c.on("REQUEST_INFORMATION",(e=>{const{channel:t,userSessionId:n}=e;"REQUEST_INFORMATION"===t&&n!==s&&o.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:o}=e,a=new URL("users/userLocation",n).href,s=new URLSearchParams(JSON.stringify(t)),r=e.getFetcher({locationType:"UriLocation",uri:a});try{if(!(await r(a,{method:"POST",body:s,signal:o.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*(o){if("none"===o){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"===o){const t=l.getRoot(e);s.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Admin",type:"subMenu",icon:u,subMenu:[{label:"Add Assembly",icon:r,onClick:e=>{e.queueDialog((t=>[St,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Delete Assembly",icon:g,onClick:e=>{e.queueDialog((t=>[Mt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Import Features",icon:f,onClick:e=>{e.queueDialog((t=>[qt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[Kt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add Assembly aliases",onClick:e=>{e.queueDialog((t=>[vt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Users",icon:h,onClick:e=>{e.queueDialog((t=>[Bt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Checks",icon:p,onClick:e=>{e.queueDialog((t=>[_t,{session:e,handleClose:()=>{t()}}]))}}]})}(t)}yield e.updateLastChangeSequenceNumber(),e.addSocketListeners();const{baseURL:a}=e,i=new URL("users/locations",a).href,c=e.getFetcher({locationType:"UriLocation",uri:i});yield c(i,{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(un)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()}}))),fn="undefined"==typeof sessionStorage;class hn extends B.BaseAdapter{refNameAliasesP;async getRefNameAliases(){if(this.refNameAliasesP)return this.refNameAliasesP;const e=o.readConfObject(this.config,"assemblyId");if(!fn){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 o=setTimeout((()=>{n(new Error("timeout"))}),2e4),a=U.nanoid(),s=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===a&&(clearTimeout(o),removeEventListener("message",s),t(n.refNameAliases))};addEventListener("message",s),rpcServer.emit("apollo",{apollo:!0,method:"getRefNameAliases",assembly:e,messageId:a})}));return this.refNameAliasesP=t,t}freeResources(){}}var pn=o.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function mn(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo}const yn="undefined"==typeof sessionStorage;class bn extends B.BaseSequenceAdapter{regions;async getRefNames(){return(await this.getRegions()).map((e=>e.refName))}async getRegions(){if(this.regions)return this.regions;const e=o.readConfObject(this.config,"assemblyId");if(!yn){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 o=await n.getRegions(e);return this.regions=o,o}const t=await new Promise(((t,n)=>{const o=setTimeout((()=>{n("timeout")}),2e4),a=U.nanoid(),s=e=>{const{data:n}=e;mn(n)&&n.messageId===a&&(clearTimeout(o),removeEventListener("message",s),t(n.regions))};addEventListener("message",s),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getRegions",assembly:e,messageId:a})}));return this.regions=t,t}getFeatures(e){const{end:t,refName:n,start:a}=e,s=o.readConfObject(this.config,"assemblyId"),r={...e,assemblyName:s};return $.ObservableCreate((async e=>{if(!yn){const o=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!o)return void e.error("No Apollo data store found");const i=o.getBackendDriver(s);if(!i)return void e.error("No backend driver found");const l=(await i.getRegions(r.assemblyName)).find((e=>e.refName===r.refName));if(!l)return void e.error("Cannot get region");r.end>l.end&&(r.end=l.end);const{seq:c}=await i.getSequence(r);return e.next(new z({id:`${n} ${a}-${t}`,data:{refName:n,start:a,end:t,seq:c}})),void e.complete()}const o=await new Promise(((e,t)=>{const n=setTimeout((()=>{t("timeout")}),2e4),o=U.nanoid(),a=t=>{const{data:s}=t;mn(s)&&s.messageId===o&&(clearTimeout(n),removeEventListener("message",a),e(s.sequence))};addEventListener("message",a),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getSequence",region:r,messageId:o})}));e.next(new z({id:`${n} ${a}-${t}`,data:{refName:n,start:a,end:t,seq:o}})),e.complete()}))}freeResources(){}}var xn=o.ConfigurationSchema("ApolloSequenceAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function wn(e,t){const{children:n,indexedIds:o,allIds:a,...s}=t;if(JSON.stringify(s).includes(e))return t;if(n)for(const t of