@cmdcolin/jbrowse-plugin-hubs 1.0.14 → 1.0.16

package/dist/configUrls.d.ts

@@ -0,0 +1 @@
+export declare function getConfigUrls(assemblyName: string): string[];

package/dist/configUrls.js

@@ -0,0 +1,44 @@
+function getGenArkConfigUrl(accession) {
+    const [base, rest] = accession.split('_');
+    if (!rest) {
+        return undefined;
+    }
+    const match = rest.match(/.{1,3}/g);
+    if (!match || match.length < 3) {
+        return undefined;
+    }
+    const [b1, b2, b3] = match;
+    return `https://jbrowse.org/hubs/genark/${base}/${b1}/${b2}/${b3}/${accession}/config.json`;
+}
+// Candidate urls for an assembly name, most preferred first. The connection
+// probe and the describe lookup each take the first that exists, so a name with
+// no hosted config anywhere is still answered by staying quiet.
+//
+// A UCSC db gets `minimal.json` ahead of `config.json`. Both carry the same
+// `assemblies` block (minimal.json is a filtered copy of config.json, tracks
+// dropped to NCBI RefSeq / GENCODE / RepeatMasker / gaps), and the assembly is
+// the whole reason this connection exists — the tracks are a bonus for the
+// panel it opens. The full config is an expensive way to learn a sequence
+// adapter: hg38 is 2.1MB against minimal's 300KB, hg19 1.35MB against 57KB,
+// hs1 603KB against 12KB, and the parse is followed by MST instantiating every
+// track config in it on the main thread (hg38 595 against 33, hs1 624 against
+// 7). hg38 alone names 239 distinct mate assemblies across its 239 synteny
+// tracks, so a session that opens a few of them pays this several times over.
+//
+// What minimal.json costs is the mate genome's long tail — conservation,
+// expression, the rest of the hub. Those are still one "Add connection" away
+// on the full config url, and nothing about this panel implied they were
+// coming. GenArk hubs have no minimal.json and don't need one; their whole
+// config is ~40KB.
+export function getConfigUrls(assemblyName) {
+    if (!/^[\w.]+$/.test(assemblyName)) {
+        return [];
+    }
+    if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {
+        const url = getGenArkConfigUrl(assemblyName);
+        return url ? [url] : [];
+    }
+    const base = `https://jbrowse.org/ucsc/${assemblyName}`;
+    return [`${base}/minimal.json`, `${base}/config.json`];
+}
+//# sourceMappingURL=configUrls.js.map

package/dist/configUrls.js.map

@@ -0,0 +1 @@
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package/dist/describeAssemblies.d.ts

@@ -0,0 +1,26 @@
+interface Description {
+    assembly: HubAssembly;
+    geneAdapter?: Record<string, unknown>;
+}
+interface HubAssembly {
+    name: string;
+    aliases?: string[];
+}
+interface HubConfig {
+    assemblies?: HubAssembly[];
+    tracks?: {
+        trackId: string;
+        adapter?: Record<string, unknown>;
+    }[];
+}
+export declare function describeFromConfig(config: HubConfig, assemblyName: string, configUrl: string): Description | undefined;
+/**
+ * Core-describeAssemblies: the assembly config and gene track adapter the
+ * hosted config of each named genome holds, read without connecting it. A
+ * name another plugin already described, or one no hosted config could hold,
+ * is left alone
+ */
+export declare function describeAssemblies(described: unknown, assemblyNames: unknown): Promise<{
+    [k: string]: Description | undefined;
+}>;
+export {};

package/dist/describeAssemblies.js

@@ -0,0 +1,91 @@
+import { getConfigUrls } from './configUrls';
+// jb2hubs' defaultGeneTrackId order, which also picks the track minimal.json
+// keeps and a hub genome's default session opens
+const GENE_TRACK_SUFFIXES = [
+    'ncbiRefSeq',
+    'ncbiRefSeqCurated',
+    'ncbiGene',
+    'refGene',
+    'ensGene',
+    'augustusGene',
+    'xenoRefGene',
+];
+// A TwoBit adapter's bare `chromSizes` resolves against the `baseUri` beside
+// its `uri`, so rewriting each `uri` alone sent jb2hubs' relative chrom.sizes
+// to the page's origin
+function withBaseUri(value, base) {
+    if (Array.isArray(value)) {
+        return value.map(item => withBaseUri(item, base));
+    }
+    if (typeof value === 'object' && value !== null) {
+        const entries = Object.entries(value).map(([key, item]) => [
+            key,
+            withBaseUri(item, base),
+        ]);
+        return Object.fromEntries(typeof value.uri === 'string' &&
+            !('baseUri' in value)
+            ? [...entries, ['baseUri', base]]
+            : entries);
+    }
+    return value;
+}
+export function describeFromConfig(config, assemblyName, configUrl) {
+    const assembly = config.assemblies?.find(a => a.name === assemblyName || a.aliases?.includes(assemblyName));
+    if (!assembly) {
+        return undefined;
+    }
+    const tracks = new Map(config.tracks?.map(track => [track.trackId, track]));
+    const geneAdapter = GENE_TRACK_SUFFIXES.map(suffix => tracks.get(`${assembly.name}-${suffix}`)?.adapter).find(adapter => adapter !== undefined);
+    return {
+        assembly: withBaseUri(assembly, configUrl),
+        geneAdapter: geneAdapter && withBaseUri(geneAdapter, configUrl),
+    };
+}
+// throws on anything but a found config or a 404, so only a definitive
+// answer is cached
+async function fetchDescription(assemblyName) {
+    for (const url of getConfigUrls(assemblyName)) {
+        const response = await fetch(url);
+        if (response.ok) {
+            const config = (await response.json());
+            return describeFromConfig(config, assemblyName, url);
+        }
+        if (response.status !== 404) {
+            throw new Error(`${url}: HTTP ${response.status}`);
+        }
+    }
+    return undefined;
+}
+const descriptions = new Map();
+function describe(assemblyName) {
+    let description = descriptions.get(assemblyName);
+    if (!description) {
+        description = fetchDescription(assemblyName).catch((error) => {
+            descriptions.delete(assemblyName);
+            console.error(error);
+            return undefined;
+        });
+        descriptions.set(assemblyName, description);
+    }
+    return description;
+}
+/**
+ * Core-describeAssemblies: the assembly config and gene track adapter the
+ * hosted config of each named genome holds, read without connecting it. A
+ * name another plugin already described, or one no hosted config could hold,
+ * is left alone
+ */
+export async function describeAssemblies(described, assemblyNames) {
+    const before = typeof described === 'object' && described !== null ? described : {};
+    const names = Array.isArray(assemblyNames)
+        ? assemblyNames.filter((name) => typeof name === 'string')
+        : [];
+    const answers = await Promise.all(names
+        .filter(name => !Object.hasOwn(before, name) && getConfigUrls(name).length > 0)
+        .map(async (name) => [name, await describe(name)]));
+    return {
+        ...before,
+        ...Object.fromEntries(answers.filter(([, description]) => description !== undefined)),
+    };
+}
+//# sourceMappingURL=describeAssemblies.js.map

