npm - @apollo-annotation/jbrowse-plugin-apollo - Versions diffs - 0.3.11 → 0.3.13 - Mend

@apollo-annotation/jbrowse-plugin-apollo 0.3.11 → 0.3.13

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Files changed (395) hide show

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

@@ -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"),a=require("@jbrowse/core/configuration"),o=require("@jbrowse/core/pluggableElementTypes"),r=require("@jbrowse/core/util"),l=require("@mui/icons-material/Add"),s=require("@mui/material"),i=require("mobx"),c=require("mobx-state-tree"),u=require("socket.io-client"),d=require("@mui/icons-material/AdminPanelSettings"),f=require("@mui/icons-material/Delete"),m=require("@mui/icons-material/Input"),g=require("@mui/icons-material/Person"),p=require("@mui/icons-material/Rule"),h=require("@mui/icons-material/Info"),y=require("@mui/icons-material/Link"),b=require("@mui/icons-material/RadioButtonChecked"),S=require("@mui/icons-material/RadioButtonUnchecked"),w=require("bson-objectid"),C=require("react"),E=require("tss-react/mui"),v=require("@gmod/gff"),x=require("@mui/icons-material/SkipNextRounded"),T=require("@mui/icons-material/SkipPreviousRounded"),A=require("@mui/x-data-grid"),F=require("@jbrowse/core/ui"),k=require("@mui/icons-material/Close"),D=require("mobx-react"),N=require("@jbrowse/core/util/types/mst"),R=require("idb/with-async-ittr"),I=require("@jbrowse/core/util/aborting"),M=require("jsonpath"),L=require("@jbrowse/core/util/io"),q=require("fast-deep-equal/es6"),P=require("file-saver"),O=require("@mui/material/Checkbox"),_=require("@mui/material/FormControlLabel"),B=require("@mui/material/LinearProgress"),U=require("nanoid"),$=require("@mui/icons-material/AccountCircle"),j=require("@jbrowse/core/pluggableElementTypes/AdapterType"),G=require("@jbrowse/core/data_adapters/BaseAdapter"),W=require("@jbrowse/core/util/rxjs"),z=require("@jbrowse/core/util/simpleFeature"),H=require("@jbrowse/core/TextSearch/BaseResults"),V=require("@mui/icons-material/ExpandMore"),J=require("@mui/icons-material/Edit"),X=require("@mui/icons-material/MoreHoriz"),K=require("@mui/icons-material/AddBox"),Z=require("@apollo-annotation/mst"),Y=require("@emotion/styled"),Q=require("@mui/icons-material/ContentCopy"),ee=require("@mui/icons-material/ContentCut"),te=require("@mui/icons-material/Remove"),ne=require("@mui/icons-material/Clear"),ae=require("@mui/icons-material/UnfoldLess"),oe=require("@jbrowse/core/util/tracks"),re=require("@mui/icons-material/ExpandLess"),le=require("@mui/icons-material/Lock"),se=require("@mui/icons-material/Error"),ie=require("@mui/icons-material/Download"),ce=require("@mui/icons-material/FactCheck"),ue=require("@mui/icons-material/FileOpen"),de=require("@mui/icons-material/Logout"),fe=require("@mui/icons-material/Redo"),me=require("@mui/icons-material/TrackChanges"),ge=require("@mui/icons-material/Undo"),pe=require("@mui/icons-material/Save");function he(e){return e&&"object"==typeof e&&"default"in e?e:{default:e}}var ye=he(n),be=he(l),Se=he(d),we=he(f),Ce=he(m),Ee=he(g),ve=he(p),xe=he(h),Te=he(y),Ae=he(b),Fe=he(S),ke=he(w),De=he(C),Ne=he(x),Re=he(T),Ie=he(k),Me=he(M),Le=he(q),qe=he(O),Pe=he(_),Oe=he(B),_e=he($),Be=he(j),Ue=he(z),$e=he(H),je=he(V),Ge=he(J),We=he(X),ze=he(K),He=he(Y),Ve=he(Q),Je=he(ee),Xe=he(te),Ke=he(ne),Ze=he(ae),Ye=he(re),Qe=he(le),et=he(se),tt=he(ie),nt=he(ce),at=he(ue),ot=he(de),rt=he(fe),lt=he(me),st=he(ge),it=he(pe);const ct=a.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:o.BaseInternetAccountConfig,explicitlyTyped:!0});async function ut(e,n,a){const o=v.parseStringSync(n,{parseSequences:!0,parseComments:!0,parseDirectives:!1,parseFeatures:!0});if(0===o.length)throw new Error("No features found in GFF3 file");let r=0,l=a.assemblies.get(e);l||(l=a.addAssembly(e,"InMemoryFileDriver"));for(const e of o)if(Array.isArray(e)){const n=t.gff3ToAnnotationFeature(e),a=l.refSeqs.get(n.refSeq)??l.addRefSeq(n.refSeq,n.refSeq);a.features.has(n._id)||a.addFeature(n)}else if("comment"in e)l.addComment(e.comment);else{r++;let t=l.refSeqs.get(e.id);t||(t=l.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===r)throw new Error("No embedded FASTA section found in GFF3");const s=await dt(l);return a.addCheckResults(s),l}async function dt(t){const n=[];for(const a of t.refSeqs.values())for(const t of a.features.values())for(const o of e.checkRegistry.getChecks().values()){const e=await o.checkFeature(c.getSnapshot(t),((e,t)=>Promise.resolve(a.getSequence(e,t))));n.push(...e)}return n}function ft(e){const{attributes:t}=e,n=t.get("gff_name");return n?n[0]:""}function mt(e){const{attributes:t}=e,n=t.get("gff_id"),a=t.get("transcript_id"),o=t.get("exon_id"),r=t.get("protein_id");return n?n[0]:a?a[0]:o?o[0]:r?r[0]:""}function gt(e){const t=ft(e),n=mt(e);return t?`: ${t}`:n?`: ${n}`:""}function pt(e,t,n=!1){const a=[];a.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))a.push(t);const o=function(e){const t=[];if(e.children)for(const[,n]of e.children)t.push(n);return t}(e);for(const e of o)e.min<t&&e.max>=t&&a.push(e);if(!n)return a;if(e.parent){const n=e.parent.children;if(n)for(const[,o]of n)o._id!=e._id&&o.min<t&&o.max>=t&&a.push(o)}return a}function ht(e,t){if(e.apolloDragging)return;e.setSelectedFeature(t);const{session:n}=e,{apolloDataStore:a}=n,{featureTypeOntology:o}=a.ontologyManager;if(!o)throw new Error("featureTypeOntology is undefined");let r=!1;for(const[,e]of t.children??[])if(o.isTypeOf(e.type,"CDS")||o.isTypeOf(e.type,"exon")){r=!0;break}(o.isTypeOf(t.type,"transcript")||o.isTypeOf(t.type,"pseudogenic_transcript"))&&r?e.showFeatureDetailsWidget(t,["ApolloTranscriptDetails","apolloTranscriptDetails"]):e.showFeatureDetailsWidget(t)}function yt(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 bt(e,t){const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"exon")}function St(e,t){const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)throw new Error("featureTypeOntology is undefined");return n.isTypeOf(e.type,"CDS")}function wt(e,t,n,a){const o=r.getContainingView(t),l=n.bp-o.bpPerPx*n.x,s=l+o.coarseTotalBp;if(!e.parent)return{upstream:void 0,downstream:void 0};const i=e.parent;if(!i.children)throw new Error(`Error getting children of ${i._id}`);const{featureTypeOntology:c}=a.apolloDataStore.ontologyManager;if(!c)throw new Error("featureTypeOntology is undefined");let u=[];for(const[,e]of i.children)c.isTypeOf(e.type,"exon")&&u.push(e);const d={upstream:void 0,downstream:void 0};u=u.sort(((e,t)=>e.min<t.min?-1:1));for(const e of u)if(e.min>s){d.downstream=e;break}u=u.sort(((e,t)=>e.min>t.min?-1:1));for(const e of u)if(e.max<l){d.upstream=e;break}if(-1===i.strand){const e=d.downstream;d.downstream=d.upstream,d.upstream=e}return d}function Ct(e,t,n){let a=Ne.default;return-1===e&&(a=Re.default),t&&(a=a===Re.default?Ne.default:Re.default),n&&(a=a===Re.default?Ne.default:Re.default),a}function Et(e,t,n,a){const o=a.bpToPx({refName:t,coord:e.min,regionNumber:n}),r=a.bpToPx({refName:t,coord:e.max,regionNumber:n});if(void 0===o||void 0===r)return;const{offsetPx:l}=a;return[o.offsetPx-l,r.offsetPx-l]}function vt(e,t,n){const[a,o]=n;if(!(Math.abs(o-a)<8))return Math.abs(a-t)<4?{feature:e,edge:"min"}:Math.abs(o-t)<4?{feature:e,edge:"max"}:void 0}function xt(e,t){return Boolean(t&&e._id===t._id)}function Tt(e,t){return!!t&&(e._id===t._id||e.hasDescendant(t._id))}function At(e){let t;t=e.attributes.get("gff_name")?e.attributes.get("gff_name")?.join(","):e.attributes.get("gff_id")?e.attributes.get("gff_id")?.join(","):e._id;const n=`(${(e.min+1).toLocaleString("en")}..${e.max.toLocaleString("en")})`;if(t&&t.length+n.length>65){const e=60-n.length;t=e>0?t.slice(0,e):"",t=`${t}[...]`}return`${t} ${n}`}function Ft(e,t){const{apolloInternetAccount:n,changeManager:a,regions:o,selectedFeature:l,session:s}=e,i=[],c=n?n.role:"admin",u="admin"===c,d=!(c&&["admin","user"].includes(c)),[f]=o,m=e.getAssemblyId(f.assemblyName),g=e.getAssemblyId(f.assemblyName);return i.push({label:At(t),type:"subHeader"},{label:"Add child feature",disabled:d,onClick:()=>{s.queueDialog((e=>[yn,{session:s,handleClose:()=>{e()},changeManager:a,sourceFeature:t,sourceAssemblyId:m,internetAccount:n}]))}},{label:"Copy features and annotations",disabled:d,onClick:()=>{s.queueDialog((e=>[Fn,{session:s,handleClose:()=>{e()},changeManager:a,sourceFeature:t,sourceAssemblyId:g}]))}},{label:"Delete feature",disabled:!u,onClick:()=>{s.queueDialog((n=>[Dn,{session:s,handleClose:()=>{n()},changeManager:a,sourceFeature:t,sourceAssemblyId:g,selectedFeature:l,setSelectedFeature:t=>{e.setSelectedFeature(t)}}]))}}),r.isSessionModelWithWidgets(s)&&i.push({label:"Open feature details",onClick:()=>{const e=s.addWidget("ApolloFeatureDetailsWidget","apolloFeatureDetailsWidget",{feature:t,assembly:g,refName:f.refName});s.showWidget(e)}}),i}function kt(e,t,n){const a=(e.max-e.min)*t,o=Math.max(e.min-a,1),r=Math.min(e.max+a,n);return{refName:e.refSeq,start:o,end:r}}function Dt(e,t,n){const a=[{featureId:e._id,oldLocation:e[n],newLocation:t}],{parent:o}=e;return o&&("min"===n&&o[n]>t||"max"===n&&o[n]<t)&&a.push(...Dt(o,t,n)),a}function Nt(e,t,n,a,o){const r=e._id,l=[{featureId:r,oldLocation:e[n],newLocation:t}],{parent:s,children:i}=e;if(i)for(const[,e]of i)e._id!==o&&("min"===n&&e[n]<t||"max"===n&&e[n]>t)&&l.push(...Nt(e,t,n,a));if(s&&a){const e=[];if(s.children)for(const[,t]of s.children)t._id!==r&&e.push(t);if(0===e.length)l.push(...Nt(s,t,n,a,r));else{const o=s[n],i=Math[n](...e.map((e=>e[n])),t);i!==o&&l.push(...Nt(s,i,n,a,r))}}return l}function Rt(e,t,n,a=!1){const o=e[n];if(t===o)throw new Error(`New and existing locations are the same: "${t}"`);return"min"===n?t>o?Nt(e,t,n,a):Dt(e,t,n):t<o?Nt(e,t,n,a):Dt(e,t,n)}function It(e){return"feature"in e}function Mt(e,t){const n=e.currentTarget,{clientX:a,clientY:o}=e,{left:r,top:l}=n.getBoundingClientRect(),s=a-r,i=o-l,{coord:c,index:u,refName:d}=t.pxToBp(s);return{x:s,y:i,refName:d,bp:c,regionNumber:u}}async function Lt(e,t){let n;try{n=await e.text()}catch{n=""}return`${t?`${t} — `:""}${e.status} ${e.statusText}${n?` (${n})`:""}`}const qt=E.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}}))),Pt=D.observer((function(e){const{classes:t}=qt(),{handleClose:n,title:a,...o}=e;return De.default.createElement(F.Dialog,{...o,header:De.default.createElement(De.default.Fragment,null,De.default.createElement(s.DialogTitle,{className:t.dialogTitle},a),De.default.createElement(s.IconButton,{"aria-label":"close",onClick:n,className:t.closeButton},De.default.createElement(Ie.default,null)))})}));var Ot;!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"}(Ot||(Ot={}));const _t=E.makeStyles()((e=>({accordion:{border:`1px solid ${e.palette.divider}`,"&:not(:last-child)":{borderBottom:0}},accordionSummary:{flexDirection:"row-reverse"},accordionDetails:{padding:e.spacing(2),borderTop:"1px solid rgba(0, 0, 0, .125)"},radioIcon:{color:e.palette.tertiary.contrastText},dialog:{minWidth:550,maxWidth:800}})));function Bt(e,t,n,a,o,r,l,s,i){return!(!e||!(t&&a||n===Ot.GFF3&&a||a&&o&&r||l&&s&&i))}function Ut({changeManager:e,handleClose:n,session:o}){const{classes:r}=_t(),{internetAccounts:l}=c.getRoot(o),{notify:i}=o,u=l.filter((e=>"ApolloInternetAccount"===e.type));if(0===u.length)throw new Error("No Apollo internet account 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o;if(a.preventDefault(),g(""),T(!0),B(!0),i(`Assembly "${d}" is being added`,"info"),n(),a.preventDefault(),y===Ot.EXTERNAL)o=new t.AddAssemblyFromExternalChange({typeName:"AddAssemblyFromExternalChange",assembly:(new ke.default).toHexString(),assemblyName:d,externalLocation:{fa:I,fai:L,gzi:P}});else{if(!A)throw new Error("Missing fasta file");if(y===Ot.GFF3&&S){const e=await W(A,Ot.GFF3);o=new t.AddAssemblyAndFeaturesFromFileChange({typeName:"AddAssemblyAndFeaturesFromFileChange",assembly:(new ke.default).toHexString(),assemblyName:d,fileIds:{fa:e}})}else if(y===Ot.GFF3){const e=await W(A,Ot.GFF3);o=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new ke.default).toHexString(),assemblyName:d,fileIds:{fa:e}})}else if(E){const e=await W(A,Ot.FASTA);o=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new ke.default).toHexString(),assemblyName:d,fileIds:{fa:e}})}else{if(!k||!N)throw new Error("Missing fasta index files");const e=await W(A,Ot.BGZIP_FASTA),n=await W(k,Ot.FAI),a=await W(N,Ot.GZI);o=new t.AddAssemblyFromFileChange({typeName:"AddAssemblyFromFileChange",assembly:(new ke.default).toHexString(),assemblyName:d,fileIds:{fa:e,fai:n,gzi:a}})}}const[{internetAccountId:r}]=u;await e.submit(o,{internetAccountId:r,updateJobsManager:!0}),T(!1),B(!1)},"data-testid":"submit-form"},De.default.createElement(s.DialogContent,{className:r.dialog},_?De.default.createElement(s.LinearProgress,null):null,De.default.createElement(s.TextField,{margin:"dense",id:"name",label:"Assembly name",type:"TextField",fullWidth:!0,variant:"outlined",onChange:e=>{T(!1),f(e.target.value),function(e){const{assemblies:t}=o;t.find((t=>a.readConfObject(t,"displayName")===e))?(h(!1),g(`Assembly ${e} already exists.`)):(h(!0),g(""))}(e.target.value)},disabled:x&&!m}),De.default.createElement(s.Accordion,{disableGutters:!0,elevation:0,square:!0,className:r.accordion,expanded:"panelFastaInput"===J,onChange:K("panelFastaInput")},De.default.createElement(s.AccordionSummary,{className:r.accordionSummary,expandIcon:"panelFastaInput"===J?De.default.createElement(Ae.default,{className:r.radioIcon,sx:{fontSize:"1.2rem",ml:5}}):De.default.createElement(Fe.default,{className:r.radioIcon,sx:{fontSize:"1.2rem",mr:5}}),"aria-controls":"panelFastaInputd-content",id:"panelFastaInputd-header"},De.default.createElement(s.Typography,{component:"span"},"FASTA input")),De.default.createElement(s.AccordionDetails,{className:r.accordionDetails},De.default.createElement(s.FormGroup,null,De.default.createElement(s.FormControlLabel,{"data-testid":"files-on-url-checkbox",control:De.default.createElement(s.Checkbox,{onChange:()=>{b(y===Ot.EXTERNAL?Ot.BGZIP_FASTA:Ot.EXTERNAL),y===Ot.EXTERNAL&&v(!1)},checked:y===Ot.EXTERNAL,disabled:E&&y!==Ot.GFF3}),label:De.default.createElement(s.Box,{display:"flex",alignItems:"center"},"Use external URLs",De.default.createElement(s.Tooltip,{title:"Use external URLs to provide FASTA and index files. 