@cmdcolin/jbrowse-plugin-hubs 1.0.2 → 1.0.3

package/dist/fetchAssemblyHub.d.ts

@@ -0,0 +1,10 @@
+export declare const fetchingAssemblies: Set<string>;
+export interface HubSession {
+    assemblyManager: {
+        get: (name: string) => unknown;
+    };
+    addSessionAssembly: (assembly: unknown) => void;
+    addTrackConf: (track: unknown) => void;
+    notifyError: (msg: string, e: unknown) => void;
+}
+export declare function fetchAssemblyHub(session: HubSession, assemblyName: string): Promise<void>;

package/dist/fetchAssemblyHub.js

@@ -0,0 +1,53 @@
+// Track assemblies we're currently fetching to avoid duplicate requests
+export const fetchingAssemblies = new Set();
+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}/${accession}/config.json`;
+}
+function getConfigUrl(assemblyName) {
+    // GenArk assemblies (GCA_* or GCF_*)
+    if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {
+        return getGenArkConfigUrl(assemblyName);
+    }
+    // UCSC assemblies (hg38, mm10, etc.)
+    return `https://jbrowse.org/ucsc/${assemblyName}/config.json`;
+}
+export async function fetchAssemblyHub(session, assemblyName) {
+    const url = getConfigUrl(assemblyName);
+    if (!url) {
+        return;
+    }
+    try {
+        const response = await fetch(url);
+        if (!response.ok) {
+            throw new Error(`HTTP ${response.status} from ${url}`);
+        }
+        const config = (await response.json());
+        // Add assemblies directly to session
+        for (const assembly of config.assemblies ?? []) {
+            if (!session.assemblyManager.get(assembly.name)) {
+                session.addSessionAssembly(assembly);
+            }
+        }
+        // Add tracks directly to session (addTrackConf handles duplicates)
+        for (const track of config.tracks ?? []) {
+            session.addTrackConf(track);
+        }
+    }
+    catch (e) {
+        console.error(e);
+        session.notifyError(`Failed to load assembly ${assemblyName}: ${e}`, e);
+    }
+    finally {
+        fetchingAssemblies.delete(assemblyName);
+    }
+}
+//# sourceMappingURL=fetchAssemblyHub.js.map

package/dist/fetchAssemblyHub.js.map

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

@@ -0,0 +1 @@
+export {};