package/dist/describeAssemblies.js.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -1,6 +1,8 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { isAbstractMenuManager, isElectron } from '@jbrowse/core/util';
 import { getRoot, getSnapshot } from '@jbrowse/mobx-state-tree';
+import { getConfigUrls } from './configUrls';
+import { describeAssemblies } from './describeAssemblies';
 import { saveAs, toDesktopSnapshot } from './util';
 import { version } from '../package.json';
 // Serializes the current web session as a desktop `.jbrowse` file. genomes
@@ -11,46 +13,6 @@ function downloadDesktopSession(session) {
     const snap = toDesktopSnapshot(getSnapshot(jbrowse), getSnapshot(session));
     saveAs(new Blob([JSON.stringify(snap, null, 2)], { type: 'application/json' }), 'session.jbrowse');
 }
-function getGenArkConfigUrl(accession) {
-    const [base, rest] = accession.split('_');
-    if (!rest) {
-        return undefined;
-    }
-    const match = rest.match(/.{1,3}/g);
-    if (!match || match.length < 3) {
-        return undefined;
-    }
-    const [b1, b2, b3] = match;
-    return `https://jbrowse.org/hubs/genark/${base}/${b1}/${b2}/${b3}/${accession}/config.json`;
-}
-// Candidate urls for an assembly name, most preferred first. The probe below
-// takes the first that exists, so a name with no hosted config anywhere is
-// still answered by staying quiet.
-//
-// A UCSC db gets `minimal.json` ahead of `config.json`. Both carry the same
-// `assemblies` block (minimal.json is a filtered copy of config.json, tracks
-// dropped to NCBI RefSeq / GENCODE / RepeatMasker / gaps), and the assembly is
-// the whole reason this connection exists — the tracks are a bonus for the
-// panel it opens. The full config is an expensive way to learn a sequence
-// adapter: hg38 is 2.1MB against minimal's 300KB, hg19 1.35MB against 57KB,
-// hs1 603KB against 12KB, and the parse is followed by MST instantiating every
-// track config in it on the main thread (hg38 595 against 33, hs1 624 against
-// 7). hg38 alone names 239 distinct mate assemblies across its 239 synteny
-// tracks, so a session that opens a few of them pays this several times over.
-//
-// What minimal.json costs is the mate genome's long tail — conservation,
-// expression, the rest of the hub. Those are still one "Add connection" away
-// on the full config url, and nothing about this panel implied they were
-// coming. GenArk hubs have no minimal.json and don't need one; their whole
-// config is ~40KB.
-function getConfigUrls(assemblyName) {
-    if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {
-        const url = getGenArkConfigUrl(assemblyName);
-        return url ? [url] : [];
-    }
-    const base = `https://jbrowse.org/ucsc/${assemblyName}`;
-    return [`${base}/minimal.json`, `${base}/config.json`];
-}
 // Every assembly name this plugin has already taken a run at, whether the probe
 // is still in flight or came back with nothing. The extension point fires on an
 // unresolved read, and `get` is read from render paths, so a name that resolves
@@ -161,6 +123,10 @@ export default class HubsViewerPlugin extends Plugin {
             // returning undefined would clobber another plugin's result.
             return defaultResult;
         });
+        // A multi-way synteny lane whose genome the session lacks asks here for
+        // its assembly config and gene track. Cores older than the point never
+        // fire it, so this is inert on them
+        pluginManager.addToExtensionPoint('Core-describeAssemblies', (described, args) => describeAssemblies(described, args.assemblyNames));
     }
     configure(pluginManager) {
         // jbrowse-web only. In desktop you'd just save the session, and an exported

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/jbrowse-plugin-hubs.umd.production.min.js

@@ -1,2 +1,2 @@
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+"use strict";var JBrowsePluginHubs=(()=>{var I=Object.create;var u=Object.defineProperty;var U=Object.getOwnPropertyDescriptor;var O=Object.getOwnPropertyNames;var P=Object.getPrototypeOf,G=Object.prototype.hasOwnProperty;var g=(n,e)=>()=>(e||n((e={exports:{}}).exports,e),e.exports),H=(n,e)=>{for(var t in e)u(n,t,{get:e[t],enumerable:!0})},w=(n,e,t,s)=>{if(e&&typeof e=="object"||typeof e=="function")for(let o of O(e))!G.call(n,o)&&o!==t&&u(n,o,{get:()=>e[o],enumerable:!(s=U(e,o))||s.enumerable});return n};var m=(n,e,t)=>(t=n!=null?I(P(n)):{},w(e||!n||!n.__esModule?u(t,"default",{value:n,enumerable:!0}):t,n)),B=n=>w(u({},"__esModule",{value:!0}),n);var h=g((Q,k)=>{k.exports=JBrowseExports["@jbrowse/core/Plugin"]});var y=g((Y,j)=>{j.exports=JBrowseExports["@jbrowse/core/util"]});var x=g((Z,A)=>{A.exports=JBrowseExports["mobx-state-tree"]});var V={};H(V,{default:()=>l});var $=m(h()),f=m(y()),a=m(x());function _(n){let[e,t]=n.split("_");if(!t)return;let s=t.match(/.{1,3}/g);if(!s||s.length<3)return;let[o,r,i]=s;return`https://jbrowse.org/hubs/genark/${e}/${o}/${r}/${i}/${n}/config.json`}function c(n){if(!/^[\w.]+$/.test(n))return[];if(n.startsWith("GCA_")||n.startsWith("GCF_")){let t=_(n);return t?[t]:[]}let e=`https://jbrowse.org/ucsc/${n}`;return[`${e}/minimal.json`,`${e}/config.json`]}var v=["ncbiRefSeq","ncbiRefSeqCurated","ncbiGene","refGene","ensGene","augustusGene","xenoRefGene"];function d(n,e){if(Array.isArray(n))return n.map(t=>d(t,e));if(typeof n=="object"&&n!==null){let t=Object.entries(n).map(([s,o])=>[s,d(o,e)]);return Object.fromEntries(typeof n.uri=="string"&&!("baseUri"in n)?[...t,["baseUri",e]]:t)}return n}function J(n,e,t){let s=n.assemblies?.find(i=>i.name===e||i.aliases?.includes(e));if(!s)return;let o=new Map(n.tracks?.map(i=>[i.trackId,i])),r=v.map(i=>o.get(`${s.name}-${i}`)?.adapter).find(i=>i!==void 0);return{assembly:d(s,t),geneAdapter:r&&d(r,t)}}async function F(n){for(let e of c(n)){let t=await fetch(e);if(t.ok){let s=await t.json();return J(s,n,e)}if(t.status!==404)throw new Error(`${e}: HTTP ${t.status}`)}}var b=new Map;function L(n){let e=b.get(n);return e||(e=F(n).catch(t=>{b.delete(n),console.error(t)}),b.set(n,e)),e}async function C(n,e){let t=typeof n=="object"&&n!==null?n:{},s=Array.isArray(e)?e.filter(r=>typeof r=="string"):[],o=await Promise.all(s.filter(r=>!Object.hasOwn(t,r)&&c(r).length>0).map(async r=>[r,await L(r)]));return{...t,...Object.fromEntries(o.filter(([,r])=>r!==void 0))}}function R(n,e){let t=URL.createObjectURL(n),s=document.createElement("a");s.href=t,s.download=e,s.rel="noopener",s.click(),setTimeout(()=>{URL.revokeObjectURL(t)},4e4)}function p(n){return Array.isArray(n)?n:[]}function S(n,e,t){let s=new Map;for(let o of[...n,...e])s.set(o[t],o);return[...s.values()]}function T(n,e){let{sessionTracks:t,sessionAssemblies:s,...o}=e;return{...n,tracks:S(p(n.tracks),p(t),"trackId"),assemblies:S(p(n.assemblies),p(s),"name"),defaultSession:o}}var E="1.0.16";function q(n){let{jbrowse:e}=(0,a.getRoot)(n),t=T((0,a.getSnapshot)(e),(0,a.getSnapshot)(n));R(new Blob([JSON.stringify(t,null,2)],{type:"application/json"}),"session.jbrowse")}var M=new WeakMap;function z(n,e){let t=M.get(n);return t||(t=new Set,M.set(n,t)),t.has(e)?!1:(t.add(e),!0)}async function K(n,e,t){let s=`jb2hub-${e}`;if(!(n.connections.find(o=>o.connectionId===s)||!z(n,e))){for(let o of t)if((await fetch(o,{method:"HEAD"})).ok){let i={type:"JB2TrackHubConnection",uri:o,name:`conn_${e}`,assemblyNames:[e],connectionId:s};n.addConnectionConf(i),n.makeConnection(i,{silent:!0});return}}}var l=class extends $.default{name="HubsViewerPlugin";version=E;install(e){e.addToExtensionPoint("Core-handleUnrecognizedAssembly",(t,s)=>{let o=s.session,r=s.assemblyName,i=r?c(r):[];return o&&r&&i.length>0?K(o,r,i).catch(D=>{console.error(D)}):t}),e.addToExtensionPoint("Core-describeAssemblies",(t,s)=>C(t,s.assemblyNames))}configure(e){if(!f.isElectron&&(0,f.isAbstractMenuManager)(e.rootModel))try{e.rootModel.appendToMenu("Tools",{label:"Download desktop session (.jbrowse)",onClick:t=>{q(t)}})}catch(t){console.error("could not add the desktop-session download item",t)}}};return B(V);})();
 //# sourceMappingURL=jbrowse-plugin-hubs.umd.production.min.js.map