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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 Wt(e,t){for(const[n,a]of t.entries())if(e.startsWith(a))return e.replace(a,String(n));return e}const zt="$PREFIXED_ID";function Ht(e,t,n){return t===zt?[Wt(e.id,n)]:Me.default.query(e,t)}function Vt(e){return e.toLowerCase().split(/[^\d:A-Za-z]+/).filter((e=>e&&!Gt.has(e)))}function*Jt(e){for(const t of e)yield*Vt(t)}function*Xt(e){for(const t of e)if("string"==typeof t)yield t;else if("object"==typeof t){const e=Me.default.query(t,"$..*");yield*Xt(e)}}function*Kt(e,t,n){for(const a of t){const t=Ht(e,a,n);if(t.length>0)for(const e of Jt(Xt(t)))yield[a,e]}}async function Zt(e,t,n){const a=await this.db,o=t??a.transaction(["nodes"]);I.checkAbortSignal(n);const r=[...Vt(e)],l=[],s=new Map;l.push(...r.map((async(e,t)=>{I.checkAbortSignal(n);const a=o.objectStore("nodes").index("full-text-words");for await(const o of a.iterate(IDBKeyRange.bound(e,`${e}`,!1,!1))){I.checkAbortSignal(n);const e=o.value,a=s.get(e.id)??[e,new Set];a[1].add(t),s.set(e.id,a)}}))),await Promise.all(l),I.checkAbortSignal(n);const i=[];for(const[,[e,t]]of 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t=a.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=a.objectStore("edges");t.createIndex("by-subject","sub"),t.createIndex("by-object","obj"),t.createIndex("by-predicate","pred")}}})}function an(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function on(e){const t=Date.now();let n,a=1;this.options.update?.("Parsing JSON",a);try{n=JSON.parse(await L.openLocation(this.sourceLocation).readFile("utf8"))}catch{throw new Error("Error in loading ontology")}a+=5,this.options.update?.("Parsing JSON complete",a);const o=Date.now(),[r,...l]=n.graphs??[];if(r){if(l.length>0)throw new Error("multiple graphs not supported");try{const n=e.transaction(["meta","nodes","edges"],"readwrite");await n.objectStore("meta").clear(),await 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recurseEdges(e,t,n,a,o){const r=new Set;return await async function t(l){await Promise.all([...l].map((async l=>{const s=(await o.objectStore("edges").index(e).getAll(l)).filter((e=>n(e))).map((e=>e[a]));if(s.length>0){for(const e of s)r.add(e);await t(s)}})))}(t),r.values()}async*expandNodeSet(e,t="is_a",n,a){const o=await this.db,r=a??o.transaction(["edges"]),l=[...e],s=await this.recurseEdges("subclasses"===n?"by-object":"by-subject",l,(e=>e.pred===t),"subclasses"===n?"sub":"obj",r);for(const e of l)yield e;for(const e of s)yield e}expandSubclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"subclasses",n)}expandSuperclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"superclasses",n)}async getClassesThat(e,t,n){const a=await this.db,o=n??a.transaction(["nodes","edges"]),r=await this.getPropertiesByLabel(e,{includeSubProperties:!0},o),l=new Set(r.map((e=>e.id))),s=await async function(e){const t=[];for await(const n of e)t.push(n);return t}(this.expandSuperclasses(t.map((e=>e.id)),"is_a",o)),i=await this.recurseEdges("by-object",s,(e=>l.has(e.pred)),"sub",o),c=this.expandSubclasses(i,"is_a",o),u=[];for await(const e of c){const t=await o.objectStore("nodes").get(e);t&&mn(t)&&!tn(t)&&u.push(t)}return u}async getClassesWithoutPropertyLabeled(e,t,n){const a=await this.db,o=n??a.transaction(["nodes","edges"]),r=o.objectStore("nodes"),l=o.objectStore("edges"),s=(await this.getPropertiesByLabel(e,t,o)).map((e=>e.id)),i=await(async()=>{const e=new Set;for(const t of s)for await(const n of l.index("by-predicate").iterate(t))e.add(n.value.sub);const t=new Set;for await(const n of this.expandSubclasses(e,"is_a",o))t.add(n);return t})(),c=[];for await(const e of r){const t=e.value;mn(t)&&!i.has(t.id)&&c.push(t.id)}const u=[];for(const e of c){const t=await o.objectStore("nodes").get(e);t&&mn(t)&&!tn(t)&&u.push(t)}return u}async getAllClasses(e){const t=await this.db,n=e??t.transaction(["nodes"]);return(await n.objectStore("nodes").index("by-type").getAll("CLASS")).filter((e=>!tn(e)))}async getAllTerms(e){const t=await this.db,n=e??t.transaction(["nodes"]);return(await n.objectStore("nodes").getAll()).filter((e=>!tn(e)))}}const cn=c.types.model("OntologyRecord",{name:c.types.string,version:"unversioned",source:c.types.union(N.LocalPathLocation,N.UriLocation,N.BlobLocation),options:c.types.frozen(),equivalentTypes:c.types.map(c.types.array(c.types.string))}).volatile((e=>({dataStore:void 0,startedEquivalentTypeRequests:new Set}))).actions((e=>({ping(){},initDataStore(){e.dataStore=new sn(e.name,e.version,c.getSnapshot(e.source),e.options)},afterCreate(){c.addDisposer(e,i.autorun((()=>{this.initDataStore()})))},setEquivalentTypes(t,n){e.equivalentTypes.set(t,n)}}))).actions((e=>({loadEquivalentTypes:c.flow((function*(t){if(!e.dataStore)return;if(e.startedEquivalentTypeRequests.has(t))return;e.startedEquivalentTypeRequests.add(t);const n=(yield 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a.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=>Wt(t,e.prefixes),expandPrefixes:t=>function(e,t){for(const[n,a]of t.entries())if(e.startsWith(String(n)))return e.replace(String(n),a);return e}(t,e.prefixes)}))).actions((e=>({addOntology(t,n,a,o){const r=e.ontologies.push({name:t,version:n,source:a,options:{prefixes:new Map(e.prefixes.entries()),...o}});e.ontologies[r-1].ping()}}))),dn=[{displayName:"Label",jsonPath:"$.lbl"},{displayName:"Synonym",jsonPath:"$.meta.synonyms[*].val"},{displayName:"Definition",jsonPath:"$.meta.definition.val"}],fn=a.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:dn}});function mn(e){return"CLASS"===e.type}function gn(e){return"PROPERTY"===e.type}async function pn(e,t,n){if(!e)return;const a=await t.getTermsWithLabelOrSynonym(e.type,{includeSubclasses:!1}),o=a.filter(mn);if(0===a.length)return;const r=await t.getClassesThat("part_of",o);return 0!==r.length?r:void 0}function hn({fetchValidTerms:e,filterTerms:t,includeDeprecated:n,onChange:a,ontologyName:o,ontologyVersion:r,renderInput:l,session:i,style:c,value:u}){const[d,f]=C.useState(!1),[m,g]=C.useState(),[p,h]=C.useState(""),[y,b]=C.useState(),{ontologyManager:S}=i.apolloDataStore,w=S.findOntology(o,r)?.dataStore,E=w&&d&&!m,v=w&&!y,x=C.useCallback((e=>(n||!tn(e))&&(!t||t(e))),[t,n]);C.useEffect((()=>{const e=new AbortController,{signal:t}=e;return v&&async function(e,t,n,a){if(!t)return;const o=(await e.getTermsWithLabelOrSynonym(t,{includeSubclasses:!1})).find((e=>(n??(()=>!0))(e)));if(!o)throw new Error(`not a valid ${e.ontologyName} term`);return o}(w,u,x).then((e=>{h(""),t.aborted||b(e)}),(e=>{t.aborted||I.isAbortException(e)||h(String(e))})),()=>{e.abort("OntologyTermAutocomplete matcher")}}),[i,u,x,w,v]),C.useEffect((()=>{const t=new AbortController,{signal:n}=t;return E&&async function(e,t,n,a){let o;if(t){const n=await t(e,a);n&&(o=n)}return o||(o=await e.getAllTerms()),n?o.filter((e=>n(e))):o}(w,e,x,n).then((e=>{e&&!n.aborted&&g(e)}),(e=>{n.aborted||I.isAbortException(e)||i.notify(e instanceof Error?e.message:String(e),"error")})),()=>{t.abort("OntologyTermAutocomplete loader")}}),[E,x,w,i,e]);const T={};return p&&(T.error=!0,T.helperText=p),De.default.createElement(s.Autocomplete,{style:c,autoComplete:!0,filterSelectedOptions:!0,disableClearable:!0,selectOnFocus:!0,clearOnBlur:!0,handleHomeEndKeys:!0,freeSolo:!0,value:u,options:m??[],onOpen:()=>{f(!0)},onClose:()=>{f(!1)},loading:E,renderInput:l??(e=>De.default.createElement(s.TextField,{...e,...T})),getOptionLabel:e=>"string"==typeof e?e:e.lbl??"",isOptionEqualToValue:(e,t)=>e.lbl===t.lbl,onChange:(e,t)=>{t&&("string"==typeof t?(b(void 0),a(u,t)):t.lbl!==u&&(h(""),b(t),a(u,t.lbl)))}})}function yn({changeManager:e,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const[l,i]=C.useState(String(r.max)),[c,u]=C.useState(String(r.min+1)),[d,f]=C.useState(""),[m,g]=C.useState(""),[p,h]=C.useState(""),y=Number(l)<=Number(c);return De.default.createElement(Pt,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},De.default.createElement("form",{onSubmit:function(s){s.preventDefault(),g("");const i=(new ke.default).toHexString(),u=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o,addedFeature:{_id:i,refSeq:r.refSeq,min:Number(c)-1,max:Number(l),type:d},parentFeatureId:r._id});e.submit(u).then((()=>{a.apolloSetSelectedFeature(i)})),n(),s.preventDefault()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:c,onChange:e=>{u(e.target.value)}}),De.default.createElement(s.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:l,onChange:e=>{i(e.target.value)},error:y,helperText:y?'"End" must be greater than "Start"':null}),De.default.createElement(hn,{session:a,ontologyName:"Sequence Ontology",style:{width:170},value:d,filterTerms:mn,fetchValidTerms:async function(e,t,n){const a=await pn(e,t);if(a)return a;h(`Type "${e?.type}" does not have any children in the ontology`)}.bind(null,r),renderInput:e=>De.default.createElement(s.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0,error:Boolean(p),helperText:p}),onChange:(e,t)=>{var n;t&&(n=t,g(""),f(n))}})),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit",disabled:y||!(c&&l&&d)},"Submit"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),m?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},m)):null)}class bn{clientStore;constructor(e){this.clientStore=e}}class Sn{dataStore;constructor(e){this.dataStore=e}recentChanges=[];undoneChanges=[];async submit(n,a={}){const{addToRecents:o=!0,submitToBackend:l=!0,updateJobsManager:s=!1}=a,i=r.getSession(this.dataStore),c=new AbortController,{jobsManager:u,isLocked:d,changeInProgress:f,setChangeInProgress:m}=r.getSession(this.dataStore);if(d)return i.notify("Cannot submit changes in locked mode"),void m(!1);if(f)return void i.notify("Could not submit change, there is another change still in progress");m(!0);const g={name:n.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{c.abort("ChangeManager")}};s&&u.runJob(g);const p=await t.validationRegistry.frontendPreValidate(n);if(!p.ok){const e=`Pre-validation failed: "${p.resultsMessages}"`;return s&&u.abortJob(g.name,e),i.notify(e,"error"),void m(!1)}try{await n.execute(this.dataStore)}catch(e){return s&&u.abortJob(g.name,String(e)),console.error(e),i.notify(`Error encountered in client: ${String(e)}. Data may be out of sync, please refresh the page`,"error"),void m(!1)}if((await t.validationRegistry.frontendPostValidate(n,this.dataStore)).ok||await this.undo(n),l){s&&u.update(g.name,"Submitting to driver");const{collaborationServerDriver:t,getBackendDriver:r}=this.dataStore,l=e.isAssemblySpecificChange(n)?r(n.assembly)??t:t;let c;try{c=await l.submitChange(n,a)}catch(e){return s&&u.abortJob(g.name,String(e)),console.error(e),i.notify(String(e),"error"),await this.undo(n,!1),void m(!1)}if(!c.ok){const e=`Post-validation failed: "${p.resultsMessages}"`;return s&&u.abortJob(g.name,e),i.notify(e,"error"),await this.undo(n,!1),void m(!1)}n.notification&&i.notify(n.notification,"success"),o&&(this.recentChanges.push(n),this.undoneChanges=[])}s&&u.done(g),m(!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=r.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=r.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 wn extends bn{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:a}=n,o=new URL("features/searchFeatures",a),r=new URLSearchParams({assemblies:t.join(","),term:e});o.search=r.toString();const l=o.toString(),s=await this.fetch(n,l);if(!s.ok){const e=await Lt(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:a,start:o}=e,{assemblyManager:l}=r.getSession(this.clientStore);if(!l.get(t))throw new Error(`Could not find assembly with name "${t}"`);const s=(await this.getRefSeqMapping(t)).get(a);if(!s)throw new Error(`Could not find refSeq "${a}"`);const i=s.id,c=this.clientStore.getInternetAccount(t),{baseURL:u}=c,d=new URL("features/getFeatures",u),f=new URLSearchParams({refSeq:i,start:String(o),end:String(n)});d.search=f.toString();const m=d.toString(),g=await this.fetch(c,m);if(!g.ok){const e=await Lt(g,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,a,c),g.json()}checkSocket(n,a,o){const{socket:r}=o,l=o.retrieveToken();if(!l)return;const s=t.makeUserSessionId(l),i=`${n}-${a}`,c=new Sn(this.clientStore);r.hasListeners(i)||r.on(i,(async t=>{if(o.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId===s)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}-${e.end}`,n=this.inFlight.get(t),{assemblyName:a,end:o,refName:l,start:s}=e,{assemblyManager:i}=r.getSession(this.clientStore);if(!i.get(a))throw new Error(`Could not find assembly with name "${a}"`);const c=(await this.getRefSeqMapping(a)).get(l);if(!c)throw new Error(`Could not find refSeq "${l}"`);const u=c.id;if(n)return{seq:await n,refSeq:u};let d=this.clientStore.assemblies.get(a);d||(d=this.clientStore.addAssembly(a));let f=d.refSeqs.get(u);f||(f=d.addRefSeq(u,l));const m=f.getSequence(s,o);if(m.length===o-s)return{seq:m,refSeq:u};const g=this.clientStore.getInternetAccount(a),{baseURL:p}=g,h=new URL("sequence",p),y=new URLSearchParams({refSeq:u,start:String(s),end:String(o)});h.search=y.toString();const b=h.toString(),S=this.getSeqFromServer(g,b,f,s,o);this.inFlight.set(t,S);const w=await S;return this.checkSocket(a,l,g),this.inFlight.delete(t),{seq:w,refSeq:u}}async getSeqFromServer(e,t,n,a,o){const r=await this.fetch(e,t);if(!r.ok){let e;try{e=await r.text()}catch{e=""}throw new Error(`getSequence failed: ${r.status} (${r.statusText})${e?` (${e})`:""}`)}const l=await r.text();return n.addSequence({sequence:l,start:a,stop:o}),l}async getRefSeqMapping(e){const t=this.refSeqMaps.get(e);if(t)return t;const{assemblyManager:n}=r.getSession(this.clientStore);if(!n.get(e))throw new Error(`Could not find assembly with name "${e}"`);const a=this.clientStore.getInternetAccount(e),{baseURL:o}=a,l=new URL("refSeqs",o),s=new URLSearchParams({assembly:e});l.search=s.toString();const i=l.toString(),c=await this.fetch(a,i);if(!c.ok){let e;try{e=await c.text()}catch{e=""}throw new Error(`getRefNameAliases failed: ${c.status} (${c.statusText})${e?` (${e})`:""}`)}const u=await c.json(),d=new Map(u.map((e=>[e.name,{refName:e.name,id:e._id,aliases:e.aliases}])));return this.refSeqMaps.set(e,d),d}async getRefNameAliases(e){return[...