package/dist/fetchAssemblyHub.test.js

@@ -0,0 +1,203 @@
+import assert from 'node:assert';
+import { beforeEach, describe, it } from 'node:test';
+import { fetchAssemblyHub, fetchingAssemblies } from "./fetchAssemblyHub.js";
+function createMockSession() {
+    const calls = {
+        addSessionAssembly: [],
+        addTrackConf: [],
+        notifyError: [],
+    };
+    return {
+        session: {
+            assemblyManager: {
+                get: (_name) => undefined,
+            },
+            addSessionAssembly: (assembly) => {
+                calls.addSessionAssembly.push(assembly);
+            },
+            addTrackConf: (track) => {
+                calls.addTrackConf.push(track);
+            },
+            notifyError: (msg, e) => {
+                calls.notifyError.push({ msg, e });
+            },
+        },
+        calls,
+    };
+}
+function mockFetch(config, ok = true, status = 200) {
+    const originalFetch = globalThis.fetch;
+    globalThis.fetch = (async () => ({
+        ok,
+        status,
+        json: async () => config,
+    }));
+    return () => {
+        globalThis.fetch = originalFetch;
+    };
+}
+describe('fetchAssemblyHub', () => {
+    beforeEach(() => {
+        fetchingAssemblies.clear();
+    });
+    it('adds assemblies from fetched config', async () => {
+        const { session, calls } = createMockSession();
+        const mockConfig = {
+            assemblies: [{ name: 'hg38', sequence: {} }],
+            tracks: [],
+        };
+        const restore = mockFetch(mockConfig);
+        fetchingAssemblies.add('hg38');
+        await fetchAssemblyHub(session, 'hg38');
+        restore();
+        assert.strictEqual(calls.addSessionAssembly.length, 1);
+        assert.deepStrictEqual(calls.addSessionAssembly[0], {
+            name: 'hg38',
+            sequence: {},
+        });
+        assert.strictEqual(fetchingAssemblies.has('hg38'), false);
+    });
+    it('adds tracks from fetched config', async () => {
+        const { session, calls } = createMockSession();
+        const mockConfig = {
+            assemblies: [],
+            tracks: [{ trackId: 'genes', type: 'FeatureTrack' }],
+        };
+        const restore = mockFetch(mockConfig);
+        fetchingAssemblies.add('hg38');
+        await fetchAssemblyHub(session, 'hg38');
+        restore();
+        assert.strictEqual(calls.addTrackConf.length, 1);
+        assert.deepStrictEqual(calls.addTrackConf[0], {
+            trackId: 'genes',
+            type: 'FeatureTrack',
+        });
+    });
+    it('skips assembly if already exists', async () => {
+        const { session, calls } = createMockSession();
+        session.assemblyManager.get = () => ({ name: 'hg38' });
+        const mockConfig = {
+            assemblies: [{ name: 'hg38', sequence: {} }],
+            tracks: [],
+        };
+        const restore = mockFetch(mockConfig);
+        fetchingAssemblies.add('hg38');
+        await fetchAssemblyHub(session, 'hg38');
+        restore();
+        assert.strictEqual(calls.addSessionAssembly.length, 0);
+    });
+    it('handles fetch error gracefully', async () => {
+        const { session, calls } = createMockSession();
+        const restore = mockFetch({}, false, 404);
+        fetchingAssemblies.add('nonexistent');
+        await fetchAssemblyHub(session, 'nonexistent');
+        restore();
+        assert.strictEqual(calls.notifyError.length, 1);
+        assert.strictEqual(fetchingAssemblies.has('nonexistent'), false);
+    });
+    it('handles network error gracefully', async () => {
+        const { session, calls } = createMockSession();
+        const originalFetch = globalThis.fetch;
+        globalThis.fetch = (async () => {
+            throw new Error('Network error');
+        });
+        fetchingAssemblies.add('hg38');
+        await fetchAssemblyHub(session, 'hg38');
+        globalThis.fetch = originalFetch;
+        assert.strictEqual(calls.notifyError.length, 1);
+        assert.strictEqual(fetchingAssemblies.has('hg38'), false);
+    });
+    it('cleans up fetchingAssemblies on success', async () => {
+        const { session } = createMockSession();
+        const mockConfig = { assemblies: [], tracks: [] };
+        const restore = mockFetch(mockConfig);
+        fetchingAssemblies.add('hg38');
+        assert.strictEqual(fetchingAssemblies.has('hg38'), true);
+        await fetchAssemblyHub(session, 'hg38');
+        restore();
+        assert.strictEqual(fetchingAssemblies.has('hg38'), false);
+    });
+});
+describe('extension point handler', () => {
+    it('fetchingAssemblies prevents duplicate requests', () => {
+        fetchingAssemblies.add('hg38');
+        const shouldFetch = !fetchingAssemblies.has('hg38');
+        assert.strictEqual(shouldFetch, false);
+    });
+    it('allows fetch for new assembly', () => {
+        fetchingAssemblies.clear();
+        const shouldFetch = !fetchingAssemblies.has('hg38');
+        assert.strictEqual(shouldFetch, true);
+    });
+});
+describe('GenArk assembly support', () => {
+    beforeEach(() => {
+        fetchingAssemblies.clear();
+    });
+    it('fetches GenArk assembly with GCF_ prefix', async () => {
+        const { session, calls } = createMockSession();
+        const mockConfig = {
+            assemblies: [{ name: 'GCF_009858895.2', sequence: {} }],
+            tracks: [],
+        };
+        let fetchedUrl = '';
+        const originalFetch = globalThis.fetch;
+        globalThis.fetch = (async (url) => {
+            fetchedUrl = url;
+            return {
+                ok: true,
+                status: 200,
+                json: async () => mockConfig,
+            };
+        });
+        fetchingAssemblies.add('GCF_009858895.2');
+        await fetchAssemblyHub(session, 'GCF_009858895.2');
+        globalThis.fetch = originalFetch;
+        assert.strictEqual(fetchedUrl, 'https://jbrowse.org/hubs/genark/GCF/009/858/895/GCF_009858895.2/config.json');
+        assert.strictEqual(calls.addSessionAssembly.length, 1);
+    });
+    it('fetches GenArk assembly with GCA_ prefix', async () => {
+        const { session, calls } = createMockSession();
+        const mockConfig = {
+            assemblies: [{ name: 'GCA_000001405.15', sequence: {} }],
+            tracks: [],
+        };
+        let fetchedUrl = '';
+        const originalFetch = globalThis.fetch;
+        globalThis.fetch = (async (url) => {
+            fetchedUrl = url;
+            return {
+                ok: true,
+                status: 200,
+                json: async () => mockConfig,
+            };
+        });
+        fetchingAssemblies.add('GCA_000001405.15');
+        await fetchAssemblyHub(session, 'GCA_000001405.15');
+        globalThis.fetch = originalFetch;
+        assert.strictEqual(fetchedUrl, 'https://jbrowse.org/hubs/genark/GCA/000/001/405/GCA_000001405.15/config.json');
+        assert.strictEqual(calls.addSessionAssembly.length, 1);
+    });
+    it('uses UCSC URL for non-GenArk assemblies', async () => {
+        const { session } = createMockSession();
+        const mockConfig = {
+            assemblies: [{ name: 'hg38', sequence: {} }],
+            tracks: [],
+        };
+        let fetchedUrl = '';
+        const originalFetch = globalThis.fetch;
+        globalThis.fetch = (async (url) => {
+            fetchedUrl = url;
+            return {
+                ok: true,
+                status: 200,
+                json: async () => mockConfig,
+            };
+        });
+        fetchingAssemblies.add('hg38');
+        await fetchAssemblyHub(session, 'hg38');
+        globalThis.fetch = originalFetch;
+        assert.strictEqual(fetchedUrl, 'https://jbrowse.org/ucsc/hg38/config.json');
+    });
+});
+//# sourceMappingURL=fetchAssemblyHub.test.js.map

package/dist/fetchAssemblyHub.test.js.map

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

@@ -4,5 +4,6 @@ export default class HubsViewerPlugin extends Plugin {
     name: string;
     version: any;
     install(pluginManager: PluginManager): void;
-    configure(pluginManager: PluginManager): void;
+    configure(_pluginManager: PluginManager): void;
 }
+export { type HubSession, fetchAssemblyHub, fetchingAssemblies, } from './fetchAssemblyHub.ts';