Object.values(n)){const n=wn(e,t);if(n)return n}}class Sn extends B.BaseAdapter{get baseURL(){return o.readConfObject(this.config,"baseURL").uri}get trackId(){return o.readConfObject(this.config,"trackId")}get assemblyNames(){return 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(${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 o=t;if(o.initialized){const{dynamicBlocks:t}=o;for(const o of t.contentBlocks){const{assemblyName:t,end:a,refName:s,start:r}=o,i=e.apolloDataStore.assemblies.get(t);i&&"CollaborationServerDriver"===i.backendDriverType&&n.push({assemblyName:t,refName:s,start:r,end:a})}}}if(0===n.length){for(const e of t)Ot(e)&&e.postUserLocation([]);return}const o=[];for(const e of t)if(Ot(e)){for(const e of n)o.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(o)}}}))).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:n,reloadPluginManagerCallback:a}=l.getRoot(e);l.addDisposer(e,c.autorun((()=>{const n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const o=t;if(o.initialized){const{dynamicBlocks:t}=o;for(const o of t.contentBlocks){const{assemblyName:t,end:a,refName:s,start:r}=o,i=e.apolloDataStore.assemblies.get(t);i&&"CollaborationServerDriver"===i.backendDriverType&&n.push({assemblyName:t,refName:s,start:r,end:a})}}}if(0===n.length){for(const e of t)Ot(e)&&e.postUserLocation([]);return}const o=[];for(const e of t)if(Ot(e)){for(const e of n)o.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(o)}}),{name:"ApolloSessionBroadcastLocations"})),l.addDisposer(e,c.autorun((async s=>{const r=n.configuration.ApolloPlugin,i=o.readConfObject(r,"hasRole"),c=o.readConfObject(r,"featureTypeOntologyName"),d=t.some((e=>Ot(e))),u=e.assemblyManager.assemblies.filter((e=>!o.getConf(e,["sequence","metadata"]).apollo));if(!d||i){const{assemblies:t}=e.assemblyManager;if(0===t.length)return;const{pluginConfiguration:n}=e.apolloDataStore;n.ontologies.find((e=>o.readConfObject(e,"name")===c))||n.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 u)e.addApolloLocalTrackConfig(t);return l.applySnapshot(e,e.previousSnapshot),void s.dispose()}const{signal:g}=e.abortController;for(const n of t){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:t}=n,o=new URL("jbrowse/config.json",t).href,r=n.getFetcher({locationType:"UriLocation",uri:o});let i,l;try{i=await r(o,{signal:g})}catch(t){e.abortController.signal.aborted||console.error(t);continue}if(i.ok){try{l=await i.json()}catch(e){console.error(e);continue}l.configuration.ApolloPlugin.hasRole&&(a(l,e.previousSnapshot),s.dispose())}else{const e=await yt(i,"Failed to fetch assemblies");console.error(e)}}}),{name:"ApolloSessionLoadConfig"}))},beforeDestroy(){e.abortController.abort(new DOMException("Clean up Apollo session","AbortError"))}}))).views((e=>{const n=e.getTrackActions;return{getTrackActions(a){if("ApolloTrack"===a.type||"ReferenceSequenceTrack"===a.type)return n?.(a);const s=o.readConfObject(a,"trackId");return s.endsWith("-sessionTrack")?[...n?.(a)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:o}=l.getRoot(e),r=l.getSnapshot(o);let i;i=t.filterJBrowseConfig(r),0===Object.keys(i).length&&(i=void 0);const c={...l.getSnapshot(a),trackId:s.slice(0,s.length-13)};for(const o of n){if("ApolloInternetAccount"!==o.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:i?.tracks&&[...i.tracks,c]}}),{internetAccountId:a}=o;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:a});const{notify:s}=e;s("Track added","success")}e.deleteTrackConf(a),o.addTrackConf(c)},icon:ue}]:[...n?.(a)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:o}=l.getRoot(e),r=l.getSnapshot(o);let i;i=t.filterJBrowseConfig(r),0===Object.keys(i).length&&(i=void 0);const c=i?.tracks?.filter((e=>e.trackId!==s));for(const o of n){if("ApolloInternetAccount"!==o.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:i,newJBrowseConfig:{...i,tracks:c}}),{internetAccountId:a}=o;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:a});const{notify:s}=e;s("Track removed","success")}e.deleteTrackConf(a),o.deleteTrackConf(a)},icon:ue}]}}}));return l.types.snapshotProcessor(i,{postProcessor(e,t){if(e.apolloSelectedFeature=void 0,e.apolloDataStore={typeName:"Client",checkResults:{}},!t)return e;const{apolloDataStore:n}=t,{checkResults:o}=n;for(const[,e]of o){const[t]=e.ids}return e}})}const as="WorkerGlobalScope"in globalThis;for(const[n,o]of Object.entries(t.changes))e.changeRegistry.registerChange(n,o);const ss=new t.CDSCheck;e.checkRegistry.registerCheck(ss.name,ss);const rs=new t.TranscriptCheck;e.checkRegistry.registerCheck(rs.name,rs),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends n{name="ApolloPlugin";version="1.0.0";configurationSchema=Da;install(e){!function(e){e.addAdapterType((()=>new O({name:"ApolloSequenceAdapter",configSchema:xn,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:bn})))}(e),function(e){e.addAdapterType((()=>new O({name:"ApolloRefNameAliasAdapter",configSchema:pn,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:hn})))}(e),function(e){e.addTextSearchAdapterType((()=>new a.