(await this.getRefSeqMapping(e)).values()].map((e=>({refName:e.refName,aliases:[...new Set([e.id,...e.aliases])],uniqueId:`alias-${e.id}`})))}async getRefSeqId(e,t){const n=await this.getRefSeqMapping(e);if(!n)return;const a=n.get(t);return a?.id}async getRegions(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${e}"`);const n=this.clientStore.getInternetAccount(e),{baseURL:a}=n,o=new URL("refSeqs",a),l=new URLSearchParams({assembly:e});o.search=l.toString();const s=o.toString(),i=await this.fetch(n,s);if(!i.ok){let e;try{e=await i.text()}catch{e=""}throw new Error(`getRegions failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,start:0,end:e.length})))}getAssemblies(e){const{assemblyManager:t}=r.getSession(this.clientStore);return t.assemblies.filter((t=>{const n=a.getConf(t,["sequence","metadata"]);return!(!(n&&n.apollo&&n.internetAccountConfigId)||e&&n.internetAccountConfigId!==e)}))}async submitChange(e,n={}){const{internetAccountId:a}=n,o=this.clientStore.getInternetAccount("assembly"in e?e.assembly:void 0,a),{baseURL:r}=o,l=new URL("changes",r).href,s=await this.fetch(o,l,{method:"POST",body:JSON.stringify(e.toJSON()),headers:{"Content-Type":"application/json"}});if(!s.ok){const e=await Lt(s,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return s.ok||(i.ok=!1),i}}class Cn extends bn{async getFeatures(){return[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=this.clientStore.assemblies.get(t);if(!r)return{seq:"",refSeq:a};const l=r.refSeqs.get(a);return l?{seq:l.getSequence(o,n),refSeq:a}:{seq:"",refSeq:a}}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[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=a.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.file&&!t.internetAccountConfigId)}))}async submitChange(e,n={}){const{clientStore:a}=this,{assemblies:o}=a;a.clearCheckResults();for(const[,e]of o)if("InMemoryFileDriver"===e.backendDriverType){const t=await dt(e);a.addCheckResults(t)}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class En extends bn{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),n=t.get(e);if(!n)throw new Error(`Assembly ${e} not found`);const{file:o}=a.getConf(n,["sequence","metadata"]),l=require("node:fs");return ut(e,await l.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${e._id}`});return n}async getFeatures(e){return await this.getAssembly(e.assemblyName),[[],[]]}async getSequence(e){const{assemblyName:t,end:n,refName:a,start:o}=e,r=(await this.getAssembly(t)).refSeqs.get(a);if(!r)throw new Error(`refSeq ${a} not found in client data store`);return{seq:r.getSequence(o,n),refSeq:a}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=a.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.internetAccountConfigId&&t.file)}))}async submitChange(n){if(!e.isAssemblySpecificChange(n))throw new Error(`Cannot use this type of change with local file: "${n.typeName}"`);const{assemblyManager:o}=r.getSession(this.clientStore),l=o.get(n.assembly);if(!l)throw new Error(`Could not find assembly with name "${n.assembly}"`);const{file:s}=a.getConf(l,["sequence","metadata"]),i=this.clientStore.assemblies.get(n.assembly);if(!i)throw new Error(`Could not find assembly in client with name "${n.assembly}"`);const u=new Set(...i.refSeqs.keys()),{checkResults:d}=this.clientStore;for(const e of d.values())u.has(e.refSeq)&&d.delete(e._id);const f=await dt(i);this.clientStore.addCheckResults(f);const m=[{directive:"gff-version",value:"3"}];for(const[,e]of i.refSeqs)m.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of i.comments)m.push({comment:e});for(const[,e]of i.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.annotationFeatureToGFF3(c.getSnapshot(e)))}for(const[,e]of i.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=v.formatSync(m),p=require("node:fs");return await p.promises.writeFile(s,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}var vn;function xn(e,t,n,a){const o={_id:(new ke.default).toHexString(),refSeq:e,type:"CDS",min:n,max:a,strand:t},r={_id:(new ke.default).toHexString(),refSeq:e,type:"exon",min:n,max:a,strand:t},l={};return l[o._id]=o,l[r._id]=r,{_id:(new ke.default).toHexString(),refSeq:e,type:"mRNA",min:n,max:a,strand:t,children:l}}function Tn({changeManager:e,handleClose:n,region:a,session:o}){const[r,l]=C.useState(String(a.end)),[i,c]=C.useState(String(a.start+1)),[u,d]=C.useState(vn.GENE_AND_SUBFEATURES),[f,m]=C.useState(""),[g,p]=C.useState(),[h,y]=C.useState(""),b=Number(r)<=Number(i);let S=Boolean(b)||!(i&&r&&u);return(u===vn.CUSTOM&&!f||!g&&u===vn.GENE_AND_SUBFEATURES||!g&&u===vn.TRANSCRIPT_AND_SUBFEATURES)&&(S=!0),De.default.createElement(Pt,{open:!0,title:"Add new feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},De.default.createElement("form",{onSubmit:async function(l){l.preventDefault(),y("");const s=o.apolloDataStore.getBackendDriver(a.assemblyName);if(!s)return void y("No backend driver found");let c=a.refName;if(s instanceof wn){const e=await s.getRefSeqId(a.assemblyName,a.refName);if(!e)return void y(`Could not find refSeq for "${a.refName}"`);c=e}if(u===vn.GENE_AND_SUBFEATURES){const l=xn(c,g,Number(i)-1,Number(r)),s={};s[l._id]=l;const u=(new ke.default).toHexString(),d=new t.AddFeatureChange({changedIds:[u],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:u,refSeq:c,min:Number(i)-1,max:Number(r),type:"gene",strand:g,children:s}});return e.submit(d).then((()=>{o.apolloSetSelectedFeature(u)})),void n()}if(u===vn.TRANSCRIPT_AND_SUBFEATURES){const l=xn(c,g,Number(i)-1,Number(r)),s=new t.AddFeatureChange({changedIds:[l._id],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:l});return e.submit(s).then((()=>{o.apolloSetSelectedFeature(l._id)})),void n()}if(!f)return void y("No type selected");const d=(new ke.default).toHexString(),m=new t.AddFeatureChange({changedIds:[d],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:d,refSeq:c,min:Number(i)-1,max:Number(r),type:f,strand:g}});e.submit(m).then((()=>{o.apolloSetSelectedFeature(d)})),n()},"data-testid":"submit-form"},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(i),onChange:e=>{c(e.target.value)}}),De.default.createElement(s.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}),De.default.createElement(s.FormControl,null,De.default.createElement(s.InputLabel,{id:"demo-simple-select-label"},"Strand"),De.default.createElement(s.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Strand",value:g?.toString(),onChange:function(e){switch(y(""),Number(e.target.value)){case 1:p(1);break;case-1:p(-1);break;default:p(void 0)}}},De.default.createElement(s.MenuItem,{value:void 0}),De.default.createElement(s.MenuItem,{value:1},"+"),De.default.createElement(s.MenuItem,{value:-1},"-"))),De.default.createElement(s.FormControl,{style:{marginTop:20}},De.default.createElement(s.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:vn.GENE_AND_SUBFEATURES,name:"radio-buttons-group",value:u,onChange:e=>{y("");const{value:t}=e.target;Object.keys(vn).includes(t)&&d(vn[t])}},De.default.createElement(s.FormControlLabel,{value:vn.GENE_AND_SUBFEATURES,control:De.default.createElement(s.Radio,null),label:De.default.createElement(s.Box,{display:"flex",alignItems:"center"},"Add gene and sub-features",De.default.createElement(s.Tooltip,{title:"This is a shortcut to create a gene with a single mRNA, exon, and CDS"},De.default.createElement(s.IconButton,{size:"small"},De.default.createElement(xe.default,{sx:{fontSize:18}}))))}),De.default.createElement(s.FormControlLabel,{value:vn.TRANSCRIPT_AND_SUBFEATURES,control:De.default.createElement(s.Radio,null),label:De.default.createElement(s.Box,{display:"flex",alignItems:"center"},"Add transcript and sub-features",De.default.createElement(s.Tooltip,{title:"This is a shortcut to create a single mRNA with exon and CDS, but without a parent gene"},De.default.createElement(s.IconButton,{size:"small"},De.default.createElement(xe.default,{sx:{fontSize:18}}))))}),De.default.createElement(s.FormControlLabel,{value:vn.CUSTOM,checked:u!==vn.GENE_AND_SUBFEATURES&&u!==vn.TRANSCRIPT_AND_SUBFEATURES,control:De.default.createElement(s.Radio,null),label:"Add feature with a sequence ontology type"}))),u===vn.CUSTOM?De.default.createElement(hn,{session:o,ontologyName:"Sequence Ontology",style:{width:170},value:f,filterTerms:mn,renderInput:e=>De.default.createElement(s.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0}),onChange:(e,t)=>{var n;t&&(n=t,y(""),m(n))}}):null),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit",disabled:S},"Submit"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),h?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},h)):null)}function An(e,t){const n=(new ke.default).toHexString();t.push(n);const a={};if(e.children)for(const n of Object.values(e.children)){const e=An(n,t);a[e._id]=e}const o="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString();return{...e,refSeq:o,children:e.children&&a,_id:n}}function Fn({changeManager:e,handleClose:n,session:o,sourceAssemblyId:r,sourceFeature:l}){const{assemblyManager:i}=o,u=i.assemblyList,[d,f]=C.useState(u.find((e=>e.name!==r))?.name),[m,g]=C.useState([]),[p,h]=C.useState(""),[y,b]=C.useState(l.min),[S,w]=C.useState("");function E(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=E(a,t);e.refSeq=p,e.min=e.min+t,e.max=e.max+t,n[e._id]=e}const a="string"==typeof e.refSeq?e.refSeq:e.refSeq.toHexString(),o="string"==typeof e._id?e._id:e._id.toHexString();return{...e,refSeq:a,children:e.children&&n,_id:o}}return C.useEffect((()=>{(async function(){if(h(""),!d)return void w("No assemblies to copy to");const e=await i.waitForAssembly(d);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})));g(n),h(n[0]?._id||"")})().catch((e=>{w(String(e))}))}),[d,i]),De.default.createElement(Pt,{open:!0,title:"Copy features and annotations",handleClose:n,maxWidth:!1,"data-testid":"copy-feature"},De.default.createElement("form",{onSubmit:async function(a){if(!d)return;a.preventDefault(),w("");const r=l.length,s=await i.waitForAssembly(d);if(!s)return void w(`Assembly not found: ${d}.`);const u=s.getCanonicalRefName(p),f=s.regions?.find((e=>e.refName===u));if(!f)return void w(`RefSeq not found: ${p}.`);const m=y+r;if(m>f.end)return void w(`Feature would extend beyond the bounds of the selected reference sequence. (Feature would end at ${m}, but reference sequence ends at ${f.end})`);if(y<f.start)return void w(`Reference sequence starts at ${f.start}, feature cannot start before that.`);const g=[],h=An(c.getSnapshot(l),g),b={...h.attributes};"Parent"in b&&delete b.Parent,h.refSeq=p;const S=y-h.min;h.min=y,h.max=y+r;const C=E(h,S),v=new t.AddFeatureChange({changedIds:[h._id],typeName:"AddFeatureChange",assembly:d,addedFeature:{_id:h._id,refSeq:h.refSeq,min:h.min,max:h.max,type:h.type,children:C.children,attributes:b,strand:h.strand},copyFeature:!0,allIds:g});e.submit(v).then((()=>{o.apolloSetSelectedFeature(h._id)})),n(),a.preventDefault()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.DialogContentText,null,"Target assembly"),De.default.createElement(s.Select,{labelId:"label",value:d,onChange:function(e){f(e.target.value)}},u.filter((e=>e.name!==r)).map((e=>De.default.createElement(s.MenuItem,{key:e.name,value:e.name},a.readConfObject(e,"displayName"))))),De.default.createElement(s.DialogContentText,null,"Target reference sequence"),De.default.createElement(s.Select,{labelId:"label",value:p,onChange:function(e){h(e.target.value)}},m.map((e=>De.default.createElement(s.MenuItem,{key:e._id,value:e._id},e.name)))),De.default.createElement(s.DialogContentText,null,"Start position in target reference sequence"),De.default.createElement(s.TextField,{margin:"dense",type:"number",fullWidth:!0,variant:"outlined",value:y,onChange:e=>{b(Number(e.target.value))}})),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{disabled:!d||!p||!y,variant:"contained",type:"submit"},"Submit"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),S?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},S)):null)}function kn({changeManager:e,handleClose:n,session:a}){const{internetAccounts:o}=c.getRoot(a),[r,l]=C.useState(""),[i,u]=C.useState(!1),[d,f]=C.useState(!1),m=o.filter((e=>"ApolloInternetAccount"===e.type));if(0===m.length)throw new Error("No Apollo internet account found");const[g,p]=C.useState(m[0]),{collaborationServerDriver:h}=a.apolloDataStore,y=h.getAssemblies(),[b,S]=C.useState(y.at(0));return De.default.createElement(Pt,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly"},De.default.createElement("form",{onSubmit:async function(a){if(a.preventDefault(),f(!0),l(""),!b)return void l("Must select assembly!");const o=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:b.name});await e.submit(o,{internetAccountId:g.internetAccountId}),n(),a.preventDefault()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},m.length>1?De.default.createElement(De.default.Fragment,null,De.default.createElement(s.DialogContentText,null,"Select account"),De.default.createElement(s.Select,{value:g.internetAccountId,onChange:function(e){f(!1);const t=m.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID "${e.target.value}"`);p(t)},disabled:d&&!r},o.map((e=>De.default.createElement(s.MenuItem,{key:e.id,value:e.internetAccountId},e.name))))):null,De.default.createElement(s.DialogContentText,null,"Select assembly"),De.default.createElement(s.Select,{labelId:"label",value:b?.name??"",onChange:function(e){const t=y.find((t=>t.name===e.target.value));S(t)},disabled:0===y.length},y.map((e=>De.default.createElement(s.MenuItem,{key:e.name,value:e.name},e.displayName)))),De.default.createElement(s.DialogContentText,null,De.default.createElement("strong",{style:{color:"red"}},"NOTE: All assembly data will be deleted and this operation cannot be undone!")),De.default.createElement(s.FormGroup,null,De.default.createElement(s.FormControlLabel,{control:De.default.createElement(s.Checkbox,{checked:i,onChange:()=>{u(!i)}}),label:"I understand that all assembly data will be deleted"}))),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{disabled:!b||!i,variant:"contained",type:"submit"},"Delete"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),r?