package/dist/index.js

@@ -1,4 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
+import { fetchAssemblyHub, fetchingAssemblies } from "./fetchAssemblyHub.js";
 import { version } from '../package.json';
 export default class HubsViewerPlugin extends Plugin {
     name = 'HubsViewerPlugin';
@@ -7,22 +8,21 @@ export default class HubsViewerPlugin extends Plugin {
         pluginManager.addToExtensionPoint('Core-handleUnrecognizedAssembly', (_defaultResult, args) => {
             const session = args.session;
             const assemblyName = args.assemblyName;
-            const jb2asm = `jb2hub-${assemblyName}`;
-            if (assemblyName &&
-                !session.connections.find((f) => f.connectionId === jb2asm)) {
-                console.log('getUnrecognizedAssembly', { assemblyName });
-                const conf = {
-                    type: 'JB2TrackHubConnection',
-                    uri: `https://jbrowse.org/ucsc/${assemblyName}/config.json`,
-                    name: `conn_${assemblyName}`,
-                    assemblyNames: [assemblyName],
-                    connectionId: jb2asm,
-                };
-                session.addConnectionConf(conf);
-                session.makeConnection(conf);
+            // Skip if missing required args
+            if (!session || !assemblyName) {
+                return;
             }
+            // Skip if already fetching (must check this first to prevent recursion)
+            if (fetchingAssemblies.has(assemblyName)) {
+                return;
+            }
+            // Mark as fetching before any other checks that might re-trigger this
+            fetchingAssemblies.add(assemblyName);
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            fetchAssemblyHub(session, assemblyName);
         });
     }
-    configure(pluginManager) { }
+    configure(_pluginManager) { }
 }
+export { fetchAssemblyHub, fetchingAssemblies, } from "./fetchAssemblyHub.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAEzC,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,MAAM;IAClD,IAAI,GAAG,kBAAkB,CAAA;IACzB,OAAO,GAAG,OAAO,CAAA;IAEjB,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,mBAAmB,CAC/B,iCAAiC,EACjC,CAAC,cAAc,EAAE,IAAI,EAAE,EAAE;YACvB,MAAM,OAAO,GAAG,IAAI,CAAC,OAAc,CAAA;YACnC,MAAM,YAAY,GAAG,IAAI,CAAC,YAAsB,CAAA;YAChD,MAAM,MAAM,GAAG,UAAU,YAAY,EAAE,CAAA;YACvC,IACE,YAAY;gBACZ,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CACvB,CAAC,CAA2B,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,KAAK,MAAM,CAC3D,EACD,CAAC;gBACD,OAAO,CAAC,GAAG,CAAC,yBAAyB,EAAE,EAAE,YAAY,EAAE,CAAC,CAAA;gBACxD,MAAM,IAAI,GAAG;oBACX,IAAI,EAAE,uBAAuB;oBAC7B,GAAG,EAAE,4BAA4B,YAAY,cAAc;oBAC3D,IAAI,EAAE,QAAQ,YAAY,EAAE;oBAC5B,aAAa,EAAE,CAAC,YAAY,CAAC;oBAC7B,YAAY,EAAE,MAAM;iBACrB,CAAA;gBACD,OAAO,CAAC,iBAAiB,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;YAC9B,CAAC;QACH,CAAC,CACF,CAAA;IACH,CAAC;IAED,SAAS,CAAC,aAA4B,IAAG,CAAC;CAC3C"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAAE,gBAAgB,EAAE,kBAAkB,EAAE,MAAM,uBAAuB,CAAA;AAC5E,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAIzC,MAAM,CAAC,OAAO,OAAO,gBAAiB,SAAQ,MAAM;IAClD,IAAI,GAAG,kBAAkB,CAAA;IACzB,OAAO,GAAG,OAAO,CAAA;IAEjB,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,mBAAmB,CAC/B,iCAAiC,EACjC,CAAC,cAAc,EAAE,IAAI,EAAE,EAAE;YACvB,MAAM,OAAO,GAAG,IAAI,CAAC,OAAiC,CAAA;YACtD,MAAM,YAAY,GAAG,IAAI,CAAC,YAAkC,CAAA;YAE5D,gCAAgC;YAChC,IAAI,CAAC,OAAO,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC9B,OAAM;YACR,CAAC;YAED,wEAAwE;YACxE,IAAI,kBAAkB,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,CAAC;gBACzC,OAAM;YACR,CAAC;YAED,sEAAsE;YACtE,kBAAkB,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAEpC,mEAAmE;YACnE,gBAAgB,CAAC,OAAO,EAAE,YAAY,CAAC,CAAA;QACzC,CAAC,CACF,CAAA;IACH,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C;AAED,OAAO,EAEL,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,uBAAuB,CAAA"}

