@apollo-annotation/jbrowse-plugin-apollo 0.3.6 → 0.3.7

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

@@ -1,2 +1,2 @@
-"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var 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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 ct(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function ut(e){const t=Date.now();let n,a=1;this.options.update?.("Parsing JSON",a);try{n=JSON.parse(await A.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 n.objectStore("nodes").clear(),await n.objectStore("edges").clear();const l=n.objectStore("nodes"),s=dt.call(this).map((e=>e.jsonPath));if(r.nodes){let e=Math.round(a);for(const[,t]of r.nodes.entries())a+=1/r.nodes.length*64,Math.round(a)!=e&&a<100&&(this.options.update?.("Processing nodes",a),e=Math.round(a)),rt(t)&&await l.add({...t,fullTextWords:ct(nt(t,s,this.prefixes))})}const i=n.objectStore("edges");if(r.edges){let e=Math.round(a);for(const[,t]of r.edges.entries())a+=1/r.edges.length*30,Math.round(a)!=e&&a<100&&(this.options.update?.("Processing edges",a),e=Math.round(a)),lt(t)&&await i.add(t)}await n.done;const c=e.transaction("meta","readwrite"),{update:u,...d}=this.options;await c.objectStore("meta").add({ontologyRecord:{name:this.ontologyName,version:this.ontologyVersion,sourceLocation:this.sourceLocation},storeOptions:d,graphMeta:r.meta,timestamp:String(new Date),schemaVersion:2,timings:{overall:Date.now()-t,load:Date.now()-o}},"meta"),await c.done}catch(t){throw await e.transaction("meta","readwrite").objectStore("meta").clear(),t}}}function dt(){return[{displayName:"ID",jsonPath:Ye},...this.options.textIndexing?.indexFields??ht]}async function ft(e){const[t]=await e.transaction("meta").objectStore("meta").getAll();return!!t&&ge.default(this.options.prefixes,t.storeOptions.prefixes)&&ge.default(this.options.textIndexing,t.storeOptions.textIndexing)}class mt{ontologyName;ontologyVersion;sourceLocation;db;options;loadOboGraphJson=ut;getTermsByFulltext=at;openDatabase=it;isDatabaseCurrent=ft;get textIndexFields(){return dt.call(this)}get prefixes(){return this.options.prefixes??new Map}DEFAULT_MAX_SEARCH_RESULTS=100;constructor(e,t,n,a){this.ontologyName=e,this.ontologyVersion=t,this.sourceLocation=n,this.options=a??{},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 determine format of ontology source file ${JSON.stringify(t)}, file name must end with ".json", ".obo", or ".owl"`)),e}get sourceType(){if(r.isUriLocation(this.sourceLocation)){if(this.sourceLocation.uri.endsWith(".json"))return"obo-graph-json"}else if(r.isLocalPathLocation(this.sourceLocation)&&this.sourceLocation.localPath.endsWith(".json"))return"obo-graph-json"}get dbName(){return`Apollo Ontology "${this.ontologyName}" "${this.ontologyVersion}"`}async prepareDatabase(){const e=this.validate();if(e.length>0)throw e;const t=await this.openDatabase(this.dbName);if(await this.isDatabaseCurrent(t))return t;try{const{options:e,sourceLocation:n,sourceType:a}=this;if("obo-graph-json"!==a)throw new Error(`ontology source file ${JSON.stringify(n)} has type ${a}, which is not yet supported`);return e.update?.("",0),await this.loadOboGraphJson(t),e.update?.("",100),t}catch(e){throw t.close(),await C.deleteDB(this.dbName),e}}async termCount(e){const t=await this.db;return(e??t.transaction("nodes")).objectStore("nodes").count()}unique(e){const t=new Map,n=[];for(const a of e)t.has(a.id)||(t.set(a.id,!0),n.push(a));return n}async getTermsWithLabelOrSynonym(e,t,n){const a=t?.includeSubclasses??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),l=r.objectStore("nodes"),s=[...await l.index("by-label").getAll(e),...await l.index("by-synonym").getAll(e)];if(a){const e=await this.recurseEdges("by-object",s.map((e=>e.id)),(e=>"is_a"===e.pred),"sub",r);for(const t of e){const e=await l.get(t);e&&s.push(e)}}return s}async getPropertiesByLabel(e,t,n){const a=t?.includeSubProperties??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),l=(await this.getTermsWithLabelOrSynonym(e,{includeSubclasses:!1},r)).filter((e=>St(e)));if(a){const e=await this.recurseEdges("by-object",l.map((e=>e.id)),(e=>"subPropertyOf"===e.pred),"sub",r),t=r.objectStore("nodes");for(const n of e){const e=await t.get(n);e&&St(e)&&l.push(e)}}return l}async 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vt({fetchValidTerms:e,filterTerms:t,includeDeprecated:n,onChange:a,ontologyName:o,ontologyVersion:r,renderInput:l,session:s,style:i,value:c}){const[u,d]=y.useState(!1),[f,m]=y.useState(),[g,h]=y.useState(""),[b,S]=y.useState(),{ontologyManager:w}=s.apolloDataStore,v=w.findOntology(o,r)?.dataStore,E=v&&u&&!f,C=v&&!b,T=y.useCallback((e=>(n||!st(e))&&(!t||t(e))),[t,n]);y.useEffect((()=>{u||m(void 0)}),[u]),y.useEffect((()=>{const e=new AbortController,{signal:t}=e;return C&&(h(""),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}(v,c,T).then((e=>{t.aborted||S(e)}),(e=>{t.aborted||x.isAbortException(e)||h(String(e))}))),()=>{e.abort()}}),[s,c,T,v,C]),y.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 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Et({changeManager:e,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const{notify:l}=a,[s,i]=y.useState(String(r.max)),[c,u]=y.useState(String(r.min+1)),[d,f]=y.useState(""),[m,g]=y.useState(""),[h,b]=y.useState(""),S=Number(s)<=Number(c);return de.default.createElement(We,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},de.default.createElement("form",{onSubmit:async function(a){a.preventDefault(),g("");const i=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o,addedFeature:{_id:(new ue.default).toHexString(),refSeq:r.refSeq,min:Number(c)-1,max:Number(s),type:d},parentFeatureId:r._id});await e.submit(i),l("Feature added 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v=Boolean(w)||!(i&&l&&u);return u!==Ct.CUSTOM||f||(v=!0),de.default.createElement(We,{open:!0,title:"Add new feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},de.default.createElement("form",{onSubmit:async function(s){let c;s.preventDefault(),S("");for(const[,e]of o.apolloDataStore.assemblies??new Map)if(e._id===a.assemblyName)for(const[,t]of e.refSeqs??new Map)t.name===a.refName&&(c=t._id);if(!c)return void S("Invalid refseq id");if(u===Ct.GENE_AND_SUBFEATURES){const o=xt(c,g,Number(i)-1,Number(l)),s={};s[o._id]=o;const u=(new ue.default).toHexString(),d=new t.AddFeatureChange({changedIds:[u],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:u,refSeq:c,min:Number(i)-1,max:Number(l),type:"gene",strand:g,children:s}});return await e.submit(d),r("Feature added successfully","success"),void n()}if(u===Ct.TRANSCRIPT_AND_SUBFEATURES){const o=xt(c,g,Number(i)-1,Number(l)),s=new t.AddFeatureChange({changedIds:[o._id],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:o});return await e.submit(s),r("Feature added successfully","success"),void n()}if(!f)return void S("No type selected");const d=(new ue.default).toHexString(),m=new t.AddFeatureChange({changedIds:[d],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:d,refSeq:c,min:Number(i)-1,max:Number(l),type:f,strand:g}});await e.submit(m),r("Feature added successfully","success"),n()},"data-testid":"submit-form"},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},de.default.createElement(p.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(p.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:l,onChange:e=>{s(e.target.value)},error:w,helperText:w?'"End" must be greater than 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0}),de.default.createElement(p.MenuItem,{value:1},"+"),de.default.createElement(p.MenuItem,{value:-1},"-"))),de.default.createElement(p.FormControl,{style:{marginTop:20}},de.default.createElement(p.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",defaultValue:Ct.GENE_AND_SUBFEATURES,name:"radio-buttons-group",value:u,onChange:e=>{S("");const{value:t}=e.target;Object.keys(Ct).includes(t)&&d(Ct[t])}},de.default.createElement(p.FormControlLabel,{value:Ct.GENE_AND_SUBFEATURES,control:de.default.createElement(p.Radio,null),label:de.default.createElement(p.Box,{display:"flex",alignItems:"center"},"Add gene and sub-features",de.default.createElement(p.Tooltip,{title:"This is a shortcut to create a gene with a single mRNA, exon, and 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Nt({changeManager:e,handleClose:n,session:o,sourceAssemblyId:r,sourceFeature:l}){const{assemblyManager:s,notify:c}=o,u=s.assemblyList,[d,f]=y.useState(u.find((e=>e.name!==r))?.name),[m,g]=y.useState([]),[h,b]=y.useState(""),[S,w]=y.useState(l.min),[v,E]=y.useState("");function C(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=C(a,t);e.refSeq=h,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 y.useEffect((()=>{b(""),async function(){if(!d)return void E("No assemblies to copy to");const e=await s.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),b(n[0]?._id||"")}().catch((e=>{E(String(e))}))}),[d,s]),de.default.createElement(We,{open:!0,title:"Copy features and 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de.default.createElement(p.TextField,{...n,type:"text",onChange:function(e){o(e.target.value)},value:a,onKeyDown:e=>{"Enter"===e.key?s?.blur():"Escape"===e.key&&(o(String(t)),l(!0))},onBlur:()=>{const n=Number(a);a!==String(t)&&(Number.isNaN(n)?o(String(t)):e(n))},inputRef:e=>{i(e)},error:c,helperText:c?"Not a valid number":void 0})})),Sn=v.observer((function({assembly:e,feature:n,session:a}){const[o,r]=y.useState(""),[l,s]=y.useState(""),{_id:i,assemblyId:c,max:u,min:d,strand:f,type:m}=n,g=e=>{a.notify(e.message,"error")},{changeManager:h}=a.apolloDataStore;function b(n){const{value:a}=n.target,o=a?Number(a):void 0,r=new t.StrandChange({typeName:"StrandChange",changedIds:[i],featureId:i,oldStrand:f,newStrand:o,assembly:e});return h.submit(r)}return de.default.createElement("div",{"data-testid":"basic_information"},de.default.createElement(bn,{margin:"dense",id:"start",label:"Start",fullWidth:!0,variant:"outlined",value:d+1,onChangeCommitted:function(n){n--;const a=new 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n=(e.lgv.bpToPx({refName:o.refName,coord:o.start+l,regionNumber:t})?.offsetPx??0)-e.lgv.offsetPx,i=1/e.lgv.bpPerPx,c=e.lgv.displayedRegions[t].reversed?n-i:n;a.beginPath(),a.fillStyle=Ua(s,e.theme),a.rect(c,3*e.sequenceRowHeight,i,e.sequenceRowHeight),a.fill(),e.lgv.bpPerPx<=.1&&(a.stroke(),$a(a,c,i,s,3*e.sequenceRowHeight));const u=r.revcom(s);a.beginPath(),a.fillStyle=Ua(u,e.theme),a.rect(c,4*e.sequenceRowHeight,i,e.sequenceRowHeight),a.fill(),e.lgv.bpPerPx<=.1&&(a.stroke(),$a(a,c,i,u,4*e.sequenceRowHeight))}for(let t=0;t<=2;t++)(o.start+l)%3===t&&ja(a,e.lgv.bpPerPx,u,e.sequenceRowHeight*((e.lgv.bpPerPx<=1?5:3)+t),n,e.sequenceRowHeight,c,l,!0,e.showStartCodons,e.showStopCodons,e.highContrast)}}}),{name:"LinearApolloDisplayRenderSequence"}))}})))}(0,t).actions((e=>({afterAttach(){i.addDisposer(e,s.autorun((()=>{const{canvas:t,featureLayouts:n,featuresHeight:a,lgv:o}=e;if(!o.initialized||e.regionCannotBeRendered())return;const{displayedRegions:l,dynamicBlocks:s}=o,i=t?.getContext("2d");if(i){i.clearRect(0,0,s.totalWidthPx,a);for(const[t,a]of n.entries()){const n=l[t];for(const[o,l]of a.entries())for(const[a,s]of l){const l=e.getAnnotationFeatureById(s);a>0||!l||r.doesIntersect2(n.start,n.end,l.min,l.max)&&e.getGlyph(l).draw(i,l,o,e,t)}}}}),{name:"LinearApolloDisplayRenderFeatures"}))}})))}(0,t);return n.named("LinearApolloDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0,apolloHover:void 0}))).views((e=>({getMousePosition(t){const n=function(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}}(t,e.lgv),{bp:a,regionNumber:o,y:r}=n,l=Math.floor(r/e.apolloRowHeight),s=e.featureLayouts[o].get(l);if(!s)return n;const i=s.find((t=>{const n=e.getAnnotationFeatureById(t[1]);return n&&a>=n.min&&a<=n.max}));if(!i)return n;const[c,u]=i,d=e.getAnnotationFeatureById(u);if(!d)return n;const f=e.getGlyph(d),{featureTypeOntology:m}=e.session.apolloDataStore.ontologyManager;if(!m)throw new Error("featureTypeOntology is undefined");const g=f.getFeatureFromLayout(d,a,c,m);return g?{...n,featureAndGlyphUnderMouse:{feature:g,topLevelFeature:d,glyph:f}}: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=>({setApolloHover(t){e.apolloHover=t},setCursor(t){e.cursor!==t&&(e.cursor=t)}}))).actions((()=>({onClick(){}})))}(0,t).actions((e=>({afterAttach(){i.addDisposer(e,s.autorun((()=>{if(!e.lgv.initialized||e.regionCannotBeRendered())return;const t=e.seqTrackOverlayCanvas?.getContext("2d");if(!t)return;t.