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},r)):null)}function Dn({changeManager:e,handleClose:n,selectedFeature:a,session:o,setSelectedFeature:r,sourceAssemblyId:l,sourceFeature:i}){const[u,d]=C.useState(""),{ontologyManager:f}=o.apolloDataStore,{featureTypeOntology:m}=f;function g(e){if(!e.parent?.children||1===e.parent.children.size)return;const t=[];for(const n of e.parent.children.values())m?.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())m?.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 a of t)if(a._id!==e._id&&a.min>=e.min){n=a.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 a of n)if(a._id!=e._id&&a.max<=e.max){t=a.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 De.default.createElement(Pt,{open:!0,title:"Delete feature",handleClose:n,maxWidth:!1,"data-testid":"delete-feature"},De.default.createElement("form",{onSubmit:o=>{!async function(o){o.preventDefault(),d(""),a?._id===i._id&&r();const s=[],u=new t.DeleteFeatureChange({changedIds:[i._id],typeName:"DeleteFeatureChange",assembly:l,changes:[{deletedFeature:c.getSnapshot(i),parentFeatureId:i.parent?._id}]});if(m&&(m.isTypeOf(i.type,"transcript")||m.isTypeOf(i.type,"pseudogenic_transcript"))){const e=g(i);e&&s.push(e)}if(m&&m.isTypeOf(i.type,"exon")){const e=function(e){if(!m)return;if(!m.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 a;for(const t of e.parent.children.values())if(t.type===n[0].type){a=t;break}if(!a)throw new Error("Unable to find CDS");const o=n[0].min,r=n[n.length-1].max;if(!(e.min>o&&e.max<r||e.max<o||e.min>r)){if(e.min<=o&&e.max>=r)return new t.DeleteFeatureChange({changedIds:[a._id],typeName:"DeleteFeatureChange",assembly:l,changes:[{deletedFeature:c.getSnapshot(a),parentFeatureId:a.parent?._id}]});if(e.min<=o&&e.max>o){let t;for(const a of n)if(a.min>e.max){t=a.min;break}if(!t)throw new Error("Error setting new CDS start");return{typeName:"LocationStartChange",changedId:a._id,featureId:a._id,oldLocation:a.min,newLocation:t}}if(e.min<r&&e.max>=r){let t;for(const a of n.reverse())if(a.max<e.min){t=a.max;break}if(!t)throw new Error("Error setting new CDS end");return{typeName:"LocationEndChange",changedId:a._id,featureId:a._id,oldLocation:a.max,newLocation:t}}throw new Error("Unexpected relationship between exon and CDS")}}(i);e&&("DeleteFeatureChange"===e.typeName?(u.changedIds.push(...e.changedIds),u.changes.push(...e.changes)):s.push(e));const n=g(i);if(n){s.push(n);const e=i.parent?.parent;if(e?.children)if("LocationStartChange"===n.typeName){let t=n.newLocation;for(const[,a]of e.children)a._id!=n.featureId&&a.min<t&&(t=a.min);t!=e.min&&s.push({typeName:n.typeName,changedId:e._id,featureId:e._id,oldLocation:e.min,newLocation:t})}else{let t=n.newLocation;for(const[,a]of e.children)a._id!=n.featureId&&a.max>t&&(t=a.max);t!=e.max&&s.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 a=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[],changes:[],assembly:n}),o=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[],changes:[],assembly:n});for(const t of e)"LocationStartChange"===t.typeName&&(a.changedIds.push(t.changedId),a.changes.push({featureId:t.featureId,oldStart:t.oldLocation,newStart:t.newLocation})),"LocationEndChange"===t.typeName&&(o.changedIds.push(t.changedId),o.changes.push({featureId:t.featureId,oldEnd:t.oldLocation,newEnd:t.newLocation}));if(a.changedIds.length>0&&0===o.changedIds.length)return a;if(o.changedIds.length>0&&0===a.changedIds.length)return o;throw new Error("Unexpected list of changes")}(s,l);await e.submit(u),f&&await e.submit(f),n(),o.preventDefault()}(o)}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.DialogContentText,null,"Are you sure you want to delete the selected feature?")),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit"},"Yes"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),u?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},u)):null)}function Nn({handleClose:e,session:n}){const[o,r]=C.useState(!1),[l,i]=C.useState(),[u,d]=C.useState(""),{collaborationServerDriver:f,getInternetAccount:m,inMemoryFileDriver:g}=n.apolloDataStore,p=[...f.getAssemblies(),...g.getAssemblies()];return De.default.createElement(Pt,{open:!0,title:"Export GFF3",handleClose:e,maxWidth:!1,"data-testid":"download-gff3"},De.default.createElement("form",{onSubmit:async function(r){if(r.preventDefault(),d(""),!l)return void d("Must select assembly to download");const{internetAccountConfigId:s}=a.getConf(l,["sequence","metadata"]);s?await async function(e){if(!l)return void d("Must select assembly to download");const t=m(l.configuration.name,e),n=new URL("export/getID",t.baseURL),a=new URLSearchParams({assembly:l.name});n.search=a.toString();const r=n.toString(),s=t.getFetcher({locationType:"UriLocation",uri:r}),i=await s(r,{method:"GET"});if(!i.ok){const e=await Lt(i,"Error when exporting ID");return void d(e)}const{exportID:c}=await i.json(),u=new URL("export",t.baseURL),f=new URLSearchParams({exportID:c,includeFASTA:o?"true":"false"});u.search=f.toString();const g=u.toString();window.open(g,"_blank")}(s):function(e){if(!l)return void d("Must select assembly to download");const{assemblies:n}=e.apolloDataStore,o=n.get(l.name),r=o?.refSeqs;if(!r)return void d(`No refSeqs found for assembly "${l.name}"`);const s=[{directive:"gff-version",value:"3"}],i=a.getConf(l,["sequence","adapter","features"]);for(const e of i){const{end:t,refName:n,start:a}=e;s.push({directive:"sequence-region",value:`${n} ${a+1} ${t}`})}for(const[,e]of r){const{features:n}=e;if(n)for(const[,e]of n)s.push(t.annotationFeatureToGFF3(c.getSnapshot(e)))}for(const e of i){const{refName:t,seq:n}=e;s.push({id:t,description:"",sequence:n})}const u=v.formatSync(s),f=new Blob([u],{type:"text/plain;charset=utf-8"});P.saveAs(f,`${l.displayName??l.name}.gff3`)}(n),e()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.DialogContentText,null,"Select assembly"),De.default.createElement(s.Select,{labelId:"label",value:l?.name??"",onChange:function(e){const t=p.find((t=>t.name===e.target.value));i(t)},disabled:0===p.length},p.map((e=>De.default.createElement(s.MenuItem,{key:e.name,value:e.name},e.displayName??e.name)))),De.default.createElement(s.DialogContentText,null,"Select assembly to export to GFF3"),De.default.createElement(s.FormGroup,null,De.default.createElement(s.FormControlLabel,{"data-testid":"include-fasta-checkbox",control:De.default.createElement(s.Checkbox,{checked:o,onChange:()=>{r(!o)}}),label:"Include fasta sequence in GFF output"}))),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{disabled:!l,variant:"contained",type:"submit"},"Download"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:e},"Cancel"))),u?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},u)):null)}function Rn({changeManager:e,handleClose:n,session:o}){const{apolloDataStore:r}=o,[l,i]=C.useState(),[c,u]=C.useState(),[d,f]=C.useState(""),[m,g]=C.useState(!1),[p,h]=C.useState(),[y,b]=C.useState(!1),[S,w]=C.useState(!1),{collaborationServerDriver:E,getInternetAccount:v}=r,x=E.getAssemblies();return C.useEffect((()=>{c&&(async()=>{const{internetAccountConfigId:e}=a.getConf(c,["sequence","metadata"]),t=v(c.name,e);if(!t)throw new Error("No Apollo internet account found");const{baseURL:n}=t,o=new URL("features/count",n),r=new URLSearchParams({assemblyId:c.name});o.search=r.toString();const l=t.getFetcher({locationType:"UriLocation",uri:o.toString()});w(!0);const s=await l(o.toString(),{method:"GET"});if(!s.ok)throw new Error(await Lt(s));{const e=await s.json();h(e.count)}w(!1)})().catch((e=>{console.error(e),f(e.message??e)}))}),[v,o,c]),De.default.createElement(Pt,{open:!0,title:"Import Features from GFF3 file",handleClose:n,maxWidth:!1,"data-testid":"import-features-dialog"},S?De.default.createElement(Oe.default,null):null,De.default.createElement("form",{onSubmit:async function(r){r.preventDefault(),f(""),w(!0),g(!0);let s="";if(!l)return void f("must select a file");if(!c)return void f("Must select assembly to download");const{internetAccountConfigId:i}=a.getConf(c,["sequence","metadata"]),u=v(c.name,i),{baseURL:d}=u,m=new URL("files",d);m.searchParams.set("type","text/x-gff3");const p=m.href,h=new FormData;h.append("file",l),h.append("fileName",l.name),h.append("type","text/x-gff3");const b=u.getFetcher({locationType:"UriLocation",uri:p});n();const{jobsManager:S}=o,C=new AbortController,E={name:`Importing features for ${c.displayName}`,statusMessage:"Uploading file, this may take awhile",progressPct:0,cancelCallback:()=>{C.abort("ImportFeatures"),S.abortJob(E.name)}};if(S.runJob(E),b){const{signal:e}=C,t=await b(p,{method:"POST",body:h,signal:e});if(!t.ok){const e=await Lt(t,"Error when inserting new features (while uploading file)");return S.abortJob(E.name,e),void f(e)}s=(await t.json())._id}const x=new t.AddFeaturesFromFileChange({typeName:"AddFeaturesFromFileChange",assembly:c.name,fileId:s,deleteExistingFeatures:y});S.done(E),await e.submit(x,{updateJobsManager:!0})}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.DialogContentText,null,"Select assembly"),De.default.createElement(s.Select,{labelId:"label",value:c?.name??"",onChange:function(e){const t=x.find((t=>t.name===e.target.value));u(t),g(!1)},disabled:m&&!d},x.map((e=>De.default.createElement(s.MenuItem,{key:e.name,value:e.name},e.displayName??e.name))))),De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.DialogContentText,null,"Upload GFF3 to load features"),De.default.createElement("input",{type:"file",onChange:function(e){g(!1),e.target.files&&i(e.target.files[0])},disabled:m&&!d})),p&&p>0?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,null,"This assembly already has ",p," features, would you like to delete the existing features before importing new ones?"),De.default.createElement(Pe.default,{label:"Yes, delete existing features",disabled:m&&!d,control:De.default.createElement(qe.default,{checked:y,onChange:function(e){b(e.target.checked)},slotProps:{input:{"aria-label":"controlled"}},color:"warning"})})):null,De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{disabled:!(c&&l&&void 0!==p)||m,variant:"contained",type:"submit"},m?"Submitting...":"Submit"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Close"))),d?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},d)):null)}function In({handleClose:e,session:t}){const{internetAccounts:n}=c.getRoot(t),[a,o]=C.useState(""),r=n.filter((e=>"ApolloInternetAccount"===e.type));if(0===r.length)throw new Error("No Apollo internet account found");const[l,i]=C.useState(r[0]);return De.default.createElement(Pt,{open:!0,title:"Log out",handleClose:e,maxWidth:!1,"data-testid":"log-out"},De.default.createElement("form",{onSubmit:function(e){e.preventDefault(),o(""),l.removeToken(),globalThis.location.reload()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},r.length>1?De.default.createElement(De.default.Fragment,null,De.default.createElement(s.DialogContentText,null,"Select 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e===u.getUserId()}C.useEffect((()=>{(async function(){const{baseURL:e}=u,t=new URL("users",e).href,n=u.getFetcher({locationType:"UriLocation",uri:t});if(n){const e=await n(t,{method:"GET"});if(!e.ok){const t=await Lt(e,"Error when getting user data from db");return void i(t)}const a=await e.json();m(a.map((e=>void 0===e.role?{...e,role:""}:e)))}})().catch((e=>{i(String(e))}))}),[u]);const p=[{field:"username",headerName:"User",width:140},{field:"email",headerName:"Email",width:160},{field:"role",headerName:"Role",width:140,type:"singleSelect",valueOptions:["readOnly","user","admin","none"],getOptionLabel(e){switch(e){case"readOnly":return"Read-only";case"user":return"User";case"admin":return"Admin";case"none":return"None";default:return"unknown"}},editable:!0},{field:"actions",type:"actions",getActions:n=>[De.default.createElement(A.GridActionsCellItem,{key:`delete-${n.id}`,icon:De.default.createElement(we.default,null),onClick:async()=>{globalThis.confirm("Delete this user?")&&await 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t.MergeExonsChange({changedIds:[l._id],typeName:"MergeExonsChange",assembly:r,firstExon:c.getSnapshot(l),secondExon:c.getSnapshot(d),parentFeatureId:i._id});e.submit(f),n(),s.preventDefault()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},0===Object.keys(m).length?"There are no neighbouring exons to merge with":"Merge with exon on:",De.default.createElement(s.FormControl,{style:{marginTop:5}},De.default.createElement(s.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",name:"radio-buttons-group",value:d,onChange:e=>{u("");const{value:t}=e.target;f(m[t])}},Object.keys(m).map((e=>De.default.createElement(s.FormControlLabel,{value:e,key:e,control:De.default.createElement(s.Radio,null),label:De.default.createElement(s.Box,{display:"flex",alignItems:"center"},qn(e,m))})))))),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit",disabled:0===Object.keys(m).length||void 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De.default.createElement(Pt,{open:!0,title:"Merge transcripts",handleClose:n,maxWidth:!1,"data-testid":"merge-transcripts"},De.default.createElement("form",{onSubmit:function(o){if(o.preventDefault(),d(""),!g)return;const s=f[g];if(a?._id===i._id&&r(),!i.parent)throw new Error("Cannot find parent");const u=new t.MergeTranscriptsChange({changedIds:[i._id],typeName:"MergeTranscriptsChange",assembly:l,firstTranscript:c.getSnapshot(i),secondTranscript:c.getSnapshot(s),parentFeatureId:i.parent._id});e.submit(u),n()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},0===Object.keys(f).length?"There are no transcripts to merge with":"Merge with 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Bn({handleClose:e,session:t}){const{apolloDataStore:n}=t,{addAssembly:a,addSessionAssembly:o,assemblyManager:l,notify:i}=t,[c,u]=C.useState(null),[d,f]=C.useState(""),[m,g]=C.useState(""),[p,h]=C.useState(!1),y=s.useTheme();return De.default.createElement(Pt,{open:!0,title:"Open local GFF3 file",handleClose:e,maxWidth:!1,"data-testid":"open-local-file"},De.default.createElement("form",{onSubmit:async function(s){if(s.preventDefault(),g(""),h(!0),!c)throw new Error("No file selected");const u=await new Response(c).text(),f=`${d}-${c.name}-${U.nanoid(8)}`;try{await ut(f,u,n)}catch(t){return console.error(t),i(`Error loading GFF3 ${c.name}, ${String(t)}`,"error"),void e()}const m={};if(r.isElectron){const{webUtils:e}=globalThis.require("electron");m.file=e.getPathForFile(c)}const p={name:f,aliases:[d],displayName:d,sequence:{trackId:`sequenceConfigId-${d}`,type:"ReferenceSequenceTrack",adapter:{type:"ApolloSequenceAdapter",assemblyId:f},metadata:{apollo:!0,...m}}};await(r.isElectron?a?.