@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.6

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 ut(e){const t=new Set;for(const[,n]of e)t.add(n);return[...t]}async function dt(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=ft.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)),lt(t)&&await l.add({...t,fullTextWords:ut(at(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)),st(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 ft(){return[{displayName:"ID",jsonPath:Ke},...this.options.textIndexing?.indexFields??yt]}async function mt(e){const[t]=await e.transaction("meta").objectStore("meta").getAll();return!!t&&he.default(this.options.prefixes,t.storeOptions.prefixes)&&he.default(this.options.textIndexing,t.storeOptions.textIndexing)}class gt{ontologyName;ontologyVersion;sourceLocation;db;options;loadOboGraphJson=dt;getTermsByFulltext=ot;openDatabase=ct;isDatabaseCurrent=mt;get textIndexFields(){return ft.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 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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=>wt(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&&wt(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,f]=g.useState(!1),[m,p]=g.useState(),[h,y]=g.useState(""),[b,S]=g.useState(),{ontologyManager:w}=s.apolloDataStore,E=w.findOntology(o,r)?.dataStore,v=E&&u&&!m,C=E&&!b,T=g.useCallback((e=>(n||!it(e))&&(!t||t(e))),[t,n]);g.useEffect((()=>{u||p(void 0)}),[u]),g.useEffect((()=>{const e=new AbortController,{signal:t}=e;return C&&(y(""),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)||y(String(e))}))),()=>{e.abort()}}),[s,c,T,E,C]),g.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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Ct({changeManager:e,handleClose:n,session:a,sourceAssemblyId:o,sourceFeature:r}){const{notify:l}=a,[s,i]=g.useState(String(r.max)),[c,u]=g.useState(String(r.min+1)),[f,m]=g.useState(""),[p,h]=g.useState(""),[y,b]=g.useState(""),S=Number(s)<=Number(c);return ie.default.createElement(ze,{open:!0,title:"Add new child feature",handleClose:n,maxWidth:!1,"data-testid":"add-feature-dialog"},ie.default.createElement("form",{onSubmit:async function(a){a.preventDefault(),h("");const i=new t.AddFeatureChange({changedIds:[r._id],typeName:"AddFeatureChange",assembly:o,addedFeature:{_id:(new se.default).toHexString(),refSeq:r.refSeq,min:Number(c)-1,max:Number(s),type:f},parentFeatureId:r._id});await e.submit(i),l("Feature added 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0}),ie.default.createElement(d.MenuItem,{value:1},"+"),ie.default.createElement(d.MenuItem,{value:-1},"-")))),ie.default.createElement(d.DialogActions,null,ie.default.createElement(d.Button,{variant:"contained",type:"submit",disabled:b||!(i&&l&&u)},"Submit"),ie.default.createElement(d.Button,{variant:"outlined",type:"submit",onClick:n},"Cancel"))),h?ie.default.createElement(d.DialogContent,null,ie.default.createElement(d.DialogContentText,{color:"error"},h)):null)}function Tt(e,t){const n=(new se.default).toHexString();t.push(n);const a={};if(e.children)for(const n of Object.values(e.children)){const e=Tt(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 At({changeManager:e,handleClose:a,session:o,sourceAssemblyId:r,sourceFeature:l}){const{assemblyManager:s,notify:c}=o,u=s.assemblyList,[f,m]=g.useState(u.find((e=>e.name!==r))?.name),[p,h]=g.useState([]),[y,b]=g.useState(""),[S,w]=g.useState(l.min),[E,v]=g.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=y,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 g.useEffect((()=>{b(""),async function(){if(!f)return void v("No assemblies to copy to");const e=await s.waitForAssembly(f);if(!e)return;const{refNameAliases:t}=e;if(!t)return;const n=[...Object.entries(t)].filter((([e,t])=>e!==t)).map((([e,t])=>({_id:e,name:t})));h(n),b(n[0]?._id||"")}().catch((e=>{v(String(e))}))}),[f,s]),ie.default.createElement(ze,{open:!0,title:"Copy features and 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0===r&&l(w[0])}),[w,r]),ie.default.createElement(ze,{open:!0,title:"Delete Assembly",handleClose:n,maxWidth:!1,"data-testid":"delete-assembly"},ie.default.createElement("form",{onSubmit:async function(a){if(a.preventDefault(),p(!0),c(""),!r)return void c("Must select assembly!");const o=new t.DeleteAssemblyChange({typeName:"DeleteAssemblyChange",assembly:r.name});await e.submit(o,{internetAccountId:y.internetAccountId}),n(),a.preventDefault()}},ie.default.createElement(d.DialogContent,{style:{display:"flex",flexDirection:"column"}},h.length>1?ie.default.createElement(ie.default.Fragment,null,ie.default.createElement(d.DialogContentText,null,"Select account"),ie.default.createElement(d.Select,{value:y.internetAccountId,onChange:function(e){p(!1);const t=h.