@cmdcolin/jbrowse-plugin-hubs 1.0.2

package/README.md

@@ -0,0 +1,3 @@
+# jbrowse-plugin-hubs
+
+For automatically adding connections to jb2hubs

package/dist/index.d.ts

@@ -0,0 +1,8 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class HubsViewerPlugin extends Plugin {
+    name: string;
+    version: any;
+    install(pluginManager: PluginManager): void;
+    configure(pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -0,0 +1,28 @@
+import Plugin from '@jbrowse/core/Plugin';
+import { version } from '../package.json';
+export default class HubsViewerPlugin extends Plugin {
+    name = 'HubsViewerPlugin';
+    version = version;
+    install(pluginManager) {
+        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);
+            }
+        });
+    }
+    configure(pluginManager) { }
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/jbrowse-plugin-hubs.umd.production.min.js

@@ -0,0 +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);})();
+//# sourceMappingURL=jbrowse-plugin-hubs.umd.production.min.js.map

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

@@ -0,0 +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"],
+  "mappings": "gpBAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,sBAAsB,ICAtD,IAAAC,EAAA,GAAAC,EAAAD,EAAA,aAAAE,IAAA,IAAAC,EAAmB,OCCjB,IAAAC,EAAW,QDIb,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,aACpBG,EAAS,UAAUD,CAAY,GACrC,GACEA,GACA,CAACD,EAAQ,YAAY,KAClBG,GAAgCA,EAAE,eAAiBD,CACtD,EACA,CACA,QAAQ,IAAI,0BAA2B,CAAE,aAAAD,CAAa,CAAC,EACvD,IAAMG,EAAO,CACX,KAAM,wBACN,IAAK,4BAA4BH,CAAY,eAC7C,KAAM,QAAQA,CAAY,GAC1B,cAAe,CAACA,CAAY,EAC5B,aAAcC,CAChB,EACAF,EAAQ,kBAAkBI,CAAI,EAC9BJ,EAAQ,eAAeI,CAAI,CAC7B,CACF,CACF,CACF,CAEA,UAAUP,EAA8B,CAAC,CAC3C",
+  "names": ["require_Plugin", "__commonJSMin", "exports", "module", "index_exports", "__export", "HubsViewerPlugin", "import_Plugin", "version", "HubsViewerPlugin", "Plugin", "version", "pluginManager", "_defaultResult", "args", "session", "assemblyName", "jb2asm", "f", "conf"]
+}

package/dist/util.d.ts

@@ -0,0 +1 @@
+export declare function textfetch(url: string, arg?: RequestInit): Promise<string>;

package/dist/util.js

@@ -0,0 +1,8 @@
+export async function textfetch(url, arg) {
+    const res = await fetch(url, arg);
+    if (!res.ok) {
+        throw new Error(`HTTP ${res.status} from ${url}`);
+    }
+    return res.text();
+}
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,GAAW,EAAE,GAAiB;IAC5D,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IACjC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,SAAS,GAAG,EAAE,CAAC,CAAA;IACnD,CAAC;IACD,OAAO,GAAG,CAAC,IAAI,EAAE,CAAA;AACnB,CAAC"}

package/package.json

@@ -0,0 +1,77 @@
+{
+  "version": "1.0.2",
+  "license": "MIT",
+  "name": "@cmdcolin/jbrowse-plugin-hubs",
+  "keywords": [
+    "jbrowse",
+    "jbrowse2"
+  ],
+  "main": "dist/index.js",
+  "module": "dist/index.esm.js",
+  "typings": "dist/index.d.ts",
+  "files": [
+    "dist",
+    "src"
+  ],
+  "scripts": {
+    "clean": "rimraf dist",
+    "start": "node esbuild.mjs",
+    "test": "vitest",
+    "format": "prettier --write .",
+    "prebuild": "npm run clean",
+    "build": "tsc && NODE_ENV=production node esbuild.mjs",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "prepack": "npm run build",
+    "postversion": "git push --follow-tags"
+  },
+  "devDependencies": {
+    "@babel/core": "^7.16.5",
+    "@babel/preset-react": "^7.10.4",
+    "@emotion/react": "^11.10.4",
+    "@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",
+    "@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",
+    "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",
+    "mobx": "^6.0.0",
+    "mobx-react": "^9.0.1",
+    "mobx-state-tree": "^5.4.1",
+    "prettier": "^3.4.2",
+    "pretty-bytes": "^7.0.0",
+    "react": "^19.0.0",
+    "react-dom": "^19.0.0",
+    "rimraf": "^6.0.1",
+    "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"
+  },
+  "publishConfig": {
+    "access": "public"
+  }
+}

package/src/declare.d.ts

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+declare module '*.json'

package/src/index.ts

@@ -0,0 +1,39 @@
+import Plugin from '@jbrowse/core/Plugin'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+import { version } from '../package.json'
+
+export default class HubsViewerPlugin extends Plugin {
+  name = 'HubsViewerPlugin'
+  version = version
+
+  install(pluginManager: PluginManager) {
+    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)
+        }
+      },
+    )
+  }
+
+  configure(pluginManager: PluginManager) {}
+}

package/src/util.ts

@@ -0,0 +1,7 @@
+export async function textfetch(url: string, arg?: RequestInit) {
+  const res = await fetch(url, arg)
+  if (!res.ok) {
+    throw new Error(`HTTP ${res.status} from ${url}`)
+  }
+  return res.text()
+}