(p):(o||a)(p));const y=await l.waitForAssembly(p.name);y?(t.addApolloTrackConfig(y),i(`Loaded GFF3 ${c.name}`,"success")):i(`Error loading GFF3 ${c.name}`,"error"),e()}},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.FormControl,null,De.default.createElement("div",{style:{flexDirection:"row"}},De.default.createElement(s.Button,{variant:"contained",component:"label",style:{marginRight:y.spacing()}},"Choose File",De.default.createElement("input",{type:"file",required:!0,hidden:!0,onChange:function(e){const t=e.target.files?.item(0);if(t&&(g(""),u(t),!d)){const e=t.name,n=e.lastIndexOf(".");f(-1===n?e:e.slice(0,n))}}})),c?c.name:"No file chosen"),De.default.createElement(s.FormHelperText,null,"Make sure your GFF3 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Error("No Apollo internet account found");const{baseURL:r}=o,{classes:l}=Un(),[i,u]=C.useState(),[d,f]=C.useState([]),{collaborationServerDriver:m}=n.apolloDataStore,g=m.getAssemblies(),[p,h]=C.useState(g.at(0)),y=[{field:"sequence"},{field:"typeName",headerName:"Change type",width:200,type:"singleSelect",valueOptions:[...e.changeRegistry.changes.keys()]},{field:"changes",headerName:"Change JSON",width:600,renderCell:({value:e})=>De.default.createElement("textarea",{className:l.changeTextarea,value:JSON.stringify(e),readOnly:!0})},{field:"user",headerName:"User",width:140},{field:"createdAt",headerName:"Time",width:160,type:"dateTime",valueGetter:e=>e&&new Date(e)}];return C.useEffect((()=>{(async function(){if(!p)return;const e=new URL("changes",r),t=new URLSearchParams({assembly:p.name});e.search=t.toString();const n=e.toString(),a=o?.getFetcher({locationType:"UriLocation",uri:n});if(a){const e=await a(n,{headers:new Headers({"Content-Type":"application/json"})});if(!e.ok){const t=await Lt(e,"Error when retrieving changes");return void u(t)}const t=await e.json();f(t)}})().catch((e=>{u(String(e))}))}),[o,r,p]),De.default.createElement(Pt,{open:!0,fullScreen:!0,title:"View change log",handleClose:t,"data-testid":"view-changelog"},De.default.createElement(s.Select,{style:{width:200,marginLeft:40},value:p?.name??"",onChange:function(e){const t=g.find((t=>t.name===e.target.value));h(t)}},g.map((e=>De.default.createElement(s.MenuItem,{key:e.name,value:e.name},e.displayName||e.name)))),De.default.createElement(s.DialogContent,null,De.default.createElement(A.DataGrid,{pagination:!0,rows:d,columns:y,getRowId:e=>e._id,slots:{toolbar:A.GridToolbar},initialState:{sorting:{sortModel:[{field:"sequence",sort:"desc"}]},columns:{columnVisibilityModel:{sequence:!1}}}})),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:t},"Close")),i?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},i)):null)}const jn=[{field:"refName",headerName:"Ref Name"},{field:"aliases",headerName:"Aliases",editable:!0,flex:1}],Gn=e=>/^[\da-f]{24}$/i.test(e),Wn=D.observer((function({changeManager:e,handleClose:n,session:a}){const o=C.useRef(null),[r,l]=C.useState(""),[i,c]=C.useState(!1),[u,d]=C.useState(),[f,m]=C.useState([]),[g,p]=C.useState(new Map),{apolloDataStore:h}=a,{collaborationServerDriver:y}=h,b=y.getAssemblies();C.useEffect((()=>{b.length>0&&(d(b[0]),y.getRefNameAliases(b[0].name).then((e=>{S(e)})).catch((()=>{p(new Map),l("Error fetching refName aliases for assembly")})))}),[]);const S=e=>{const t=new Map;for(const n of e){const e=n.refName;Gn(e)||t.set(e,n.aliases)}p(t)},w=()=>[...g].map(((e,t)=>({id:t,refName:e[0],aliases:e[1].filter((t=>t!==e[0])).join(", ")})));return De.default.createElement(Pt,{open:!0,title:"Add reference sequence aliases",handleClose:n,maxWidth:"sm","data-testid":"add-refseq-alias",fullWidth:!0},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column"}},De.default.createElement(s.Grid,{container:!0,spacing:2},De.default.createElement(s.Grid,null,De.default.createElement(s.FormControl,{disabled:i&&!r,fullWidth:!0},De.default.createElement(s.InputLabel,{id:"demo-simple-select-label"},"Assembly"),De.default.createElement(s.Select,{labelId:"demo-simple-select-label",id:"demo-simple-select",label:"Assembly",value:u?.name??"",onChange:e=>{const t=b.find((t=>t.name===e.target.value));d(t),t?.name&&(y.getRefNameAliases(t.name).then((e=>{S(e),l("")})).catch((()=>{p(new Map),l("Error fetching refName aliases for assembly")})),c(!1),o.current&&(o.current.value=""))},style:{minWidth:150}},b.map((e=>De.default.createElement(s.MenuItem,{key:e.name,value:e.name},e.displayName)))))),De.default.createElement(s.Grid,null,De.default.createElement(s.InputLabel,null,"Load RefName alias"),De.default.createElement("input",{type:"file",onChange:e=>{(async e=>{if(!e.target.files)return;const t=e.target.files[0],n=(await t.text()).split("\n"),a=new Map(g);l("");for(const e of n){const t=e.split("\t");for(const e of t)a.has(e)&&a.set(e,[...a.get(e)??[],...t])}p(a)})(e).catch((()=>{l("Error reading file")}))},ref:o,disabled:i&&!r||!u}))),u&&g.size>0?De.default.createElement("div",{style:{height:200,width:"100%",marginTop:20}},De.default.createElement(s.InputLabel,null,"Refname aliases found for selected assembly."),De.default.createElement(A.DataGrid,{rows:w(),columns:jn,initialState:{pagination:{paginationModel:{page:0,pageSize:5}}},pageSizeOptions:[5,10],onRowSelectionModelChange:e=>{const{ids:t}=e;if(t.size>0){c(!0);const e=[...t.values()].flatMap((e=>w().filter((t=>String(t.id)===String(e)))));m(e)}else c(!1),m([])},processRowUpdate:(e,t)=>{const n=new Map(g);return n.set(e.refName,e.aliases.split(",")),p(n),e},checkboxSelection:!0,disableRowSelectionExcludeModel:!0})):null),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"contained",type:"submit",disabled:!i,onClick:()=>{const a=[];for(const e of f){const{refName:t}=e,n=e.aliases.split(",").map((e=>e.trim())).filter((e=>e.length>0));a.push({refName:t,aliases:n})}if(l(""),!u)return void l("No assembly selected");const o=new t.AddRefSeqAliasesChange({typeName:"AddRefSeqAliasesChange",assembly:u.name,refSeqAliases:a});e.submit(o).catch((()=>{l("Error submitting change")})),n()}},"Submit"),De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:n},"Close")),r?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},r)):null)}));function zn({handleClose:e,session:t}){const{internetAccounts:n}=c.getRoot(t),{collaborationServerDriver:a}=t.apolloDataStore,o=n.find((e=>"ApolloInternetAccount"===e.type));if(!o)throw new Error("No Apollo internet account found");const{baseURL:r}=o,[l,i]=C.useState(),[u,d]=C.useState([]),f=a.getAssemblies(),[m,g]=C.useState(f.at(0));return C.useEffect((()=>{(async function(){const e=m?.name;if(!e)return;const t=new URL("checks",r),n=new URLSearchParams({assembly:e});t.search=n.toString();const a=t.toString(),l=o?.getFetcher({locationType:"UriLocation",uri:a});if(l){const e=await l(a,{headers:new Headers({"Content-Type":"application/json"})});if(!e.ok){const t=await Lt(e,"Error when retrieving checks");return void i(t)}const t=await e.json();d(t)}})().catch((e=>{i(String(e))}))}),[m,o,r]),De.default.createElement(Pt,{open:!0,fullScreen:!0,title:"View check 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c0.708,-2.127,2.692,-3.71,5.036,-3.71 l0,0 z",fill:"#EA4335"})))}function Xn(e){const{color:t}=e;return De.default.createElement(s.SvgIcon,{viewBox:"0 0 21 21",style:{fontSize:21},...e},De.default.createElement("rect",{x:"1",y:"1",width:"9",height:"9",fill:"disabled"===t?"#7B7B7B":"#F25022"}),De.default.createElement("rect",{x:"1",y:"11",width:"9",height:"9",fill:"disabled"===t?"#7B7B7B":"#00A4EF"}),De.default.createElement("rect",{x:"11",y:"1",width:"9",height:"9",fill:"disabled"===t?"#939393":"#7FBA00"}),De.default.createElement("rect",{x:"11",y:"11",width:"9",height:"9",fill:"disabled"===t?"#B9B9B9":"#FFB900"}))}const Kn=E.makeStyles()((e=>({loginButton:{marginBottom:e.spacing(1),width:"220px",height:"40px",fontSize:"16px",textTransform:"none",justifyContent:"left",padding:"3px 12px"}})));function Zn(e){const{classes:t}=Kn(),{disabled:n}=e;return De.default.createElement(s.Button,{className:t.loginButton,variant:"outlined",startIcon:De.default.createElement(Jn,{color:n?"disabled":void 0}),...e},"Sign in with Google")}function Yn(e){const{classes:t}=Kn(),{disabled:n}=e;return De.default.createElement(s.Button,{className:t.loginButton,variant:"outlined",startIcon:De.default.createElement(Xn,{color:n?"disabled":void 0}),...e},"Sign in with Microsoft")}function Qn(e){const{classes:t}=Kn();return De.default.createElement(s.Button,{className:t.loginButton,variant:"outlined",startIcon:De.default.createElement(_e.default,{fontSize:"small"}),...e},"Continue as Guest")}const ea=E.makeStyles()((e=>({divider:{marginTop:e.spacing(4),marginBottom:e.spacing(5)}}))),ta=({baseURL:e,handleClose:t,name:n})=>{const{classes:a}=ea(),[o,r]=C.useState(""),[l,i]=C.useState([]);function c(e){t("google"===e?"google":"microsoft"===e?"microsoft":"guest")}C.useEffect((()=>{const t=new AbortController,{signal:n}=t;return async function(){const t=new URL("auth/types",e).href,a=await fetch(t,{method:"GET",signal:n});if(!a.ok){const e=await Lt(a,"Error when retrieving auth types from server");return void r(e)}const o=await a.json();i(o)}().catch((e=>{I.isAbortException(e)||r(String(e))})),()=>{t.abort("AuthTypeSelector")}}),[e]);const u=l.includes("google"),d=l.includes("microsoft"),f=l.includes("guest");return De.default.createElement(Pt,{open:!0,title:`Log in to ${n}`,handleClose:t,maxWidth:!1,"data-testid":"login-apollo"},De.default.createElement(s.DialogContent,{style:{display:"flex",flexDirection:"column",paddingTop:8}},u?De.default.createElement(Zn,{disabled:!u,onClick:()=>{c("google")}}):null,d?De.default.createElement(Yn,{disabled:!d,onClick:()=>{c("microsoft")}}):null,f?De.default.createElement(De.default.Fragment,null,De.default.createElement(s.Divider,{className:a.divider}),De.default.createElement(Qn,{onClick:()=>{c("guest")}})):null),De.default.createElement(s.DialogActions,null,De.default.createElement(s.Button,{variant:"outlined",type:"submit",onClick:()=>{t()}},"Cancel")),o?De.default.createElement(s.DialogContent,null,De.default.createElement(s.DialogContentText,{color:"error"},o)):null)},na="undefined"==typeof sessionStorage,aa=n=>o.InternetAccount.named("ApolloInternetAccount").props({type:c.types.literal("ApolloInternetAccount"),configuration:a.ConfigurationReference(n)}).views((e=>({get baseURL(){return a.getConf(e,"baseURL")},getUserId(){const n=e.retrieveToken();if(n)return t.getDecodedToken(n).id}}))).volatile((()=>({role:void 0,controller:new AbortController}))).actions((e=>({setRole(){const n=e.retrieveToken();if(!n)return void(e.role=void 0);const a=t.getDecodedToken(n),{role:o}=a;e.role!==o&&(e.role=o)}}))).actions((e=>{let t;return{addMessageChannel(e,n){t=t=>{this.finishOAuthWindow(t,e,n)},window.addEventListener("message",t)},deleteMessageChannel(){window.removeEventListener("message",t)},finishOAuthWindow(t,n,a){if(t.data.name!==`JBrowseAuthWindow-${e.internetAccountId}`)return void this.deleteMessageChannel();const o=t.data.redirectUri.replace("#","?"),r=new URL(o),l=new URLSearchParams(r.search).get("access_token");this.deleteMessageChannel(),l?(e.storeToken(l),e.setRole(),n(l)):a(new Error("Error with token endpoint"))},async openAuthWindow(t,n,a){const o=r.isElectron?"http://localhost/auth":globalThis.location.origin+globalThis.location.pathname,l=new URL("auth/login",e.baseURL),s=new URLSearchParams({type:t,redirect_uri:o});l.search=s.toString();const i=`JBrowseAuthWindow-${e.internetAccountId}`;if(r.isElectron){const{ipcRenderer:t}=globalThis.require("electron"),r=await t.invoke("openAuthWindow",{internetAccountId:e.internetAccountId,data:{redirect_uri:o},url:l.toString()}),s=new MessageEvent("message",{data:{name:i,redirectUri:r}});this.finishOAuthWindow(s,n,a)}else this.addMessageChannel(n,a),window.open(l,i,"width=500,height=600")}}})).actions((e=>({async getTokenFromUser(t,n){const{baseURL:a}=e,o=await new Promise(((t,n)=>{const{session:a}=c.getRoot(e),{baseURL:o,name:r}=e;a.queueDialog((e=>[ta,{name:r,handleClose:a=>{a?a instanceof Error?n(a):t(a):n(new Error("user cancelled entry")),e()},baseURL:o}]))}));if("guest"!==o)return void e.openAuthWindow(o,t,n);const r=new URL("auth/login",a),l=new URLSearchParams({type:o});r.search=l.toString();const s=r.toString(),i=await fetch(s,{signal:e.controller.signal});if(!i.ok){const e=await Lt(i,"Error when logging in");return void n(new Error(e))}const{token:u}=await i.json();t(u)}}))).volatile((()=>({lastChangeSequenceNumber:void 0}))).actions((e=>({setLastChangeSequenceNumber(t){e.lastChangeSequenceNumber=t}}))).actions((t=>({updateLastChangeSequenceNumber:c.flow((function*(){const{baseURL:e}=t,n=new URL("changes",e),a=new URLSearchParams({limit:"1"});n.search=a.toString();const o=n.toString(),r=t.getFetcher({locationType:"UriLocation",uri:o});let l;try{l=yield r(o,{method:"GET",signal:t.controller.signal})}catch(e){return void(t.controller.signal.aborted||console.error(e))}if(!l.ok){const e=yield Lt(l,"Error when fetching server LastChangeSequence");throw new Error(e)}const s=yield l.json();t.setLastChangeSequenceNumber(s.length>0?s[0].sequence:0)})),getMissingChanges:c.flow((function*(){const{session:n}=c.getRoot(t),{changeManager:a}=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:o,lastChangeSequenceNumber:r}=t,l=new URL("changes",o),s=new URLSearchParams({since:String(r),sort:"1"});l.search=s.toString();const i=l.toString(),u=t.getFetcher({locationType:"UriLocation",uri:i});let d;try{d=yield u(i,{method:"GET",signal:t.controller.signal})}catch(e){return void(t.controller.signal.aborted||console.error(e))}if(!d.ok)return void console.error(`Error when fetching the last updates to recover socket connection — ${d.status}`);const f=yield d.json();for(const t of f){const n=e.Change.fromJSON(t);a.submit(n,{submitToBackend:!1})}}))}))).volatile((e=>{const{origin:t,pathname:n}=new URL("socket.io/",e.baseURL);return{socket:u.io(t,{path:n})}})).actions((n=>({addSocketListeners(){const{session:a}=c.getRoot(n),{notify:o}=a,r=n.retrieveToken();if(!r)throw new Error("No Token found");const l=t.getDecodedToken(r),s=t.makeUserSessionId(l),{socket:i}=n,{addCheckResult:u,changeManager:d,deleteCheckResult:f}=a.apolloDataStore;i.on("connect",(()=>{n.getMissingChanges()})),i.on("connect_error",(e=>{console.error(e),o("Could not connect to the Apollo server.","error")})),i.on("COMMON",(t=>{if("checkResult"in t)return void(t.deleted?f(t.checkResult._id.toString()):u(t.checkResult));if(sessionStorage.setItem("LastChangeSequence",String(t.changeSequence)),t.userSessionId===s)return;const n=e.Change.fromJSON(t.changeInfo);d.submit(n,{submitToBackend:!1})})),i.on("USER_LOCATION",(e=>{const{channel:t,locations:n,userName:o,userSessionId:r}=e;"USER_LOCATION"===t&&r!