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID 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g.useEffect((()=>{i&&(async()=>{const{internetAccountConfigId:e}=n.getConf(i,["sequence","metadata"]),t=C(i.name,e);if(!t)throw new Error("No Apollo internet account found");const{baseURL:a}=t,o=new URL("features/count",a),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 Ge(s));{const e=await s.json();y(e.count)}E(!1)})().catch((e=>{console.error(e),f(e.message??e)}))}),[C,o,i]),ie.default.createElement(ze,{open:!0,title:"Import Features from GFF3 file",handleClose:a,maxWidth:!1,"data-testid":"import-features-dialog"},w?ie.default.createElement(Se.default,null):null,ie.default.createElement("form",{onSubmit:async function(r){r.preventDefault(),f(""),E(!0),p(!0);let s="";if(!l)return void f("must select a file");if(!i)return void f("Must select assembly to 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e.submit(x,{updateJobsManager:!0})}},ie.default.createElement(d.DialogContent,{style:{display:"flex",flexDirection:"column"}},ie.default.createElement(d.DialogContentText,null,"Select assembly"),ie.default.createElement(d.Select,{labelId:"label",value:i?.name??"",onChange:function(e){const t=x.find((t=>t.name===e.target.value));c(t),p(!1)},disabled:m&&!u},x.map((e=>ie.default.createElement(d.MenuItem,{key:e.name,value:e.name},e.displayName??e.name))))),ie.default.createElement(d.DialogContent,{style:{display:"flex",flexDirection:"column"}},ie.default.createElement(d.DialogContentText,null,"Upload GFF3 to load features"),ie.default.createElement("input",{type:"file",onChange:function(e){p(!1),e.target.files&&s(e.target.files[0])},disabled:m&&!u})),h&&h>0?ie.default.createElement(d.DialogContent,null,ie.default.createElement(d.DialogContentText,null,"This assembly already has ",h," features, would you like to delete the existing features before importing new 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out",handleClose:e,maxWidth:!1,"data-testid":"log-out"},ie.default.createElement("form",{onSubmit:function(e){e.preventDefault(),o(""),l.removeToken(),globalThis.location.reload()}},ie.default.createElement(d.DialogContent,{style:{display:"flex",flexDirection:"column"}},r.length>1?ie.default.createElement(ie.default.Fragment,null,ie.default.createElement(d.DialogContentText,null,"Select account"),ie.default.createElement(d.Select,{value:l.internetAccountId,onChange:function(e){const t=r.find((t=>t.internetAccountId===e.target.value));if(!t)throw new Error(`Could not find internetAccount with ID "${e.target.value}"`);s(t)}},n.map((e=>ie.default.createElement(d.MenuItem,{key:e.id,value:e.internetAccountId},e.name))))):null,ie.default.createElement(d.DialogContentText,null,"Are you sure you want to log out?")),ie.default.createElement(d.DialogActions,null,ie.default.createElement(d.Button,{disabled:!l,variant:"contained",type:"submit"},"Log 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qt({handleClose:e,session:t}){const{apolloDataStore:n}=t,{addAssembly:a,addSessionAssembly:o,assemblyManager:l,notify:s}=t,[i,c]=g.useState(null),[u,f]=g.useState(""),[m,p]=g.useState(""),[h,y]=g.useState(!1),b=d.useTheme();return ie.default.createElement(ze,{open:!0,title:"Open local GFF3 file",handleClose:e,maxWidth:!1,"data-testid":"open-local-file"},ie.default.createElement("form",{onSubmit:async function(c){if(c.preventDefault(),p(""),y(!0),!i)throw new Error("No file selected");const d=await new Response(i).text(),f=`${u}-${i.name}-${q.nanoid(8)}`;try{await Be(f,d,n)}catch(t){return console.error(t),s(`Error loading GFF3 ${i.name}, ${String(t)}`,"error"),void e()}const m={name:f,aliases:[u],displayName:u,sequence:{trackId:`sequenceConfigId-${u}`,type:"ReferenceSequenceTrack",adapter:{type:"ApolloSequenceAdapter",assemblyId:f},metadata:{apollo:!0,...r.isElectron?{file:i.path}:{}}}};await(o||a)(m);const g=await l.waitForAssembly(m.name);g?(t.addApolloTrackConfig(g),s(`Loaded GFF3 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o=e.session.apolloDataStore.getBackendDriver(a.assemblyName);if(!o)throw new Error("Failed to get the backend driver");const{seq:l}=await o.getSequence(a);if(!l)return;for(const[o,s]of[...l].entries()){const i=(e.lgv.bpToPx({refName:a.refName,coord:a.start+o,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx,c=3/e.lgv.bpPerPx,u=e.lgv.displayedRegions[n].reversed?i-c:i;for(let n=2;n>=0;n--)(a.start+o)%3===n&&eo(t,e.lgv.bpPerPx,u,e.sequenceRowHeight*(2-n),c,e.sequenceRowHeight,l,o,!1);if(e.lgv.bpPerPx<=1){const l=(e.lgv.bpToPx({refName:a.refName,coord:a.start+o,regionNumber:n})?.offsetPx??0)-e.lgv.offsetPx,i=1/e.lgv.bpPerPx,c=e.lgv.displayedRegions[n].reversed?l-i:l;t.beginPath(),t.fillStyle=Ka(s,e.theme),t.rect(c,3*e.sequenceRowHeight,i,e.sequenceRowHeight),t.fill(),e.lgv.bpPerPx<=.1&&(t.stroke(),Qa(t,c,i,s,3*e.sequenceRowHeight));const 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o.