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.lgv.bpPerPx<=1?125:95);const{apolloHover:n,lgv:a,regions:o,sequenceRowHeight:l,session:s,theme:i}=e;if(!n)return;const{feature:c}=n,{featureTypeOntology:u}=s.apolloDataStore.ontologyManager;if(!u)throw new Error("featureTypeOntology is undefined");for(const[e,n]of o.entries())if(u.isTypeOf(c.type,"CDS")){const o=c.parent;if(!o)continue;const s=o.cdsLocations.find((e=>c.min===e.at(0)?.min&&c.max===e.at(-1)?.max));if(!s)continue;for(const o of s){const s=Wa(r.getFrame(o.min,o.max,c.strand??1,o.phase),a.bpPerPx),u=(a.bpToPx({refName:n.refName,coord:o.min,regionNumber:e})?.offsetPx??0)-a.offsetPx,d=(o.max-o.min)/a.bpPerPx;za(t,i,a.displayedRegions[e].reversed?u-d:u,l,s,d)}}else{const o=Ha(c.strand,a.bpPerPx),r=(a.bpToPx({refName:n.refName,coord:c.min,regionNumber:e})?.offsetPx??0)-a.offsetPx,s=c.length/a.bpPerPx;za(t,i,a.displayedRegions[e].reversed?r-s:r,l,o,s)}}),{name:"LinearApolloDisplayRenderSeqHighlight"}))}})))}(0,n);return l.views((e=>({contextMenuItems(t){const{apolloHover:n}=e;if(!n||!t)return[];const{topLevelFeature:a}=n;return e.getGlyph(a).getContextMenuItems(e)}}))).actions((e=>({startDrag(t,n,a){e.apolloDragging={start:t,current:t,feature:n,edge:a}},endDrag(){if(!e.apolloDragging)throw new Error("endDrag() called with no current drag in progress");const{current:n,edge:a,feature:o,start:r}=e.apolloDragging;if(Math.abs(n.x-r.x)<=4)return e.setDragging(),void e.setCursor();const{displayedRegions:l}=e.lgv,s=e.getAssemblyId(l[r.regionNumber].assemblyName);let i;if("max"===a){const e=o._id;i=new t.LocationEndChange({typeName:"LocationEndChange",changedIds:[e],featureId:e,oldEnd:o.max,newEnd:n.bp,assembly:s})}else{const e=o._id;i=new t.LocationStartChange({typeName:"LocationStartChange",changedIds:[e],featureId:e,oldStart:o.min,newStart:n.bp,assembly:s})}e.changeManager.submit(i),e.setDragging(),e.setCursor()}}))).actions((e=>({onMouseDown(t){const n=e.getMousePosition(t);Ga(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseDown(e,n,t)},onMouseMove(t){const n=e.getMousePosition(t);if(e.apolloDragging)return e.setCursor("col-resize"),void e.continueDrag(n,t);Ga(n)?n.featureAndGlyphUnderMouse.glyph.onMouseMove(e,n,t):(e.setApolloHover(),e.setCursor())},onMouseLeave(t){e.setDragging(),e.setApolloHover();const n=e.getMousePosition(t);Ga(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseLeave(e,n,t)},onMouseUp(t){const n=e.getMousePosition(t);Ga(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseUp(e,n,t),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.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,apolloHover:a}=e;if(!a)return;const{glyph:o}=a;o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:i.types.optional(ra,{})}).named("LinearApolloDisplay")}const Va=a.ConfigurationSchema("LinearApolloSixFrameDisplay",{},{explicitIdentifier:"displayId",explicitlyTyped:!0});let Xa=null,Ka=null,Ya=null,Za=null;if("document"in globalThis)for(const e of["forward","backward"])for(const t of["light","dark"]){const n=document.createElement("canvas"),a=10;n.width=n.height=a;const o=n.getContext("2d");if(o){const r="light"===t?"rgba(0,0,0,0)":"rgba(0,0,0,0.75)",l="light"===t?"rgba(255,255,255,0.25)":"rgba(0,0,0,0.50)",s="forward"===e?o.createLinearGradient(0,a,a,0):o.createLinearGradient(0,0,a,a);s.addColorStop(0,r),s.addColorStop(.25,r),s.addColorStop(.25,l),s.addColorStop(.5,l),s.addColorStop(.5,r),s.addColorStop(.75,r),s.addColorStop(.75,l),s.addColorStop(1,l),o.fillStyle=s,o.fillRect(0,0,10,10),"forward"===e?"light"===t?Xa=o.createPattern(n,"repeat"):Ya=o.createPattern(n,"repeat"):"light"===t?Ka=o.createPattern(n,"repeat"):Za=o.createPattern(n,"repeat")}}function Qa(e,t){for(const n of e)if(ge.default(n,t))return!0;return!1}function eo(e,t,n,a){const{session:o}=a,{apolloDataStore:l}=o,{featureTypeOntology:s}=l.ontologyManager;if(!s)throw new Error("featureTypeOntology is undefined");const 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to={draw:function(e,t,n,a,o){const{apolloRowHeight:l,lgv:s,session:i,theme:c,highestRow:u}=a,{bpPerPx:d,displayedRegions:f,offsetPx:m}=s,g=f[o],{refName:h,reversed:y}=g,b=l,S=Math.round(.6*b),w=Math.round(.7*b),{children:v,min:E,strand:C,_id:x}=t;if(!v)return;const{apolloSelectedFeature:T}=i,{apolloDataStore:A}=i,{featureTypeOntology:N}=A.ontologyManager;if(!N)throw new Error("featureTypeOntology is undefined");const F=(s.bpToPx({refName:h,coord:E,regionNumber:o})?.offsetPx??0)-m,k=t.length/d,D=y?F-k:F,R=(1==C?3:4)*b,M=Math.round(.7*b);e.fillStyle=c?.palette.text.primary??"black",e.fillRect(D,R,k,M),e.fillStyle=p.alpha(T&&x===T._id?"rgb(0,0,0)":c?.palette.background.paper??"#ffffff",.7),e.fillRect(D+1,R+1,k-2,M-2);const I="dark"===c?.palette.mode?Ya:Xa,P="dark"===c?.palette.mode?Za:Ka,q=y?-1:1;let L=null,B=null;C&&([L,B]=C*q==1?[I,P]:[P,I]),L&&B&&(e.fillStyle=L,e.fillRect(D+1,R+1,k-2,(M-2)/2),e.fillStyle=B,e.fillRect(D+1,R+(M-2)/2,k-2,(M-2)/2));const O=new Set;for(const[,t]of v){if(!N.isTypeOf(t.type,"transcript")&&!N.isTypeOf(t.type,"pseudogenic_transcript"))continue;const{children:n,cdsLocations:a,_id:l}=t;if(n){for(const[,t]of n){if(!N.isTypeOf(t.type,"exon"))continue;const n=(s.bpToPx({refName:h,coord:t.min,regionNumber:o})?.offsetPx??0)-m,a=t.length/d,r=y?n-a:n,l=R+(M-S)/2;e.fillStyle=c?.palette.text.primary??"black",e.fillRect(r,l,a,S),a>2&&(e.clearRect(r+1,l+1,a-2,S-2),e.fillStyle=T&&t._id===T._id?"rgb(0,0,0)":p.alpha("#f5f500",.6),e.fillRect(r+1,l+1,a-2,S-2),L&&B&&(e.fillStyle=L,e.fillRect(r+1,l+1,a-2,(S-2)/2),e.fillStyle=B,e.fillRect(r+1,l+1+(S-2)/2,a-2,(S-2)/2)))}for(const n of a){let a=0,i=0,f=1;for(const g of n.sort(((e,t)=>e.max-t.max)))if(T&&N.isTypeOf(T.type,"CDS")&&l===T.parent?._id||!Qa(O,g)){const n=(g.max-g.min)/d,p=(s.bpToPx({refName:h,coord:g.min,regionNumber:o})?.offsetPx??0)-m,S=y?p-n:p;e.fillStyle=c?.palette.text.primary??"black";const v=r.getFrame(g.min,g.max,t.strand??1,g.phase),E=((v<0?-1*v+5:v)-1)*b+(b-w)/2;if(e.fillRect(S,E,n,w),n>2){e.clearRect(S+1,E+1,n-2,w-2);const t=c?.palette.framesCDS.at(v)?.main,o=t??"rgb(171,71,188)";if(e.fillStyle=o,e.fillStyle=T&&N.isTypeOf(T.type,"CDS")&&l===T.parent?._id?"rgb(0,0,0)":o,e.fillRect(S+1,E+1,n-2,w-2),f>1){const t=[(S-i)/2+i,Math.max(v<0?b*u+1:1,Math.min(a,E)-b/2)];e.strokeStyle="rgb(0, 128, 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c=e.getFeatureLayoutPosition(i);if(!c)return;const{layoutIndex:u}=c,{bpPerPx:d,displayedRegions:f,offsetPx:m}=o,g=f[u],{refName:h,reversed:y}=g,b=a,S=Math.round(.7*b);let w="Loc: ";const{strand:v}=i,{max:E,min:C,phase:x}=s;w+=`${C+1}–${E}`;let T=(o.bpToPx({refName:h,coord:y?E:C,regionNumber:u})?.offsetPx??0)-m;const A=r.getFrame(C,E,v??1,x),N=((A<0?-1*A+5:A)-1)*b+(b-S)/2,F=(E-C)/d,k=`Type: ${s.type}`,{attributes:D}=i,R=D.get("gff_name")?.find((e=>""!==e)),M=[t.measureText(k).width,t.measureText(w).width];R&&M.push(t.measureText(`Parent Type: ${i.type}`).width,t.measureText(`Parent Name: ${R}`).width);const I=Math.max(...M);T=T+F+5,t.fillStyle=p.alpha(l?.palette.text.primary??"rgb(1, 1, 1)",.7),t.fillRect(T,N,I+4,4===M.length?55:35),t.beginPath(),t.moveTo(T,N),t.lineTo(T-5,N+5),t.lineTo(T,N+10),t.fill(),t.fillStyle=l?.palette.background.default??"rgba(255, 255, 255)";let P=N+12;t.fillText(k,T+2,P),R&&(P+=12,t.fillText(`Parent Type: ${i.type}`,T+2,P),P+=12,t.fillText(`Parent Name: 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o)if(a.isTypeOf(e.type,"transcript")){const{cdsLocations:t,strand:n,children:o}=e;if(o)for(const[,e]of o){if(!a.isTypeOf(e.type,"exon"))continue;const t=1==e.strand?4:5,n=l.get(t);n?.push({rowNum:t,feature:e,cds:null})}for(const a of t)for(const t of a){let a=r.getFrame(t.min,t.max,n??1,t.phase);a=a<0?-1*a+5:a,l.get(a)||l.set(a,[]);const o=l.get(a);o?.push({rowNum:a,feature:e,cds:t})}}}}return l}))},getFeatureLayoutPosition(e){const{featureLayouts:t}=this;for(const[n,a]of t.entries())for(const[,t]of a)for(const{feature:a}of t)if(e._id===a._id)return{layoutIndex:n,layoutRow:0,featureRow:0}}}))).views((e=>({get highestRow(){return 5}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.autorun((()=>{if(e.lgv.initialized&&!e.regionCannotBeRendered())for(const t of e.regions){const n=e.session.apolloDataStore.assemblies.get(t.assemblyName),a=n?.getByRefName(t.refName),o=a?.features;if(o)for(const[,n]of 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n;const{feature:c,cds:u}=i,{topLevelFeature:d}=c,f=e.getGlyph(c);return{...n,featureAndGlyphUnderMouse:{cds:u,feature:c,topLevelFeature:d,glyph:f}}}}))).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=>({setApolloHover(t){e.apolloHover=t},setCursor(t){e.cursor!==t&&(e.cursor=t)}}))).actions((()=>({onClick(){}})))}(0,n);return l.views((e=>({contextMenuItems(t){const{apolloHover:n}=e;if(!n||!t)return[];const{topLevelFeature:a}=n;return e.getGlyph(a).getContextMenuItems(e)}}))).actions((e=>({startDrag(t,n,a){e.apolloDragging={start:t,current:t,feature:n,edge:a}},endDrag(){if(!e.apolloDragging)throw new Error("endDrag() called with no current drag in progress");const{current:n,edge:a,feature:o,start:r}=e.apolloDragging;if(Math.abs(n.x-r.x)<=4)return e.setDragging(),void 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n=e.getMousePosition(t);no(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseUp(e,n,t),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.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,apolloHover:a}=e;if(!a)return;const{glyph:o}=a;o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloSixFrameDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:i.types.optional(ra,{})}).named("LinearApolloSixFrameDisplay")}const oo=a.ConfigurationSchema("ApolloPlugin",{ontologies:i.types.array(yt),featureTypeOntologyName:{description:"Name of the feature type ontology",type:"string",defaultValue:"Sequence Ontology"}});function ro(e){if("LinearPileupDisplay"!==e.name)return e;const{stateModel:n}=e,a=n.views((e=>({getFirstRegion:()=>r.getContainingView(e).dynamicBlocks.contentBlocks[0],getAssembly(){const t=e.getFirstRegion(),n=r.getSession(e),{assemblyManager:a}=n,{assemblyName:o}=t,l=a.get(o);if(!l)throw new Error(`Could not find assembly named ${o}`);return l},getRefSeqId(t){const n=e.getFirstRegion(),{refName:a}=n,{refNameAliases:o}=t;if(!o)throw new Error(`Could not find aliases for ${t.name}`);const r=[...Object.entries(o)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t}))),l=r.find((e=>e.name===a))?._id;if(!l)throw new Error(`Could not find refSeqId named ${a}`);return l},createFeature(){const t=e.contextMenuFeature,n=e.getAssembly(),a=e.getRefSeqId(n),o=(t.get("CIGAR").toUpperCase().match(/\d+\D/g)??[]).map((e=>[(/\D/.exec(e)??[])[0],Number.parseInt(e,10)]));let r=0;const l=t.get("start");let s;const i=[];for(const[e,t]of o)"M"===e||"="===e?void 0===s&&(s=r+l):"N"===e&&void 0!==s&&(i.push({start:s,end:r+s}),s=void 0),"I"!==e&&(r+=t);void 0!==s&&i.push({start:s,end:r+l});const c={_id:ue.default().toHexString(),refSeq:a,min:t.get("start"),max:t.get("end"),type:"mRNA",strand:t.get("strand")};if(0===i.length)return c;c.children={};const[u]=i,d={_id:ue.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"CDS",strand:t.get("strand")};if(c.children[d._id]=d,1===i.length){const e={_id:ue.default().toHexString(),refSeq:a,min:u.start,max:u.end,type:"exon",strand:t.get("strand")};return c.children[e._id]=e,c}for(const e of i){d.min=Math.min(d.min,e.start),d.max=Math.max(d.max,e.end);const{end:n,start:o}=e,r={_id:ue.default().toHexString(),refSeq:a,min:o,max:n,type:"exon",strand:t.get("strand")};c.children[r._id]=r}return c},async onPileupFeatureContext(){const n=e.createFeature(),a=e.getAssembly(),o=new t.AddFeatureChange({changedIds:[n._id],typeName:"AddFeatureChange",assembly:a.name,addedFeature:n}),l=r.getSession(e);await l.apolloDataStore.changeManager.submit(o),l.notify("Annotation added 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n?n[0]:e.type},uo=(e,t)=>{const{featureTypeOntology:n}=t.apolloDataStore.ontologyManager;if(!n)return co(e);let a="";n.isTypeOf(e.type,"gene")&&(a="gene_name"),n.isTypeOf(e.type,"transcript")&&(a="transcript_name");const{attributes:o}=e,r=o?.[a];return r?r[0]:co(e)};function fo({annotationFeature:e,assembly:n,handleClose:a,refSeqId:o,session:r}){const l=r,s=y.useMemo((()=>Object.keys(e.children??