==s&&a.addOrUpdateCollaborator({name:o,id:r,locations:n})})),i.on("REQUEST_INFORMATION",(e=>{const{channel:t,userSessionId:n}=e;"REQUEST_INFORMATION"===t&&n!==r&&a.broadcastLocations()}))}}))).actions((e=>({postUserLocation:(t=>{let n;return t=>{clearTimeout(n),n=setTimeout((()=>{!async function(t){if(!c.isAlive(e)||"none"===e.role)return;const{baseURL:n,controller:a}=e,o=new URL("users/userLocation",n).href,r=new URLSearchParams(JSON.stringify(t)),l=e.getFetcher({locationType:"UriLocation",uri:o});try{if(!(await l(o,{method:"POST",body:r,signal:a.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}=c.getRoot(e);t.broadcastLocations()}}return{initialize:c.flow((function*(a){if("none"===a){if(!e.roleNotificationSent){const{session:t}=c.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"===a){const t=c.getRoot(e);r.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Admin",type:"subMenu",icon:Se.default,subMenu:[{label:"Add Assembly",icon:be.default,onClick:e=>{e.queueDialog((t=>[Ut,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Delete Assembly",icon:we.default,onClick:e=>{e.queueDialog((t=>[kn,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Import Features",icon:Ce.default,onClick:e=>{e.queueDialog((t=>[Rn,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[Wn,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Add Assembly aliases",onClick:e=>{e.queueDialog((t=>[jt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Users",icon:Ee.default,onClick:e=>{e.queueDialog((t=>[Ln,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}},{label:"Manage Checks",icon:ve.default,onClick:e=>{e.queueDialog((t=>[Mn,{session:e,handleClose:()=>{t()}}]))}}]})}(t)}yield e.updateLastChangeSequenceNumber(),e.addSocketListeners();const{baseURL:o}=e,l=new URL("users/locations",o).href,s=e.getFetcher({locationType:"UriLocation",uri:l});yield s(l,{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(),i.autorun((async t=>{if(na)return;const{session:n}=c.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("internet account beforeDestroy"),e.socket.close()}}))),oa="undefined"==typeof sessionStorage;class ra extends G.BaseAdapter{refNameAliases;async getRefNameAliases(){const e=a.readConfObject(this.config,"assemblyId");if(!oa){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 a=setTimeout((()=>{n(new Error("timeout"))}),2e4),o=U.nanoid(),r=e=>{const n=e.data;(function(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo&&"refNameAliases"in e})(n)&&n.messageId===o&&(clearTimeout(a),removeEventListener("message",r),t(n.refNameAliases))};addEventListener("message",r),rpcServer.emit("apollo",{apollo:!0,method:"getRefNameAliases",assembly:e,messageId:o})}));return this.refNameAliases=t,t}freeResources(){}}var la=a.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function sa(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo}const ia="undefined"==typeof sessionStorage;class ca extends G.BaseSequenceAdapter{regions;async getRefNames(){return(await this.getRegions()).map((e=>e.refName))}async getRegions(){if(this.regions)return this.regions;const e=a.readConfObject(this.config,"assemblyId");if(!ia){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 a=await n.getRegions(e);return this.regions=a,a}const t=await new Promise(((t,n)=>{const a=setTimeout((()=>{n("timeout")}),2e4),o=U.nanoid(),r=e=>{const{data:n}=e;sa(n)&&n.messageId===o&&(clearTimeout(a),removeEventListener("message",r),t(n.regions))};addEventListener("message",r),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getRegions",assembly:e,messageId:o})}));return this.regions=t,t}getFeatures(e){const{end:t,refName:n,start:o}=e,r=a.readConfObject(this.config,"assemblyId"),l={...e,assemblyName:r};return W.ObservableCreate((async e=>{if(!ia){const a=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!a)return void e.error("No Apollo data store found");const s=a.getBackendDriver(r);if(!s)return void e.error("No backend driver found");const i=(await s.getRegions(l.assemblyName)).find((e=>e.refName===l.refName));if(!i)return void e.error("Cannot get region");l.end>i.end&&(l.end=i.end);const{seq:c}=await s.getSequence(l);return e.next(new Ue.default({id:`${n} ${o}-${t}`,data:{refName:n,start:o,end:t,seq:c}})),void e.complete()}const a=await new Promise(((e,t)=>{const n=setTimeout((()=>{t("timeout")}),2e4),a=U.nanoid(),o=t=>{const{data:r}=t;sa(r)&&r.messageId===a&&(clearTimeout(n),removeEventListener("message",o),e(r.sequence))};addEventListener("message",o),globalThis.rpcServer.emit("apollo",{apollo:!0,method:"getSequence",region:l,messageId:a})}));e.next(new Ue.default({id:`${n} ${o}-${t}`,data:{refName:n,start:o,end:t,seq:a}})),e.complete()}))}freeResources(){}}var ua=a.ConfigurationSchema("ApolloSequenceAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});class da extends G.BaseAdapter{get baseURL(){return a.readConfObject(this.config,"baseURL").uri}get trackId(){return a.readConfObject(this.config,"trackId")}get assemblyNames(){return a.readConfObject(this.config,"assemblyNames")}mapBaseResult(e,t,n){return e.map((e=>{const a=t.getCanonicalRefName(e.refSeq);return new $e.default({label:n,trackId:this.trackId,locString:`${a}:${e.min+1}..${e.max}`})}))}async searchIndex(e){const t=e.queryString,n=[],a=this.pluginManager?.rootModel?.session;if(!a)return n;const{apolloDataStore:o}=a,{assemblyManager:r}=a;for(const a of this.assemblyNames){const l=o.getBackendDriver(a),s=r.get(a);if(!l||!s)continue;const i=await l.searchFeatures(e.queryString,[a]);n.push(...this.mapBaseResult(i,s,t))}return n}freeResources(){}}var fa=a.ConfigurationSchema("ApolloTextSearchAdapter",{assemblyNames:{type:"stringArray",defaultValue:[],description:"List of assemblies covered by text search adapter"},trackId:{type:"string",defaultValue:""},baseURL:{type:"fileLocation",defaultValue:{uri:"",locationType:"UriLocation"}}},{explicitlyTyped:!0,explicitIdentifier:"textSearchAdapterId"});const ma=E.makeStyles()((e=>({attributeKey:{fontWeight:"bold",marginRight:e.spacing(2)}})));function ga({attributeKey:e}){const{classes:n}=ma(),a=/^[A-Z]/.test(e);let o,r=e;return t.isGFFInternalAttribute(e)?(r=t.internalToGFF[e],o=`On GFF3 export, this will be assigned to the GFF3's reserved "${r}" attribute`):t.isGFFColumnInternal(e)?(r=t.gffInternalToColumn[e],o=`On GFF3 export, this will be placed in the GFF3's "${r}" column`):a&&(o="On GFF3 export, this attribute will be changed to start with a lower-case letter because attributes starting with an upper-case letter are reserved in GFF3"),De.default.createElement("div",{style:{display:"flex"}},De.default.createElement(s.Typography,{className:n.attributeKey},r),o?De.default.createElement(s.Tooltip,{title:o},De.default.createElement(s.Chip,{icon:De.default.createElement(xe.default,null),label:"GFF3",size:"small",variant:"outlined"})):null)}const pa="Custom",ha={[pa]:"custom"};for(const[e,n]of Object.entries(t.gffToInternal))ha[`GFF ${n}`]=e;for(const[e,n]of Object.entries(t.gffColumnToInternal))ha[`GFF ${n}`]=e;const 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n.named("LinearApolloReferenceSequenceDisplayRendering").volatile((()=>({seqTrackCanvas:null,seqTrackOverlayCanvas:null,theme:s.createTheme()}))).actions((e=>({setSeqTrackCanvas(t){e.seqTrackCanvas=t},setSeqTrackOverlayCanvas(t){e.seqTrackOverlayCanvas=t},setTheme(t){e.theme=t},afterAttach(){c.addDisposer(e,i.autorun((()=>{const{lgv:t,seqTrackCanvas:n,theme:a,highContrast:o,showStartCodons:l,showStopCodons:s,sequenceRowHeight:i,session:c}=e;if(!t.initialized||e.regionCannotBeRendered()||!n)return;if(3/t.bpPerPx<1)return;const{bpPerPx:u,offsetPx:d,dynamicBlocks:f}=t;!function(e,t,n,a,o,l,s,i,c,u){const d=e.getContext("2d");if(!d)return;d.clearRect(0,0,e.width,e.height);const{apolloDataStore:f}=u;for(const e of o.contentBlocks){const o=e.offsetPx-a;ir(d,n,t,l,o,e.widthPx,c,e.reversed);const u=f.assemblies.get(e.assemblyName),m=u?.getByRefName(e.refName),g=Math.floor(e.start),p=Math.ceil(e.end);let h=m?.getSequence(g,p);if(!h)return;h=h.toUpperCase(),e.reversed&&(h=r.revcom(h));const 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t.LocationEndChange({typeName:"LocationEndChange",changedIds:c.map((e=>e.featureId)),changes:c.map((e=>({featureId:e.featureId,oldEnd:e.oldLocation,newEnd:e.newLocation}))),assembly:i}):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:i});e.changeManager.submit(u),e.setDragging(),e.setCursor()}}))).actions((e=>({onMouseDown(t){const n=e.getMousePosition(t);It(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);It(n)?e.getGlyph(n.feature).onMouseMove(e,n,t):(e.setHoveredFeature(),e.setCursor())},onMouseLeave(t){e.setDragging(),e.setHoveredFeature();const n=e.getMousePosition(t);It(n)&&e.getGlyph(n.feature).onMouseLeave(e,n,t)},onMouseUp(t){const n=e.getMousePosition(t);It(n)?e.getGlyph(n.feature).onMouseUp(e,n,t):e.setSelectedFeature(),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){c.addDisposer(e,i.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:a}=e;if(!a)return;const o=e.getGlyph(a.feature);o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloSixFrameDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:c.types.optional(co,{})}).named("LinearApolloSixFrameDisplay")}const Tr=a.ConfigurationSchema("ApolloPlugin",{ontologies:c.types.array(fn),featureTypeOntologyName:{description:"Name of the feature type ontology",type:"string",defaultValue:"Sequence Ontology"},hasRole:{description:"Flag used internally by 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n=r.getSession(e),a=e.getAssembly(),o=e.getFirstRegion();return e.contextMenuFeature?[...t(),{label:"Create Apollo annotation",icon:be.default,onClick:()=>{n.queueDialog((t=>[Rr,{session:n,handleClose:()=>{t()},annotationFeature:e.getAnnotationFeature(a),assembly:a,refSeqId:e.getRefSeqId(a),region:o}]))}}]:t()}}}));return e.stateModel=n,e}function Mr(e,t){const n=JSON.parse(JSON.stringify(e)),a=n.subfeatures;return[{start:n.start+1,end:n.end,seq_id:t,source:n.source??null,type:n.type??null,score:n.score??null,strand:n.strand?1===n.strand?"+":"-":null,phase:null!==n.phase||void 0!==n.phase?n.phase:null,attributes:qr(n),derived_features:[],child_features:a?a.map((e=>Mr(e,t))):[]}]}function Lr(e,n){return t.gff3ToAnnotationFeature(Mr(e,n))}function qr(e){const t={},n=new Set(["start","end","type","strand","refName","subfeatures","derived_features","phase","source","score"]);for(const[a,o]of Object.entries(e))n.has(a)||(t[a]=Array.isArray(o)?o.map(String):[String(o)]);return t}function 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n=e.getTrackActionMenuItems;return{getTrackActionMenuItems(o){if("ApolloTrack"===o.type||"ReferenceSequenceTrack"===o.type)return n?.(o);const r=a.readConfObject(o,"trackId");return r.endsWith("-sessionTrack")?[...n?.(o)??[],{label:"Save track to Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=c.getRoot(e),l=c.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const i={...c.getSnapshot(o),trackId:r.slice(0,r.length-13)};for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:s,newJBrowseConfig:{...s,tracks:s?.tracks&&[...s.tracks,i]}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track added","success")}e.deleteTrackConf(o),a.addTrackConf(i)},icon:it.default}]:[...n?.(o)??[],{label:"Remove track from 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o){const[n]=t.ids;if(!n)continue;const o=a.assemblies.get(n.assemblyId);o&&"InMemoryFileDriver"===o.backendDriverType&&(e.apolloDataStore.checkResults[t._id]=c.getSnapshot(t))}return e}})}const Xr="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const Kr=new t.CDSCheck;e.checkRegistry.registerCheck(Kr.name,Kr);const Zr=new t.TranscriptCheck;e.checkRegistry.registerCheck(Zr.name,Zr),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends ye.default{name="ApolloPlugin";version="0.3.11";configurationSchema=Tr;install(e){!function(e){e.addAdapterType((()=>new Be.default({name:"ApolloSequenceAdapter",configSchema:ua,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:ca})))}(e),function(e){e.addAdapterType((()=>new Be.default({name:"ApolloRefNameAliasAdapter",configSchema:la,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:ra})))}(e),function(e){e.addTextSearchAdapterType((()=>new o.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:fa,AdapterClass:da,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new o.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:Na,ReactComponent:Da})})),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloTranscriptDetails",{});return new o.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:Ra,ReactComponent:Ha})})),e.addTrackType((()=>{const t=a.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:o.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new o.TrackType({name:"ApolloTrack",configSchema:t,stateModel:o.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new o.InternetAccountType({name:"ApolloInternetAccount",configSchema:ct,stateModel:aa(ct)}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloDisplay",configSchema:Va,stateModel:Qo(0,Va),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:zr}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:mr,stateModel:xr(0,mr),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Hr}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloReferenceSequenceDisplay",configSchema:er,stateModel:dr(0,er),displayName:"Apollo reference sequence display",trackType:"ReferenceSequenceTrack",viewType:"LinearGenomeView",ReactComponent:fr}))),e.addToExtensionPoint("Core-extendSession",Jr.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:be.