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() 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n=e.getMousePosition(t);to(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,o).props({tabularEditor:i.types.optional(ya,{})}).named("LinearApolloDisplay")}const lo=f.makeStyles()((e=>({canvasContainer:{position:"relative",left:0},canvas:{position:"absolute",left:0},ellipses:{textOverflow:"ellipsis",overflow:"hidden"},avatar:{position:"absolute",color:e.palette.warning.light,backgroundColor:e.palette.warning.contrastText},loading:{position:"absolute",right:e.spacing(3),zIndex:10,pointerEvents:"none",textAlign:"right"}}))),so=y.observer((function(e){const t=d.useTheme(),{model:n}=e,{loading:a,apolloDragging:o,apolloRowHeight:l,contextMenuItems:s,cursor:i,featuresHeight:c,isShown:u,onMouseDown:f,onMouseLeave:m,onMouseMove:h,onMouseUp:y,regionCannotBeRendered:b,session:S,setCanvas:w,setCollaboratorCanvas:E,setOverlayCanvas:v,setSeqTrackCanvas:C,setSeqTrackOverlayCanvas:x,setTheme:T}=n,{classes:A}=lo(),k=r.getContainingView(n);g.useEffect((()=>{T(t)}),[t,T]);const[N,D]=g.useState(),[F,R]=g.useState([]),I=b();if(!u)return null;const{assemblyManager:M}=S;return ie.default.createElement(ie.default.Fragment,null,k.bpPerPx<=3?ie.default.createElement("div",{className:A.canvasContainer,style:{width:k.dynamicBlocks.totalWidthPx,height:k.bpPerPx<=1?125:95}},ie.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),C(e)},width:k.dynamicBlocks.totalWidthPx,height:k.bpPerPx<=1?125:95,className:A.canvas,"data-testid":"seqTrackCanvas"}),ie.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),x(e)},width:k.dynamicBlocks.totalWidthPx,height:k.bpPerPx<=1?125:95,className:A.canvas,"data-testid":"seqTrackOverlayCanvas"})):null,ie.default.createElement("div",{className:A.canvasContainer,style:{width:k.dynamicBlocks.totalWidthPx,height:c},onContextMenu:e=>{if(e.preventDefault(),F.length>0)R([]);else{const t=[e.clientX,e.clientY];D(t),R(s(t))}}},a?ie.default.createElement("div",{className:A.loading},ie.default.createElement(d.CircularProgress,{size:"18px"})):null,I?ie.default.createElement(d.Alert,{severity:"warning",classes:{message:A.ellipses}},ie.default.createElement(d.Tooltip,{title:I},ie.default.createElement("div",null,I))):ie.default.createElement(ie.default.Fragment,null,ie.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),E(e)},width:k.dynamicBlocks.totalWidthPx,height:c,className:A.canvas,"data-testid":"collaboratorCanvas"}),ie.default.createElement("canvas",{ref:async e=>{await Promise.resolve(),w(e)},width:k.dynamicBlocks.totalWidthPx,height:c,className:A.canvas,"data-testid":"canvas"}),ie.default.createElement("canvas",{ref:async e=>{await 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ie.default.createElement("div",{style:{position:"absolute",left:0,top:t/2,width:"100%"}},ie.default.createElement("hr",{style:{margin:0,top:0,color:"black"}}))})),co=f.makeStyles()((e=>({shading:{background:d.alpha(e.palette.primary.main,.2),overflowY:"scroll",overflowX:"hidden"},details:{background:e.palette.background.paper},accordionControl:{height:12,width:"100%","&:hover":{background:e.palette.action.hover},display:"flex",alignItems:"center",justifyContent:"center"},accordionRoot:{background:e.palette.divider},resizeHandle:{width:"100%",height:4,position:"absolute",cursor:"row-resize",zIndex:100},expandIcon:{},title:{userSelect:"none"},alertContainer:{display:"flex",alignItems:"center",justifyContent:"center"}}))),uo=({onResize:e})=>{const{classes:t}=co(),n=g.useCallback((t=>{t.stopPropagation(),t.preventDefault(),e(t.movementY)}),[e]),a=g.useCallback((e=>{e.stopPropagation(),e.preventDefault(),globalThis.removeEventListener("mousemove",n),globalThis.removeEventListener("mouseup",a),globalThis.removeEventListener("mouseleave",a)}),[n]);return ie.default.createElement("div",{onMouseDown:e=>{e.stopPropagation(),globalThis.addEventListener("mousemove",n),globalThis.addEventListener("mouseup",a),globalThis.addEventListener("mouseleave",a)},onClick:e=>{e.stopPropagation(),e.preventDefault()},className:t.resizeHandle})},fo=y.observer((function({onClick:e,onResize:t,open:n,title:a}){const{classes:o}=co();return ie.default.createElement("div",{className:o.accordionRoot},n&&t?ie.default.createElement(uo,{onResize:t}):null,ie.default.createElement("div",{className:o.accordionControl,onClick:e},ie.default.createElement(n?qe.default:Te.default,{className:o.expandIcon}),a?ie.default.createElement(d.Typography,{className:o.title,variant:"caption",component:"span"},a):null))})),mo=y.observer((function({model:e,...t}){const