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

@@ -1,2 +1,2 @@
-"use strict";var JBrowsePluginHubs=(()=>{var g=Object.create;var a=Object.defineProperty;var f=Object.getOwnPropertyDescriptor;var y=Object.getOwnPropertyNames;var j=Object.getPrototypeOf,h=Object.prototype.hasOwnProperty;var w=(n,e)=>()=>(e||n((e={exports:{}}).exports,e),e.exports),x=(n,e)=>{for(var s in e)a(n,s,{get:e[s],enumerable:!0})},d=(n,e,s,r)=>{if(e&&typeof e=="object"||typeof e=="function")for(let i of y(e))!h.call(n,i)&&i!==s&&a(n,i,{get:()=>e[i],enumerable:!(r=f(e,i))||r.enumerable});return n};var v=(n,e,s)=>(s=n!=null?g(j(n)):{},d(e||!n||!n.__esModule?a(s,"default",{value:n,enumerable:!0}):s,n)),k=n=>d(a({},"__esModule",{value:!0}),n);var p=w((N,m)=>{m.exports=JBrowseExports["@jbrowse/core/Plugin"]});var P={};x(P,{default:()=>l});var b=v(p());var u="1.0.2";var l=class extends b.default{name="HubsViewerPlugin";version=u;install(e){e.addToExtensionPoint("Core-handleUnrecognizedAssembly",(s,r)=>{let i=r.session,t=r.assemblyName,c=`jb2hub-${t}`;if(t&&!i.connections.find(o=>o.connectionId===c)){console.log("getUnrecognizedAssembly",{assemblyName:t});let o={type:"JB2TrackHubConnection",uri:`https://jbrowse.org/ucsc/${t}/config.json`,name:`conn_${t}`,assemblyNames:[t],connectionId:c};i.addConnectionConf(o),i.makeConnection(o)}})}configure(e){}};return k(P);})();
+"use strict";var JBrowsePluginHubs=(()=>{var g=Object.create;var a=Object.defineProperty;var y=Object.getOwnPropertyDescriptor;var h=Object.getOwnPropertyNames;var w=Object.getPrototypeOf,x=Object.prototype.hasOwnProperty;var j=(e,s)=>()=>(s||e((s={exports:{}}).exports,s),s.exports),k=(e,s)=>{for(var n in s)a(e,n,{get:s[n],enumerable:!0})},u=(e,s,n,t)=>{if(s&&typeof s=="object"||typeof s=="function")for(let r of h(s))!x.call(e,r)&&r!==n&&a(e,r,{get:()=>s[r],enumerable:!(t=y(s,r))||t.enumerable});return e};var A=(e,s,n)=>(n=e!=null?g(w(e)):{},u(s||!e||!e.__esModule?a(n,"default",{value:e,enumerable:!0}):n,e)),v=e=>u(a({},"__esModule",{value:!0}),e);var m=j((M,d)=>{d.exports=JBrowseExports["@jbrowse/core/Plugin"]});var S={};k(S,{default:()=>c,fetchAssemblyHub:()=>l,fetchingAssemblies:()=>o});var f=A(m());var o=new Set;function H(e){let[s,n]=e.split("_");if(!n)return;let t=n.match(/.{1,3}/g);if(!t||t.length<3)return;let[r,i,p]=t;return`https://jbrowse.org/hubs/genark/${s}/${r}/${i}/${p}/${e}/config.json`}function $(e){return e.startsWith("GCA_")||e.startsWith("GCF_")?H(e):`https://jbrowse.org/ucsc/${e}/config.json`}async function l(e,s){let n=$(s);if(n)try{let t=await fetch(n);if(!t.ok)throw new Error(`HTTP ${t.status} from ${n}`);let r=await t.json();for(let i of r.assemblies??[])e.assemblyManager.get(i.name)||e.addSessionAssembly(i);for(let i of r.tracks??[])e.addTrackConf(i)}catch(t){console.error(t),e.notifyError(`Failed to load assembly ${s}: ${t}`,t)}finally{o.delete(s)}}var b="1.0.3";var c=class extends f.default{name="HubsViewerPlugin";version=b;install(s){s.addToExtensionPoint("Core-handleUnrecognizedAssembly",(n,t)=>{let r=t.session,i=t.assemblyName;!r||!i||o.has(i)||(o.add(i),l(r,i))})}configure(s){}};return v(S);})();
 //# 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", "../src/index.ts", "../package.json"],
-  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nimport { version } from '../package.json'\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 any\n        const assemblyName = args.assemblyName as string\n        const jb2asm = `jb2hub-${assemblyName}`\n        if (\n          assemblyName &&\n          !session.connections.find(\n            (f: { connectionId: string }) => f.connectionId === jb2asm,\n          )\n        ) {\n          console.log('getUnrecognizedAssembly', { assemblyName })\n          const conf = {\n            type: 'JB2TrackHubConnection',\n            uri: `https://jbrowse.org/ucsc/${assemblyName}/config.json`,\n            name: `conn_${assemblyName}`,\n            assemblyNames: [assemblyName],\n            connectionId: jb2asm,\n          }\n          session.addConnectionConf(conf)\n          session.makeConnection(conf)\n        }\n      },\n    )\n  }\n\n  configure(pluginManager: PluginManager) {}\n}\n", "{\n  \"version\": \"1.0.2\",\n  \"license\": \"MIT\",\n  \"name\": \"@cmdcolin/jbrowse-plugin-hubs\",\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\",\n    \"test\": \"vitest\",\n    \"format\": \"prettier --write .\",\n    \"prebuild\": \"npm run clean\",\n    \"build\": \"tsc && NODE_ENV=production node esbuild.mjs\",\n    \"lint\": \"eslint --report-unused-disable-directives --max-warnings 0\",\n    \"prepack\": \"npm run build\",\n    \"postversion\": \"git push --follow-tags\"\n  },\n  \"devDependencies\": {\n    \"@babel/core\": \"^7.16.5\",\n    \"@babel/preset-react\": \"^7.10.4\",\n    \"@emotion/react\": \"^11.10.4\",\n    \"@fal-works/esbuild-plugin-global-externals\": \"^2.1.2\",\n    \"@jbrowse/core\": \"^3.0.1\",\n    \"@jbrowse/plugin-data-management\": \"^3.0.1\",\n    \"@jbrowse/plugin-linear-genome-view\": \"^3.0.1\",\n    \"@mui/material\": \"^7.0.1\",\n    \"@mui/system\": \"^7.0.1\",\n    \"@mui/x-data-grid\": \"^8.2.0\",\n    \"@types/d3-array\": \"^3.2.1\",\n    \"@types/d3-hierarchy\": \"^3.1.7\",\n    \"@types/node\": \"^22.15.16\",\n    \"@types/react\": \"^19.0.1\",\n    \"chalk\": \"^5.3.0\",\n    \"esbuild\": \"^0.25.0\",\n    \"eslint\": \"^9.17.0\",\n    \"eslint-plugin-import\": \"^2.31.0\",\n    \"eslint-plugin-react\": \"^7.20.3\",\n    \"eslint-plugin-react-hooks\": \"^5.1.0\",\n    \"eslint-plugin-unicorn\": \"^60.0.0\",\n    \"mobx\": \"^6.0.0\",\n    \"mobx-react\": \"^9.0.1\",\n    \"mobx-state-tree\": \"^5.4.1\",\n    \"prettier\": \"^3.4.2\",\n    \"pretty-bytes\": \"^7.0.0\",\n    \"react\": \"^19.0.0\",\n    \"react-dom\": \"^19.0.0\",\n    \"rimraf\": \"^6.0.1\",\n    \"rxjs\": \"^7.8.1\",\n    \"serve\": \"^14.2.0\",\n    \"tss-react\": \"^4.9.18\",\n    \"typescript\": \"^5.1.6\",\n    \"typescript-eslint\": \"^8.18.0\",\n    \"vitest\": \"^3.2.1\"\n  },\n  \"dependencies\": {\n    \"@gmod/bgzf-filehandle\": \"^4.0.0\",\n    \"abortable-promise-cache\": \"^1.5.0\",\n    \"buffer\": \"^6.0.3\",\n    \"d3-array\": \"^3.2.4\",\n    \"d3-hierarchy\": \"^3.1.2\",\n    \"fast-deep-equal\": \"^3.1.3\",\n    \"generic-filehandle2\": \"^2.0.1\",\n    \"long\": \"^5.2.3\"\n  },\n  \"publishConfig\": {\n    \"access\": \"public\"\n  }\n}\n"],
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-  "names": ["require_Plugin", "__commonJSMin", "exports", "module", "index_exports", "__export", "HubsViewerPlugin", "import_Plugin", "version", "HubsViewerPlugin", "Plugin", "version", "pluginManager", "_defaultResult", "args", "session", "assemblyName", "jb2asm", "f", "conf"]
