@cmdcolin/jbrowse-plugin-hubs 1.0.6 → 1.0.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.d.ts +2 -2
- package/dist/index.js +28 -1
- package/dist/index.js.map +1 -1
- package/dist/jbrowse-plugin-hubs.umd.production.min.js +1 -1
- package/dist/jbrowse-plugin-hubs.umd.production.min.js.map +4 -4
- package/dist/util.d.ts +1 -0
- package/dist/util.js +27 -0
- package/dist/util.js.map +1 -1
- package/package.json +20 -11
- package/src/index.ts +38 -2
- package/src/util.ts +45 -0
package/dist/index.d.ts
CHANGED
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@@ -1,8 +1,8 @@
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import Plugin from '@jbrowse/core/Plugin';
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-
import PluginManager from '@jbrowse/core/PluginManager';
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import type PluginManager from '@jbrowse/core/PluginManager';
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export default class HubsViewerPlugin extends Plugin {
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name: string;
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version: any;
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install(pluginManager: PluginManager): void;
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configure(
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configure(pluginManager: PluginManager): void;
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}
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package/dist/index.js
CHANGED
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@@ -1,5 +1,20 @@
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import Plugin from '@jbrowse/core/Plugin';
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import { isAbstractMenuManager, isElectron } from '@jbrowse/core/util';
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import { getRoot, getSnapshot } from '@jbrowse/mobx-state-tree';
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import { toDesktopSnapshot } from './util';
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import { version } from '../package.json';
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// Serializes the current web session as a desktop `.jbrowse` file. genomes
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// sessions are config-shaped already, so this just folds the live session into
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// a defaultSession and downloads it; desktop opens it via File > Open session.
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function downloadDesktopSession(session) {
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const { jbrowse } = getRoot(session);
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const snap = toDesktopSnapshot(getSnapshot(jbrowse), getSnapshot(session));
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const anchor = document.createElement('a');
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anchor.href = URL.createObjectURL(new Blob([JSON.stringify(snap, null, 2)], { type: 'application/json' }));
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anchor.download = 'session.jbrowse';
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anchor.click();
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URL.revokeObjectURL(anchor.href);
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}
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function getGenArkConfigUrl(accession) {
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const [base, rest] = accession.split('_');
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if (!rest) {
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@@ -46,6 +61,18 @@ export default class HubsViewerPlugin extends Plugin {
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}
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});
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}
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configure(
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configure(pluginManager) {
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// jbrowse-web only. In desktop you'd just save the session, and an exported
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// .jbrowse file carries this plugin in its plugins list, so an older desktop
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// would otherwise load and run this menu code when opening that file.
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if (!isElectron && isAbstractMenuManager(pluginManager.rootModel)) {
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pluginManager.rootModel.appendToMenu('File', {
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label: 'Download desktop session (.jbrowse)',
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onClick: (session) => {
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downloadDesktopSession(session);
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},
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});
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}
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}
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}
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//# sourceMappingURL=index.js.map