package/dist/jbrowse-plugin-hubs.umd.production.min.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["global-externals:@jbrowse/core/Plugin", "global-externals:@jbrowse/core/util", "global-externals:@jbrowse/mobx-state-tree", "../src/index.ts", "../src/util.ts", "../package.json"],
-  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util\"];", "module.exports = JBrowseExports[\"mobx-state-tree\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport { isAbstractMenuManager, isElectron } from '@jbrowse/core/util'\nimport { getRoot, getSnapshot } from '@jbrowse/mobx-state-tree'\n\nimport { saveAs, toDesktopSnapshot } from './util'\nimport { version } from '../package.json'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\nimport type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree'\n\ninterface Session {\n  makeConnection: (conf: unknown, initialSnapshot?: unknown) => void\n  addConnectionConf: (conf: unknown) => void\n  connections: { connectionId: string }[]\n}\n\n// Serializes the current web session as a desktop `.jbrowse` file. genomes\n// sessions are config-shaped already, so this just folds the live session into\n// a defaultSession and downloads it; desktop opens it via File > Open session.\nfunction downloadDesktopSession(session: AbstractSessionModel) {\n  const { jbrowse } = getRoot<{ jbrowse: IAnyStateTreeNode }>(session)\n  const snap = toDesktopSnapshot(\n    getSnapshot<Record<string, unknown>>(jbrowse),\n    getSnapshot<Record<string, unknown>>(session),\n  )\n  saveAs(\n    new Blob([JSON.stringify(snap, null, 2)], { type: 'application/json' }),\n    'session.jbrowse',\n  )\n}\n\nfunction getGenArkConfigUrl(accession: string) {\n  const [base, rest] = accession.split('_')\n  if (!rest) {\n    return undefined\n  }\n  const match = rest.match(/.{1,3}/g)\n  if (!match || match.length < 3) {\n    return undefined\n  }\n  const [b1, b2, b3] = match\n  return `https://jbrowse.org/hubs/genark/${base}/${b1}/${b2}/${b3}/${accession}/config.json`\n}\n\n// Candidate urls for an assembly name, most preferred first. The probe below\n// takes the first that exists, so a name with no hosted config anywhere is\n// still answered by staying quiet.\n//\n// A UCSC db gets `minimal.json` ahead of `config.json`. Both carry the same\n// `assemblies` block (minimal.json is a filtered copy of config.json, tracks\n// dropped to NCBI RefSeq / GENCODE / RepeatMasker / gaps), and the assembly is\n// the whole reason this connection exists \u2014 the tracks are a bonus for the\n// panel it opens. The full config is an expensive way to learn a sequence\n// adapter: hg38 is 2.1MB against minimal's 300KB, hg19 1.35MB against 57KB,\n// hs1 603KB against 12KB, and the parse is followed by MST instantiating every\n// track config in it on the main thread (hg38 595 against 33, hs1 624 against\n// 7). hg38 alone names 239 distinct mate assemblies across its 239 synteny\n// tracks, so a session that opens a few of them pays this several times over.\n//\n// What minimal.json costs is the mate genome's long tail \u2014 conservation,\n// expression, the rest of the hub. Those are still one \"Add connection\" away\n// on the full config url, and nothing about this panel implied they were\n// coming. GenArk hubs have no minimal.json and don't need one; their whole\n// config is ~40KB.\nfunction getConfigUrls(assemblyName: string) {\n  if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {\n    const url = getGenArkConfigUrl(assemblyName)\n    return url ? [url] : []\n  }\n  const base = `https://jbrowse.org/ucsc/${assemblyName}`\n  return [`${base}/minimal.json`, `${base}/config.json`]\n}\n\n// Every assembly name this plugin has already taken a run at, whether the probe\n// is still in flight or came back with nothing. The extension point fires on an\n// unresolved read, and `get` is read from render paths, so a name that resolves\n// to no hosted config is asked about again and again \u2014 GenArk strain hubs\n// (mouseStrains and friends) live under /hubs/genark/<hub>/<strain>/ and are not\n// at the url guessed from the name, and a session can name an assembly this host\n// has never heard of at all. Clearing this once the probe settled (what an\n// earlier `finally` did) meant the next read re-probed, i.e. one HEAD per render\n// forever for exactly the names nothing can supply.\n//\n// A name that DID resolve is also in here, and is separately deduped by\n// connectionId once the connection exists. Nothing is ever removed within a\n// session: a probe answers a question about a url that does not change within a\n// page load.\n//\n// Keyed by session, because the connection a probe created belongs to the\n// session and goes with it. A flat Set would remember a name across\n// `setSession` and leave the new session unable to resolve a genome the old one\n// had. WeakMap so a replaced session is still collectable.\n//\n// jbrowse-core@main reports each unknown name to the extension point once per\n// session, which makes this redundant there \u2014 but this plugin runs against\n// whatever core the host page shipped, down to the v4.0.0 floor, where it is\n// the only thing standing between a mistyped assembly name and an unbounded\n// request stream.\nconst attempted = new WeakMap<Session, Set<string>>()\n\nfunction markAttempted(session: Session, assemblyName: string) {\n  let names = attempted.get(session)\n  if (!names) {\n    names = new Set()\n    attempted.set(session, names)\n  }\n  if (names.has(assemblyName)) {\n    return false\n  }\n  names.add(assemblyName)\n  return true\n}\n\n// Connect to the first of `uris` that exists. Connecting to a config that 404s\n// puts a red error snackbar over a session that is otherwise working, so probe\n// first and stay quiet when there's nothing there \u2014 some other handler, or the\n// session itself, may be supplying the assembly.\nasync function connectIfConfigExists(\n  session: Session,\n  assemblyName: string,\n  uris: string[],\n) {\n  const connectionId = `jb2hub-${assemblyName}`\n  if (\n    session.connections.find(f => f.connectionId === connectionId) ||\n    !markAttempted(session, assemblyName)\n  ) {\n    return\n  }\n  for (const uri of uris) {\n    const response = await fetch(uri, { method: 'HEAD' })\n    if (response.ok) {\n      const conf = {\n        type: 'JB2TrackHubConnection',\n        uri,\n        name: `conn_${assemblyName}`,\n        assemblyNames: [assemblyName],\n        connectionId,\n      }\n      session.addConnectionConf(conf)\n      // `silent`: no \"Successfully loaded\" snackbar. Nobody asked for this\n      // connection \u2014 it exists because a track referenced an assembly the\n      // session didn't have \u2014 so announcing it is noise over whatever the\n      // user was doing, and it lands on top of any screenshot of a hub\n      // genome. The property is newer than every released core (it landed\n      // after v4.3.0) and this plugin runs against whatever core the host\n      // page shipped, down to the v4.0.0 floor, but passing it is safe\n      // regardless: MST drops an undeclared key off a model snapshot rather\n      // than rejecting it (verified against the fork \u2014 the instance is\n      // created, the key is neither readable on it nor in its snapshot), so\n      // an older core makes the same connection it always did and keeps its\n      // toast.\n      session.makeConnection(conf, { silent: true })\n      return\n    }\n  }\n}\n\nexport default class HubsViewerPlugin extends Plugin {\n  name = 'HubsViewerPlugin'\n  version = version\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addToExtensionPoint(\n      'Core-handleUnrecognizedAssembly',\n      (defaultResult, args) => {\n        const session = args.session as Session | undefined\n        const assemblyName = args.assemblyName as string | undefined\n        const uris = assemblyName ? getConfigUrls(assemblyName) : []\n        if (session && assemblyName && uris.length > 0) {\n          // The probe and the connection it may create land after this returns,\n          // which is fine because assemblyManager re-reads reactively once the\n          // assembly shows up.\n          //\n          // Returning the promise rather than the accumulator: a core that\n          // knows to look (jbrowse-core > 4.3.0) awaits it in waitForAssembly,\n          // which is what lets that wait end on an event instead of a 10s\n          // timeout. Nothing observable happens between being asked and the\n          // HEAD coming back, so a core with only the session to watch has to\n          // guess, and 10s is both too long to fail in and too short for a cold\n          // CDN. Older cores fold the return value into an accumulator they\n          // then discard, so this is inert there.\n          //\n          // Nothing else registers on this point (checked across the plugin\n          // ecosystem), so replacing the accumulator costs no other plugin its\n          // result; if that changes, a handler registered after this one still\n          // receives and can pass on whatever it is given.\n          return connectIfConfigExists(session, assemblyName, uris).catch(\n            (e: unknown) => {\n              console.error(e)\n            },\n          )\n        }\n        // Pass the accumulator through: this extension point chains handlers, so\n        // returning undefined would clobber another plugin's result.