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[Tn,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Ir),e.addToExtensionPoint("Core-extendPluggableElement",Pr),Xr||e.addToExtensionPoint("Core-extendWorker",(t=>"on"in t&&t.on?(t.on("apollo",(async n=>{if("object"!=typeof(a=n)||null===a||!("apollo"in a)||!0!==a.apollo)return;var a;const{apollo:o,messageId:r,method:l}=n;switch(l){case"getSequence":{const{region:a}=n,{assemblyName:l}=a,s=e.rootModel?.session?.apolloDataStore;if(!s)break;const i=s.getBackendDriver(l);if(!i)break;const{seq:c}=await i.getSequence(a);t.workers[0].postMessage({apollo:o,messageId:r,sequence:c});break}case"getRegions":{const{assembly:a}=n,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const s=l.getBackendDriver(a);if(!s)break;const i=await s.getRegions(a);t.workers[0].postMessage({apollo:o,messageId:r,regions:i});break}case"getRefNameAliases":{const{assembly:a}=n,l=e.rootModel?.session?.apolloDataStore;if(!l)break;const s=l.getBackendDriver(a);if(!s)break;const i=await s.getRefNameAliases(a);t.workers[0].postMessage({apollo:o,messageId:r,refNameAliases:i});break}}})),t):t))}configure(e){var t;r.isAbstractMenuManager(e.rootModel)&&(e.jexl.addFunction("geneBackgroundColor",(e=>"pseudogene"===e?s.alpha("rgb(148, 203, 236)",.6):"ncRNA_gene"===e?s.alpha("rgb(194, 106, 119)",.6):void 0)),(t=e.rootModel).insertInMenu("Apollo",{label:"Redo",icon:rt.default,onClick(e){const{apolloDataStore:t}=e;t.changeManager.redoLastChange()}},0),t.insertInMenu("Apollo",{label:"Undo",icon:st.default,onClick(e){const{apolloDataStore:t}=e;t.changeManager.undoLastChange()}},0),t.appendToMenu("Apollo",{label:"Download GFF3",icon:tt.default,onClick:e=>{e.queueDialog((t=>[Nn,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"View Change Log",icon:lt.default,onClick:e=>{e.queueDialog((t=>[$n,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"Open local GFF3 file",icon:at.default,onClick:e=>{e.queueDialog((t=>[Bn,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),t.appendToMenu("Apollo",{label:"View check results",icon:nt.default,onClick:e=>{e.queueDialog((t=>[zn,{session:e,handleClose:()=>{t()}}]))}}),t.appendToMenu("Apollo",{label:"Lock/Unlock session",onClick:e=>{e.toggleLocked()}}),t.appendToMenu("Apollo",{label:"Log out",icon:ot.default,onClick:e=>{e.queueDialog((t=>[In,{session:e,handleClose:()=>{t()}}]))}}))}};
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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?`: ${n}`:""}function Se(e,t,n=!1){const o=[];o.push(e);for(const t of function(e){const 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URL(W);"http:"!==e.protocol&&"https:"!==e.protocol||(te=!0)}catch{}const[ne,oe]=v.useState("panelFastaInput"),ae=e=>(t,n)=>{n&&oe(e)};return m.jsxs(Ue,{open:!0,handleClose:n,"data-testid":"add-assembly-dialog",title:"Add new assembly",maxWidth:!1,children:[m.jsxs("form",{onSubmit:async function(o){let a;if(o.preventDefault(),h(""),R(!0),V(!0),c(`Assembly "${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 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e.replace(o,String(n));return e}const Ke="$PREFIXED_ID";function Ze(e,t,n){if(t===Ke)return[Xe(e.id,n)];let o;try{o=L.query(e,t)}catch{o=L.query(JSON.parse(JSON.stringify(e)),t)}return o}function Ye(e){return e.toLowerCase().split(/[^\d:A-Za-z]+/).filter((e=>e&&!Je.has(e)))}function*Qe(e){for(const t of e)yield*Ye(t)}function*et(e){for(const t of e)if("string"==typeof t)yield t;else if("object"==typeof t){const e=L.query(t,"$..*");yield*et(e)}}function*tt(e,t,n){for(const o of t){const t=Ze(e,o,n);if(t.length>0)for(const e of Qe(et(t)))yield[o,e]}}async function nt(e,t,n){const o=await this.db,a=t??o.transaction(["nodes"]);M.checkAbortSignal(n);const s=[...Ye(e)],r=[],i=new Map;r.push(...s.map((async(e,t)=>{M.checkAbortSignal(n);const o=a.objectStore("nodes").index("full-text-words");for await(const a of o.iterate(IDBKeyRange.bound(e,`${e}`,!1,!1))){M.checkAbortSignal(n);const e=a.value,o=i.get(e.id)??[e,new Set];o[1].add(t),i.set(e.id,o)}}))),await 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e.transaction("meta","readwrite").objectStore("meta").clear(),t}}}function dt(){return[{displayName:"ID",jsonPath:Ke},...this.options.textIndexing?.indexFields??pt]}async function ut(e){const[t]=await e.transaction("meta").objectStore("meta").getAll();return!!t&&q(this.options.prefixes,t.storeOptions.prefixes)&&q(this.options.textIndexing,t.storeOptions.textIndexing)}class ft{ontologyName;ontologyVersion;sourceLocation;db;options;loadOboGraphJson=ct;getTermsByFulltext=nt;openDatabase=it;isDatabaseCurrent=ut;get textIndexFields(){return dt.call(this)}get prefixes(){return this.options.prefixes??new Map}DEFAULT_MAX_SEARCH_RESULTS=100;constructor(e,t,n,o){this.ontologyName=e,this.ontologyVersion=t,this.sourceLocation=n,this.options=o??{},this.db=this.prepareDatabase()}validate(){const e=[],{sourceLocation:t,sourceType:n}=this;return n?"obo-graph-json"!==n&&e.push(new Error(`ontology source file ${JSON.stringify(t)} has type ${n}, which is not yet supported`)):e.push(new Error(`unable to 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recurseEdges(e,t,n,o,a){const s=new Set;return await async function t(r){await Promise.all([...r].map((async r=>{const i=(await a.objectStore("edges").index(e).getAll(r)).filter((e=>n(e))).map((e=>e[o]));if(i.length>0){for(const e of i)s.add(e);await t(i)}})))}(t),s.values()}async*expandNodeSet(e,t="is_a",n,o){const a=await this.db,s=o??a.transaction(["edges"]),r=[...e],i=await this.recurseEdges("subclasses"===n?"by-object":"by-subject",r,(e=>e.pred===t),"subclasses"===n?"sub":"obj",s);for(const e of r)yield e;for(const e of i)yield e}expandSubclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"subclasses",n)}expandSuperclasses(e,t="is_a",n){return this.expandNodeSet(e,t,"superclasses",n)}async getClassesThat(e,t,n){const o=await this.db,a=n??o.transaction(["nodes","edges"]),s=await this.getPropertiesByLabel(e,{includeSubProperties:!0},a),r=new Set(s.map((e=>e.id))),i=await async function(e){const t=[];for await(const n of e)t.push(n);return t}(this.expandSuperclasses(t.map((e=>e.id)),"is_a",a)),l=await this.recurseEdges("by-object",i,(e=>r.has(e.pred)),"sub",a),c=this.expandSubclasses(l,"is_a",a),d=[];for await(const e of c){const t=await a.objectStore("nodes").get(e);t&&yt(t)&&!rt(t)&&d.push(t)}return d}async getClassesWithoutPropertyLabeled(e,t,n){const o=await this.db,a=n??o.transaction(["nodes","edges"]),s=a.objectStore("nodes"),r=a.objectStore("edges"),i=(await this.getPropertiesByLabel(e,t,a)).map((e=>e.id)),l=await(async()=>{const e=new Set;for(const t of i)for await(const n of r.index("by-predicate").iterate(t))e.add(n.value.sub);const t=new Set;for await(const n of this.expandSubclasses(e,"is_a",a))t.add(n);return t})(),c=[];for await(const e of s){const t=e.value;yt(t)&&!l.has(t.id)&&c.push(t.id)}const d=[];for(const e of c){const t=await a.objectStore("nodes").get(e);t&&yt(t)&&!rt(t)&&d.push(t)}return d}async getAllClasses(e){const t=await this.db,n=e??t.transaction(["nodes"]);return(await n.objectStore("nodes").index("by-type").getAll("CLASS")).filter((e=>!rt(e)))}async getAllTerms(e){const t=await this.db,n=e??t.transaction(["nodes"]);return(await n.objectStore("nodes").getAll()).filter((e=>!rt(e)))}}const gt=l.types.model("OntologyRecord",{name:l.types.string,version:"unversioned",source:l.types.union(R.LocalPathLocation,R.UriLocation,R.BlobLocation),options:l.types.frozen(),equivalentTypes:l.types.map(l.types.array(l.types.string))}).volatile((e=>({dataStore:void 0,startedEquivalentTypeRequests:new Set}))).actions((e=>({ping(){},initDataStore(){e.dataStore=new ft(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 o=e.equivalentTypes.get(n);return o?o.includes(t):(e.loadEquivalentTypes(n),!1)}}))),ht=l.types.model("OntologyManager",{ontologies:l.types.array(gt),prefixes:l.types.optional(l.types.map(l.types.string),{"GO:":"http://purl.obolibrary.org/obo/GO_","SO:":"http://purl.obolibrary.org/obo/SO_"})}).views((e=>({get featureTypeOntologyName(){const t=l.getRoot(e).jbrowse.configuration;return 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 and sub-features",m.jsx(i.Tooltip,{title:"This is a shortcut to create a single mRNA with exon and CDS, but without a parent gene",children:m.jsx(i.IconButton,{size:"small",children:m.jsx(b,{sx:{fontSize:18}})})})]})}),m.jsx(i.FormControlLabel,{value:Ft.CUSTOM,checked:d!==Ft.GENE_AND_SUBFEATURES&&d!==Ft.TRANSCRIPT_AND_SUBFEATURES,control:m.jsx(i.Radio,{}),label:"Add feature with a sequence ontology type"})]})}),d===Ft.CUSTOM?m.jsx(St,{session:a,ontologyName:"Sequence Ontology",style:{width:170},value:f,filterTerms:yt,renderInput:e=>m.jsx(i.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0}),onChange:(e,t)=>{var n;t&&(n=t,x(""),g(n))}}):null]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{variant:"contained",type:"submit",disabled:w,children:"Submit"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:n,children:"Cancel"})]})]}),y?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:y})}):null]})}function Nt(e,t){const n=(new 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 assembly"}),m.jsx(i.Select,{labelId:"label",value:u,onChange:function(e){f(e.target.value)},children:d.filter((e=>e.name!==s)).map((e=>m.jsx(i.MenuItem,{value:e.name,children:o.readConfObject(e,"displayName")},e.name)))}),m.jsx(i.DialogContentText,{children:"Target reference sequence"}),m.jsx(i.Select,{labelId:"label",value:p,onChange:function(e){y(e.target.value)},children:g.map((e=>m.jsx(i.MenuItem,{value:e._id,children:e.name},e._id)))}),m.jsx(i.DialogContentText,{children:"Start position in target reference sequence"}),m.jsx(i.TextField,{margin:"dense",type:"number",fullWidth:!0,variant:"outlined",value:b,onChange:e=>{x(Number(e.target.value))}})]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{disabled:!u||!p||!b,variant:"contained",type:"submit",children:"Submit"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:n,children:"Cancel"})]})]}),S?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:S})}):null]})}function 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 account"}),m.jsx(i.Select,{value:h.internetAccountId,onChange:function(e){f(!1);const t=g.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID "${e.target.value}"`);p(t)},disabled:u&&!s,children:a.map((e=>m.jsx(i.MenuItem,{value:e.internetAccountId,children:e.name},e.id)))})]}):null,m.jsx(i.DialogContentText,{children:"Select assembly"}),m.jsx(i.Select,{labelId:"label",value:x?.name??"",onChange:function(e){const t=b.find((t=>t.name===e.target.value));S(t)},disabled:0===b.length,children:b.map((e=>m.jsx(i.MenuItem,{value:e.name,children:e.displayName},e.name)))}),m.jsx(i.DialogContentText,{children:m.jsx("strong",{style:{color:"red"},children:"NOTE: All assembly data will be deleted and this operation cannot be undone!"})}),m.jsx(i.FormGroup,{children:m.jsx(i.FormControlLabel,{control:m.jsx(i.Checkbox,{checked:c,onChange:()=>{d(!c)}}),label:"I understand that all assembly data will be deleted"})})]}),m.jsxs(i.DialogActions,{children:[m.jsx(i.Button,{disabled:!x||!c,variant:"contained",type:"submit",children:"Delete"}),m.jsx(i.Button,{variant:"outlined",type:"submit",onClick:n,children:"Cancel"})]})]}),s?m.jsx(i.DialogContent,{children:m.jsx(i.DialogContentText,{color:"error",children:s})}):null]})}function Mt({changeManager:e,handleClose:n,selectedFeature:o,session:a,setSelectedFeature:s,sourceAssemblyId:r,sourceFeature:c}){const[d,u]=v.useState(""),{ontologyManager:f}=a.apolloDataStore,{featureTypeOntology:g}=f;function h(e){if(!e.parent?.children||1===e.parent.children.size)return;const t=[];for(const n of e.parent.children.values())g?.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())g?.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(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 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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. 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m.jsx(m.Fragment,{children:e?.map(((e,t)=>m.jsx(i.Typography,{variant:"body2",color:"textSecondary",children:e},`${t}.${e}`)))})}const kn=y.makeStyles()((e=>({list:{"li:nth-of-type(odd)":{backgroundColor:e.palette.action.focus},"li:nth-of-type(even)":{backgroundColor:e.palette.action.hover}}}))),Nn=N.observer((function({assembly:e,editable:n,feature:o,session:a}){const{pluginManager:r}=s.getEnv(a),{classes:d}=kn(),[u,g]=v.useState(null),[h,p]=v.useState(null),[y,b]=v.useState(null),[x,S]=v.useState(!1),[w,C]=v.useState(),j=Boolean(u),{changeManager:T}=a.apolloDataStore,{notify:A}=a;function F(){g(null),p(null)}const{_id:D,attributes:k}=o,N=r.evaluateExtensionPoint("Apollo-AttributeEditorComponent",Fn,{key:w});return m.jsxs(m.Fragment,{children:[m.jsxs(i.List,{className:d.list,children:[c.entries(k).map((([s,c])=>{const d=r.evaluateExtensionPoint("Apollo-AttributeEditorComponent",Fn,{key:s}),u=r.evaluateExtensionPoint("Apollo-AttributeViewerComponent",Dn,{key:s});return 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n=e.session;e.session.queueDialog((o=>[ea,{session:n,handleClose:()=>{o()},featureTypes:l.getSnapshot(t),onUpdate:t=>{e.updateFilteredFeatureTypes(t)}}]))}}]}}})).actions((e=>({setSelectedFeature(t){e.session.apolloSetSelectedFeature(t)},setHoveredFeature(t){e.session.apolloSetHoveredFeature(t)},showFeatureDetailsWidget(t,n){const[o]=e.regions,{assemblyName:a,refName:s}=o,r=e.getAssemblyId(a);if(!r)return;const{session:i}=e,{changeManager:l}=i.apolloDataStore,[c,d]=n??["ApolloFeatureDetailsWidget","apolloFeatureDetailsWidget"],u=i.addWidget(c,d,{feature:t,assembly:r,refName:s,changeManager:l});i.showWidget(u)},afterAttach(){l.addDisposer(e,c.autorun((()=>{e.lgv.initialized&&!e.regionCannotBeRendered()&&(e.setLoading(!0),e.session.apolloDataStore.loadFeatures(e.regions).then((()=>{setTimeout((()=>{e.setLoading(!1)}),1e3)})))}),{name:"LinearApolloDisplayLoadFeatures",delay:1e3}))}})))}(0,t);return n.named("LinearApolloDisplayLayouts").props({cleanupBoundary:2e5}).volatile((()=>({seenFeatures:c.observable.map()}))).views((e=>({getAnnotationFeatureById:t=>e.seenFeatures.get(t),getGlyph(e){const{topLevelFeature:t}=e;return t.looksLikeGene?Bo:t.children?.size?Qo:vo}}))).actions((e=>({addSeenFeature(t){e.seenFeatures.set(t._id,t)},deleteSeenFeature(t){e.seenFeatures.delete(t)}}))).views((e=>({get featureLayouts(){const{assemblyManager:t}=e.session;return e.lgv.displayedRegions.map((n=>{const o=t.get(n.assemblyName),a=new Map,r=new Map,{end:i,refName:c,start:d}=n;for(const[t,n]of e.seenFeatures.entries()){if(!l.isAlive(n)){e.deleteSeenFeature(t);continue}if(c!