n=r.getSession(e),{ontologyManager:a}=n.apolloDataStore,{featureTypeOntology:o}=a,l=o?.dataStore,{classes:s}=co(),{graphical:i,height:c,isShown:u,selectedFeature:f,table:m,tabularEditor:p,toggleShown:h}=e,y=g.useRef(null);g.useEffect((()=>{!function(e,t){const{apolloRowHeight:n,selectedFeature:a}=e;if(t.current&&a){const o=e.getFeatureLayoutPosition(a);o&&t.current.scroll({top:(o.layoutRow+o.featureRow)*n,behavior:"smooth"})}}(e,y)}),[e,f]);const b=t=>{e.setDetailsHeight(e.detailsHeight-t)};if(!l)return ie.default.createElement("div",{className:s.alertContainer},ie.default.createElement(d.Alert,{severity:"error"},"Could not load feature type ontology."));if(i&&m){const n=p.isShown?e.detailsHeight:0,a=u?c-e.detailsHeight-24:0;return ie.default.createElement("div",{style:{height:c}},ie.default.createElement(fo,{open:u,title:"Graphical",onClick:h}),ie.default.createElement("div",{className:s.shading,ref:y,style:{height:a}},ie.default.createElement(so,{model:e,...t})),ie.default.createElement(fo,{title:"Table",open:p.isShown,onClick:p.togglePane,onResize:b}),ie.default.createElement("div",{className:s.details,style:{height:n}},ie.default.createElement(ha,{model:e})))}return i?ie.default.createElement("div",{className:s.shading,ref:y,style:{height:c}},ie.default.createElement(so,{model:e,...t})):ie.default.createElement("div",{className:s.details,style:{height:c}},ie.default.createElement(ha,{model:e}))})),go=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 po{clientStore;constructor(e){this.clientStore=e}}class ho{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: "${f.resultsMessages}"`;return s&&u.abortJob(d.name,e),void i.notify(e,"error")}try{await n.execute(this.dataStore)}catch(e){return s&&u.abortJob(d.name,String(e)),console.error(e),void i.notify(String(e),"error")}if((await t.validationRegistry.frontendPostValidate(n,this.dataStore)).ok||await this.revert(n),l){s&&u.update(d.name,"Submitting to driver");const{collaborationServerDriver:t,getBackendDriver:o}=this.dataStore,r=e.isAssemblySpecificChange(n)?o(n.assembly):t;let l;try{l=await r.submitChange(n,a)}catch(e){return s&&u.abortJob(d.name,String(e)),console.error(e),i.notify(String(e),"error"),void await this.revert(n,!1)}if(!l.ok){const e=`Post-validation failed: "${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 yo extends po{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 Ge(s,"searchFeatures failed");throw new Error(e)}return s.json()}async getFeatures(e){const{assemblyName:t,end:a,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 "${t}"`);const{ids:c}=n.getConf(i,["sequence","metadata"]),u=c[o];if(!u)throw new Error(`Could not find refSeq "${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(a)});m.search=g.toString();const p=m.toString(),h=await this.fetch(d,p);if(!h.ok){const e=await Ge(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 ho(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}-${e.end}`,a=this.inFlight.get(t),{assemblyName:o,end:l,refName:s,start:i}=e,{assemblyManager:c}=r.getSession(this.clientStore),u=c.get(o);if(!u)throw new Error(`Could not find assembly with name "${o}"`);const{ids:d}=n.getConf(u,["sequence","metadata"]),f=d[s];if(!f)throw new Error(`Could not find refSeq "${s}"`);if(a)return{seq:await a,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 a=n.getConf(t,["sequence","metadata"]);return!(!(a&&a.apollo&&a.internetAccountConfigId)||e&&a.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 Ge(s,"submitChange failed");throw new Error(e)}const i=new t.ValidationResultSet;return s.ok||(i.ok=!1),i}}class bo extends po{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=n.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 So extends po{async loadAssembly(e){const{assemblyManager:t}=r.getSession(this.clientStore),a=t.get(e);if(!a)throw new Error(`Assembly ${e} not found`);const{file:o}=n.getConf(a,["sequence","metadata"]),l=require("node:fs");return Be(e,await l.promises.readFile(o,"utf8"),this.clientStore)}async getAssembly(e){let t=this.clientStore.assemblies.get(e);return t||(t=await this.loadAssembly(e)),t}async getRefNameAliases(e){const t=await this.getAssembly(e),n=[];for(const[,e]of t.refSeqs)n.push({refName:e.name,aliases:[e._id],uniqueId:`alias-${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 ${a} not found in client data store`);return{seq:r.getSequence(o,n),refSeq:a}}async getRegions(e){const t=await this.getAssembly(e),n=[];for(const[,a]of t.refSeqs)n.push({assemblyName:e,refName:a.name,start:a.sequence[0].start,end:a.sequence[0].stop});return n}getAssemblies(){const{assemblyManager:e}=r.getSession(this.clientStore);return e.assemblies.filter((e=>{const t=n.getConf(e,["sequence","metadata"]);return Boolean(t&&t.apollo&&!t.internetAccountConfigId&&t.file)}))}async submitChange(a){if(!e.isAssemblySpecificChange(a))throw new Error(`Cannot use this type of change with local file: "${a.typeName}"`);const{assemblyManager:o}=r.getSession(this.clientStore),l=o.get(a.assembly);if(!l)throw new Error(`Could not find assembly with name "${a.assembly}"`);const{file:s}=n.getConf(l,["sequence","metadata"]),c=this.clientStore.assemblies.get(a.assembly);if(!c)throw new Error(`Could not find assembly in client with name "${a.