+  "sources": ["global-externals:@jbrowse/core/Plugin", "../src/index.ts", "../src/fetchAssemblyHub.ts", "../package.json"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nimport { fetchAssemblyHub, fetchingAssemblies } from './fetchAssemblyHub.ts'\nimport { version } from '../package.json'\n\nimport type { HubSession } from './fetchAssemblyHub.ts'\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 HubSession | undefined\n        const assemblyName = args.assemblyName as string | undefined\n\n        // Skip if missing required args\n        if (!session || !assemblyName) {\n          return\n        }\n\n        // Skip if already fetching (must check this first to prevent recursion)\n        if (fetchingAssemblies.has(assemblyName)) {\n          return\n        }\n\n        // Mark as fetching before any other checks that might re-trigger this\n        fetchingAssemblies.add(assemblyName)\n\n        // eslint-disable-next-line @typescript-eslint/no-floating-promises\n        fetchAssemblyHub(session, assemblyName)\n      },\n    )\n  }\n\n  configure(_pluginManager: PluginManager) {}\n}\n\nexport {\n  type HubSession,\n  fetchAssemblyHub,\n  fetchingAssemblies,\n} from './fetchAssemblyHub.ts'\n", "// Track assemblies we're currently fetching to avoid duplicate requests\nexport const fetchingAssemblies = new Set<string>()\n\nexport interface HubSession {\n  assemblyManager: { get: (name: string) => unknown }\n  addSessionAssembly: (assembly: unknown) => void\n  addTrackConf: (track: unknown) => void\n  notifyError: (msg: string, e: unknown) => void\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\nfunction getConfigUrl(assemblyName: string) {\n  // GenArk assemblies (GCA_* or GCF_*)\n  if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {\n    return getGenArkConfigUrl(assemblyName)\n  }\n  // UCSC assemblies (hg38, mm10, etc.)\n  return `https://jbrowse.org/ucsc/${assemblyName}/config.json`\n}\n\nexport async function fetchAssemblyHub(\n  session: HubSession,\n  assemblyName: string,\n) {\n  const url = getConfigUrl(assemblyName)\n  if (!url) {\n    return\n  }\n  try {\n    const response = await fetch(url)\n    if (!response.ok) {\n      throw new Error(`HTTP ${response.status} from ${url}`)\n    }\n    const config = (await response.json()) as {\n      assemblies?: { name: string }[]\n      tracks?: unknown[]\n    }\n\n    // Add assemblies directly to session\n    for (const assembly of config.assemblies ?? []) {\n      if (!session.assemblyManager.get(assembly.name)) {\n        session.addSessionAssembly(assembly)\n      }\n    }\n\n    // Add tracks directly to session (addTrackConf handles duplicates)\n    for (const track of config.tracks ?? []) {\n      session.addTrackConf(track)\n    }\n  } catch (e) {\n    console.error(e)\n    session.notifyError(`Failed to load assembly ${assemblyName}: ${e}`, e)\n  } finally {\n    fetchingAssemblies.delete(assemblyName)\n  }\n}\n", "{\n  \"version\": \"1.0.3\",\n  \"license\": \"MIT\",\n  \"name\": \"@cmdcolin/jbrowse-plugin-hubs\",\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\": \"node --experimental-strip-types --test src/fetchAssemblyHub.test.ts\",\n    \"format\": \"prettier --write .\",\n    \"prebuild\": \"npm run clean\",\n    \"build\": \"tsc && NODE_ENV=production node esbuild.mjs\",\n    \"lint\": \"eslint --report-unused-disable-directives --max-warnings 0\",\n    \"prepack\": \"npm run build\",\n    \"postversion\": \"git push --follow-tags\"\n  },\n  \"devDependencies\": {\n    \"@babel/core\": \"^7.28.6\",\n    \"@babel/preset-react\": \"^7.10.4\",\n    \"@emotion/react\": \"^11.10.4\",\n    \"@emotion/styled\": \"^11.14.1\",\n    \"@eslint/js\": \"^9.39.2\",\n    \"@fal-works/esbuild-plugin-global-externals\": \"^2.1.2\",\n    \"@jbrowse/core\": \"^4.1.3\",\n    \"@jbrowse/plugin-data-management\": \"^4.1.3\",\n    \"@jbrowse/plugin-linear-genome-view\": \"^4.1.3\",\n    \"@mui/material\": \"^7.3.7\",\n    \"@mui/system\": \"^7.3.7\",\n    \"@mui/x-data-grid\": \"^8.26.0\",\n    \"@types/d3-array\": \"^3.2.1\",\n    \"@types/d3-hierarchy\": \"^3.1.7\",\n    \"@types/node\": \"^25.1.0\",\n    \"@types/react\": \"^19.2.10\",\n    \"esbuild\": \"^0.27.2\",\n    \"eslint\": \"^9.39.2\",\n    \"eslint-plugin-import\": \"^2.31.0\",\n    \"eslint-plugin-unicorn\": \"^62.0.0\",\n    \"mobx\": \"^6.0.0\",\n    \"mobx-react\": \"^9.0.1\",\n    \"mobx-state-tree\": \"^7.0.2\",\n    \"prettier\": \"^3.8.1\",\n    \"pretty-bytes\": \"^7.0.0\",\n    \"react\": \"^19.2.4\",\n    \"react-dom\": \"^19.2.4\",\n    \"rimraf\": \"^6.1.2\",\n    \"rxjs\": \"^7.8.1\",\n    \"serve\": \"^14.2.0\",\n    \"typescript\": \"^5.1.6\",\n    \"typescript-eslint\": \"^8.54.0\"\n  },\n  \"publishConfig\": {\n    \"access\": \"public\"\n  }\n}\n"],
+  "mappings": "gpBAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,sBAAsB,ICAtD,IAAAC,EAAA,GAAAC,EAAAD,EAAA,aAAAE,EAAA,qBAAAC,EAAA,uBAAAC,IAAA,IAAAC,EAAmB,OCCZ,IAAMC,EAAqB,IAAI,IAStC,SAASC,EAAmBC,EAAmB,CAC7C,GAAM,CAACC,EAAMC,CAAI,EAAIF,EAAU,MAAM,GAAG,EACxC,GAAI,CAACE,EACH,OAEF,IAAMC,EAAQD,EAAK,MAAM,SAAS,EAClC,GAAI,CAACC,GAASA,EAAM,OAAS,EAC3B,OAEF,GAAM,CAACC,EAAIC,EAAIC,CAAE,EAAIH,EACrB,MAAO,mCAAmCF,CAAI,IAAIG,CAAE,IAAIC,CAAE,IAAIC,CAAE,IAAIN,CAAS,cAC/E,CAEA,SAASO,EAAaC,EAAsB,CAE1C,OAAIA,EAAa,WAAW,MAAM,GAAKA,EAAa,WAAW,MAAM,EAC5DT,EAAmBS,CAAY,EAGjC,4BAA4BA,CAAY,cACjD,CAEA,eAAsBC,EACpBC,EACAF,EACA,CACA,IAAMG,EAAMJ,EAAaC,CAAY,EACrC,GAAKG,EAGL,GAAI,CACF,IAAMC,EAAW,MAAM,MAAMD,CAAG,EAChC,GAAI,CAACC,EAAS,GACZ,MAAM,IAAI,MAAM,QAAQA,EAAS,MAAM,SAASD,CAAG,EAAE,EAEvD,IAAME,EAAU,MAAMD,EAAS,KAAK,EAMpC,QAAWE,KAAYD,EAAO,YAAc,CAAC,EACtCH,EAAQ,gBAAgB,IAAII,EAAS,IAAI,GAC5CJ,EAAQ,mBAAmBI,CAAQ,EAKvC,QAAWC,KAASF,EAAO,QAAU,CAAC,EACpCH,EAAQ,aAAaK,CAAK,CAE9B,OAASC,EAAG,CACV,QAAQ,MAAMA,CAAC,EACfN,EAAQ,YAAY,2BAA2BF,CAAY,KAAKQ,CAAC,GAAIA,CAAC,CACxE,QAAE,CACAlB,EAAmB,OAAOU,CAAY,CACxC,CACF,CClEE,IAAAS,EAAW,QFOb,IAAqBC,EAArB,cAA8C,EAAAC,OAAO,CACnD,KAAO,mBACP,QAAUC,EAEV,QAAQC,EAA8B,CACpCA,EAAc,oBACZ,kCACA,CAACC,EAAgBC,IAAS,CACxB,IAAMC,EAAUD,EAAK,QACfE,EAAeF,EAAK,aAGtB,CAACC,GAAW,CAACC,GAKbC,EAAmB,IAAID,CAAY,IAKvCC,EAAmB,IAAID,CAAY,EAGnCE,EAAiBH,EAASC,CAAY,EACxC,CACF,CACF,CAEA,UAAUG,EAA+B,CAAC,CAC5C",
+  "names": ["require_Plugin", "__commonJSMin", "exports", "module", "index_exports", "__export", "HubsViewerPlugin", "fetchAssemblyHub", "fetchingAssemblies", "import_Plugin", "fetchingAssemblies", "getGenArkConfigUrl", "accession", "base", "rest", "match", "b1", "b2", "b3", "getConfigUrl", "assemblyName", "fetchAssemblyHub", "session", "url", "response", "config", "assembly", "track", "e", "version", "HubsViewerPlugin", "Plugin", "version", "pluginManager", "_defaultResult", "args", "session", "assemblyName", "fetchingAssemblies", "fetchAssemblyHub", "_pluginManager"]
 }