\n        return defaultResult\n      },\n    )\n  }\n\n  configure(pluginManager: PluginManager) {\n    // jbrowse-web only. In desktop you'd just save the session, and an exported\n    // .jbrowse file carries this plugin in its plugins list, so an older desktop\n    // would otherwise load and run this menu code when opening that file.\n    if (!isElectron && isAbstractMenuManager(pluginManager.rootModel)) {\n      // 'Tools', not 'File'. Every released core from v4.0.0 to latest defines\n      // the File menu as a thunk and appends with `menu.menuItems.push()`, which\n      // throws on a function; the throw escapes configure() and renders the app\n      // as an error page rather than costing just this menu item. Because the\n      // plugin store serves `latest/` no-cache, that took out every\n      // jbrowse.org/ucsc launch on hg38/hg19/mm39/hs1 the moment 1.0.9 shipped.\n      // core@main resolves item contributions lazily and accepts either form,\n      // but this plugin has to keep working on the releases already in the wild.\n      //\n      // Belt and braces on the same reasoning: a cosmetic menu item should never\n      // be able to cost a user their whole session.\n      try {\n        pluginManager.rootModel.appendToMenu('Tools', {\n          label: 'Download desktop session (.jbrowse)',\n          onClick: (session: AbstractSessionModel) => {\n            downloadDesktopSession(session)\n          },\n        })\n      } catch (e) {\n        console.error('could not add the desktop-session download item', e)\n      }\n    }\n  }\n}\n", "// Trigger a browser download of `blob` as `filename`. Mirrors the anchor-download\n// path of @jbrowse/core's saveAs: the deferred revoke avoids canceling the\n// download before the browser has read the blob (the read is async in some\n// browsers). Inlined until a published core release exports saveAs from its util.\nexport function saveAs(blob: Blob, filename: string) {\n  const url = URL.createObjectURL(blob)\n  const anchor = document.createElement('a')\n  anchor.href = url\n  anchor.download = filename\n  anchor.rel = 'noopener'\n  anchor.click()\n  setTimeout(() => {\n    URL.revokeObjectURL(url)\n  }, 40000)\n}\n\nfunction asObjArray(value: unknown): Record<string, unknown>[] {\n  return Array.isArray(value) ? (value as Record<string, unknown>[]) : []\n}\n\n// Merges two lists of config objects by an id key, with `overrides` winning so\n// a session-scoped track/assembly that shadows a config one (same id) replaces\n// it rather than duplicating.\nfunction mergeById(\n  base: Record<string, unknown>[],\n  overrides: Record<string, unknown>[],\n  key: string,\n): Record<string, unknown>[] {\n  const merged = new Map<unknown, Record<string, unknown>>()\n  for (const item of [...base, ...overrides]) {\n    merged.set(item[key], item)\n  }\n  return [...merged.values()]\n}\n\n// Builds a desktop `.jbrowse` snapshot (a config plus a defaultSession) from a\n// web root config and its live session. Session-scoped tracks/assemblies are\n// hoisted into the config arrays so they open as first-class config entries in\n// desktop; the rest of the session becomes the defaultSession. Web sessions are\n// always UriLocation-based, so the result is fully portable to desktop.\nexport function toDesktopSnapshot(\n  jbrowse: Record<string, unknown>,\n  session: Record<string, unknown>,\n): Record<string, unknown> {\n  const { sessionTracks, sessionAssemblies, ...defaultSession } = session\n  return {\n    ...jbrowse,\n    tracks: mergeById(\n      asObjArray(jbrowse.tracks),\n      asObjArray(sessionTracks),\n      'trackId',\n    ),\n    assemblies: mergeById(\n      asObjArray(jbrowse.assemblies),\n      asObjArray(sessionAssemblies),\n      'name',\n    ),\n    defaultSession,\n  }\n}\n", "{\n  \"version\": \"1.0.14\",\n  \"license\": \"MIT\",\n  \"name\": \"@cmdcolin/jbrowse-plugin-hubs\",\n  \"repository\": {\n    \"type\": \"git\",\n    \"url\": \"git+https://github.com/GMOD/jbrowse-plugin-hubs.git\"\n  },\n  \"keywords\": [\n    \"jbrowse\",\n    \"jbrowse2\"\n  ],\n  \"main\": \"dist/index.js\",\n  \"module\": \"dist/index.esm.js\",\n  \"typings\": \"dist/index.d.ts\",\n  \"files\": [\n    \"dist\",\n    \"src\"\n  ],\n  \"scripts\": {\n    \"clean\": \"rimraf dist\",\n    \"start\": \"node esbuild.mjs --watch\",\n    \"test\": \"echo 'no tests'\",\n    \"format\": \"pnpm prettier --write .\",\n    \"prebuild\": \"pnpm clean\",\n    \"build\": \"tsc && NODE_ENV=production node esbuild.mjs\",\n    \"lint\": \"eslint src --report-unused-disable-directives --max-warnings 0\",\n    \"prepack\": \"pnpm build\",\n    \"postversion\": \"git push --follow-tags\",\n    \"preversion\": \"pnpm lint && pnpm build && pnpm host-compat\",\n    \"host-compat\": \"node scripts/host-compat-probe.mjs --bundle dist/jbrowse-plugin-hubs.umd.production.min.js\"\n  },\n  \"devDependencies\": {\n    \"@eslint/js\": \"^10.0.1\",\n    \"@fal-works/esbuild-plugin-global-externals\": \"^2.1.2\",\n    \"@jbrowse/core\": \"^4.3.0\",\n    \"@jbrowse/mobx-state-tree\": \"^5.11.1\",\n    \"@mui/material\": \"^7.3.11\",\n    \"@mui/system\": \"^7.3.11\",\n    \"@mui/x-data-grid\": \"^8.29.1\",\n    \"@types/node\": \"^25.9.3\",\n    \"@types/react\": \"^19.2.17\",\n    \"@typescript-eslint/eslint-plugin\": \"^8.61.1\",\n    \"@typescript-eslint/parser\": \"^8.61.1\",\n    \"esbuild\": \"^0.27.7\",\n    \"eslint\": \"^10.5.0\",\n    \"eslint-plugin-import-x\": \"^4.16.2\",\n    \"eslint-plugin-react\": \"^7.37.5\",\n    \"eslint-plugin-react-hooks\": \"^7.1.1\",\n    \"eslint-plugin-unicorn\": \"^64.0.0\",\n    \"mobx\": \"^6.16.1\",\n    \"mobx-react\": \"^9.2.2\",\n    \"prettier\": \"^3.8.4\",\n    \"pretty-bytes\": \"^7.1.0\",\n    \"puppeteer-core\": \"^25.4.0\",\n    \"react\": \"^19.2.7\",\n    \"react-dom\": \"^19.2.7\",\n    \"rimraf\": \"^6.1.3\",\n    \"rxjs\": \"^7.8.2\",\n    \"serve\": \"^14.2.6\",\n    \"typescript\": \"^5.9.3\",\n    \"typescript-eslint\": \"^8.61.1\"\n  },\n  \"publishConfig\": {\n    \"access\": \"public\"\n  }\n}\n"],
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-  "names": ["require_Plugin", "__commonJSMin", "exports", "module", "require_util", "__commonJSMin", "exports", "module", "require_mobx_state_tree", "__commonJSMin", "exports", "module", "index_exports", "__export", "HubsViewerPlugin", "import_Plugin", "import_util", "import_mobx_state_tree", "saveAs", "blob", "filename", "url", "anchor", "asObjArray", "value", "mergeById", "base", "overrides", "key", "merged", "item", "toDesktopSnapshot", "jbrowse", "session", "sessionTracks", "sessionAssemblies", "defaultSession", "version", "downloadDesktopSession", "session", "jbrowse", "snap", "toDesktopSnapshot", "saveAs", "getGenArkConfigUrl", "accession", "base", "rest", "match", "b1", "b2", "b3", "getConfigUrls", "assemblyName", "url", "attempted", "markAttempted", "names", "connectIfConfigExists", "uris", "connectionId", "f", "uri", "conf", "HubsViewerPlugin", "Plugin", "version", "pluginManager", "defaultResult", "args", "e"]
+  "sources": ["global-externals:@jbrowse/core/Plugin", "global-externals:@jbrowse/core/util", "global-externals:@jbrowse/mobx-state-tree", "../src/index.ts", "../src/configUrls.ts", "../src/describeAssemblies.ts", "../src/util.ts", "../package.json"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util\"];", "module.exports = JBrowseExports[\"mobx-state-tree\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport { isAbstractMenuManager, isElectron } from '@jbrowse/core/util'\nimport { getRoot, getSnapshot } from '@jbrowse/mobx-state-tree'\n\nimport { getConfigUrls } from './configUrls'\nimport { describeAssemblies } from './describeAssemblies'\nimport { saveAs, toDesktopSnapshot } from './util'\nimport { version } from '../package.json'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\nimport type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree'\n\ninterface Session {\n  makeConnection: (conf: unknown, initialSnapshot?: unknown) => void\n  addConnectionConf: (conf: unknown) => void\n  connections: { connectionId: string }[]\n}\n\n// Serializes the current web session as a desktop `.jbrowse` file. genomes\n// sessions are config-shaped already, so this just folds the live session into\n// a defaultSession and downloads it; desktop opens it via File > Open session.\nfunction downloadDesktopSession(session: AbstractSessionModel) {\n  const { jbrowse } = getRoot<{ jbrowse: IAnyStateTreeNode }>(session)\n  const snap = toDesktopSnapshot(\n    getSnapshot<Record<string, unknown>>(jbrowse),\n    getSnapshot<Record<string, unknown>>(session),\n  )\n  saveAs(\n    new Blob([JSON.stringify(snap, null, 2)], { type: 'application/json' }),\n    'session.jbrowse',\n  )\n}\n\n// Every assembly name this plugin has already taken a run at, whether the probe\n// is still in flight or came back with nothing. The extension point fires on an\n// unresolved read, and `get` is read from render paths, so a name that resolves\n// to no hosted config is asked about again and again \u2014 GenArk strain hubs\n// (mouseStrains and friends) live under /hubs/genark/<hub>/<strain>/ and are not\n// at the url guessed from the name, and a session can name an assembly this host\n// has never heard of at all. Clearing this once the probe settled (what an\n// earlier `finally` did) meant the next read re-probed, i.e. one HEAD per render\n// forever for exactly the names nothing can supply.