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 ${e.sequence[0].stop}`});for(const e of c.comments)m.push({comment:e});for(const[,e]of c.refSeqs){const{features:n}=e;for(const[,e]of n)m.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const[,e]of c.refSeqs){const[n]=e.sequence,a=t.splitStringIntoChunks(n.sequence,80).join("\n");m.push({id:e.name,description:e.description,sequence:a})}const g=le.default.formatSync(m),p=require("node:fs");return await p.promises.writeFile(s,g,"utf8"),new t.ValidationResultSet}async searchFeatures(e,t){return[]}}function wo(e,a){const o=new AbortController,{signal:l}=o,c=e.evaluateExtensionPoint("Apollo-extendAnnotationFeature",z.AnnotationFeatureModel),u=function(e){return i.types.model("ClientDataStore",{typeName:i.types.optional(i.types.literal("Client"),"Client"),assemblies:i.types.map(z.ApolloAssembly),checkResults:i.types.map(z.CheckResult),ontologyManager:i.types.optional(ht,{})}).views((t=>({get internetAccounts(){return i.getRoot(t).internetAccounts},get pluginConfiguration(){return i.getRoot(t).jbrowse.configuration.ApolloPlugin},getFeature:n=>i.resolveIdentifier(e,t.assemblies,n)}))).actions((e=>({addAssembly(t,n){const a={_id:t,refSeqs:{}};return n&&(a.backendDriverType=n),e.assemblies.put(a)},addFeature(t,n){const a=e.assemblies.get(t);if(!a)throw new Error(`Could not find assembly "${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,z.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 ho(e),collaborationServerDriver:new yo(e),inMemoryFileDriver:new bo(e),desktopFileDriver:r.isElectron?new So(e):void 0}))).actions((e=>({afterCreate(){i.addDisposer(e,s.autorun((()=>{const{ontologyManager:t,pluginConfiguration:a}=e,o=a.ontologies;for(const a of o||[]){const[o,l,s,i]=[n.readConfObject(a,"name"),n.readConfObject(a,"version"),n.readConfObject(a,"source"),n.readConfObject(a,"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 a=r.getSession(e),{assemblyManager:o}=a,l=o.get(t);if(!l)return e.collaborationServerDriver;const{file:s,internetAccountConfigId:i}=n.getConf(l,["sequence","metadata"]);return r.isElectron&&s?e.desktopFileDriver:i?e.collaborationServerDriver:e.inMemoryFileDriver},getInternetAccount(t,a){if(!(t??a))throw new Error("Must provide either assemblyName or internetAccountId");let o=a;if(t&&!o){const{assemblyManager:a}=r.getSession(e),l=a.get(t);if(!l)throw new Error(`No assembly found with name ${t}`);({internetAccountConfigId:o}=n.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 ${a}`);return s}}))).actions((e=>({loadFeatures:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const[a,o]=yield t.getFeatures(n);if(0===a.length)continue;const{assemblyName:r,refName:l}=n;let s=e.assemblies.get(r);s||(s=e.assemblies.put({_id:r,refSeqs:{}}));const[i]=a;let c=s.refSeqs.get(i.refSeq);c||(c=s.refSeqs.put({_id:i.refSeq,name:l,features:{}}));for(const e of a)c.features.has(e._id)||c.features.put(e);e.addCheckResults(o)}})),loadRefSeq:i.flow((function*(t){for(const n of t){const t=e.getBackendDriver(n.assemblyName);if(!t)return;const{refSeq:a,seq:o}=yield t.getSequence(n),{assemblyName:r,end:l,refName:s,start:i}=n;let c=e.assemblies.get(r);c||(c=e.assemblies.put({_id:r,refSeqs:{}}));let u=c.refSeqs.get(a);u||(u=c.refSeqs.put({_id:a,name:s,sequence:[]})),u.addSequence({start:i,stop:l,sequence:o})}}))})))}(c),d=a.props({apolloDataStore:i.types.optional(u,{typeName:"Client"}),apolloSelectedFeature:i.types.safeReference(c),jobsManager:i.types.optional(go,{})}).extend((()=>{const e=s.observable.array([]);return{views:{get collaborators(){return e}},actions:{addOrUpdateCollaborator(t){const n=e.find((e=>e.id===t.id));n?n.locations=t.locations:e.push(t)}}}})).actions((e=>({apolloSetSelectedFeature(t){e.apolloSelectedFeature=t},addApolloTrackConfig(t,a){const o=`apollo_track_${t.name}`;e.tracks.some((e=>e.trackId===o))||e.addTrackConf({type:"ApolloTrack",trackId:o,name:`Annotations (${n.getConf(t,"displayName")||t.name})`,assemblyNames:[t.name],textSearching:{textSearchAdapter:{type:"ApolloTextSearchAdapter",trackId:o,assemblyNames:[t.name],textSearchAdapterId:`apollo_search_${t.name}`,...a?