{})),[e]),c=y.useMemo((()=>{for(const[,e]of l.apolloDataStore.assemblies)if(e._id===n.name)for(const[,t]of e.refSeqs)if(t._id===o)return t.features;return[]}),[]),[u,d]=y.useState(!0),[f,m]=y.useState(s),[g,h]=y.useState(""),[b,S]=y.useState([]),[w,v]=y.useState();return y.useEffect((()=>{h("");let t=[],n=[];if(e.children){const a=Object.values(e.children).filter((e=>io(e,l))).filter((e=>f.includes(e._id)));t=a.map((e=>e.min)),n=a.map((e=>e.max))}const{featureTypeOntology:a}=l.apolloDataStore.ontologyManager;a&&a.isTypeOf(e.type,"transcript")&&(t=[e.min,...t],n=[e.max,...n]);const 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c?de.default.createElement("div",{className:s.shading,ref:b,style:{height:u}},de.default.createElement(vo,{model:e,...t})):de.default.createElement("div",{className:s.details,style:{height:u}},de.default.createElement(oa,{model:e}))})),Fo=i.types.model("JobsManager",{}).views((e=>({get jobStatusWidget(){const{widgets:t}=r.getSession(e);let n=t.get("JobsList");return n||(n=r.getSession(e).addWidget("JobsListWidget","JobsList")),n}}))).actions((e=>({update(t,n,a){e.jobStatusWidget.updateJobStatusMessage(t,n),a&&e.jobStatusWidget.updateJobProgressPct(t,a)},abortJob(t,n){const a=r.getSession(e);if(r.isSessionModelWithWidgets(a)){a.showWidget(e.jobStatusWidget),e.jobStatusWidget.updateJobStatusMessage(t,n??"Aborted unexpectedly");const o=e.jobStatusWidget.jobs.findIndex((e=>e.name===t));e.jobStatusWidget.addAbortedJob({...e.jobStatusWidget.jobs[o]}),e.jobStatusWidget.removeJob(t),a.notify("Job aborted","info")}},runJob(t){const 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this.revert(e);r.getSession(this.dataStore).notify("No changes to undo!","warning")}}class Ro extends ko{inFlight=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 je(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:o,start:l}=e,{assemblyManager:s}=r.getSession(this.clientStore),i=s.get(t);if(!i)throw new Error(`Could not find assembly with name "${t}"`);const{ids:c}=a.getConf(i,["sequence","metadata"]),u=c[o];if(!u)throw new Error(`Could not find refSeq "${o}"`);const d=this.clientStore.getInternetAccount(t),{baseURL:f}=d,m=new URL("features/getFeatures",f),g=new URLSearchParams({refSeq:u,start:String(l),end:String(n)});m.search=g.toString();const p=m.toString(),h=await this.fetch(d,p);if(!h.ok){const e=await je(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,d),h.json()}checkSocket(t,n,a){const{socket:o}=a,r=a.retrieveToken(),l=`${t}-${n}`,s=new Do(this.clientStore);o.hasListeners(l)||o.on(l,(async t=>{if(a.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId!==r&&t.channel===l){const n=e.Change.fromJSON(t.changeInfo);await s.submit(n,{submitToBackend:!1})}}))}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,n=this.inFlight.get(t),{assemblyName:o,end:l,refName:s,start:i}=e,{assemblyManager:c}=r.getSession(this.clientStore),u=c.get(o);if(!u)throw new Error(`Could not find assembly with name "${o}"`);const{ids:d}=a.getConf(u,["sequence","metadata"]),f=d[s];if(!f)throw new Error(`Could not find refSeq "${s}"`);if(n)return{seq:await n,refSeq:f};let m=this.clientStore.assemblies.get(o);m||(m=this.clientStore.addAssembly(o));let g=m.refSeqs.get(f);g||(g=m.addRefSeq(f,s));const p=g.getSequence(i,l);if(p.length===l-i)return{seq:p,refSeq:f};const h=this.clientStore.getInternetAccount(o),{baseURL:y}=h,b=new URL("sequence",y),S=new URLSearchParams({refSeq:f,start:String(i),end:String(l)});b.search=S.toString();const w=b.toString(),v=this.getSeqFromServer(h,w,g,i,l);this.inFlight.set(t,v);const E=await v;return this.checkSocket(o,s,h),this.inFlight.delete(t),{seq:E,refSeq:f}}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 getRefNameAliases(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(`getRefNameAliases failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,aliases:[e._id,...e.aliases],uniqueId:`alias-${e._id}`})))}async getRegions(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${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 je(s,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return s.ok||(i.ok=!1),i}}class Mo extends ko{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 Oe(e);a.addCheckResults(t)}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class Io extends ko{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),n=t.get(e);if(!n)throw new Error(`Assembly ${e} not found`);const{file:o}=a.getConf(n,["sequence","metadata"]),l=require("node:fs");return Be(e,await l.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${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 "${n.assembly}"`);const{file:s}=a.getConf(l,["sequence","metadata"]),c=this.clientStore.assemblies.get(n.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${n.assembly}"`);const u=new Set(...c.refSeqs.keys()),{checkResults:d}=this.clientStore;for(const e of d.values())u.has(e.refSeq)&&d.delete(e._id);const f=await Oe(c);this.clientStore.addCheckResults(f);const m=[{directive:"gff-version",value:"3"}];for(const[,e]of c.refSeqs)m.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of c.comments)m.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=re.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(s,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function Po(e,n){const o=new AbortController,{signal:l}=o,c=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",H.AnnotationFeatureModel),u=function(e){return i.types.model("ClientDataStore",{typeName:i.types.optional(i.types.literal("Client"),"Client"),assemblies:i.types.map(H.ApolloAssembly),checkResults:i.types.map(H.CheckResult),ontologyManager:i.types.optional(pt,{})}).views((t=>({get internetAccounts(){return i.getRoot(t).internetAccounts},get pluginConfiguration(){return i.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>i.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const a={_id:t,refSeqs:{}};return n&&(a.backendDriverType=n),e.assemblies.put(a)},addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const o=a.refSeqs.get(n.refSeq);if(!o)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);o.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:a,parent:o}=n;o?o.deleteChild(t):i.getParentOfType(n,H.ApolloRefSeq).deleteFeature(a)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)},clearCheckResults(){e.checkResults.clear()}}))).volatile((e=>({changeManager:new Do(e),collaborationServerDriver:new Ro(e),inMemoryFileDriver:new Mo(e),desktopFileDriver:r.isElectron?new Io(e):void 0}))).actions((e=>({afterCreate(){i.addDisposer(e,s.autorun((()=>{const{ontologyManager:t,pluginConfiguration:n}=e,o=n.ontologies;for(const n of o||[]){const[o,l,s,i]=[a.readConfObject(n,"name"),a.readConfObject(n,"version"),a.readConfObject(n,"source"),a.readConfObject(n,"textIndexFields")];if(!t.findOntology(o)){const n=r.getSession(e),{jobsManager:a}=n,c=new AbortController,u=`Loading ontology "${o}"`,d={name:u,statusMessage:`Loading ontology "${o}", version "${l}", this may take a while`,progressPct:0,cancelCallback:()=>{c.abort(),a.abortJob(d.name)}};t.addOntology(o,l,s,{textIndexing:{indexFields:i},update:(e,t)=>{0!==t?100!==t?a.update(u,e,t):a.done(d):a.runJob(d)}})}}})))}}))).views((e=>({getBackendDriver(t){if(!t)return e.collaborationServerDriver;const n=r.getSession(e),{assemblyManager:o}=n,l=o.get(t);if(!l)return e.collaborationServerDriver;const{file:s,internetAccountConfigId:i}=a.getConf(l,["sequence","metadata"]);return r.isElectron&&s?e.desktopFileDriver:i?e.collaborationServerDriver:e.inMemoryFileDriver},getInternetAccount(t,n){if(!(t??n))throw new Error("Must provide either assemblyName or internetAccountId");let o=n;if(t&&!o){const{assemblyManager:n}=r.getSession(e),l=n.get(t);if(!l)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:o}=a.getConf(l,["sequence","metadata"]))}const{internetAccounts:l}=e,s=l.find((e=>e.internetAccountId===o));if(!s)throw new Error(`No InternetAccount found with config id ${n}`);return s}}))).actions((e=>({loadFeatures:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:l}=n;let s=e.assemblies.get(r);s||(s=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=s.refSeqs.get(i.refSeq);c||(c=s.refSeqs.put({_id:i.refSeq,name:l,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:l,refName:s,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:s,sequence:[]})),u.addSequence({start:i,stop:l,sequence:o})}}))})))}(c),d=n.props({apolloDataStore:i.types.optional(u,{typeName:"Client"}),apolloSelectedFeature:i.types.safeReference(c),jobsManager:i.types.optional(Fo,{})}).extend((()=>{const e=s.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},addApolloTrackConfig(t,n){const o=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===o))||e.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations (${a.getConf(t,"displayName")||t.name})`,assemblyNames:[t.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:o,assemblyNames:[t.name],textSearchAdapterId:`apollo_search_${t.name}`,...n?{baseURL:{uri:n,locationType:"UriLocation"}}:{}}}})},broadcastLocations(){const{internetAccounts:t}=i.getRoot(e),n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const a=t;if(a.initialized){const{dynamicBlocks:t}=a;t.forEach((t=>{if(void 0!==t.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=t,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&n.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===n.length){for(const e of t)"baseURL"in e&&e.postUserLocation([]);return}const a=[];for(const e of t)if("baseURL"in e){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}}))).actions((e=>({afterCreate:i.flow((function*(){const t=i.getSnapshot(e),{id:n,name:a}=t;i.applySnapshot(e,{name:a,id:n});const{internetAccounts:o,jbrowse:r}=i.getRoot(e);s.autorun((()=>{const t=[];for(const n of e.views){if("LinearGenomeView"!==n.type)return;const a=n;if(a.initialized){const{dynamicBlocks:n}=a;n.forEach((n=>{if(void 0!==n.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=n,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&t.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===t.length){for(const e of o)"baseURL"in e&&e.postUserLocation([]);return}const n=[];for(const e of o)if("baseURL"in e){for(const e of t)n.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(n)}}),{name:"ApolloSession"});for(const n of o){if("ApolloInternetAccount"!==n.type)continue;const{baseURL:a}=n,o=new URL("jbrowse/config.json",a).href,s=n.getFetcher({locationType:"UriLocation",uri:o});let c,u;try{c=yield s(o,{signal:l})}catch(e){console.error(e);continue}if(c.ok){try{u=yield c.json()}catch(e){console.error(e);continue}i.applySnapshot(r,u),i.applySnapshot(e,t)}else{const e=yield je(c,"Failed to fetch assemblies");console.error(e)}}})),beforeDestroy(){o.abort("destroying session model")}}))).views((e=>{const 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}=i.getRoot(e),l=i.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const c={...i.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,c]}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track added","success")}e.deleteTrackConf(o),a.addTrackConf(c)},icon:qe.default}]:[...n?.(o)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),l=i.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const c=s?.tracks?.filter((e=>e.trackId!==r));for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:s,newJBrowseConfig:{...s,tracks:c}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track removed","success")}e.deleteTrackConf(o),a.deleteTrackConf(o)},icon:qe.default}]}}}));return i.types.snapshotProcessor(d,{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:a}=t,{checkResults:o}=a;for(const[,t]of o){const[n]=t.ids;if(!n)continue;const o=a.assemblies.get(n.assemblyId);o&&"InMemoryFileDriver"===o.backendDriverType&&(e.apolloDataStore.checkResults[t._id]=i.getSnapshot(t))}return e}})}const qo="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const Lo=new t.CDSCheck;e.checkRegistry.registerCheck(Lo.name,Lo),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends ae.default{name="ApolloPlugin";version="0.3.6";configurationSchema=oo;install(e){!function(e){e.addAdapterType((()=>new we.default({name:"ApolloSequenceAdapter",configSchema:on,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:an})))}(e),function(e){e.addAdapterType((()=>new we.default({name:"ApolloRefNameAliasAdapter",configSchema:en,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Qt})))}(e),function(e){e.addTextSearchAdapterType((()=>new o.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:ln,AdapterClass:rn,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:Tn,ReactComponent:xn})})),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloTranscriptDetails",{});return new o.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:An,ReactComponent:$n})})),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:Le,stateModel:Yt(Le)}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloDisplay",configSchema:jn,stateModel:Ja(0,jn),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Ao}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:Va,stateModel:ao(0,Va),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:No}))),e.addToExtensionPoint("Core-extendSession",Po.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:oe.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[Tt,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",ro),e.addToExtensionPoint("Core-extendPluggableElement",ho),qo||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),{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),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),i=await s.getRefNameAliases(a);t.workers[0].postMessage({apollo:o,messageId:r,refNameAliases:i});break}}})),t):t))}configure(e){r.isAbstractMenuManager(e.rootModel)&&(e.rootModel.appendToMenu("Apollo",{label:"Download GFF3",onClick:e=>{e.queueDialog((t=>[Dt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Manage Checks",onClick:e=>{e.queueDialog((t=>[It,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View Change Log",onClick:e=>{e.queueDialog((t=>[Bt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 file",onClick:e=>{e.queueDialog((t=>[qt,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View check results",onClick:e=>{e.queueDialog((t=>[$t,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Log out",onClick:e=>{e.queueDialog((t=>[Mt,{session:e,handleClose:()=>{t()}}]))}}))}};