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.0.2",
+  "version": "1.0.3",
   "license": "MIT",
   "name": "@cmdcolin/jbrowse-plugin-hubs",
   "keywords": [
@@ -15,8 +15,8 @@
   ],
   "scripts": {
     "clean": "rimraf dist",
-    "start": "node esbuild.mjs",
-    "test": "vitest",
+    "start": "node esbuild.mjs --watch",
+    "test": "node --experimental-strip-types --test src/fetchAssemblyHub.test.ts",
     "format": "prettier --write .",
     "prebuild": "npm run clean",
     "build": "tsc && NODE_ENV=production node esbuild.mjs",
@@ -25,51 +25,38 @@
     "postversion": "git push --follow-tags"
   },
   "devDependencies": {
-    "@babel/core": "^7.16.5",
+    "@babel/core": "^7.28.6",
     "@babel/preset-react": "^7.10.4",
     "@emotion/react": "^11.10.4",
+    "@emotion/styled": "^11.14.1",
+    "@eslint/js": "^9.39.2",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^3.0.1",
-    "@jbrowse/plugin-data-management": "^3.0.1",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.1",
-    "@mui/material": "^7.0.1",
-    "@mui/system": "^7.0.1",
-    "@mui/x-data-grid": "^8.2.0",
+    "@jbrowse/core": "^4.1.3",
+    "@jbrowse/plugin-data-management": "^4.1.3",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.3",
+    "@mui/material": "^7.3.7",
+    "@mui/system": "^7.3.7",
+    "@mui/x-data-grid": "^8.26.0",
     "@types/d3-array": "^3.2.1",
     "@types/d3-hierarchy": "^3.1.7",
-    "@types/node": "^22.15.16",
-    "@types/react": "^19.0.1",
-    "chalk": "^5.3.0",
-    "esbuild": "^0.25.0",
-    "eslint": "^9.17.0",
+    "@types/node": "^25.1.0",
+    "@types/react": "^19.2.10",
+    "esbuild": "^0.27.2",
+    "eslint": "^9.39.2",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-react": "^7.20.3",
-    "eslint-plugin-react-hooks": "^5.1.0",
-    "eslint-plugin-unicorn": "^60.0.0",
+    "eslint-plugin-unicorn": "^62.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.1",
-    "mobx-state-tree": "^5.4.1",
-    "prettier": "^3.4.2",
+    "mobx-state-tree": "^7.0.2",
+    "prettier": "^3.8.1",
     "pretty-bytes": "^7.0.0",
-    "react": "^19.0.0",
-    "react-dom": "^19.0.0",
-    "rimraf": "^6.0.1",
+    "react": "^19.2.4",
+    "react-dom": "^19.2.4",
+    "rimraf": "^6.1.2",
     "rxjs": "^7.8.1",
     "serve": "^14.2.0",
-    "tss-react": "^4.9.18",
     "typescript": "^5.1.6",
-    "typescript-eslint": "^8.18.0",
-    "vitest": "^3.2.1"
-  },
-  "dependencies": {
-    "@gmod/bgzf-filehandle": "^4.0.0",
-    "abortable-promise-cache": "^1.5.0",
-    "buffer": "^6.0.3",
-    "d3-array": "^3.2.4",
-    "d3-hierarchy": "^3.1.2",
-    "fast-deep-equal": "^3.1.3",
-    "generic-filehandle2": "^2.0.1",
-    "long": "^5.2.3"
+    "typescript-eslint": "^8.54.0"
   },
   "publishConfig": {
     "access": "public"