{baseURL:{uri:a,locationType:"UriLocation"}}:{}}},displays:[{type:"LinearApolloDisplay",displayId:`${o}-LinearApolloDisplay`},{type:"SixFrameFeatureDisplay",displayId:`${o}-SixFrameFeatureDisplay`}]})},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 Ge(c,"Failed to fetch assemblies");console.error(e)}}})),beforeDestroy(){o.abort("destroying session model")}}))).views((e=>{const a=e.getTrackActionMenuItems;return{getTrackActionMenuItems(o){if("ApolloTrack"===o.type||"ReferenceSequenceTrack"===o.type)return a?.(o);const r=n.readConfObject(o,"trackId");return r.endsWith("-sessionTrack")?[...a?.(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}]:[...a?.(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 Eo={0:2,1:1,2:0},vo={3:0,4:1,5:2};function Co(e,t){const a=e.getPlugin("LinearGenomeViewPlugin"),{BaseLinearDisplay:o}=a.exports;return o.named("SixFrameFeatureDisplay").props({type:i.types.literal("SixFrameFeatureDisplay"),configuration:n.ConfigurationReference(t),apolloRowHeight:20,detailsMinHeight:200,showStartCodons:!1,showStopCodons:!0,showIntronLines:!0}).volatile((()=>({apolloFeatureUnderMouse:void 0,apolloRowUnderMouse:void 0}))).views((e=>{const{configuration:t,renderProps:n}=e;return{renderProps:()=>({...n(),...K.getParentRenderProps(e),config:t.renderer})}})).views((e=>({get regions(){let t;try{({blockDefinitions:t}=e)}catch{return[]}return t.contentBlocks.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))},regionCannotBeRendered(){const t=r.getContainingView(e);if(t&&t.bpPerPx>=200)return"Zoom in to see annotations"},get session(){return r.getSession(e)}}))).actions((e=>{let t=[];return{afterAttach(){i.addDisposer(e,s.autorun((()=>{const n=r.getSession(e);if(r.getContainingView(e).initialized){if(e.regionCannotBeRendered())return;const a=[],o=[];for(const n of e.blockDefinitions.contentBlocks)a.push(n.key),t.includes(n.key)||o.push(n);n.apolloDataStore.loadFeatures(o.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))),n.apolloDataStore.loadRefSeq(o.map((({assemblyName:e,end:t,refName:n,start:a})=>({assemblyName:e,refName:n,start:a,end:t})))),t=a}}),{name:"SixFrameFeatureDisplay"}))}}})).views((e=>({get rendererTypeName(){return e.configuration.renderer.type},get changeManager(){return r.getSession(e).apolloDataStore.changeManager},get sequence(){const{regions:t}=e,n=r.getSession(e),a=new Map;for(const e of t){const t=n.apolloDataStore.assemblies.get(e.assemblyName),o=t?.getByRefName(e.refName),r=o?.getSequence(e.start,e.end);a.set(e.start,r??"")}return a},get features(){const{regions:t}=e,n=r.getSession(e),a=new Map;for(const e of t){const t=n.apolloDataStore.assemblies.get(e.assemblyName),o=t?.getByRefName(e.refName);let r=a.get(e.refName);r||(r=new Map,a.set(e.refName,r));for(const[t,n]of o?.features.entries()??new Map)e.start<n.end&&e.end>n.start&&r.set(t,n)}return a},get featuresMinMax(){const e={};for(const[t,n]of this.features||[]){let a,o;for(const[,e]of n)void 0===a&&({min:a}=e),void 0===o&&({max:o}=e),e.min<a&&({min:a}=e),e.max>o&&({max:o}=e);void 0!==a&&void 0!==o&&(e[t]=[a,o])}return e},get codonLayout(){const e=new Map;let t="",n=0;for(const[e,a]of this.sequence||[])a&&(t||(n=e),t+=a);for(let a=0;a<6;a++){const o=[],l=[],s=a in vo;let i,c,u;s?(i=(t.length+n)%3,c=(vo[a]+i+3)%3,u=r.reverse(t).slice(c)):(i=3-n%3,c=(Eo[a]+i+3)%3,u=t.slice(c));for(let e=0;e<u.length;e+=3){const t=u.slice(e,e+3),a=s?r.reverse(r.revcom(t)):t,i=s?n+u.length-(3+e):n+e+c;r.defaultStarts.includes(a.toUpperCase())?o.push(i):r.defaultStops.includes(a.toUpperCase())&&l.push(i)}e.set(a,{starts:o,stops:l})}return e},get featureLayout(){const{featureTypeOntology:t}=e.session.apolloDataStore.ontologyManager;if(!t)throw new Error("featureTypeOntology is undefined");const n=new Map;for(const[e,a]of this.features||[]){if(!a)continue;const o=this.featuresMinMax[e];if(!o)continue;const[r,l]=o,s=[],i=6;for(let e=0;e<i;e++){const e=s.length;s[e]=Array.from({length:l-r}),n.set(e,[])}for(const e of[...a.values()].sort(((e,t)=>{const{max:n,min:a}=e,{max:o,min:r}=t;return a-r||n-o})))for(const[,a]of e.children??new Map)if(t.isTypeOf(a.type,"transcript")||t.isTypeOf(e.type,"pseudogenic_transcript"))for(const[,o]of a.children||new Map){let r;if(t.isTypeOf(o.type,"CDS")){let t;o.discontinuousLocations.length>0?