==o?.getCanonicalRefName(n.refSeq)||!s.doesIntersect2(d,i,n.min,n.max)||e.filteredFeatureTypes.length>0&&!e.filteredFeatureTypes.includes(n.type))continue;const{featureTypeOntology:u}=e.session.apolloDataStore.ontologyManager;if(!u)throw new Error("featureTypeOntology is undefined");const f=e.getGlyph(n).getRowCount(n,u,e.lgv.bpPerPx);let g=0,h=!1;for(;!h;){let e=ra(g,f,r);if(e.length<f){for(let t=0;t<f-e.length;t++){const e=r.size;r.set(e,[]),a.set(e,[])}e=ra(g,f,r)}if(ia(e,n)){for(let e=g;e<g+f;e++){r.get(e)?.push([n.min,n.max]);const t=a.get(e);t?.push([e-g,n._id])}h=!0}else g+=1}}return a}))},getFeatureLayoutPosition(t){const{featureLayouts:n}=this,{featureTypeOntology:o}=e.session.apolloDataStore.ontologyManager;for(const[a,s]of n.entries())for(const[n,r]of s)for(const[s,i]of r){if(0!==s)continue;const r=e.getAnnotationFeatureById(i);if(r){if(t._id===r._id)return{layoutIndex:a,layoutRow:n,featureRow:s};if(r.hasDescendant(t._id)){if(!o)throw new Error("featureTypeOntology is undefined");const s=e.getGlyph(r).getRowForFeature(r,t,o);if(void 0!==s)return{layoutIndex:a,layoutRow:n,featureRow:s}}}}}}))).views((e=>({get highestRow(){return 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featuresHeight(){return(e.highestRow+1)*e.apolloRowHeight+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:"LinearApolloDisplayRenderCollaborators"})),l.addDisposer(e,c.autorun((()=>{const{canvas:t,featureLayouts:n,featuresHeight:o,lgv:a}=e;if(!a.initialized||e.regionCannotBeRendered())return;const{displayedRegions:r,dynamicBlocks:i}=a,l=t?.getContext("2d");if(l){l.clearRect(0,0,i.totalWidthPx,o);for(const[t,o]of n.entries()){const n=r[t];for(const[a,r]of o.entries())for(const[o,i]of r){const r=e.getAnnotationFeatureById(i);o>0||!r||s.doesIntersect2(n.start,n.end,r.min,r.max)&&e.getGlyph(r).draw(l,r,a,e,t)}}}}),{name:"LinearApolloDisplayRenderFeatures"}))}})))}(0,t);return n.named("LinearApolloDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0}))).views((e=>({getMousePosition(t){const n=Oe(t,e.lgv),{bp:o,regionNumber:a,y:s}=n,r=Math.floor(s/e.apolloRowHeight),i=e.featureLayouts[a].get(r);if(!i)return n;const l=i.find((t=>{const n=e.getAnnotationFeatureById(t[1]);return n&&o>=n.min&&o<=n.max}));if(!l)return n;const[c,d]=l,u=e.getAnnotationFeatureById(d);if(!u)return n;const f=e.getGlyph(u),{featureTypeOntology:g}=e.session.apolloDataStore.ontologyManager;if(!g)throw new Error("featureTypeOntology is undefined");const h=f.getFeatureFromLayout(u,o,c,g);return h?{...n,feature:h}:n}}))).actions((e=>({continueDrag(t,n){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in progress");n.stopPropagation(),e.apolloDragging={...e.apolloDragging,current:t}},setDragging(t){e.apolloDragging=t??null}}))).actions((e=>({setCursor(t){e.cursor!==t&&(e.cursor=t)},updateFilteredTranscripts(e){}}))).actions((()=>({onClick(){}})))}(0,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 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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:"LinearApolloDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:l.types.optional(xo,{})}).named("LinearApolloDisplay")}const ca=o.ConfigurationSchema("LinearApolloReferenceSequenceDisplay",{},{explicitIdentifier:"displayId",explicitlyTyped:!0});function da(e,t,n){const o=t<=1?[2,1,0,7,6,5]:[2,1,0,5,4,3];n&&o.reverse(),o.unshift(0);const a=o.at(e);if(void 0===a)throw new Error("could not find row");return a}function ua(e,t,n,o){return o.offsetPx-n+(o.reversed?o.end-e.max:e.min-o.start)/t}function fa(e,t,n,o,a,s,r=!1){e.fillStyle=r?s.palette.action.disabled:s.palette.action.focus,e.fillRect(t,n,o,a),e.strokeStyle=r?s.palette.text.secondary:s.palette.text.primary,e.strokeStyle=s.palette.text.primary,e.strokeRect(t,n,o,a)}function ga(e,t,n,o,a,s,r,i=!1){const l=function(e,t,n){if(!(t>1||void 0===e))return 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ba(e,t,n,o,a,r,i){if(1/a<1)return;const l=Math.round(o+n/a),c=Math.round(o+(n+1)/a)-l,d=[-1,1];for(const n of d){const o=(1===n?3:4)*r,d=1===n?t:s.revcom(t);e.fillStyle=sa(d,i),e.fillRect(l,o,c,r),1/a>=12&&(pa(e,l,o,c,r,i.palette.text.disabled),ma(e,l,o,c,d))}}function xa(e,t,n,o,a,r,i,l,c,d,u){const f=(i<=1?[0,2,1,0,7,6,5]:[0,2,1,0,5,4,3]).map((e=>e*c)),g=[-1,1];for(const h of g){const g=s.getFrame(l,l+3,h,0),p=f.at(g);if(void 0===p)continue;const m=Math.round(n+o/i),y=Math.round(n+(o+3)/i)-m,b=1===h?t:s.revcom(t),x=s.defaultCodonTable[b],S=aa(x,a,r);S&&(u&&"*"==x||d&&"*"!=x)&&(e.fillStyle=S,e.fillRect(m,p,y,c)),1/i>=4&&(pa(e,m,p,y,c,a.palette.text.disabled),ma(e,m,p,y,x))}}function Sa(e,t){return function(e,t){const n=function(e,t){return a.BaseDisplay.named("BaseLinearApolloReferenceSequenceDisplay").props({type:l.types.literal("LinearApolloReferenceSequenceDisplay"),configuration:o.ConfigurationReference(t),showStartCodons:!1,showStopCodons:!0,highContrast:!1,heightPreConfig:l.types.maybe(l.types.refinement("displayHeight",l.types.number,(e=>e>=20))),sequenceRowHeight:15}).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...ne.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get lgv(){return s.getContainingView(e)}}))).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get session(){return s.getSession(e)},get regions(){return e.lgv.dynamicBlocks.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:o})=>({assemblyName:e,refName:n,start:Math.round(o),end:Math.round(t)})))},regionCannotBeRendered(){if(e.lgv&&e.lgv.bpPerPx>=3)return"Zoom in to see sequence"}}))).views((e=>({get apolloInternetAccount(){const[t]=e.regions,{internetAccounts:n}=l.getRoot(e),{assemblyName:a}=t,{assemblyManager:s}=e.session,r=s.get(a);if(!r)throw new Error(`No assembly found with name ${a}`);const{internetAccountConfigId:i}=o.getConf(r,["sequence","metadata"]);return n.find((e=>o.getConf(e,"internetAccountId")===i))},get changeManager(){return e.session.apolloDataStore.changeManager},getAssemblyId(t){const{assemblyManager:n}=e.session,o=n.get(t);if(!o)throw new Error(`Could not find assembly named ${t}`);return o.name},get selectedFeature(){return e.session.apolloSelectedFeature},get hoveredFeature(){return e.session.apolloHoveredFeature},get height(){const{sequenceRowHeight:t}=e;return e.lgv.bpPerPx<=1?8*t:6*t}}))).volatile((()=>({scrollTop:0}))).actions((e=>({setScrollTop(t){e.scrollTop=t},setHeight:t=>(e.heightPreConfig=Math.max(t,20),e.height),resizeHeight(t){const n=e.height;return this.setHeight(e.height+t)-n},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleHighContrast(){e.highContrast=!e.highContrast}}))).views((e=>{const{trackMenuItems:t}=e;return{trackMenuItems(){const{showStartCodons:n,showStopCodons:o,highContrast:a}=e;return[...t(),{type:"subMenu",label:"Appearance",subMenu:[{label:"Show start codons",type:"checkbox",checked:n,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:o,onClick:()=>{e.toggleShowStopCodons()}},{label:"Use high contrast colors",type:"checkbox",checked:a,onClick:()=>{e.toggleHighContrast()}}]}]}}})).actions((e=>({afterAttach(){l.addDisposer(e,c.autorun((()=>{e.lgv.initialized&&!e.regionCannotBeRendered()&&e.lgv.bpPerPx<=3&&e.session.apolloDataStore.loadRefSeq(e.regions)}),{name:"LinearApolloReferenceSequenceDisplayLoadFeatures",delay:1e3}))}})))}(0,t);return 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this.setHeight(e.height+t)-n},showGraphicalOnly(){e.graphical=!0,e.table=!1},showTableOnly(){e.graphical=!1,e.table=!0},showGraphicalAndTable(){e.graphical=!0,e.table=!0},toggleShowFeatureLabels(){e.showFeatureLabels=!e.showFeatureLabels},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleShowCheckResults(){e.showCheckResults=!e.showCheckResults},updateFilteredFeatureTypes(t){e.filteredFeatureTypes=l.cast(t)},setZoomThresholdSetting({zoomThreshold:t}){e.zoomThreshold=t}}))).views((e=>{const{filteredFeatureTypes:t,trackMenuItems:n}=e;return{trackMenuItems(){const{graphical:o,table:a,showFeatureLabels:r,showStartCodons:i,showStopCodons:c,showCheckResults:d}=e;return[...n(),{type:"subMenu",label:"Appearance",subMenu:[{label:"Show graphical display",type:"radio",checked:o&&!a,onClick:()=>{e.showGraphicalOnly()}},{label:"Show table display",type:"radio",checked:a&&!o,onClick:()=>{e.showTableOnly()}},{label:"Show both graphical and table display",type:"radio",checked:a&&o,onClick:()=>{e.showGraphicalAndTable()}},{label:"Feature Labels",type:"checkbox",checked:r,onClick:()=>{e.toggleShowFeatureLabels()}},{label:"Show start codons",type:"checkbox",checked:i,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:c,onClick:()=>{e.toggleShowStopCodons()}},{label:"Check Results",type:"checkbox",checked:d,onClick:()=>{e.toggleShowCheckResults()}},{label:"Change zoom threshold",onClick:()=>{s.getSession(e).queueDialog((t=>[ta,{model:e,handleClose:t}]))}}]},{label:"Filter features by type",onClick:()=>{const n=e.session;e.session.queueDialog((o=>[ea,{session:n,handleClose:()=>{o()},featureTypes:l.getSnapshot(t),onUpdate:t=>{e.updateFilteredFeatureTypes(t)}}]))}}]}}})).actions((e=>({setSelectedFeature(t){e.session.apolloSetSelectedFeature(t)},setHoveredFeature(t){e.session.apolloSetHoveredFeature(t)},showFeatureDetailsWidget(t,n){const[o]=e.regions,{assemblyName:a,refName:s}=o,r=e.getAssemblyId(a);if(!r)return;const{session:i}=e,{changeManager:l}=i.apolloDataStore,[c,d]=n??["ApolloFeatureDetailsWidget","apolloFeatureDetailsWidget"],u=i.addWidget(c,d,{feature:t,assembly:r,refName:s,changeManager:l});i.showWidget(u)},afterAttach(){l.addDisposer(e,c.autorun((()=>{e.lgv.initialized&&!e.regionCannotBeRendered()&&(e.session.apolloDataStore.loadFeatures(e.regions),e.lgv.bpPerPx<=e.zoomThreshold&&e.session.apolloDataStore.loadRefSeq(e.regions))}),{name:"LinearApolloSixFrameDisplayLoadFeatures",delay:1e3}))}})))}(0,t);return n.named("LinearApolloSixFrameDisplayLayouts").props({featuresMinMaxLimit:5e5}).volatile((()=>({seenFeatures:c.observable.map()}))).views((e=>({get featuresMinMax(){const{assemblyManager:t}=e.session;return e.lgv.displayedRegions.map((n=>{const o=t.get(n.assemblyName);let a,r;const{end:i,refName:l,start:c}=n;for(const[,t]of e.seenFeatures)l!==o?.getCanonicalRefName(t.refSeq)||!s.doesIntersect2(c,i,t.min,t.max)||t.length>e.featuresMinMaxLimit||(void 0===a&&({min:a}=t),void 0===r&&({max:r}=t),t.minWithChildren<a&&({min:a}=t),t.maxWithChildren>r&&({max:r}=t));if(void 0!==a&&void 0!==r)return[a,r]}))},getGlyph:e=>Ra,featureLabelSpacer:t=>e.showFeatureLabels?2*t-1:t}))).actions((e=>({addSeenFeature(t){e.seenFeatures.set(t._id,t)},deleteSeenFeature(t){e.seenFeatures.delete(t)}}))).views((e=>({get geneTrackRowNums(){return[4,5].map((t=>e.featureLabelSpacer(t)))}}))).views((e=>({get featureLayouts(){const{assemblyManager:t}=e.session;return e.lgv.displayedRegions.map(((n,o)=>{const a=t.get(n.assemblyName),r=new Map;if(!e.featuresMinMax[o])return r;const{end:i,refName:c,start:d}=n;for(const[t,n]of e.seenFeatures.entries()){if(!l.isAlive(n)){e.deleteSeenFeature(t);continue}if(c!==a?.getCanonicalRefName(n.refSeq)||!s.doesIntersect2(d,i,n.min,n.max))continue;const{featureTypeOntology:o}=e.session.apolloDataStore.ontologyManager;if(!o)throw new Error("featureTypeOntology is undefined");if(n.looksLikeGene){const t=1==n.strand?e.geneTrackRowNums[0]:e.geneTrackRowNums[1];r.get(t)||r.set(t,[]);const a=r.get(t);a?.push({rowNum:t,feature:n});const{children:i}=n;if(!i)continue;for(const[,t]of i)if(o.isTypeOf(t.type,"transcript")){const{cdsLocations:n,strand:a,children:i}=t;if(i)for(const[,t]of i){if(!o.isTypeOf(t.type,"exon"))continue;const n=1==t.strand?e.geneTrackRowNums[0]:e.geneTrackRowNums[1],a=r.get(n);a?.push({rowNum:n,feature:t})}for(const o of n)for(const n of o){const 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)} 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${n}`);return i}}))).actions((e=>({loadFeatures:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[o,a]=yield t.getFeatures(n);if(0===o.length)continue;const{assemblyName:s,refName:r}=n;let i=e.assemblies.get(s);i||(i=e.assemblies.put({_id:s,refSeqs:{}}));const[l]=o;let c=i.refSeqs.get(l.refSeq);c||(c=i.refSeqs.put({_id:l.refSeq,name:r,features:{}}));for(const e of o)c.features.has(e._id)||c.features.put(e);e.addCheckResults(a)}})),loadRefSeq:l.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:o,seq:a}=yield t.getSequence(n),{assemblyName:s,end:r,refName:i,start:l}=n;let c=e.assemblies.get(s);c||(c=e.assemblies.put({_id:s,refSeqs:{}}));let d=c.refSeqs.get(o);d||(d=c.refSeqs.put({_id:o,name:i,sequence:[]})),d.addSequence({start:l,stop:r,sequence:a})}}))})))}(a),i=n.props({apolloDataStore:l.types.optional(r,{typeName:"Client"}),apolloSelectedFeature:l.types.safeReference(a),jobsManager:l.types.optional(ns,{}),isLocked:l.types.optional(l.types.boolean,!1),changeInProgress:l.types.optional(l.types.boolean,!1)}).volatile((()=>({apolloHoveredFeature:void 0,abortController:new AbortController}))).extend((()=>{const e=c.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},apolloSetHoveredFeature(t){e.apolloHoveredFeature=t},addApolloTrackConfig(t,n){const a=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===a))||e.addTrackConf({type:"ApolloTrack",trackId:a,name:`Annotations (${o.getConf(t,"displayName")||t.name})`,assemblyNames:[t.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:a,assemblyNames:[t.name],textSearchAdapterId:`apollo_search_${t.name}`,...n?{baseURL:{uri:n,locationType:"UriLocation"}}:{}}}})},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)"baseURL"in e&&e.postUserLocation([]);return}const o=[];for(const e of t)if("baseURL"in 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)"baseURL"in e&&e.postUserLocation([]);return}const o=[];for(const e of t)if("baseURL"in 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=>{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()}}]))}}))}};
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