\n//\n// A name that DID resolve is also in here, and is separately deduped by\n// connectionId once the connection exists. Nothing is ever removed within a\n// session: a probe answers a question about a url that does not change within a\n// page load.\n//\n// Keyed by session, because the connection a probe created belongs to the\n// session and goes with it. A flat Set would remember a name across\n// `setSession` and leave the new session unable to resolve a genome the old one\n// had. WeakMap so a replaced session is still collectable.\n//\n// jbrowse-core@main reports each unknown name to the extension point once per\n// session, which makes this redundant there \u2014 but this plugin runs against\n// whatever core the host page shipped, down to the v4.0.0 floor, where it is\n// the only thing standing between a mistyped assembly name and an unbounded\n// request stream.\nconst attempted = new WeakMap<Session, Set<string>>()\n\nfunction markAttempted(session: Session, assemblyName: string) {\n  let names = attempted.get(session)\n  if (!names) {\n    names = new Set()\n    attempted.set(session, names)\n  }\n  if (names.has(assemblyName)) {\n    return false\n  }\n  names.add(assemblyName)\n  return true\n}\n\n// Connect to the first of `uris` that exists. Connecting to a config that 404s\n// puts a red error snackbar over a session that is otherwise working, so probe\n// first and stay quiet when there's nothing there \u2014 some other handler, or the\n// session itself, may be supplying the assembly.\nasync function connectIfConfigExists(\n  session: Session,\n  assemblyName: string,\n  uris: string[],\n) {\n  const connectionId = `jb2hub-${assemblyName}`\n  if (\n    session.connections.find(f => f.connectionId === connectionId) ||\n    !markAttempted(session, assemblyName)\n  ) {\n    return\n  }\n  for (const uri of uris) {\n    const response = await fetch(uri, { method: 'HEAD' })\n    if (response.ok) {\n      const conf = {\n        type: 'JB2TrackHubConnection',\n        uri,\n        name: `conn_${assemblyName}`,\n        assemblyNames: [assemblyName],\n        connectionId,\n      }\n      session.addConnectionConf(conf)\n      // `silent`: no \"Successfully loaded\" snackbar. Nobody asked for this\n      // connection \u2014 it exists because a track referenced an assembly the\n      // session didn't have \u2014 so announcing it is noise over whatever the\n      // user was doing, and it lands on top of any screenshot of a hub\n      // genome. The property is newer than every released core (it landed\n      // after v4.3.0) and this plugin runs against whatever core the host\n      // page shipped, down to the v4.0.0 floor, but passing it is safe\n      // regardless: MST drops an undeclared key off a model snapshot rather\n      // than rejecting it (verified against the fork \u2014 the instance is\n      // created, the key is neither readable on it nor in its snapshot), so\n      // an older core makes the same connection it always did and keeps its\n      // toast.\n      session.makeConnection(conf, { silent: true })\n      return\n    }\n  }\n}\n\nexport default class HubsViewerPlugin extends Plugin {\n  name = 'HubsViewerPlugin'\n  version = version\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addToExtensionPoint(\n      'Core-handleUnrecognizedAssembly',\n      (defaultResult, args) => {\n        const session = args.session as Session | undefined\n        const assemblyName = args.assemblyName as string | undefined\n        const uris = assemblyName ? getConfigUrls(assemblyName) : []\n        if (session && assemblyName && uris.length > 0) {\n          // The probe and the connection it may create land after this returns,\n          // which is fine because assemblyManager re-reads reactively once the\n          // assembly shows up.\n          //\n          // Returning the promise rather than the accumulator: a core that\n          // knows to look (jbrowse-core > 4.3.0) awaits it in waitForAssembly,\n          // which is what lets that wait end on an event instead of a 10s\n          // timeout. Nothing observable happens between being asked and the\n          // HEAD coming back, so a core with only the session to watch has to\n          // guess, and 10s is both too long to fail in and too short for a cold\n          // CDN. Older cores fold the return value into an accumulator they\n          // then discard, so this is inert there.\n          //\n          // Nothing else registers on this point (checked across the plugin\n          // ecosystem), so replacing the accumulator costs no other plugin its\n          // result; if that changes, a handler registered after this one still\n          // receives and can pass on whatever it is given.\n          return connectIfConfigExists(session, assemblyName, uris).catch(\n            (e: unknown) => {\n              console.error(e)\n            },\n          )\n        }\n        // Pass the accumulator through: this extension point chains handlers, so\n        // returning undefined would clobber another plugin's result.\n        return defaultResult\n      },\n    )\n    // A multi-way synteny lane whose genome the session lacks asks here for\n    // its assembly config and gene track. Cores older than the point never\n    // fire it, so this is inert on them\n    pluginManager.addToExtensionPoint(\n      'Core-describeAssemblies',\n      (described: unknown, args) =>\n        describeAssemblies(described, args.assemblyNames),\n    )\n  }\n\n  configure(pluginManager: PluginManager) {\n    // jbrowse-web only. In desktop you'd just save the session, and an exported\n    // .jbrowse file carries this plugin in its plugins list, so an older desktop\n    // would otherwise load and run this menu code when opening that file.\n    if (!isElectron && isAbstractMenuManager(pluginManager.rootModel)) {\n      // 'Tools', not 'File'. Every released core from v4.0.0 to latest defines\n      // the File menu as a thunk and appends with `menu.menuItems.push()`, which\n      // throws on a function; the throw escapes configure() and renders the app\n      // as an error page rather than costing just this menu item. Because the\n      // plugin store serves `latest/` no-cache, that took out every\n      // jbrowse.org/ucsc launch on hg38/hg19/mm39/hs1 the moment 1.0.9 shipped.\n      // core@main resolves item contributions lazily and accepts either form,\n      // but this plugin has to keep working on the releases already in the wild.\n      //\n      // Belt and braces on the same reasoning: a cosmetic menu item should never\n      // be able to cost a user their whole session.\n      try {\n        pluginManager.rootModel.appendToMenu('Tools', {\n          label: 'Download desktop session (.jbrowse)',\n          onClick: (session: AbstractSessionModel) => {\n            downloadDesktopSession(session)\n          },\n        })\n      } catch (e) {\n        console.error('could not add the desktop-session download item', e)\n      }\n    }\n  }\n}\n", "function getGenArkConfigUrl(accession: string) {\n  const [base, rest] = accession.split('_')\n  if (!rest) {\n    return undefined\n  }\n  const match = rest.match(/.{1,3}/g)\n  if (!match || match.length < 3) {\n    return undefined\n  }\n  const [b1, b2, b3] = match\n  return `https://jbrowse.org/hubs/genark/${base}/${b1}/${b2}/${b3}/${accession}/config.json`\n}\n\n// Candidate urls for an assembly name, most preferred first. The connection\n// probe and the describe lookup each take the first that exists, so a name with\n// no hosted config anywhere is still answered by staying quiet.\n//\n// A UCSC db gets `minimal.json` ahead of `config.json`. Both carry the same\n// `assemblies` block (minimal.json is a filtered copy of config.json, tracks\n// dropped to NCBI RefSeq / GENCODE / RepeatMasker / gaps), and the assembly is\n// the whole reason this connection exists \u2014 the tracks are a bonus for the\n// panel it opens. The full config is an expensive way to learn a sequence\n// adapter: hg38 is 2.1MB against minimal's 300KB, hg19 1.35MB against 57KB,\n// hs1 603KB against 12KB, and the parse is followed by MST instantiating every\n// track config in it on the main thread (hg38 595 against 33, hs1 624 against\n// 7). hg38 alone names 239 distinct mate assemblies across its 239 synteny\n// tracks, so a session that opens a few of them pays this several times over.\n//\n// What minimal.json costs is the mate genome's long tail \u2014 conservation,\n// expression, the rest of the hub. Those are still one \"Add connection\" away\n// on the full config url, and nothing about this panel implied they were\n// coming. GenArk hubs have no minimal.json and don't need one; their whole\n// config is ~40KB.\nexport function getConfigUrls(assemblyName: string) {\n  if (!/^[\\w.]+$/.test(assemblyName)) {\n    return []\n  }\n  if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {\n    const url = getGenArkConfigUrl(assemblyName)\n    return url ? [url] : []\n  }\n  const base = `https://jbrowse.org/ucsc/${assemblyName}`\n  return [`${base}/minimal.json`, `${base}/config.json`]\n}\n", "import { getConfigUrls } from './configUrls'\n\ninterface Description {\n  assembly: HubAssembly\n  geneAdapter?: Record<string, unknown>\n}\n\ninterface HubAssembly {\n  name: string\n  aliases?: string[]\n}\n\ninterface HubConfig {\n  assemblies?: HubAssembly[]\n  tracks?: { trackId: string; adapter?: Record<string, unknown> }[]\n}\n\n// jb2hubs' defaultGeneTrackId order, which also picks the track minimal.json\n// keeps and a hub genome's default session opens\nconst GENE_TRACK_SUFFIXES = [\n  'ncbiRefSeq',\n  'ncbiRefSeqCurated',\n  'ncbiGene',\n  'refGene',\n  'ensGene',\n  'augustusGene',\n  'xenoRefGene',\n]\n\n// A TwoBit adapter's bare `chromSizes` resolves against the `baseUri` beside\n// its `uri`, so rewriting each `uri` alone sent jb2hubs' relative chrom.sizes\n// to the page's origin\nfunction withBaseUri<T>(value: T, base: string): T {\n  if (Array.isArray(value)) {\n    return value.map(item => withBaseUri(item, base)) as T\n  }\n  if (typeof value === 'object' && value !