({discontinuousLocations:t}=o):t=[o];for(const o of t){const t=o.start+3,l=o.end-3;for(const[s,{stops:i}]of this.codonLayout)if((s<3&&1===e.strand||s>=3&&-1===e.strand)&&0===i.filter((e=>e>=t&&e<=l)).length){r=s;const e=n.get(r);e?.push([a.featureId,o]);break}}}}}return n},getAssemblyId(t){const{assemblyManager:n}=r.getSession(e),a=n.get(t);if(!a)throw new Error(`Could not find assembly named ${t}`);return a.name},get selectedFeature(){return r.getSession(e).apolloSelectedFeature},get setSelectedFeature(){return r.getSession(e).apolloSetSelectedFeature}}))).actions((e=>({setSelectedFeature(t){r.getSession(e).apolloSetSelectedFeature(t)},setApolloFeatureUnderMouse(t){e.apolloFeatureUnderMouse=t},setApolloRowUnderMouse(t){e.apolloRowUnderMouse=t},toggleShowStartCodons(){e.showStartCodons=!e.showStartCodons},toggleShowStopCodons(){e.showStopCodons=!e.showStopCodons},toggleShowIntronLines(){e.showIntronLines=!e.showIntronLines}}))).views((e=>({get highestRow(){return 0===e.featureLayout.size?0:Math.max(...e.featureLayout.keys())},get featuresHeight(){return(this.highestRow+1)*e.apolloRowHeight},get detailsHeight(){return Math.max(e.detailsMinHeight,e.height-this.featuresHeight)},trackMenuItems:()=>[{label:"Show start codons",type:"checkbox",checked:e.showStartCodons,onClick:()=>{e.toggleShowStartCodons()}},{label:"Show stop codons",type:"checkbox",checked:e.showStopCodons,onClick:()=>{e.toggleShowStopCodons()}},{label:"Show intron lines",type:"checkbox",checked:e.showIntronLines,onClick:()=>{e.toggleShowIntronLines()}}]})))}var xo=n.ConfigurationSchema("ApolloRefNameAliasAdapter",{assemblyId:{type:"string",defaultValue:""}},{explicitlyTyped:!0});const To="undefined"==typeof sessionStorage;class Ao extends O.BaseAdapter{refNameAliases;async getRefNameAliases(){const e=n.readConfObject(this.config,"assemblyId");if(!To){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=q.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(){}}const ko="WorkerGlobalScope"in globalThis;for(const[n,a]of Object.entries(t.changes))e.changeRegistry.registerChange(n,a);const No=new t.CDSCheck;e.checkRegistry.registerCheck(No.name,No),t.validationRegistry.registerValidation(new t.CoreValidation),t.validationRegistry.registerValidation(new t.ParentChildValidation),exports.default=class extends oe.default{name="ApolloPlugin";version="0.3.5";configurationSchema=sn;install(e){!function(e){e.addAdapterType((()=>new ve.default({name:"ApolloSequenceAdapter",configSchema:en,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Qt})))}(e),function(e){e.addAdapterType((()=>new ve.default({name:"ApolloRefNameAliasAdapter",configSchema:xo,adapterMetadata:{category:void 0,hiddenFromGUI:!0,description:void 0},AdapterClass:Ao})))}(e),function(e){e.addTextSearchAdapterType((()=>new a.TextSearchAdapterType({name:"ApolloTextSearchAdapter",displayName:"Apollo text search adapter",configSchema:ln,AdapterClass:rn,description:"Apollo Text Search adapter"})))}(e),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloFeatureDetailsWidget",{});return new a.WidgetType({name:"ApolloFeatureDetailsWidget",heading:"Apollo feature details",configSchema:e,stateModel:Bn,ReactComponent:On})})),e.addWidgetType((()=>{const e=n.ConfigurationSchema("ApolloTranscriptDetails",{});return new a.WidgetType({name:"ApolloTranscriptDetails",heading:"Apollo transcript details",configSchema:e,stateModel:_n,ReactComponent:Qn})})),e.addTrackType((()=>{const t=n.ConfigurationSchema("ApolloTrack",{adapter:""},{baseConfiguration:a.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new a.TrackType({name:"ApolloTrack",configSchema:t,stateModel:a.createBaseTrackModel(e,"ApolloTrack",t)})})),e.addInternetAccountType((()=>new a.InternetAccountType({name:"ApolloInternetAccount",configSchema:Oe,stateModel:Zt(Oe)}))),e.addDisplayType((()=>new a.DisplayType({name:"LinearApolloDisplay",configSchema:ea,stateModel:ro(0,ea),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:mo}))),e.addDisplayType((()=>{const t=function(e){const t=e.getPlugin("LinearGenomeViewPlugin"),{baseLinearDisplayConfigSchema:a}=t.exports;return n.ConfigurationSchema("SixFrameFeatureDisplay",{renderer:an,height:{type:"number",defaultValue:120}},{baseConfiguration:a,explicitlyTyped:!0})}(e),o=function(e){const t=e.getPlugin("LinearGenomeViewPlugin");if(!t)throw new Error("LinearGenomeView plugin not found");const{BaseLinearDisplayComponent:n}=t.exports;return y.observer((function({model:e,...t}){const{classes:a}=co(),{height:o,selectedFeature:r}=e;let{detailsHeight:l}=e;return r||(l=0),ie.default.createElement("div",{style:{height:e.height}},ie.default.createElement("div",{className:a.shading,style:{height:o-l}},ie.default.createElement(n,{model:e,...t})),ie.default.createElement("div",{className:"testTrackLines"},ie.default.createElement(io,{model:e})))}))}(e);return new a.DisplayType({name:"SixFrameFeatureDisplay",configSchema:t,stateModel:Co(e,t),trackType:"ApolloTrack",viewType:"LinearGenomeView",ReactComponent:o})})),e.addRendererType((()=>new on({name:"ApolloSixFrameRenderer",ReactComponent:nn,configSchema:an,pluginManager:e}))),e.addToExtensionPoint("Core-extendSession",wo.