+"use strict";Object.defineProperty(exports,"__esModule",{value:!0});var e=require("@apollo-annotation/common"),t=require("@apollo-annotation/shared"),n=require("@jbrowse/core/Plugin"),a=require("@jbrowse/core/configuration"),o=require("@jbrowse/core/pluggableElementTypes"),r=require("@jbrowse/core/util"),l=require("@mui/icons-material/Add"),s=require("mobx"),i=require("mobx-state-tree"),c=require("socket.io-client"),u=require("@gmod/gff"),d=require("@mui/icons-material/Info"),f=require("@mui/icons-material/Link"),m=require("@mui/icons-material/RadioButtonChecked"),g=require("@mui/icons-material/RadioButtonUnchecked"),p=require("@mui/material"),h=require("bson-objectid"),y=require("react"),b=require("tss-react/mui"),S=require("@jbrowse/core/ui"),w=require("@mui/icons-material/Close"),E=require("mobx-react"),v=require("@jbrowse/core/util/types/mst"),C=require("idb/with-async-ittr"),x=require("@jbrowse/core/util/aborting"),T=require("jsonpath"),A=require("@jbrowse/core/util/io"),F=require("fast-deep-equal/es6"),D=require("file-saver"),k=require("@mui/material/Checkbox"),N=require("@mui/material/FormControlLabel"),I=require("@mui/material/LinearProgress"),R=require("@mui/icons-material/Delete"),M=require("@mui/x-data-grid"),L=require("nanoid"),P=require("@mui/icons-material/AccountCircle"),q=require("@jbrowse/core/pluggableElementTypes/AdapterType"),O=require("@jbrowse/core/data_adapters/BaseAdapter"),_=require("@jbrowse/core/util/rxjs"),B=require("@jbrowse/core/util/simpleFeature"),U=require("@jbrowse/core/TextSearch/BaseResults"),$=require("@mui/icons-material/ExpandMore"),G=require("@mui/icons-material/Edit"),j=require("@mui/icons-material/MoreHoriz"),W=require("@mui/icons-material/AddBox"),H=require("@apollo-annotation/mst"),z=require("@emotion/styled"),J=require("@mui/icons-material/ContentCopy"),V=require("@mui/icons-material/ContentCut"),X=require("@mui/icons-material/Remove"),K=require("@mui/icons-material/Clear"),Y=require("@mui/icons-material/UnfoldLess"),Z=require("@jbrowse/core/util/tracks"),Q=require("@mui/icons-material/ExpandLess"),ee=require("@mui/icons-material/Error"),te=require("@mui/icons-material/Save");function 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s)x.checkAbortSignal(n),i.push(...ut(this.textIndexFields,e,t,r,this.prefixes));return i.sort(((e,t)=>t.score-e.score)),i.slice(0,this.options.maxSearchResults??this.DEFAULT_MAX_SEARCH_RESULTS)}function ut(e,t,n,a,o){const r=[...n].sort().map((e=>a[e])),l=r.map((e=>{const t=e.replaceAll(/[$()*+./?[\\\]^{|}-]/g,String.raw`\$&`);return new RegExp(`\\b${t}`,"gi")}));let s=[],i=0;for(const[n,r]of e.entries()){const c=new Set,u=e.length-n-1,d=[...st(ot(t,r.jsonPath,o))];for(const e of d){let n=0;const o=[];for(const[t,r]of l.entries())for(const l of e.matchAll(r)){n+=1+1*u,c.add(t);const r=l.index,s=a[t];void 0!==r&&(n+=.01*s.length,n+=s.length/e.length*100*.05,o.push({wordIndex:t,position:r}))}n+=100*c.size,i<n&&(i=n),o.sort(((e,t)=>e.position-t.position)),o.length>0&&s.push({term:t,field:r,str:e,score:n,wordMatches:o})}}s=s.filter((e=>e.score===i));for(const e of s){const{wordMatches:t}=e;for(let n=0;n<t.length-1;n++){const a=t[n],o=t[n+1],l=o.wordIndex-a.wordIndex;if(1===l||-1===l){e.score+=1,1===l&&(e.score+=1);const t=Math.abs(o.position-(a.position+r[a.wordIndex].length))-1;e.score-=.05*t}}}return s}function dt(e){return"string"==typeof e.id}function ft(e){return"string"==typeof e.sub&&"string"==typeof e.pred&&"string"==typeof e.obj}function mt(e){return Boolean(e.meta?.deprecated)}async function gt(e){return C.openDB(e,2,{upgrade(e,t,n,a,o){if(t<2&&(e.objectStoreNames.contains("meta")&&e.deleteObjectStore("meta"),e.objectStoreNames.contains("nodes")&&e.deleteObjectStore("nodes"),e.objectStoreNames.contains("edges")&&e.deleteObjectStore("edges")),e.objectStoreNames.contains("meta")||e.createObjectStore("meta"),!e.objectStoreNames.contains("nodes")){e.createObjectStore("nodes",{keyPath:"id"});const t=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 pt(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function ht(e){const t=Date.now();let n,a=1;this.options.update?.("Parsing JSON",a);try{n=JSON.parse(await A.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 n.objectStore("nodes").clear(),await n.objectStore("edges").clear();const l=n.objectStore("nodes"),s=yt.call(this).map((e=>e.jsonPath));if(r.nodes){let e=Math.round(a);for(const[,t]of r.nodes.entries())a+=1/r.nodes.length*64,Math.round(a)!=e&&a<100&&(this.options.update?.("Processing nodes",a),e=Math.round(a)),dt(t)&&await l.add({...t,fullTextWords:pt(it(t,s,this.prefixes))})}const i=n.objectStore("edges");if(r.edges){let e=Math.round(a);for(const[,t]of r.edges.entries())a+=1/r.edges.length*30,Math.round(a)!=e&&a<100&&(this.options.update?.("Processing edges",a),e=Math.round(a)),ft(t)&&await i.add(t)}await n.done;const c=e.transaction("meta","readwrite"),{update:u,...d}=this.options;await c.objectStore("meta").add({ontologyRecord:{name:this.ontologyName,version:this.ontologyVersion,sourceLocation:this.sourceLocation},storeOptions:d,graphMeta:r.meta,timestamp:String(new Date),schemaVersion:2,timings:{overall:Date.now()-t,load:Date.now()-o}},"meta"),await c.done}catch(t){throw await e.transaction("meta","readwrite").objectStore("meta").clear(),t}}}function yt(){return[{displayName:"ID",jsonPath:at},...this.options.textIndexing?.indexFields??vt]}async function bt(e){const[t]=await e.transaction("meta").objectStore("meta").getAll();return!!t&&ge.default(this.options.prefixes,t.storeOptions.prefixes)&&ge.default(this.options.textIndexing,t.storeOptions.textIndexing)}class St{ontologyName;ontologyVersion;sourceLocation;db;options;loadOboGraphJson=ht;getTermsByFulltext=ct;openDatabase=gt;isDatabaseCurrent=bt;get textIndexFields(){return yt.call(this)}get prefixes(){return this.options.prefixes??new Map}DEFAULT_MAX_SEARCH_RESULTS=100;constructor(e,t,n,a){this.ontologyName=e,this.ontologyVersion=t,this.sourceLocation=n,this.options=a??{},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 determine format of ontology source file ${JSON.stringify(t)}, file name must end with ".json", ".obo", or ".owl"`)),e}get sourceType(){if(r.isUriLocation(this.sourceLocation)){if(this.sourceLocation.uri.endsWith(".json"))return"obo-graph-json"}else if(r.isLocalPathLocation(this.sourceLocation)&&this.sourceLocation.localPath.endsWith(".json"))return"obo-graph-json"}get dbName(){return`Apollo Ontology "${this.ontologyName}" "${this.ontologyVersion}"`}async prepareDatabase(){const e=this.validate();if(e.length>0)throw e;const t=await this.openDatabase(this.dbName);if(await this.isDatabaseCurrent(t))return t;try{const{options:e,sourceLocation:n,sourceType:a}=this;if("obo-graph-json"!==a)throw new Error(`ontology source file ${JSON.stringify(n)} has type ${a}, which is not yet supported`);return e.update?.("",0),await this.loadOboGraphJson(t),e.update?.("",100),t}catch(e){throw t.close(),await C.deleteDB(this.dbName),e}}async termCount(e){const t=await this.db;return(e??t.transaction("nodes")).objectStore("nodes").count()}unique(e){const t=new Map,n=[];for(const a of e)t.has(a.id)||(t.set(a.id,!0),n.push(a));return n}async getTermsWithLabelOrSynonym(e,t,n){const a=t?.includeSubclasses??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),l=r.objectStore("nodes"),s=[...await l.index("by-label").getAll(e),...await l.index("by-synonym").getAll(e)];if(a){const e=await this.recurseEdges("by-object",s.map((e=>e.id)),(e=>"is_a"===e.pred),"sub",r);for(const t of e){const e=await l.get(t);e&&s.push(e)}}return s}async getPropertiesByLabel(e,t,n){const a=t?.includeSubProperties??!0,o=await this.db,r=n??o.transaction(["nodes","edges"]),l=(await this.getTermsWithLabelOrSynonym(e,{includeSubclasses:!1},r)).filter((e=>Tt(e)));if(a){const e=await this.recurseEdges("by-object",l.map((e=>e.id)),(e=>"subPropertyOf"===e.pred),"sub",r),t=r.objectStore("nodes");for(const n of e){const e=await t.get(n);e&&Tt(e)&&l.push(e)}}return l}async 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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&&xt(t)&&!mt(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;xt(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&&xt(t)&&!mt(t)&&u.push(t)}return u}async getAllClasses(e){const t=await this.db,n=e??t.transaction(["nodes"]);return(await 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Ft({fetchValidTerms:e,filterTerms:t,includeDeprecated:n,onChange:a,ontologyName:o,ontologyVersion:r,renderInput:l,session:s,style:i,value:c}){const[u,d]=y.useState(!1),[f,m]=y.useState(),[g,h]=y.useState(""),[b,S]=y.useState(),{ontologyManager:w}=s.apolloDataStore,E=w.findOntology(o,r)?.dataStore,v=E&&u&&!f,C=E&&!b,T=y.useCallback((e=>(n||!mt(e))&&(!t||t(e))),[t,n]);y.useEffect((()=>{u||m(void 0)}),[u]),y.useEffect((()=>{const e=new AbortController,{signal:t}=e;return C&&(h(""),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}(E,c,T).then((e=>{t.aborted||S(e)}),(e=>{t.aborted||x.isAbortException(e)||h(String(e))}))),()=>{e.abort()}}),[s,c,T,E,C]),y.useEffect((()=>{const t=new AbortController,{signal:n}=t;return v&&async function(e,t,n,a){let o;if(t){const n=await t(e,a);n&&(o=n)}return o||(o=await 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Dt({changeManager:e,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const[l,s]=y.useState(String(r.max)),[i,c]=y.useState(String(r.min+1)),[u,d]=y.useState(""),[f,m]=y.useState(""),[g,h]=y.useState(""),b=Number(l)<=Number(i);return de.default.createElement(Ke,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},de.default.createElement("form",{onSubmit:function(a){a.preventDefault(),m("");const s=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o,addedFeature:{_id:(new 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t.AddFeatureChange({changedIds:[u],typeName:"AddFeatureChange",assembly:a.assemblyName,addedFeature:{_id:u,refSeq:i,min:Number(s)-1,max:Number(r),type:d,strand:m}});e.submit(f),n()},"data-testid":"submit-form"},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},de.default.createElement(p.TextField,{margin:"dense",id:"start",label:"Start",type:"number",fullWidth:!0,variant:"outlined",value:Number(s),onChange:e=>{i(e.target.value)}}),de.default.createElement(p.TextField,{margin:"dense",id:"end",label:"End",type:"number",fullWidth:!0,variant:"outlined",value:r,onChange:e=>{l(e.target.value)},error:S,helperText:S?'"End" must be greater than 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Ontology",style:{width:170},value:"",filterTerms:xt,renderInput:e=>de.default.createElement(p.TextField,{...e,label:"Type",variant:"outlined",fullWidth:!0}),onChange:(e,t)=>{var n;t&&(n=t,b(""),f(n))}}):null),de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{variant:"contained",type:"submit",disabled:w},"Submit"),de.default.createElement(p.