== null) {\n    const entries = Object.entries(value).map(([key, item]) => [\n      key,\n      withBaseUri(item, base),\n    ])\n    return Object.fromEntries(\n      typeof (value as { uri?: unknown }).uri === 'string' &&\n        !('baseUri' in value)\n        ? [...entries, ['baseUri', base]]\n        : entries,\n    ) as T\n  }\n  return value\n}\n\nexport function describeFromConfig(\n  config: HubConfig,\n  assemblyName: string,\n  configUrl: string,\n): Description | undefined {\n  const assembly = config.assemblies?.find(\n    a => a.name === assemblyName || a.aliases?.includes(assemblyName),\n  )\n  if (!assembly) {\n    return undefined\n  }\n  const tracks = new Map(config.tracks?.map(track => [track.trackId, track]))\n  const geneAdapter = GENE_TRACK_SUFFIXES.map(\n    suffix => tracks.get(`${assembly.name}-${suffix}`)?.adapter,\n  ).find(adapter => adapter !== undefined)\n  return {\n    assembly: withBaseUri(assembly, configUrl),\n    geneAdapter: geneAdapter && withBaseUri(geneAdapter, configUrl),\n  }\n}\n\n// throws on anything but a found config or a 404, so only a definitive\n// answer is cached\nasync function fetchDescription(assemblyName: string) {\n  for (const url of getConfigUrls(assemblyName)) {\n    const response = await fetch(url)\n    if (response.ok) {\n      const config = (await response.json()) as HubConfig\n      return describeFromConfig(config, assemblyName, url)\n    }\n    if (response.status !== 404) {\n      throw new Error(`${url}: HTTP ${response.status}`)\n    }\n  }\n  return undefined\n}\n\nconst descriptions = new Map<string, Promise<Description | undefined>>()\n\nfunction describe(assemblyName: string) {\n  let description = descriptions.get(assemblyName)\n  if (!description) {\n    description = fetchDescription(assemblyName).catch((error: unknown) => {\n      descriptions.delete(assemblyName)\n      console.error(error)\n      return undefined\n    })\n    descriptions.set(assemblyName, description)\n  }\n  return description\n}\n\n/**\n * Core-describeAssemblies: the assembly config and gene track adapter the\n * hosted config of each named genome holds, read without connecting it. A\n * name another plugin already described, or one no hosted config could hold,\n * is left alone\n */\nexport async function describeAssemblies(\n  described: unknown,\n  assemblyNames: unknown,\n) {\n  const before =\n    typeof described === 'object' && described !== null ? described : {}\n  const names = Array.isArray(assemblyNames)\n    ? assemblyNames.filter((name): name is string => typeof name === 'string')\n    : []\n  const answers = await Promise.all(\n    names\n      .filter(\n        name => !Object.hasOwn(before, name) && getConfigUrls(name).length > 0,\n      )\n      .map(async name => [name, await describe(name)] as const),\n  )\n  return {\n    ...before,\n    ...Object.fromEntries(\n      answers.filter(([, description]) => description !== undefined),\n    ),\n  }\n}\n", "// Trigger a browser download of `blob` as `filename`. Mirrors the anchor-download\n// path of @jbrowse/core's saveAs: the deferred revoke avoids canceling the\n// download before the browser has read the blob (the read is async in some\n// browsers). Inlined until a published core release exports saveAs from its util.\nexport function saveAs(blob: Blob, filename: string) {\n  const url = URL.createObjectURL(blob)\n  const anchor = document.createElement('a')\n  anchor.href = url\n  anchor.download = filename\n  anchor.rel = 'noopener'\n  anchor.click()\n  setTimeout(() => {\n    URL.revokeObjectURL(url)\n  }, 40000)\n}\n\nfunction asObjArray(value: unknown): Record<string, unknown>[] {\n  return Array.isArray(value) ? (value as Record<string, unknown>[]) : []\n}\n\n// Merges two lists of config objects by an id key, with `overrides` winning so\n// a session-scoped track/assembly that shadows a config one (same id) replaces\n// it rather than duplicating.\nfunction mergeById(\n  base: Record<string, unknown>[],\n  overrides: Record<string, unknown>[],\n  key: string,\n): Record<string, unknown>[] {\n  const merged = new Map<unknown, Record<string, unknown>>()\n  for (const item of [...base, ...overrides]) {\n    merged.set(item[key], item)\n  }\n  return [...merged.values()]\n}\n\n// Builds a desktop `.jbrowse` snapshot (a config plus a defaultSession) from a\n// web root config and its live session. Session-scoped tracks/assemblies are\n// hoisted into the config arrays so they open as first-class config entries in\n// desktop; the rest of the session becomes the defaultSession. Web sessions are\n// always UriLocation-based, so the result is fully portable to desktop.\nexport function toDesktopSnapshot(\n  jbrowse: Record<string, unknown>,\n  session: Record<string, unknown>,\n): Record<string, unknown> {\n  const { sessionTracks, sessionAssemblies, ...defaultSession } = session\n  return {\n    ...jbrowse,\n    tracks: mergeById(\n      asObjArray(jbrowse.tracks),\n      asObjArray(sessionTracks),\n      'trackId',\n    ),\n    assemblies: mergeById(\n      asObjArray(jbrowse.assemblies),\n      asObjArray(sessionAssemblies),\n      'name',\n    ),\n    defaultSession,\n  }\n}\n", "{\n  \"version\": \"1.0.16\",\n  \"license\": \"MIT\",\n  \"name\": \"@cmdcolin/jbrowse-plugin-hubs\",\n  \"repository\": {\n    \"type\": \"git\",\n    \"url\": \"git+https://github.com/GMOD/jbrowse-plugin-hubs.git\"\n  },\n  \"keywords\": [\n    \"jbrowse\",\n    \"jbrowse2\"\n  ],\n  \"main\": \"dist/index.js\",\n  \"module\": \"dist/index.esm.js\",\n  \"typings\": \"dist/index.d.ts\",\n  \"files\": [\n    \"dist\",\n    \"src\"\n  ],\n  \"scripts\": {\n    \"clean\": \"rimraf dist\",\n    \"start\": \"node esbuild.mjs --watch\",\n    \"test\": \"echo 'no tests'\",\n    \"format\": \"pnpm prettier --write .\",\n    \"prebuild\": \"pnpm clean\",\n    \"build\": \"tsc && NODE_ENV=production node esbuild.mjs\",\n    \"lint\": \"eslint src --report-unused-disable-directives --max-warnings 0\",\n    \"prepack\": \"pnpm build\",\n    \"postversion\": \"git push --follow-tags\",\n    \"preversion\": \"pnpm lint && pnpm build && pnpm host-compat\",\n    \"host-compat\": \"node scripts/host-compat-probe.mjs --bundle dist/jbrowse-plugin-hubs.umd.production.min.js\"\n  },\n  \"devDependencies\": {\n    \"@eslint/js\": \"^10.0.1\",\n    \"@fal-works/esbuild-plugin-global-externals\": \"^2.1.2\",\n    \"@jbrowse/core\": \"^4.3.0\",\n    \"@jbrowse/mobx-state-tree\": \"^5.11.1\",\n    \"@mui/material\": \"^7.3.11\",\n    \"@mui/system\": \"^7.3.11\",\n    \"@mui/x-data-grid\": \"^8.29.1\",\n    \"@types/node\": \"^25.9.3\",\n    \"@types/react\": \"^19.2.17\",\n    \"@typescript-eslint/eslint-plugin\": \"^8.61.1\",\n    \"@typescript-eslint/parser\": \"^8.61.1\",\n    \"esbuild\": \"^0.27.7\",\n    \"eslint\": \"^10.5.0\",\n    \"eslint-plugin-import-x\": \"^4.16.2\",\n    \"eslint-plugin-react\": \"^7.37.5\",\n    \"eslint-plugin-react-hooks\": \"^7.1.1\",\n    \"eslint-plugin-unicorn\": \"^64.0.0\",\n    \"mobx\": \"^6.16.1\",\n    \"mobx-react\": \"^9.2.2\",\n    \"prettier\": \"^3.8.4\",\n    \"pretty-bytes\": \"^7.1.0\",\n    \"puppeteer-core\": \"^25.4.0\",\n    \"react\": \"^19.2.7\",\n    \"react-dom\": \"^19.2.7\",\n    \"rimraf\": \"^6.1.3\",\n    \"rxjs\": \"^7.8.2\",\n    \"serve\": \"^14.2.6\",\n    \"typescript\": \"^5.9.3\",\n    \"typescript-eslint\": \"^8.61.1\"\n  },\n  \"publishConfig\": {\n    \"access\": \"public\"\n  }\n}\n"],
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+  "names": ["require_Plugin", "__commonJSMin", "exports", "module", "require_util", "__commonJSMin", "exports", "module", "require_mobx_state_tree", "__commonJSMin", "exports", "module", "index_exports", "__export", "HubsViewerPlugin", "import_Plugin", "import_util", "import_mobx_state_tree", "getGenArkConfigUrl", "accession", "base", "rest", "match", "b1", "b2", "b3", "getConfigUrls", "assemblyName", "url", "GENE_TRACK_SUFFIXES", "withBaseUri", "value", "base", "item", "entries", "key", "describeFromConfig", "config", "assemblyName", "configUrl", "assembly", "a", "tracks", "track", "geneAdapter", "suffix", "adapter", "fetchDescription", "url", "getConfigUrls", "response", "descriptions", "describe", "description", "error", "describeAssemblies", "described", "assemblyNames", "before", "names", "name", "answers", "saveAs", "blob", "filename", "url", "anchor", "asObjArray", "value", "mergeById", "base", "overrides", "key", "merged", "item", "toDesktopSnapshot", "jbrowse", "session", "sessionTracks", "sessionAssemblies", "defaultSession", "version", "downloadDesktopSession", "session", "jbrowse", "snap", "toDesktopSnapshot", "saveAs", "attempted", "markAttempted", "assemblyName", "names", "connectIfConfigExists", "uris", "connectionId", "f", "uri", "conf", "HubsViewerPlugin", "Plugin", "version", "pluginManager", "defaultResult", "args", "getConfigUrls", "e", "described", "describeAssemblies"]
 }