package/src/fetchAssemblyHub.test.ts

@@ -0,0 +1,255 @@
+import assert from 'node:assert'
+import { beforeEach, describe, it } from 'node:test'
+
+import { fetchAssemblyHub, fetchingAssemblies } from './fetchAssemblyHub.ts'
+
+import type { HubSession } from './fetchAssemblyHub.ts'
+
+function createMockSession(): {
+  session: HubSession
+  calls: {
+    addSessionAssembly: unknown[]
+    addTrackConf: unknown[]
+    notifyError: unknown[]
+  }
+} {
+  const calls = {
+    addSessionAssembly: [] as unknown[],
+    addTrackConf: [] as unknown[],
+    notifyError: [] as unknown[],
+  }
+  return {
+    session: {
+      assemblyManager: {
+        get: (_name: string) => undefined as unknown,
+      },
+      addSessionAssembly: (assembly: unknown) => {
+        calls.addSessionAssembly.push(assembly)
+      },
+      addTrackConf: (track: unknown) => {
+        calls.addTrackConf.push(track)
+      },
+      notifyError: (msg: string, e: unknown) => {
+        calls.notifyError.push({ msg, e })
+      },
+    },
+    calls,
+  }
+}
+
+function mockFetch(config: unknown, ok = true, status = 200) {
+  const originalFetch = globalThis.fetch
+  globalThis.fetch = (async () => ({
+    ok,
+    status,
+    json: async () => config,
+  })) as unknown as typeof fetch
+  return () => {
+    globalThis.fetch = originalFetch
+  }
+}
+
+describe('fetchAssemblyHub', () => {
+  beforeEach(() => {
+    fetchingAssemblies.clear()
+  })
+
+  it('adds assemblies from fetched config', async () => {
+    const { session, calls } = createMockSession()
+    const mockConfig = {
+      assemblies: [{ name: 'hg38', sequence: {} }],
+      tracks: [],
+    }
+    const restore = mockFetch(mockConfig)
+
+    fetchingAssemblies.add('hg38')
+    await fetchAssemblyHub(session, 'hg38')
+    restore()
+
+    assert.strictEqual(calls.addSessionAssembly.length, 1)
+    assert.deepStrictEqual(calls.addSessionAssembly[0], {
+      name: 'hg38',
+      sequence: {},
+    })
+    assert.strictEqual(fetchingAssemblies.has('hg38'), false)
+  })
+
+  it('adds tracks from fetched config', async () => {
+    const { session, calls } = createMockSession()
+    const mockConfig = {
+      assemblies: [],
+      tracks: [{ trackId: 'genes', type: 'FeatureTrack' }],
+    }
+    const restore = mockFetch(mockConfig)
+
+    fetchingAssemblies.add('hg38')
+    await fetchAssemblyHub(session, 'hg38')
+    restore()
+
+    assert.strictEqual(calls.addTrackConf.length, 1)
+    assert.deepStrictEqual(calls.addTrackConf[0], {
+      trackId: 'genes',
+      type: 'FeatureTrack',
+    })
+  })
+
+  it('skips assembly if already exists', async () => {
+    const { session, calls } = createMockSession()
+    session.assemblyManager.get = () => ({ name: 'hg38' })
+    const mockConfig = {
+      assemblies: [{ name: 'hg38', sequence: {} }],
+      tracks: [],
+    }
+    const restore = mockFetch(mockConfig)
+
+    fetchingAssemblies.add('hg38')
+    await fetchAssemblyHub(session, 'hg38')
+    restore()
+
+    assert.strictEqual(calls.addSessionAssembly.length, 0)
+  })
+
+  it('handles fetch error gracefully', async () => {
+    const { session, calls } = createMockSession()
+    const restore = mockFetch({}, false, 404)
+
+    fetchingAssemblies.add('nonexistent')
+    await fetchAssemblyHub(session, 'nonexistent')
+    restore()
+
+    assert.strictEqual(calls.notifyError.length, 1)
+    assert.strictEqual(fetchingAssemblies.has('nonexistent'), false)
+  })
+
+  it('handles network error gracefully', async () => {
+    const { session, calls } = createMockSession()
+    const originalFetch = globalThis.fetch
+    globalThis.fetch = (async () => {
+      throw new Error('Network error')
+    }) as unknown as typeof fetch
+
+    fetchingAssemblies.add('hg38')
+    await fetchAssemblyHub(session, 'hg38')
+    globalThis.fetch = originalFetch
+
+    assert.strictEqual(calls.notifyError.length, 1)
+    assert.strictEqual(fetchingAssemblies.has('hg38'), false)
+  })
+
+  it('cleans up fetchingAssemblies on success', async () => {
+    const { session } = createMockSession()
+    const mockConfig = { assemblies: [], tracks: [] }
+    const restore = mockFetch(mockConfig)
+
+    fetchingAssemblies.add('hg38')
+    assert.strictEqual(fetchingAssemblies.has('hg38'), true)
+
+    await fetchAssemblyHub(session, 'hg38')
+    restore()
+
+    assert.strictEqual(fetchingAssemblies.has('hg38'), false)
+  })
+})
+
+describe('extension point handler', () => {
+  it('fetchingAssemblies prevents duplicate requests', () => {
+    fetchingAssemblies.add('hg38')
+    const shouldFetch = !fetchingAssemblies.has('hg38')
+    assert.strictEqual(shouldFetch, false)
+  })
+
+  it('allows fetch for new assembly', () => {
+    fetchingAssemblies.clear()
+    const shouldFetch = !fetchingAssemblies.has('hg38')
+    assert.strictEqual(shouldFetch, true)
+  })
+})
+
+describe('GenArk assembly support', () => {
+  beforeEach(() => {
+    fetchingAssemblies.clear()
+  })
+
+  it('fetches GenArk assembly with GCF_ prefix', async () => {
+    const { session, calls } = createMockSession()
+    const mockConfig = {
+      assemblies: [{ name: 'GCF_009858895.2', sequence: {} }],
+      tracks: [],
+    }
+
+    let fetchedUrl = ''
+    const originalFetch = globalThis.fetch
+    globalThis.fetch = (async (url: string) => {
+      fetchedUrl = url
+      return {
+        ok: true,
+        status: 200,
+        json: async () => mockConfig,
+      }
+    }) as unknown as typeof fetch
+
+    fetchingAssemblies.add('GCF_009858895.2')
+    await fetchAssemblyHub(session, 'GCF_009858895.2')
+    globalThis.fetch = originalFetch
+
+    assert.strictEqual(
+      fetchedUrl,
+      'https://jbrowse.org/hubs/genark/GCF/009/858/895/GCF_009858895.2/config.json',
+    )
+    assert.strictEqual(calls.addSessionAssembly.length, 1)
+  })
+
+  it('fetches GenArk assembly with GCA_ prefix', async () => {
+    const { session, calls } = createMockSession()
+    const mockConfig = {
+      assemblies: [{ name: 'GCA_000001405.15', sequence: {} }],
+      tracks: [],
+    }
+
+    let fetchedUrl = ''
+    const originalFetch = globalThis.fetch
+    globalThis.fetch = (async (url: string) => {
+      fetchedUrl = url
+      return {
+        ok: true,
+        status: 200,
+        json: async () => mockConfig,
+      }
+    }) as unknown as typeof fetch
+
+    fetchingAssemblies.add('GCA_000001405.15')
+    await fetchAssemblyHub(session, 'GCA_000001405.15')
+    globalThis.fetch = originalFetch
+
+    assert.strictEqual(
+      fetchedUrl,
+      'https://jbrowse.org/hubs/genark/GCA/000/001/405/GCA_000001405.15/config.json',
+    )
+    assert.strictEqual(calls.addSessionAssembly.length, 1)
+  })
+
+  it('uses UCSC URL for non-GenArk assemblies', async () => {
+    const { session } = createMockSession()
+    const mockConfig = {
+      assemblies: [{ name: 'hg38', sequence: {} }],
+      tracks: [],
+    }
+
+    let fetchedUrl = ''
+    const originalFetch = globalThis.fetch
+    globalThis.fetch = (async (url: string) => {
+      fetchedUrl = url
+      return {
+        ok: true,
+        status: 200,
+        json: async () => mockConfig,
+      }
+    }) as unknown as typeof fetch
+
+    fetchingAssemblies.add('hg38')
+    await fetchAssemblyHub(session, 'hg38')
+    globalThis.fetch = originalFetch
+
+    assert.strictEqual(fetchedUrl, 'https://jbrowse.org/ucsc/hg38/config.json')
+  })
+})