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),h?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,{color:"error"},h)):null)}function Rt(e,t){const n=(new ue.default).toHexString();t.push(n);const a={};if(e.children)for(const n of Object.values(e.children)){const e=Rt(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 Mt({changeManager:e,handleClose:n,session:o,sourceAssemblyId:r,sourceFeature:l}){const{assemblyManager:s}=o,c=s.assemblyList,[u,d]=y.useState(c.find((e=>e.name!==r))?.name),[f,m]=y.useState([]),[g,h]=y.useState(""),[b,S]=y.useState(l.min),[w,E]=y.useState("");function v(e,t){const n={};if(e.children)for(const a of Object.values(e.children)){const e=v(a,t);e.refSeq=g,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 y.useEffect((()=>{h(""),async function(){if(!u)return void E("No assemblies to copy to");const e=await s.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})));m(n),h(n[0]?._id||"")}().catch((e=>{E(String(e))}))}),[u,s]),de.default.createElement(Ke,{open:!0,title:"Copy features and annotations",handleClose:n,maxWidth:!1,"data-testid":"copy-feature"},de.default.createElement("form",{onSubmit:async function(a){if(!u)return;a.preventDefault(),E("");const o=l.length,r=await s.waitForAssembly(u);if(!r)return void E(`Assembly not found: ${u}.`);const c=r.getCanonicalRefName(g),d=r.regions?.find((e=>e.refName===c));if(!d)return void E(`RefSeq not found: ${g}.`);const f=b+o;if(f>d.end)return void E(`Feature would extend beyond the bounds of the selected reference sequence. (Feature would end at ${f}, but reference sequence ends at ${d.end})`);if(b<d.start)return void E(`Reference sequence starts at ${d.start}, feature cannot start before that.`);const m=[],p=Rt(i.getSnapshot(l),m),h={...p.attributes};"Parent"in h&&delete h.Parent,p.refSeq=g;const y=b-p.min;p.min=b,p.max=b+o;const S=v(p,y),w=new t.AddFeatureChange({changedIds:[p._id],typeName:"AddFeatureChange",assembly:u,addedFeature:{_id:p._id,refSeq:p.refSeq,min:p.min,max:p.max,type:p.type,children:S.children,attributes:h,strand:p.strand},copyFeature:!0,allIds:m});e.submit(w),n(),a.preventDefault()}},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},de.default.createElement(p.DialogContentText,null,"Target assembly"),de.default.createElement(p.Select,{labelId:"label",value:u,onChange:function(e){d(e.target.value)}},c.filter((e=>e.name!==r)).map((e=>de.default.createElement(p.MenuItem,{key:e.name,value:e.name},a.readConfObject(e,"displayName"))))),de.default.createElement(p.DialogContentText,null,"Target reference sequence"),de.default.createElement(p.Select,{labelId:"label",value:g,onChange:function(e){h(e.target.value)}},f.map((e=>de.default.createElement(p.MenuItem,{key:e._id,value:e._id},e.name)))),de.default.createElement(p.DialogContentText,null,"Start position in target reference sequence"),de.default.createElement(p.TextField,{margin:"dense",type:"number",fullWidth:!0,variant:"outlined",value:b,onChange:e=>{S(Number(e.target.value))}})),de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{disabled:!u||!g||!b,variant:"contained",type:"submit"},"Submit"),de.default.createElement(p.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),w?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,{color:"error"},w)):null)}function Lt({changeManager:e,handleClose:n,session:a}){const{internetAccounts:o}=i.getRoot(a),[r,l]=y.useState(),[s,c]=y.useState(""),[u,d]=y.useState(!1),[f,m]=y.useState(!1),g=o.filter((e=>"ApolloInternetAccount"===e.type));if(0===g.length)throw new Error("No Apollo internet account found");const[h,b]=y.useState(g[0]),{collaborationServerDriver:S}=a.apolloDataStore,w=S.getAssemblies();return y.useEffect((()=>{w.length>0&&void 0===r&&l(w[0])}),[w,r]),de.default.createElement(Ke,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly"},de.default.createElement("form",{onSubmit:async function(a){if(a.preventDefault(),m(!0),c(""),!r)return void c("Must select assembly!");const o=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:r.name});await e.submit(o,{internetAccountId:h.internetAccountId}),n(),a.preventDefault()}},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},g.length>1?de.default.createElement(de.default.Fragment,null,de.default.createElement(p.DialogContentText,null,"Select account"),de.default.createElement(p.Select,{value:h.internetAccountId,onChange:function(e){m(!1);const t=g.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID 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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(Ke,{open:!0,title:"Delete feature",handleClose:n,maxWidth:!1,"data-testid":"delete-feature"},de.default.createElement("form",{onSubmit:o=>{!async function(o){o.preventDefault(),u(""),a?._id===s._id&&r();const c=[],d=new t.DeleteFeatureChange({changedIds:[s._id],typeName:"DeleteFeatureChange",assembly:l,changes:[{deletedFeature:i.getSnapshot(s),parentFeatureId:s.parent?._id}]});if(f&&(f.isTypeOf(s.type,"transcript")||f.isTypeOf(s.type,"pseudogenic_transcript"))){const e=m(s);e&&c.push(e)}if(f&&f.isTypeOf(s.type,"exon")){const e=function(e){if(!f)return;if(!f.isTypeOf(e.type,"exon"))return;if(!e.parent?.cdsLocations||0===e.parent.cdsLocations.length||0===e.parent.cdsLocations[0].length)return;if(!e.parent.children)throw new Error("Unable to find parent of CDS");if(1!=e.parent.cdsLocations.length)throw new Error("Unable to handle a transcript with multiple CDSs");const n=(e.parent.cdsLocations.at(0)??[]).sort((({min:e},{min:t})=>e-t));let 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:i.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 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e.submit(g),n(),o.preventDefault()}(o)}},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},de.default.createElement(p.DialogContentText,null,"Are you sure you want to delete the selected feature?")),de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{variant:"contained",type:"submit"},"Yes"),de.default.createElement(p.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),c?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,{color:"error"},c)):null)}function qt({handleClose:e,session:n}){const[o,r]=y.useState(!1),[l,s]=y.useState(),[c,u]=y.useState(""),{collaborationServerDriver:d,getInternetAccount:f,inMemoryFileDriver:m}=n.apolloDataStore,g=[...d.getAssemblies(),...m.getAssemblies()];return de.default.createElement(Ke,{open:!0,title:"Export GFF3",handleClose:e,maxWidth:!1,"data-testid":"download-gff3"},de.default.createElement("form",{onSubmit:async function(r){if(r.preventDefault(),u(""),!l)return void u("Must select assembly to download");const{internetAccountConfigId:s}=a.getConf(l,["sequence","metadata"]);s?await async function(e){if(!l)return void u("Must select assembly to download");const t=f(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 Ve(i,"Error when exporting ID");return void u(e)}const{exportID:c}=await i.json(),d=new URL("export",t.baseURL),m=new URLSearchParams({exportID:c,includeFASTA:o?"true":"false"});d.search=m.toString();const g=d.toString();window.open(g,"_blank")}(s):function(e){if(!l)return void u("Must select assembly to download");const{assemblies:n}=e.apolloDataStore,o=n.get(l.name),r=o?.refSeqs;if(!r)return void u(`No refSeqs found for assembly "${l.name}"`);const s=[{directive:"gff-version",value:"3"}],c=a.getConf(l,["sequence","adapter","features"]);for(const e of c){const{end:t,refName:n,start:a}=e;s.push({directive:"sequence-region",value:`${n} ${a+1} ${t}`})}for(const[,e]of r){const{features:n}=e;if(n)for(const[,e]of n)s.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const e of c){const{refName:t,seq:n}=e;s.push({id:t,description:"",sequence:n})}const d=re.default.formatSync(s),f=new Blob([d],{type:"text/plain;charset=utf-8"});D.saveAs(f,`${l.displayName??l.name}.gff3`)}(n),e()}},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},de.default.createElement(p.DialogContentText,null,"Select assembly"),de.default.createElement(p.Select,{labelId:"label",value:l?.name??"",onChange:function(e){const t=g.find((t=>t.name===e.target.value));s(t)},disabled:0===g.length},g.map((e=>de.default.createElement(p.MenuItem,{key:e.name,value:e.name},e.displayName??e.name)))),de.default.createElement(p.DialogContentText,null,"Select assembly to export to GFF3"),de.default.createElement(p.FormGroup,null,de.default.createElement(p.FormControlLabel,{"data-testid":"include-fasta-checkbox",control:de.default.createElement(p.Checkbox,{checked:o,onChange:()=>{r(!o)}}),label:"Include fasta sequence in GFF output"}))),de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{disabled:!l,variant:"contained",type:"submit"},"Download"),de.default.createElement(p.Button,{variant:"outlined",type:"submit",onClick:e},"Cancel"))),c?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,{color:"error"},c)):null)}function Ot({changeManager:e,handleClose:n,session:o}){const{apolloDataStore:r}=o,[l,s]=y.useState(),[i,c]=y.useState(),[u,d]=y.useState(""),[f,m]=y.useState(!1),[g,h]=y.useState(),[b,S]=y.useState(!1),[w,E]=y.useState(!1),{collaborationServerDriver:v,getInternetAccount:C}=r,x=v.getAssemblies();return y.useEffect((()=>{i&&(async()=>{const{internetAccountConfigId:e}=a.getConf(i,["sequence","metadata"]),t=C(i.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:i.name});o.search=r.toString();const l=t.getFetcher({locationType:"UriLocation",uri:o.toString()});E(!0);const s=await l(o.toString(),{method:"GET"});if(!s.ok)throw new Error(await Ve(s));{const e=await s.json();h(e.count)}E(!1)})().catch((e=>{console.error(e),d(e.message??e)}))}),[C,o,i]),de.default.createElement(Ke,{open:!0,title:"Import Features from GFF3 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features"),de.default.createElement("input",{type:"file",onChange:function(e){m(!1),e.target.files&&s(e.target.files[0])},disabled:f&&!u})),g&&g>0?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,null,"This assembly already has ",g," features, would you like to delete the existing features before importing new ones?"),de.default.createElement(he.default,{label:"Yes, delete existing features",disabled:f&&!u,control:de.default.createElement(pe.default,{checked:b,onChange:function(e){S(e.target.checked)},inputProps:{"aria-label":"controlled"},color:"warning"})})):null,de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{disabled:!(i&&l&&void 0!==g)||f,variant:"contained",type:"submit"},f?"Submitting...":"Submit"),de.default.createElement(p.Button,{variant:"outlined",type:"submit",onClick:n},"Close"))),u?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,{color:"error"},u)):null)}function _t({handleClose:e,session:t}){const{internetAccounts:n}=i.getRoot(t),[a,o]=y.useState(""),r=n.filter((e=>"ApolloInternetAccount"===e.type));if(0===r.length)throw new Error("No Apollo internet account found");const[l,s]=y.useState(r[0]);return de.default.createElement(Ke,{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(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},r.length>1?de.default.createElement(de.default.Fragment,null,de.default.createElement(p.DialogContentText,null,"Select 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s=await r.json();b(s.checks)})().catch((e=>{l(String(e))}))}),[a,d]),de.default.createElement(Ke,{open:!0,title:"Manage Checks",handleClose:e,"data-testid":"manage-checks"},de.default.createElement("form",{onSubmit:async function(n){if(n.preventDefault(),!a)return void l("Must select assembly!");const{notify:o}=t,{baseURL:r,getFetcher:s}=d,i=new URL("assemblies/checks",r).href,c=s({locationType:"UriLocation",uri:i}),u=await c(i,{method:"POST",body:JSON.stringify({_id:a.name,checks:h,name:""}),headers:{"Content-Type":"application/json"}});if(u.ok)o("Assembly checks updated successfully","success"),e();else{const e=await Ve(u,"Error when updating assembly checks");l(e)}}},de.default.createElement(p.DialogContent,null,u.length>1?de.default.createElement(de.default.Fragment,null,de.default.createElement(p.DialogContentText,null,"Select account"),de.default.createElement(p.Select,{value:d.internetAccountId,onChange:function(e){c(!1);const 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t.MergeExonsChange({changedIds:[l._id],typeName:"MergeExonsChange",assembly:r,firstExon:i.getSnapshot(l),secondExon:i.getSnapshot(u),parentFeatureId:d._id});e.submit(f),n(),s.preventDefault()}},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},0===Object.keys(f).length?"There are no neighbouring exons to merge with":"Merge with exon on:",de.default.createElement(p.FormControl,{style:{marginTop:5}},de.default.createElement(p.RadioGroup,{"aria-labelledby":"demo-radio-buttons-group-label",name:"radio-buttons-group",value:u,onChange:e=>{c("");const{value:t}=e.target;d(f[t])}},Object.keys(f).map((e=>de.default.createElement(p.FormControlLabel,{value:e,key:e,control:de.default.createElement(p.Radio,null),label:de.default.createElement(p.Box,{display:"flex",alignItems:"center"},$t(e,f))})))))),de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{variant:"contained",type:"submit",disabled:0===Object.keys(f).length||void 0===u},"Submit"),de.default.createElement(p.