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.0.14",
+  "version": "1.0.16",
   "license": "MIT",
   "name": "@cmdcolin/jbrowse-plugin-hubs",
   "repository": {

package/src/configUrls.ts

@@ -0,0 +1,44 @@
+function getGenArkConfigUrl(accession: string) {
+  const [base, rest] = accession.split('_')
+  if (!rest) {
+    return undefined
+  }
+  const match = rest.match(/.{1,3}/g)
+  if (!match || match.length < 3) {
+    return undefined
+  }
+  const [b1, b2, b3] = match
+  return `https://jbrowse.org/hubs/genark/${base}/${b1}/${b2}/${b3}/${accession}/config.json`
+}
+
+// Candidate urls for an assembly name, most preferred first. The connection
+// probe and the describe lookup each take the first that exists, so a name with
+// no hosted config anywhere is still answered by staying quiet.
+//
+// A UCSC db gets `minimal.json` ahead of `config.json`. Both carry the same
+// `assemblies` block (minimal.json is a filtered copy of config.json, tracks
+// dropped to NCBI RefSeq / GENCODE / RepeatMasker / gaps), and the assembly is
+// the whole reason this connection exists — the tracks are a bonus for the
+// panel it opens. The full config is an expensive way to learn a sequence
+// adapter: hg38 is 2.1MB against minimal's 300KB, hg19 1.35MB against 57KB,
+// hs1 603KB against 12KB, and the parse is followed by MST instantiating every
+// track config in it on the main thread (hg38 595 against 33, hs1 624 against
+// 7). hg38 alone names 239 distinct mate assemblies across its 239 synteny
+// tracks, so a session that opens a few of them pays this several times over.
+//
+// What minimal.json costs is the mate genome's long tail — conservation,
+// expression, the rest of the hub. Those are still one "Add connection" away
+// on the full config url, and nothing about this panel implied they were
+// coming. GenArk hubs have no minimal.json and don't need one; their whole
+// config is ~40KB.
+export function getConfigUrls(assemblyName: string) {
+  if (!/^[\w.]+$/.test(assemblyName)) {
+    return []
+  }
+  if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {
+    const url = getGenArkConfigUrl(assemblyName)
+    return url ? [url] : []
+  }
+  const base = `https://jbrowse.org/ucsc/${assemblyName}`
+  return [`${base}/minimal.json`, `${base}/config.json`]
+}