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:re.default,onClick:()=>{const t=r.getSession(e),{leftOffset:n,rightOffset:a}=e,o=e.getSelectedRegions(n,a);t.queueDialog((e=>[xt,{session:t,handleClose:()=>{e()},region:o[0],changeManager:t.apolloDataStore.changeManager}]))}}]}}));e.stateModel=n}return e})),e.addToExtensionPoint("Core-extendPluggableElement",cn),e.addToExtensionPoint("Core-extendPluggableElement",Sn),ko||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=>[Pt,{session:e,handleClose:()=>{t()}}]))}}),e.rootModel.appendToMenu("Apollo",{label:"Open local GFF3 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s)x.checkAbortSignal(n),i.push(...ot(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 ot(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=[...tt(Ze(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 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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 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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 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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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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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0===r&&l(w[0])}),[w,r]),de.default.createElement(We,{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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c=[{directive:"gff-version",value:"3"}],u=a.getConf(o,["sequence","adapter","features"]);for(const e of u){const{end:t,refName:n,start:a}=e;c.push({directive:"sequence-region",value:`${n} ${a+1} ${t}`})}for(const[,e]of l){const{features:n}=e;if(n)for(const[,e]of n)c.push(t.annotationFeatureToGFF3(i.getSnapshot(e)))}for(const e of u){const{refName:t,seq:n}=e;c.push({id:t,description:"",sequence:n})}const d=re.default.formatSync(c),f=new Blob([d],{type:"text/plain;charset=utf-8"});F.saveAs(f,`${o.displayName??o.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:o?.name??"",onChange:function(e){const 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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()});v(!0);const s=await l(o.toString(),{method:"GET"});if(!s.ok)throw new Error(await je(s));{const e=await s.json();h(e.count)}v(!1)})().catch((e=>{console.error(e),d(e.message??e)}))}),[C,o,i]),de.default.createElement(We,{open:!0,title:"Import Features from GFF3 file",handleClose:n,maxWidth:!1,"data-testid":"import-features-dialog"},w?de.default.createElement(ye.default,null):null,de.default.createElement("form",{onSubmit:async function(r){r.preventDefault(),d(""),v(!0),m(!0);let s="";if(!l)return void d("must select a file");if(!i)return void d("Must select assembly to 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e.submit(x,{updateJobsManager:!0})}},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:i?.name??"",onChange:function(e){const t=x.find((t=>t.name===e.target.value));c(t),m(!1)},disabled:f&&!u},x.map((e=>de.default.createElement(p.MenuItem,{key:e.name,value:e.name},e.displayName??e.name))))),de.default.createElement(p.DialogContent,{style:{display:"flex",flexDirection:"column"}},de.default.createElement(p.DialogContentText,null,"Upload GFF3 to load 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 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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:"LinearApolloDisplayRenderCollaborators"}))}})))}(0,t);return n.actions((e=>({afterAttach(){i.addDisposer(e,s.autorun((()=>{const{theme:t}=e;if(!e.lgv.initialized||e.regionCannotBeRendered())return;const n=3/e.lgv.bpPerPx;if(n<1)return;const a=e.seqTrackCanvas?.getContext("2d");if(!a)return;a.clearRect(0,0,e.lgv.dynamicBlocks.totalWidthPx,e.lgv.bpPerPx<=1?125:95);const o=e.lgv.bpPerPx<=1?[3,2,1,0,0,-1,-2,-3]:[3,2,1,-1,-2,-3];let l=0;if(t)for(const n of o){let o=t.palette.framesCDS.at(n)?.main;if(o){let 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&&ja(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=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 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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 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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 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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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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()}}]))}}))}};
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