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),s?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,{color:"error"},s)):null)}function jt(e){let t;return t=e.attributes.get("gff_name")?e.attributes.get("gff_name")?.join(","):e.attributes.get("gff_id")?e.attributes.get("gff_id")?.join(","):e._id,`${t} [${e.min+1}-${e.max}]`}function Wt({changeManager:e,handleClose:n,selectedFeature:a,session:o,setSelectedFeature:r,sourceAssemblyId:l,sourceFeature:s}){const{notify:c}=o,[u,d]=y.useState(""),[f,m]=y.useState(),g=function(e,t){const n=e.parent;if(!n)throw new Error("Unable to find parent of reference transcript");const{featureTypeOntology:a}=t.apolloDataStore.ontologyManager;if(!a)throw new Error("featureTypeOntology is undefined");const o={};if(n.children)for(const[,t]of n.children)a.isTypeOf(t.type,"transcript")&&t._id!==e._id&&(o[t._id]=t);return o}(s,o);return de.default.createElement(Ke,{open:!0,title:"Merge transcripts",handleClose:n,maxWidth:!1,"data-testid":"merge-transcripts"},de.default.createElement("form",{onSubmit:async function(o){if(o.preventDefault(),d(""),!f)return;if(a?._id===s._id&&r(),!s.parent)throw new Error("Cannot find parent");const u=new t.MergeTranscriptsChange({changedIds:[s._id],typeName:"MergeTranscriptsChange",assembly:l,firstTranscript:i.getSnapshot(s),secondTranscript:i.getSnapshot(f),parentFeatureId:s.parent._id});await e.submit(u),c("Transcripts successfully merged","success"),n(),o.preventDefault()}},de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},0===Object.keys(g).length?"There are no transcripts to merge with":"Merge with 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Ht({handleClose:e,session:t}){const{apolloDataStore:n}=t,{addAssembly:a,addSessionAssembly:o,assemblyManager:l,notify:s}=t,[i,c]=y.useState(null),[u,d]=y.useState(""),[f,m]=y.useState(""),[g,h]=y.useState(!1),b=p.useTheme();return de.default.createElement(Ke,{open:!0,title:"Open local GFF3 file",handleClose:e,maxWidth:!1,"data-testid":"open-local-file"},de.default.createElement("form",{onSubmit:async function(c){if(c.preventDefault(),m(""),h(!0),!i)throw new Error("No file selected");const d=await new Response(i).text(),f=`${u}-${i.name}-${L.nanoid(8)}`;try{await Oe(f,d,n)}catch(t){return console.error(t),s(`Error loading GFF3 ${i.name}, ${String(t)}`,"error"),void e()}const g={name:f,aliases:[u],displayName:u,sequence:{trackId:`sequenceConfigId-${u}`,type:"ReferenceSequenceTrack",adapter:{type:"ApolloSequenceAdapter",assemblyId:f},metadata:{apollo:!0,...r.isElectron?{file:i.path}:{}}}};await(o||a)(g);const p=await l.waitForAssembly(g.name);p?(t.addApolloTrackConfig(p),s(`Loaded GFF3 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log",handleClose:t,"data-testid":"view-changelog"},de.default.createElement(p.Select,{style:{width:200,marginLeft:40},value:f,onChange:function(e){m(e.target.value)}},u.map((e=>de.default.createElement(p.MenuItem,{key:e._id,value:e._id},e.name)))),de.default.createElement(p.DialogContent,null,de.default.createElement(M.DataGrid,{pagination:!0,rows:g,columns:b,getRowId:e=>e._id,slots:{toolbar:M.GridToolbar},initialState:{sorting:{sortModel:[{field:"sequence",sort:"desc"}]},columns:{columnVisibilityModel:{sequence:!1}}}})),de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{variant:"outlined",type:"submit",onClick:t},"Close")),s?de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,{color:"error"},s)):null)}const Vt=[{field:"refName",headerName:"Ref Name"},{field:"aliases",headerName:"Aliases",editable:!0}],Xt=e=>/^[\da-f]{24}$/i.test(e);function Kt({changeManager:e,handleClose:n,session:a}){const o=y.useRef(null),[r,l]=y.useState(""),[s,i]=y.useState(!1),[c,u]=y.useState(),[d,f]=y.useState([]),[m,g]=y.useState(new Map),{apolloDataStore:h}=a,{collaborationServerDriver:b}=h,S=b.getAssemblies();y.useEffect((()=>{let e=0;const t=()=>{if(!c)return;const n=new Map;if(e<2&&!c.refNames&&(e++,setTimeout(t,50)),!c.refNames)return;const a=c.refNameAliases;for(const e in a){const t=a[e];if(t&&!Xt(e))if(n.has(t)){const a=n.get(t)??[];n.set(t,[...a,e])}else n.set(t,[e])}g(n)};t()}),[c]);const w=()=>[...m].map(((e,t)=>({id:t,refName:e[0],aliases:e[1].filter((t=>t!==e[0])).join(", ")})));return de.default.createElement(Ke,{open:!0,title:"Add reference sequence 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t.text()).split("\n"),a=new Map(m);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])}g(a)})(e).catch((()=>{l("Error reading file")}))},ref:o,disabled:s&&!r||!c}))),c&&m.size>0?de.default.createElement("div",{style:{height:200,width:"100%",marginTop:20}},de.default.createElement(p.InputLabel,null,"Refname aliases found for selected assembly."),de.default.createElement(M.DataGrid,{rows:w(),columns:Vt,initialState:{pagination:{paginationModel:{page:0,pageSize:5}}},pageSizeOptions:[5,10],onRowSelectionModelChange:e=>{(e=>{if(e.length>0){i(!0);const t=e.flatMap((e=>w().filter((t=>t.id===e))));f(t)}else i(!1),f([])})(e)},processRowUpdate:(e,t)=>{const n=new Map(m);return n.set(e.refName,e.aliases.split(",")),g(n),e},checkboxSelection:!0})):null),de.default.createElement(p.DialogActions,null,de.default.createElement(p.Button,{variant:"contained",type:"submit",disabled:!s,onClick:()=>{const a=[];for(const e of 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de.default.createElement(p.Button,{className:t.loginButton,variant:"outlined",startIcon:de.default.createElement(an,{color:n?"disabled":void 0}),...e},"Sign in with Microsoft")}function sn(e){const{classes:t}=on();return de.default.createElement(p.Button,{className:t.loginButton,variant:"outlined",startIcon:de.default.createElement(Se.default,{fontSize:"small"}),...e},"Continue as Guest")}const cn=b.makeStyles()((e=>({divider:{marginTop:e.spacing(4),marginBottom:e.spacing(5)}}))),un=({baseURL:e,handleClose:t,name:n})=>{const{classes:a}=cn(),[o,r]=y.useState(""),[l,s]=y.useState([]);function i(e){t("google"===e?"google":"microsoft"===e?"microsoft":"guest")}y.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 Ve(a,"Error when retrieving auth types from server");return void r(e)}const o=await a.json();s(o)}().catch((e=>{x.isAbortException(e)||r(String(e))})),()=>{t.abort()}}),[e]);const c=l.includes("google"),u=l.includes("microsoft"),d=l.includes("guest");return de.default.createElement(Ke,{open:!0,title:`Log in to 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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 c=l.toString(),u=t.getFetcher({locationType:"UriLocation",uri:c}),d=yield u(c,{method:"GET"});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:c.io(t,{path:n})}})).actions((n=>({addSocketListeners(){const{session:a}=i.getRoot(n),{notify:o}=a,r=n.retrieveToken();if(!r)throw new Error("No Token found");const{socket:l}=n,{addCheckResult:s,changeManager:c,deleteCheckResult:u}=a.apolloDataStore;l.on("connect",(async()=>{await n.getMissingChanges()})),l.on("connect_error",(e=>{console.error(e),o("Could not connect to the 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Error("ignore")}catch{console.error("Broadcasting user location failed")}}(t)}),300)}})()}))).actions((e=>({initialize:i.flow((function*(t){if("admin"===t){const t=i.getRoot(e);r.isAbstractMenuManager(t)&&function(e){e.appendToMenu("Apollo",{label:"Add Assembly",onClick:e=>{e.queueDialog((t=>[et,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Delete Assembly",onClick:e=>{e.queueDialog((t=>[Lt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Import Features",onClick:e=>{e.queueDialog((t=>[Ot,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Add reference sequence aliases",onClick:e=>{e.queueDialog((t=>[Kt,{session:e,handleClose:()=>{t()},changeManager:e.apolloDataStore.changeManager}]))}}),e.appendToMenu("Apollo",{label:"Add Assembly 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o(a,{method:"GET"}),window.addEventListener("beforeunload",(()=>{e.postUserLocation([])})),document.addEventListener("visibilitychange",(()=>{if("hidden"===document.visibilityState&&e.postUserLocation([]),"visible"===document.visibilityState){const{session:t}=i.getRoot(e);t.broadcastLocations()}}))}))}))).actions((e=>({afterAttach(){e.setRole(),s.autorun((async t=>{if(dn)return;const{session:n}=i.getRoot(e);n&&e.role&&(await e.initialize(e.role),t.dispose())}),{name:"ApolloInternetAccount"})}}))),mn="undefined"==typeof sessionStorage;class gn extends O.BaseAdapter{refNameAliases;async getRefNameAliases(){const e=a.readConfObject(this.config,"assemblyId");if(!mn){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e);return await n.getRefNameAliases(e)}const t=await new Promise(((t,n)=>{const a=setTimeout((()=>{n(new Error("timeout"))}),2e4),o=L.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 pn=a.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});function hn(e){return"object"==typeof e&&null!==e&&"apollo"in e&&!0===e.apollo}const yn="undefined"==typeof sessionStorage;class bn extends O.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(!yn){const t=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!t)throw new Error("No Apollo data store found");const n=t.getBackendDriver(e),a=await n.getRegions(e);return this.regions=a,a}const t=await new Promise(((t,n)=>{const a=setTimeout((()=>{n("timeout")}),2e4),o=L.nanoid(),r=e=>{const{data:n}=e;hn(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 _.ObservableCreate((async e=>{if(!yn){const a=this.pluginManager?.rootModel?.session?.apolloDataStore;if(!a)return void e.error("No Apollo data store found");const s=a.getBackendDriver(r),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 Ee.default({id:`${n} 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n=0;e.highContrast&&(o="white",n=1,a.fillStyle=t.palette.grey[200],a.fillRect(0,l,e.lgv.dynamicBlocks.totalWidthPx,e.sequenceRowHeight)),a.fillStyle=o,a.fillRect(0+n,l+n,e.lgv.dynamicBlocks.totalWidthPx-2*n,e.sequenceRowHeight-2*n)}l+=e.sequenceRowHeight}for(const[t,o]of e.regions.entries()){const{apolloDataStore:l}=e.session,s=l.assemblies.get(o.assemblyName),i=s?.getByRefName(o.refName),c=i?.getSequence(o.start,o.end);if(!c)return;for(const[l,s]of[...c].entries()){const i=(e.lgv.bpToPx({refName:o.refName,coord:o.start+l,regionNumber:t})?.offsetPx??0)-e.lgv.offsetPx,u=e.lgv.displayedRegions[t].reversed?i-n:i;for(let t=2;t>=0;t--)(o.start+l)%3===t&&io(a,e.lgv.bpPerPx,u,e.sequenceRowHeight*(2-t),n,e.sequenceRowHeight,c,l,!1,e.showStartCodons,e.showStopCodons,e.highContrast);if(e.lgv.bpPerPx<=1){const n=(e.lgv.bpToPx({refName:o.refName,coord:o.start+l,regionNumber:t})?.offsetPx??0)-e.lgv.offsetPx,i=1/e.lgv.bpPerPx,c=e.lgv.displayedRegions[t].reversed?n-i:n;a.beginPath(),a.fillStyle=lo(s,e.theme),a.rect(c,3*e.sequenceRowHeight,i,e.sequenceRowHeight),a.fill(),e.lgv.bpPerPx<=.1&&(a.stroke(),so(a,c,i,s,3*e.sequenceRowHeight));const u=r.revcom(s);a.beginPath(),a.fillStyle=lo(u,e.theme),a.rect(c,4*e.sequenceRowHeight,i,e.sequenceRowHeight),a.fill(),e.lgv.bpPerPx<=.1&&(a.stroke(),so(a,c,i,u,4*e.sequenceRowHeight))}for(let 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s=uo(r.getFrame(o.min,o.max,c.strand??1,o.phase),a.bpPerPx),u=(a.bpToPx({refName:n.refName,coord:o.min,regionNumber:e})?.offsetPx??0)-a.offsetPx,d=(o.max-o.min)/a.bpPerPx;mo(t,i,a.displayedRegions[e].reversed?u-d:u,l,s,d)}}else{const o=fo(c.strand,a.bpPerPx),r=(a.bpToPx({refName:n.refName,coord:c.min,regionNumber:e})?.offsetPx??0)-a.offsetPx,s=c.length/a.bpPerPx;mo(t,i,a.displayedRegions[e].reversed?r-s:r,l,o,s)}}),{name:"LinearApolloDisplayRenderSeqHighlight"}))}})))}(0,n);return l.views((e=>({contextMenuItems(t){const{apolloHover:n}=e;if(!n)return[];const a=e.getMousePosition(t),{topLevelFeature:o}=n,r=e.getGlyph(o);return co(a)?r.getContextMenuItems(e,a):[]}}))).actions((e=>({startDrag(t,n,a,o=!1){e.apolloDragging={start:t,current:t,feature:n,edge:a,shrinkParent:o}},endDrag(){if(!e.apolloDragging)throw new Error("endDrag() called with no current drag in progress");const{current:n,edge:a,feature:o,start:r,shrinkParent:l}=e.apolloDragging;if(Math.abs(n.x-r.x)<=4)return e.setDragging(),void e.setCursor();const{displayedRegions:s}=e.lgv,i=e.getAssemblyId(s[r.regionNumber].assemblyName),c=Je(o,n.bp,a,l),u="max"===a?