package/src/describeAssemblies.ts

@@ -0,0 +1,132 @@
+import { getConfigUrls } from './configUrls'
+
+interface Description {
+  assembly: HubAssembly
+  geneAdapter?: Record<string, unknown>
+}
+
+interface HubAssembly {
+  name: string
+  aliases?: string[]
+}
+
+interface HubConfig {
+  assemblies?: HubAssembly[]
+  tracks?: { trackId: string; adapter?: Record<string, unknown> }[]
+}
+
+// jb2hubs' defaultGeneTrackId order, which also picks the track minimal.json
+// keeps and a hub genome's default session opens
+const GENE_TRACK_SUFFIXES = [
+  'ncbiRefSeq',
+  'ncbiRefSeqCurated',
+  'ncbiGene',
+  'refGene',
+  'ensGene',
+  'augustusGene',
+  'xenoRefGene',
+]
+
+// A TwoBit adapter's bare `chromSizes` resolves against the `baseUri` beside
+// its `uri`, so rewriting each `uri` alone sent jb2hubs' relative chrom.sizes
+// to the page's origin
+function withBaseUri<T>(value: T, base: string): T {
+  if (Array.isArray(value)) {
+    return value.map(item => withBaseUri(item, base)) as T
+  }
+  if (typeof value === 'object' && value !== null) {
+    const entries = Object.entries(value).map(([key, item]) => [
+      key,
+      withBaseUri(item, base),
+    ])
+    return Object.fromEntries(
+      typeof (value as { uri?: unknown }).uri === 'string' &&
+        !('baseUri' in value)
+        ? [...entries, ['baseUri', base]]
+        : entries,
+    ) as T
+  }
+  return value
+}
+
+export function describeFromConfig(
+  config: HubConfig,
+  assemblyName: string,
+  configUrl: string,
+): Description | undefined {
+  const assembly = config.assemblies?.find(
+    a => a.name === assemblyName || a.aliases?.includes(assemblyName),
+  )
+  if (!assembly) {
+    return undefined
+  }
+  const tracks = new Map(config.tracks?.map(track => [track.trackId, track]))
+  const geneAdapter = GENE_TRACK_SUFFIXES.map(
+    suffix => tracks.get(`${assembly.name}-${suffix}`)?.adapter,
+  ).find(adapter => adapter !== undefined)
+  return {
+    assembly: withBaseUri(assembly, configUrl),
+    geneAdapter: geneAdapter && withBaseUri(geneAdapter, configUrl),
+  }
+}
+
+// throws on anything but a found config or a 404, so only a definitive
+// answer is cached
+async function fetchDescription(assemblyName: string) {
+  for (const url of getConfigUrls(assemblyName)) {
+    const response = await fetch(url)
+    if (response.ok) {
+      const config = (await response.json()) as HubConfig
+      return describeFromConfig(config, assemblyName, url)
+    }
+    if (response.status !== 404) {
+      throw new Error(`${url}: HTTP ${response.status}`)
+    }
+  }
+  return undefined
+}
+
+const descriptions = new Map<string, Promise<Description | undefined>>()
+
+function describe(assemblyName: string) {
+  let description = descriptions.get(assemblyName)
+  if (!description) {
+    description = fetchDescription(assemblyName).catch((error: unknown) => {
+      descriptions.delete(assemblyName)
+      console.error(error)
+      return undefined
+    })
+    descriptions.set(assemblyName, description)
+  }
+  return description
+}
+
+/**
+ * Core-describeAssemblies: the assembly config and gene track adapter the
+ * hosted config of each named genome holds, read without connecting it. A
+ * name another plugin already described, or one no hosted config could hold,
+ * is left alone
+ */
+export async function describeAssemblies(
+  described: unknown,
+  assemblyNames: unknown,
+) {
+  const before =
+    typeof described === 'object' && described !== null ? described : {}
+  const names = Array.isArray(assemblyNames)
+    ? assemblyNames.filter((name): name is string => typeof name === 'string')
+    : []
+  const answers = await Promise.all(
+    names
+      .filter(
+        name => !Object.hasOwn(before, name) && getConfigUrls(name).length > 0,
+      )
+      .map(async name => [name, await describe(name)] as const),
+  )
+  return {
+    ...before,
+    ...Object.fromEntries(
+      answers.filter(([, description]) => description !== undefined),
+    ),
+  }
+}

package/src/index.ts

@@ -2,6 +2,8 @@ import Plugin from '@jbrowse/core/Plugin'
 import { isAbstractMenuManager, isElectron } from '@jbrowse/core/util'
 import { getRoot, getSnapshot } from '@jbrowse/mobx-state-tree'
 
+import { getConfigUrls } from './configUrls'
+import { describeAssemblies } from './describeAssemblies'
 import { saveAs, toDesktopSnapshot } from './util'
 import { version } from '../package.json'
 
@@ -30,48 +32,6 @@ function downloadDesktopSession(session: AbstractSessionModel) {
   )
 }
 
-function getGenArkConfigUrl(accession: string) {
-  const [base, rest] = accession.split('_')
-  if (!rest) {
-    return undefined
-  }
-  const match = rest.match(/.{1,3}/g)
-  if (!match || match.length < 3) {
-    return undefined
-  }
-  const [b1, b2, b3] = match
-  return `https://jbrowse.org/hubs/genark/${base}/${b1}/${b2}/${b3}/${accession}/config.json`
-}
-
-// Candidate urls for an assembly name, most preferred first. The probe below
-// takes the first that exists, so a name with no hosted config anywhere is
-// still answered by staying quiet.
-//
-// A UCSC db gets `minimal.json` ahead of `config.json`. Both carry the same
-// `assemblies` block (minimal.json is a filtered copy of config.json, tracks
-// dropped to NCBI RefSeq / GENCODE / RepeatMasker / gaps), and the assembly is
-// the whole reason this connection exists — the tracks are a bonus for the
-// panel it opens. The full config is an expensive way to learn a sequence
-// adapter: hg38 is 2.1MB against minimal's 300KB, hg19 1.35MB against 57KB,
-// hs1 603KB against 12KB, and the parse is followed by MST instantiating every
-// track config in it on the main thread (hg38 595 against 33, hs1 624 against
-// 7). hg38 alone names 239 distinct mate assemblies across its 239 synteny
-// tracks, so a session that opens a few of them pays this several times over.
-//
-// What minimal.json costs is the mate genome's long tail — conservation,
-// expression, the rest of the hub. Those are still one "Add connection" away
-// on the full config url, and nothing about this panel implied they were
-// coming. GenArk hubs have no minimal.json and don't need one; their whole
-// config is ~40KB.
-function getConfigUrls(assemblyName: string) {
-  if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {
-    const url = getGenArkConfigUrl(assemblyName)
-    return url ? [url] : []
-  }
-  const base = `https://jbrowse.org/ucsc/${assemblyName}`
-  return [`${base}/minimal.json`, `${base}/config.json`]
-}
-
 // Every assembly name this plugin has already taken a run at, whether the probe
 // is still in flight or came back with nothing. The extension point fires on an
 // unresolved read, and `get` is read from render paths, so a name that resolves
@@ -197,6 +157,14 @@ export default class HubsViewerPlugin extends Plugin {
         return defaultResult
       },
     )
+    // A multi-way synteny lane whose genome the session lacks asks here for
+    // its assembly config and gene track. Cores older than the point never
+    // fire it, so this is inert on them
+    pluginManager.addToExtensionPoint(
+      'Core-describeAssemblies',
+      (described: unknown, args) =>
+        describeAssemblies(described, args.assemblyNames),
+    )
   }
 
   configure(pluginManager: PluginManager) {