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:Cn,AdapterClass:Sn,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=o.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new a.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:Bn,ReactComponent:On})})),e.addWidgetType((()=>{const e=o.ConfigurationSchema("ApolloTranscriptDetails",{});return new a.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:Un,ReactComponent:ao})})),e.addTrackType((()=>{const t=o.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:a.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new a.TrackType({name:"ApolloTrack",configSchema:t,stateModel:a.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new a.InternetAccountType({name:"ApolloInternetAccount",configSchema:ge,stateModel:gn(ge)}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloDisplay",configSchema:so,stateModel:aa(0,so),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:es}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:ya,stateModel:ka(0,ya),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:ts}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloReferenceSequenceDisplay",configSchema:sa,stateModel:pa(0,sa),displayName:"Apollo reference sequence display",trackType:"ReferenceSequenceTrack",viewType:"LinearGenomeView",ReactComponent:ma}))),e.addToExtensionPoint("Core-extendSession",os.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:r,onClick:()=>{const t=s.getSession(e),{leftOffset:n,rightOffset:o}=e,a=e.getSelectedRegions(n,o);t.queueDialog((e=>[Rt,{session:t,handleClose:()=>{e()},region:a[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Pa),e.addToExtensionPoint("Core-extendPluggableElement",za),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 o=t.toSpliced(n,1);return o.unshift({type:"LinearApolloReferenceSequenceDisplay",displayId:`${e.trackId}-LinearApolloReferenceSequenceDisplay`}),{...e,displays:o}})),e.addToExtensionPoint("LinearGenomeView-searchResultSelected",((e,t)=>{const{session:n,result:o}=t,a=o.getTrackId(),s=o.matchedObject;return a?.startsWith("apollo_track_")&&s&&n.apolloSetEventualSelectedFeature(s._id),e})),as||e.addToExtensionPoint("Core-extendWorker",(t=>"on"in t&&t.on?(t.on("apollo",(async n=>{if("object"!=typeof(o=n)||null===o||!("apollo"in o)||!0!==o.apollo)return;var o;const{apollo:a,messageId:s,method:r}=n;switch(r){case"getSequence":{const{region:o}=n,{assemblyName:r}=o,i=e.rootModel?.session?.apolloDataStore;if(!i)break;const l=i.getBackendDriver(r);if(!l)break;const{seq:c}=await l.getSequence(o);t.workers[0].postMessage({apollo:a,messageId:s,sequence:c});break}case"getRegions":{const{assembly:o}=n,r=e.rootModel?.session?.apolloDataStore;if(!r)break;const i=r.getBackendDriver(o);if(!i)break;const l=await i.getRegions(o);t.workers[0].postMessage({apollo:a,messageId:s,regions:l});break}case"getRefNameAliases":{const{assembly:o}=n,r=e.rootModel?.session?.apolloDataStore;if(!r)break;const i=r.getBackendDriver(o);if(!i)break;const l=await i.getRefNameAliases(o);t.workers[0].postMessage({apollo:a,messageId:s,refNameAliases:l});break}}})),t):t))}configure(e){s.isAbstractMenuManager(e.rootModel)&&(e.jexl.addFunction("geneBackgroundColor",(e=>"pseudogene"===e?i.alpha("rgb(148, 203, 236)",.6):"ncRNA_gene"===e?i.alpha("rgb(194, 106, 119)",.6):void 0)),function(e){e.insertInMenu("Apollo",{label:"Redo",icon:ce,onClick(e){const{apolloDataStore:t}=e;t.changeManager.redoLastChange()}},0),e.insertInMenu("Apollo",{label:"Undo",icon:de,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=>Ot(e)))&&e.appendToMenu("Apollo",{label:"Log out",icon:le,onClick:e=>{e.queueDialog((t=>[Pt,{session:e,handleClose:()=>{t()}}]))}})}(e.rootModel))}};
 //# sourceMappingURL=jbrowse-plugin-apollo.cjs.production.min.js.map