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: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);co(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseDown(e,n,t)},onMouseMove(t){const n=e.getMousePosition(t);if(e.apolloDragging)return e.setCursor("col-resize"),void e.continueDrag(n,t);co(n)?n.featureAndGlyphUnderMouse.glyph.onMouseMove(e,n,t):(e.setApolloHover(),e.setCursor())},onMouseLeave(t){e.setDragging(),e.setApolloHover();const n=e.getMousePosition(t);co(n)&&n.featureAndGlyphUnderMouse.glyph.onMouseLeave(e,n,t)},onMouseUp(t){const n=e.getMousePosition(t);co(n)?n.featureAndGlyphUnderMouse.glyph.onMouseUp(e,n,t):e.setSelectedFeature(),e.apolloDragging&&e.endDrag()}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.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,apolloHover:a}=e;if(!a)return;const{glyph:o}=a;o.drawHover(e,t),o.drawTooltip(e,t),n&&e.getGlyph(n.feature.topLevelFeature).drawDragPreview(e,t)}),{name:"LinearApolloDisplayRenderMouseoverAndDrag"}))}})))}(0,n).props({tabularEditor:i.types.optional(wa,{})}).named("LinearApolloDisplay")}const po=a.ConfigurationSchema("LinearApolloSixFrameDisplay",{},{explicitIdentifier:"displayId",explicitlyTyped:!0}),ho=E.observer((function({sourceFeature:e,filteredTranscripts:t,handleClose:n,onUpdate:a}){const o=[];if(e.children)for(const[,t]of e.children){const e=t.attributes.get("gff_id")?.toString();e&&o.push(e)}const[r,l]=y.useState(t);return de.default.createElement(Ke,{open:!0,maxWidth:!1,"data-testid":"filter-transcripts-dialog",title:"Filter transcripts by ID",handleClose:n},de.default.createElement(p.DialogContent,null,de.default.createElement(p.DialogContentText,null,"Select the alternate transcripts you want to display in the apollo track"),de.default.createElement(p.Grid2,{container:!0,spacing:2},de.default.createElement(p.Grid2,{size:8},de.default.createElement(p.FormGroup,null,o.map((e=>de.default.createElement(p.FormControlLabel,{control:de.default.createElement(p.Checkbox,{checked:!r.includes(e),onChange:()=>{(e=>{const 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e.seenFeatures.entries()){if(!i.isAlive(n)){e.deleteSeenFeature(t);continue}if(c!==o?.getCanonicalRefName(n.refSeq)||!r.doesIntersect2(u,s,n.min,n.max))continue;const{featureTypeOntology:a}=e.session.apolloDataStore.ontologyManager;if(!a)throw new Error("featureTypeOntology is undefined");if(n.looksLikeGene){const t=1==n.strand?e.geneTrackRowNums[0]:e.geneTrackRowNums[1];l.get(t)||l.set(t,[]);const o=l.get(t);o?.push({rowNum:t,feature:n,cds:null});const{children:s}=n;if(!s)continue;for(const[,t]of s)if(a.isTypeOf(t.type,"transcript")){const{cdsLocations:n,strand:o,children:s}=t;if(s)for(const[,t]of s){if(!a.isTypeOf(t.type,"exon"))continue;const n=1==t.strand?e.geneTrackRowNums[0]:e.geneTrackRowNums[1],o=l.get(n);o?.push({rowNum:n,feature:t,cds:null})}for(const a of n)for(const n of a){let a=r.getFrame(n.min,n.max,o??1,n.phase);a=e.featureLabelSpacer(a<0?-1*a+5:a),l.get(a)||l.set(a,[]);const s=l.get(a);s?.push({rowNum:a,feature:t,cds:n})}}}}return l}))},getFeatureLayoutPosition(e){const{featureLayouts:t}=this;for(const[n,a]of t.entries())for(const[,t]of a)for(const{feature:a}of t)if(e._id===a._id)return{layoutIndex:n,layoutRow:0,featureRow:0}}}))).views((e=>({get highestRow(){return 5}}))).actions((e=>({afterAttach(){i.addDisposer(e,s.autorun((()=>{if(e.lgv.initialized&&!e.regionCannotBeRendered())for(const t of e.regions){const n=e.session.apolloDataStore.assemblies.get(t.assemblyName),a=n?.getByRefName(t.refName),o=a?.features;if(o)for(const[,n]of o)r.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({sequenceRowHeight:15,apolloRowHeight:20,detailsMinHeight:200,detailsHeight:200,lastRowTooltipBufferHeight:80,isShown:!0,filteredTranscripts:i.types.array(i.types.string)}).volatile((()=>({canvas:null,overlayCanvas:null,collaboratorCanvas:null,theme:void 0}))).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},afterAttach(){i.addDisposer(e,s.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:a}=n;if(0===a.length)continue;let o=0;for(const r of e.lgv.displayedRegions){for(const l of a){if(l.refSeq!==r.refName)continue;const{end:a,refSeq:s,start:i}=l,c=e.lgv.bpToPx({refName:s,coord:i,regionNumber:o});if(!c)continue;const u=c.offsetPx-e.lgv.offsetPx,d=(a-i)/e.lgv.bpPerPx;t.fillStyle="rgba(0,255,0,.2)",t.fillRect(u,1,d,100),t.fillStyle="black",t.fillText(n.name,u+1,11,d-2)}o++}}}}),{name:"LinearApolloSixFrameDisplayRenderCollaborators"}))}})))}(0,t);return n.actions((e=>({afterAttach(){i.addDisposer(e,s.autorun((()=>{const{canvas:t,featureLayouts:n,featuresHeight:a,lgv:o}=e;if(!o.initialized||e.regionCannotBeRendered())return;const{displayedRegions:l,dynamicBlocks:s}=o,i=t?.getContext("2d");if(i){i.clearRect(0,0,s.totalWidthPx,a);for(const[t,a]of n.entries()){const n=l[t];for(const[o,l]of a.entries())for(const{feature:a}of l){if(!a.looksLikeGene)continue;if(!r.doesIntersect2(n.start,n.end,a.min,a.max))continue;const{topLevelFeature:l}=a,s=e.getGlyph(l);void 0!==s&&s.draw(i,l,o,e,t)}}}}),{name:"LinearApolloSixFrameDisplayRenderFeatures"}))}})))}(0,t).named("LinearApolloSixFrameDisplayMouseEvents").volatile((()=>({apolloDragging:null,cursor:void 0,apolloHover:void 0}))).views((e=>({getMousePosition(t){const n=function(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}}(t,e.lgv),{bp:a,regionNumber:o,y:r}=n,l=Math.floor(r/e.apolloRowHeight)+1,s=e.featureLayouts[o].get(l);if(!s)return n;let i;if(e.geneTrackRowNums.includes(l)?(i=s.find((e=>"exon"==e.feature.type&&a>=e.feature.min&&a<=e.feature.max)),i||(i=s.find((e=>a>=e.feature.min&&a<=e.feature.max)))):i=s.find((t=>{const n=t.feature.attributes.get("gff_id")?.toString();return null!=t.cds&&a>=t.cds.min&&a<=t.cds.max&&(void 0===n||!e.filteredTranscripts.includes(n))})),!i)return n;const{feature:c,cds:u}=i,{topLevelFeature:d}=c,f=e.getGlyph(c);return{...n,featureAndGlyphUnderMouse:{cds:u,feature:c,topLevelFeature:d,glyph:f}}}}))).actions((e=>({continueDrag(t,n){if(!e.apolloDragging)throw new Error("continueDrag() called with no current drag in 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de.default.createElement("div",{style:{height:c}},de.default.createElement(Vo,{open:u,title:"Graphical",onClick:g}),de.default.createElement("div",{className:s.shading,ref:h,style:{height:a}},de.default.createElement($o,{model:e,...t})),de.default.createElement(Vo,{title:"Table",open:m.isShown,onClick:m.togglePane,onResize:b}),de.default.createElement("div",{className:s.details,style:{height:n}},de.default.createElement(Sa,{model:e})))}return i?de.default.createElement("div",{className:s.shading,ref:h,style:{height:c}},de.default.createElement($o,{model:e,...t})):de.default.createElement("div",{className:s.details,style:{height:c}},de.default.createElement(Sa,{model:e}))})),Ko=E.observer((function({model:e,...t}){const n=r.getSession(e),{ontologyManager:a}=n.apolloDataStore,{featureTypeOntology:o}=a,l=o?.dataStore,{classes:s}=Ho(),{detailsHeight:i,graphical:c,height:u,isShown:d,selectedFeature:f,table:m,tabularEditor:g,toggleShown:h}=e,b=y.useRef(null);y.useEffect((()=>{zo(e,b)}),[e,f]);const S=t=>{e.setDetailsHeight(i-t)};if(!l)return de.default.createElement("div",{className:s.alertContainer},de.default.createElement(p.Alert,{severity:"error"},"Could not load feature type ontology."));if(c&&m){const n=g.isShown?i:0,a=d?u-i-24:0;return de.default.createElement("div",{style:{height:u}},de.default.createElement(Vo,{open:d,title:"Graphical",onClick:h}),de.default.createElement("div",{className:s.shading,ref:b,style:{height:a}},de.default.createElement(Wo,{model:e,...t})),de.default.createElement(Vo,{title:"Table",open:g.isShown,onClick:g.togglePane,onResize:S}),de.default.createElement("div",{className:s.details,style:{height:n}},de.default.createElement(Sa,{model:e})))}return c?de.default.createElement("div",{className:s.shading,ref:b,style:{height:u}},de.default.createElement(Wo,{model:e,...t})):de.default.createElement("div",{className:s.details,style:{height:u}},de.default.createElement(Sa,{model:e}))})),Yo=i.types.model("JobsManager",{}).views((e=>({get jobStatusWidget(){const{widgets:t}=r.getSession(e);let n=t.get("JobsList");return n||(n=r.getSession(e).addWidget("JobsListWidget","JobsList")),n}}))).actions((e=>({update(t,n,a){e.jobStatusWidget.updateJobStatusMessage(t,n),a&&e.jobStatusWidget.updateJobProgressPct(t,a)},abortJob(t,n){const a=r.getSession(e);if(r.isSessionModelWithWidgets(a)){a.showWidget(e.jobStatusWidget),e.jobStatusWidget.updateJobStatusMessage(t,n??"Aborted unexpectedly");const o=e.jobStatusWidget.jobs.findIndex((e=>e.name===t));e.jobStatusWidget.addAbortedJob({...e.jobStatusWidget.jobs[o]}),e.jobStatusWidget.removeJob(t),a.notify("Job aborted","info")}},runJob(t){const n=r.getSession(e);r.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.addJob(t))},done(t){const n=r.getSession(e);r.isSessionModelWithWidgets(n)&&(n.showWidget(e.jobStatusWidget),e.jobStatusWidget.removeJob(t.name),e.jobStatusWidget.addFinishedJob({name:t.name,statusMessage:"All operations successful",progressPct:100,cancelCallback:t.cancelCallback}))}})));class Zo{clientStore;constructor(e){this.clientStore=e}}class Qo{dataStore;constructor(e){this.dataStore=e}recentChanges=[];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}=r.getSession(this.dataStore),d={name:n.typeName,statusMessage:"Pre-validating",progressPct:0,cancelCallback:()=>{c.abort()}};s&&u.runJob(d);const f=await t.validationRegistry.frontendPreValidate(n);if(!f.ok){const e=`Pre-validation failed: "${f.resultsMessages}"`;return s&&u.abortJob(d.name,e),void i.notify(e,"error")}try{await n.execute(this.dataStore)}catch(e){return s&&u.abortJob(d.name,String(e)),console.error(e),void i.notify(`Error encountered in client: ${String(e)}. Data may be out of sync, please refresh the page`,"error")}if((await t.validationRegistry.frontendPostValidate(n,this.dataStore)).ok||await this.revert(n),l){s&&u.update(d.name,"Submitting to driver");const{collaborationServerDriver:t,getBackendDriver:r}=this.dataStore,l=e.isAssemblySpecificChange(n)?r(n.assembly):t;let c;try{c=await l.submitChange(n,a)}catch(e){return s&&u.abortJob(d.name,String(e)),console.error(e),i.notify(String(e),"error"),void await this.revert(n,!1)}if(!c.ok){const e=`Post-validation failed: "${f.resultsMessages}"`;return s&&u.abortJob(d.name,e),i.notify(e,"error"),void await this.revert(n,!1)}n.notification&&i.notify(n.notification,"success"),o&&this.recentChanges.push(n)}s&&u.done(d)}async revert(e,t=!0){const n=e.getInverse();return this.submit(n,{submitToBackend:t,addToRecents:!1})}async revertLastChange(){const e=this.recentChanges.pop();if(e)return this.revert(e);r.getSession(this.dataStore).notify("No changes to undo!","warning")}}class er extends Zo{inFlight=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 Ve(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:n,refName:o,start:l}=e,{assemblyManager:s}=r.getSession(this.clientStore),i=s.get(t);if(!i)throw new Error(`Could not find assembly with name "${t}"`);const{ids:c}=a.getConf(i,["sequence","metadata"]),u=c[o];if(!u)throw new Error(`Could not find refSeq "${o}"`);const d=this.clientStore.getInternetAccount(t),{baseURL:f}=d,m=new URL("features/getFeatures",f),g=new URLSearchParams({refSeq:u,start:String(l),end:String(n)});m.search=g.toString();const p=m.toString(),h=await this.fetch(d,p);if(!h.ok){const e=await Ve(h,"getFeatures failed");throw new Error(e)}return this.checkSocket(t,o,d),h.json()}checkSocket(t,n,a){const{socket:o}=a,r=a.retrieveToken(),l=`${t}-${n}`,s=new Qo(this.clientStore);o.hasListeners(l)||o.on(l,(async t=>{if(a.setLastChangeSequenceNumber(Number(t.changeSequence)),t.userSessionId!