package/src/fetchAssemblyHub.ts

@@ -0,0 +1,68 @@
+// Track assemblies we're currently fetching to avoid duplicate requests
+export const fetchingAssemblies = new Set<string>()
+
+export interface HubSession {
+  assemblyManager: { get: (name: string) => unknown }
+  addSessionAssembly: (assembly: unknown) => void
+  addTrackConf: (track: unknown) => void
+  notifyError: (msg: string, e: unknown) => void
+}
+
+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}/${accession}/config.json`
+}
+
+function getConfigUrl(assemblyName: string) {
+  // GenArk assemblies (GCA_* or GCF_*)
+  if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {
+    return getGenArkConfigUrl(assemblyName)
+  }
+  // UCSC assemblies (hg38, mm10, etc.)
+  return `https://jbrowse.org/ucsc/${assemblyName}/config.json`
+}
+
+export async function fetchAssemblyHub(
+  session: HubSession,
+  assemblyName: string,
+) {
+  const url = getConfigUrl(assemblyName)
+  if (!url) {
+    return
+  }
+  try {
+    const response = await fetch(url)
+    if (!response.ok) {
+      throw new Error(`HTTP ${response.status} from ${url}`)
+    }
+    const config = (await response.json()) as {
+      assemblies?: { name: string }[]
+      tracks?: unknown[]
+    }
+
+    // Add assemblies directly to session
+    for (const assembly of config.assemblies ?? []) {
+      if (!session.assemblyManager.get(assembly.name)) {
+        session.addSessionAssembly(assembly)
+      }
+    }
+
+    // Add tracks directly to session (addTrackConf handles duplicates)
+    for (const track of config.tracks ?? []) {
+      session.addTrackConf(track)
+    }
+  } catch (e) {
+    console.error(e)
+    session.notifyError(`Failed to load assembly ${assemblyName}: ${e}`, e)
+  } finally {
+    fetchingAssemblies.delete(assemblyName)
+  }
+}

package/src/index.ts

@@ -1,8 +1,11 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 
+import { fetchAssemblyHub, fetchingAssemblies } from './fetchAssemblyHub.ts'
 import { version } from '../package.json'
 
+import type { HubSession } from './fetchAssemblyHub.ts'
+
 export default class HubsViewerPlugin extends Plugin {
   name = 'HubsViewerPlugin'
   version = version
@@ -11,29 +14,33 @@ export default class HubsViewerPlugin extends Plugin {
     pluginManager.addToExtensionPoint(
       'Core-handleUnrecognizedAssembly',
       (_defaultResult, args) => {
-        const session = args.session as any
-        const assemblyName = args.assemblyName as string
-        const jb2asm = `jb2hub-${assemblyName}`
-        if (
-          assemblyName &&
-          !session.connections.find(
-            (f: { connectionId: string }) => f.connectionId === jb2asm,
-          )
-        ) {
-          console.log('getUnrecognizedAssembly', { assemblyName })
-          const conf = {
-            type: 'JB2TrackHubConnection',
-            uri: `https://jbrowse.org/ucsc/${assemblyName}/config.json`,
-            name: `conn_${assemblyName}`,
-            assemblyNames: [assemblyName],
-            connectionId: jb2asm,
-          }
-          session.addConnectionConf(conf)
-          session.makeConnection(conf)
+        const session = args.session as HubSession | undefined
+        const assemblyName = args.assemblyName as string | undefined
+
+        // Skip if missing required args
+        if (!session || !assemblyName) {
+          return
+        }
+
+        // Skip if already fetching (must check this first to prevent recursion)
+        if (fetchingAssemblies.has(assemblyName)) {
+          return
         }
+
+        // Mark as fetching before any other checks that might re-trigger this
+        fetchingAssemblies.add(assemblyName)
+
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        fetchAssemblyHub(session, assemblyName)
       },
     )
   }
 
-  configure(pluginManager: PluginManager) {}
+  configure(_pluginManager: PluginManager) {}
 }
+
+export {
+  type HubSession,
+  fetchAssemblyHub,
+  fetchingAssemblies,
+} from './fetchAssemblyHub.ts'