==r&&t.channel===l){const n=e.Change.fromJSON(t.changeInfo);await s.submit(n,{submitToBackend:!1})}}))}async getSequence(e){const t=`${e.refName}:${e.start}-${e.end}`,n=this.inFlight.get(t),{assemblyName:o,end:l,refName:s,start:i}=e,{assemblyManager:c}=r.getSession(this.clientStore),u=c.get(o);if(!u)throw new Error(`Could not find assembly with name "${o}"`);const{ids:d}=a.getConf(u,["sequence","metadata"]),f=d[s];if(!f)throw new Error(`Could not find refSeq "${s}"`);if(n)return{seq:await n,refSeq:f};let m=this.clientStore.assemblies.get(o);m||(m=this.clientStore.addAssembly(o));let g=m.refSeqs.get(f);g||(g=m.addRefSeq(f,s));const p=g.getSequence(i,l);if(p.length===l-i)return{seq:p,refSeq:f};const h=this.clientStore.getInternetAccount(o),{baseURL:y}=h,b=new URL("sequence",y),S=new URLSearchParams({refSeq:f,start:String(i),end:String(l)});b.search=S.toString();const w=b.toString(),E=this.getSeqFromServer(h,w,g,i,l);this.inFlight.set(t,E);const v=await E;return this.checkSocket(o,s,h),this.inFlight.delete(t),{seq:v,refSeq:f}}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 getRefNameAliases(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(`getRefNameAliases failed: ${i.status} (${i.statusText})${e?` (${e})`:""}`)}return(await i.json()).map((e=>({refName:e.name,aliases:[e._id,...e.aliases],uniqueId:`alias-${e._id}`})))}async getRegions(e){const{assemblyManager:t}=r.getSession(this.clientStore);if(!t.get(e))throw new Error(`Could not find assembly with name "${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 Ve(s,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return s.ok||(i.ok=!1),i}}class tr extends Zo{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 _e(e);a.addCheckResults(t)}return new t.ValidationResultSet}async searchFeatures(e,t){return[]}}class nr extends Zo{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),n=t.get(e);if(!n)throw new Error(`Assembly ${e} not found`);const{file:o}=a.getConf(n,["sequence","metadata"]),l=require("node:fs");return Oe(e,await l.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${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 "${n.assembly}"`);const{file:s}=a.getConf(l,["sequence","metadata"]),c=this.clientStore.assemblies.get(n.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${n.assembly}"`);const u=new Set(...c.refSeqs.keys()),{checkResults:d}=this.clientStore;for(const e of d.values())u.has(e.refSeq)&&d.delete(e._id);const f=await _e(c);this.clientStore.addCheckResults(f);const m=[{directive:"gff-version",value:"3"}];for(const[,e]of c.refSeqs)m.push({directive:"sequence-region",value:`${e.name} 1 ${e.sequence[0].stop}`});for(const e of c.comments)m.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=re.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(s,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function ar(e,n){const o=new AbortController,{signal:l}=o,c=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",H.AnnotationFeatureModel),u=function(e){return i.types.model("ClientDataStore",{typeName:i.types.optional(i.types.literal("Client"),"Client"),assemblies:i.types.map(H.ApolloAssembly),checkResults:i.types.map(H.CheckResult),ontologyManager:i.types.optional(Et,{})}).views((t=>({get internetAccounts(){return i.getRoot(t).internetAccounts},get pluginConfiguration(){return i.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>i.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const a={_id:t,refSeqs:{}};return n&&(a.backendDriverType=n),e.assemblies.put(a)},addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${t}" to add feature "${n._id}"`);const o=a.refSeqs.get(n.refSeq);if(!o)throw new Error(`Could not find refSeq "${n.refSeq}" to add feature "${n._id}"`);o.features.put(n)},deleteFeature(t){const n=e.getFeature(t);if(!n)throw new Error(`Could not find feature "${t}" to delete`);const{_id:a,parent:o}=n;o?o.deleteChild(t):i.getParentOfType(n,H.ApolloRefSeq).deleteFeature(a)},deleteAssembly(t){e.assemblies.delete(t)},addCheckResult(t){e.checkResults.put(t)},addCheckResults(t){for(const n of t)e.checkResults.has(n._id)||e.checkResults.put(n)},deleteCheckResult(t){e.checkResults.delete(t)},clearCheckResults(){e.checkResults.clear()}}))).volatile((e=>({changeManager:new Qo(e),collaborationServerDriver:new er(e),inMemoryFileDriver:new tr(e),desktopFileDriver:r.isElectron?new nr(e):void 0}))).actions((e=>({afterCreate(){i.addDisposer(e,s.autorun((()=>{const{ontologyManager:t,pluginConfiguration:n}=e,o=n.ontologies;for(const n of o||[]){const[o,l,s,i]=[a.readConfObject(n,"name"),a.readConfObject(n,"version"),a.readConfObject(n,"source"),a.readConfObject(n,"textIndexFields")];if(!t.findOntology(o)){const n=r.getSession(e),{jobsManager:a}=n,c=new AbortController,u=`Loading ontology "${o}"`,d={name:u,statusMessage:`Loading ontology "${o}", version "${l}", this may take a while`,progressPct:0,cancelCallback:()=>{c.abort(),a.abortJob(d.name)}};t.addOntology(o,l,s,{textIndexing:{indexFields:i},update:(e,t)=>{0!==t?100!==t?a.update(u,e,t):a.done(d):a.runJob(d)}})}}})))}}))).views((e=>({getBackendDriver(t){if(!t)return e.collaborationServerDriver;const n=r.getSession(e),{assemblyManager:o}=n,l=o.get(t);if(!l)return e.collaborationServerDriver;const{file:s,internetAccountConfigId:i}=a.getConf(l,["sequence","metadata"]);return r.isElectron&&s?e.desktopFileDriver:i?e.collaborationServerDriver:e.inMemoryFileDriver},getInternetAccount(t,n){if(!(t??n))throw new Error("Must provide either assemblyName or internetAccountId");let o=n;if(t&&!o){const{assemblyManager:n}=r.getSession(e),l=n.get(t);if(!l)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:o}=a.getConf(l,["sequence","metadata"]))}const{internetAccounts:l}=e,s=l.find((e=>e.internetAccountId===o));if(!s)throw new Error(`No InternetAccount found with config id ${n}`);return s}}))).actions((e=>({loadFeatures:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:l}=n;let s=e.assemblies.get(r);s||(s=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=s.refSeqs.get(i.refSeq);c||(c=s.refSeqs.put({_id:i.refSeq,name:l,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:l,refName:s,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:s,sequence:[]})),u.addSequence({start:i,stop:l,sequence:o})}}))})))}(c),d=n.props({apolloDataStore:i.types.optional(u,{typeName:"Client"}),apolloSelectedFeature:i.types.safeReference(c),jobsManager:i.types.optional(Yo,{})}).extend((()=>{const e=s.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},addApolloTrackConfig(t,n){const o=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===o))||e.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations (${a.getConf(t,"displayName")||t.name})`,assemblyNames:[t.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:o,assemblyNames:[t.name],textSearchAdapterId:`apollo_search_${t.name}`,...n?{baseURL:{uri:n,locationType:"UriLocation"}}:{}}}})},broadcastLocations(){const{internetAccounts:t}=i.getRoot(e),n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const a=t;if(a.initialized){const{dynamicBlocks:t}=a;t.forEach((t=>{if(void 0!==t.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=t,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&n.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===n.length){for(const e of t)"baseURL"in e&&e.postUserLocation([]);return}const a=[];for(const e of t)if("baseURL"in e){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}}))).actions((e=>({afterCreate:i.flow((function*(){s.autorun((()=>{const n=[];for(const t of e.views){if("LinearGenomeView"!==t.type)return;const a=t;if(a.initialized){const{dynamicBlocks:t}=a;t.forEach((t=>{if(void 0!==t.regionNumber){const{assemblyName:a,end:o,refName:r,start:l}=t,s=e.apolloDataStore.assemblies.get(a);s&&"CollaborationServerDriver"===s.backendDriverType&&n.push({assemblyName:a,refName:r,start:l,end:o})}}))}}if(0===n.length){for(const e of t)"baseURL"in e&&e.postUserLocation([]);return}const a=[];for(const e of t)if("baseURL"in e){for(const e of n)a.push({assemblyId:e.assemblyName,refSeq:e.refName,start:e.start,end:e.end});e.postUserLocation(a)}}),{name:"ApolloSession"});const{internetAccounts:t,jbrowse:n,reloadPluginManagerCallback:o}=i.getRoot(e);if(a.readConfObject(n.configuration.ApolloPlugin,"hasRole"))return;const r=i.getSnapshot(e),{id:c,name:u}=r;i.applySnapshot(e,{name:u,id:c});for(const e of t){if("ApolloInternetAccount"!==e.type)continue;const{baseURL:t}=e,n=new URL("jbrowse/config.json",t).href,a=e.getFetcher({locationType:"UriLocation",uri:n});let s,i;try{s=yield a(n,{signal:l})}catch(e){console.error(e);continue}if(s.ok){try{i=yield s.json()}catch(e){console.error(e);continue}o(i,r)}else{const e=yield Ve(s,"Failed to fetch assemblies");console.error(e)}}})),beforeDestroy(){o.abort("destroying session model")}}))).views((e=>{const 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}=i.getRoot(e),l=i.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const c={...i.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,c]}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track added","success")}e.deleteTrackConf(o),a.addTrackConf(c)},icon:Pe.default}]:[...n?.(o)??[],{label:"Remove track from Apollo",onClick:async()=>{const{internetAccounts:n,jbrowse:a}=i.getRoot(e),l=i.getSnapshot(a);let s;s=t.filterJBrowseConfig(l),0===Object.keys(s).length&&(s=void 0);const c=s?.tracks?.filter((e=>e.trackId!==r));for(const a of n){if("ApolloInternetAccount"!==a.type)continue;const n=new t.ImportJBrowseConfigChange({typeName:"ImportJBrowseConfigChange",oldJBrowseConfig:s,newJBrowseConfig:{...s,tracks:c}}),{internetAccountId:o}=a;await e.apolloDataStore.changeManager.submit(n,{internetAccountId:o});const{notify:r}=e;r("Track removed","success")}e.deleteTrackConf(o),a.deleteTrackConf(o)},icon:Pe.default}]}}}));return i.types.snapshotProcessor(d,{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:a}=t,{checkResults:o}=a;for(const[,t]of o){const[n]=t.ids;if(!n)continue;const o=a.assemblies.get(n.assemblyId);o&&"InMemoryFileDriver"===o.backendDriverType&&(e.apolloDataStore.checkResults[t._id]=i.getSnapshot(t))}return e}})}const or="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const rr=new t.CDSCheck;e.checkRegistry.registerCheck(rr.name,rr),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends ae.default{name="ApolloPlugin";version="0.3.7";configurationSchema=Do;install(e){!function(e){e.addAdapterType((()=>new we.default({name:"ApolloSequenceAdapter",configSchema:Sn,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:bn})))}(e),function(e){e.addAdapterType((()=>new we.default({name:"ApolloRefNameAliasAdapter",configSchema:pn,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:gn})))}(e),function(e){e.addTextSearchAdapterType((()=>new o.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:En,AdapterClass:wn,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:Bn,ReactComponent:_n})})),e.addWidgetType((()=>{const e=a.ConfigurationSchema("ApolloTranscriptDetails",{});return new o.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:Un,ReactComponent:na})})),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:qe,stateModel:fn(qe)}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloDisplay",configSchema:aa,stateModel:go(0,aa),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Xo}))),e.addDisplayType((()=>new o.DisplayType({name:"LinearApolloSixFrameDisplay",configSchema:po,stateModel:Fo(0,po),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:Ko}))),e.addToExtensionPoint("Core-extendSession",ar.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:oe.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[It,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",Po),e.addToExtensionPoint("Core-extendPluggableElement",Bo),or||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),{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),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),i=await s.getRefNameAliases(a);t.workers[0].postMessage({apollo:o,messageId:r,refNameAliases:i});break}}})),t):t))}configure(e){r.isAbstractMenuManager(e.rootModel)&&(e.rootModel.appendToMenu("Apollo",{label:"Download GFF3",onClick:e=>{e.queueDialog((t=>[qt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Manage Checks",onClick:e=>{e.queueDialog((t=>[Bt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View Change Log",onClick:e=>{e.queueDialog((t=>[Jt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 file",onClick:e=>{e.queueDialog((t=>[Ht,{session:e,handleClose:()=>{t()},inMemoryFileDriver:e.apolloDataStore.inMemoryFileDriver}]))}}),e.rootModel.appendToMenu("Apollo",{label:"View check results",onClick:e=>{e.queueDialog((t=>[Yt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Log out",onClick:e=>{e.queueDialog((t=>[_t,{session:e,handleClose:()=>{t()}}]))}}))}};
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