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package/dist/index.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AACzC,OAAO,EAAE,qBAAqB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AACtE,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AAE/D,OAAO,EAAE,iBAAiB,EAAE,MAAM,QAAQ,CAAA;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AAYzC,2EAA2E;AAC3E,+EAA+E;AAC/E,+EAA+E;AAC/E,SAAS,sBAAsB,CAAC,OAA6B;IAC3D,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAiC,OAAO,CAAC,CAAA;IACpE,MAAM,IAAI,GAAG,iBAAiB,CAC5B,WAAW,CAA0B,OAAO,CAAC,EAC7C,WAAW,CAA0B,OAAO,CAAC,CAC9C,CAAA;IACD,MAAM,MAAM,GAAG,QAAQ,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;IAC1C,MAAM,CAAC,IAAI,GAAG,GAAG,CAAC,eAAe,CAC/B,IAAI,IAAI,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC,CACxE,CAAA;IACD,MAAM,CAAC,QAAQ,GAAG,iBAAiB,CAAA;IACnC,MAAM,CAAC,KAAK,EAAE,CAAA;IACd,GAAG,CAAC,eAAe,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;AAClC,CAAC;AAED,SAAS,kBAAkB,CAAC,SAAiB;IAC3C,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACzC,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;IACnC,IAAI,CAAC,KAAK,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC/B,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,GAAG,KAAK,CAAA;IAC1B,OAAO,mCAAmC,IAAI,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,SAAS,cAAc,CAAA;AAC7F,CAAC;AAED,SAAS,YAAY,CAAC,YAAoB;IACxC,IAAI,YAAY,CAAC,UAAU,CAAC,MAAM,CAAC,IAAI,YAAY,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;QACvE,OAAO,kBAAkB,CAAC,YAAY,CAAC,CAAA;IACzC,CAAC;IACD,OAAO,4BAA4B,YAAY,cAAc,CAAA;AAC/D,CAAC;AAED,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,OAA8B,CAAA;YACnD,MAAM,YAAY,GAAG,IAAI,CAAC,YAAkC,CAAA;YAC5D,IAAI,CAAC,OAAO,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC9B,OAAM;YACR,CAAC;YACD,MAAM,GAAG,GAAG,YAAY,CAAC,YAAY,CAAC,CAAA;YACtC,IAAI,CAAC,GAAG,EAAE,CAAC;gBACT,OAAM;YACR,CAAC;YACD,MAAM,YAAY,GAAG,UAAU,YAAY,EAAE,CAAA;YAC7C,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,YAAY,KAAK,YAAY,CAAC,EAAE,CAAC;gBACpE,MAAM,IAAI,GAAG;oBACX,IAAI,EAAE,uBAAuB;oBAC7B,GAAG;oBACH,IAAI,EAAE,QAAQ,YAAY,EAAE;oBAC5B,aAAa,EAAE,CAAC,YAAY,CAAC;oBAC7B,YAAY;iBACb,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;QACpC,4EAA4E;QAC5E,6EAA6E;QAC7E,sEAAsE;QACtE,IAAI,CAAC,UAAU,IAAI,qBAAqB,CAAC,aAAa,CAAC,SAAS,CAAC,EAAE,CAAC;YAClE,aAAa,CAAC,SAAS,CAAC,YAAY,CAAC,MAAM,EAAE;gBAC3C,KAAK,EAAE,qCAAqC;gBAC5C,OAAO,EAAE,CAAC,OAA6B,EAAE,EAAE;oBACzC,sBAAsB,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;aACF,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;CACF"}
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"use strict";var JBrowsePluginHubs=(()=>{var
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"use strict";var JBrowsePluginHubs=(()=>{var S=Object.create;var u=Object.defineProperty;var v=Object.getOwnPropertyDescriptor;var $=Object.getOwnPropertyNames;var E=Object.getPrototypeOf,I=Object.prototype.hasOwnProperty;var g=(n,e)=>()=>(e||n((e={exports:{}}).exports,e),e.exports),T=(n,e)=>{for(var t in e)u(n,t,{get:e[t],enumerable:!0})},b=(n,e,t,o)=>{if(e&&typeof e=="object"||typeof e=="function")for(let s of $(e))!I.call(n,s)&&s!==t&&u(n,s,{get:()=>e[s],enumerable:!(o=v(e,s))||o.enumerable});return n};var m=(n,e,t)=>(t=n!=null?S(E(n)):{},b(e||!n||!n.__esModule?u(t,"default",{value:n,enumerable:!0}):t,n)),P=n=>b(u({},"__esModule",{value:!0}),n);var k=g((N,w)=>{w.exports=JBrowseExports["@jbrowse/core/Plugin"]});var j=g((G,h)=>{h.exports=JBrowseExports["@jbrowse/core/util"]});var x=g((L,y)=>{y.exports=JBrowseExports["mobx-state-tree"]});var _={};T(_,{default:()=>l});var A=m(k()),p=m(j()),i=m(x());function d(n){return Array.isArray(n)?n:[]}function R(n,e,t){let o=new Map;for(let s of[...n,...e])o.set(s[t],s);return[...o.values()]}function C(n,e){let{sessionTracks:t,sessionAssemblies:o,...s}=e;return{...n,tracks:R(d(n.tracks),d(t),"trackId"),assemblies:R(d(n.assemblies),d(o),"name"),defaultSession:s}}var M="1.0.9";function U(n){let{jbrowse:e}=(0,i.getRoot)(n),t=C((0,i.getSnapshot)(e),(0,i.getSnapshot)(n)),o=document.createElement("a");o.href=URL.createObjectURL(new Blob([JSON.stringify(t,null,2)],{type:"application/json"})),o.download="session.jbrowse",o.click(),URL.revokeObjectURL(o.href)}function B(n){let[e,t]=n.split("_");if(!t)return;let o=t.match(/.{1,3}/g);if(!o||o.length<3)return;let[s,r,c]=o;return`https://jbrowse.org/hubs/genark/${e}/${s}/${r}/${c}/${n}/config.json`}function O(n){return n.startsWith("GCA_")||n.startsWith("GCF_")?B(n):`https://jbrowse.org/ucsc/${n}/config.json`}var l=class extends A.default{name="HubsViewerPlugin";version=M;install(e){e.addToExtensionPoint("Core-handleUnrecognizedAssembly",(t,o)=>{let s=o.session,r=o.assemblyName;if(!s||!r)return;let c=O(r);if(!c)return;let f=`jb2hub-${r}`;if(!s.connections.find(a=>a.connectionId===f)){let a={type:"JB2TrackHubConnection",uri:c,name:`conn_${r}`,assemblyNames:[r],connectionId:f};s.addConnectionConf(a),s.makeConnection(a)}})}configure(e){!p.isElectron&&(0,p.isAbstractMenuManager)(e.rootModel)&&e.rootModel.appendToMenu("File",{label:"Download desktop session (.jbrowse)",onClick:t=>{U(t)}})}};return P(_);})();
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//# sourceMappingURL=jbrowse-plugin-hubs.umd.production.min.js.map
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{
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"version": 3,
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"sources": ["global-externals:@jbrowse/core/Plugin", "../src/index.ts", "../package.json"],
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"sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport
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"mappings": "gpBAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,sBAAsB,ICAtD,IAAAC,EAAA,GAAAC,EAAAD,EAAA,aAAAE,IAAA,IAAAC,EAAmB,
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"names": ["require_Plugin", "__commonJSMin", "exports", "module", "index_exports", "__export", "HubsViewerPlugin", "import_Plugin", "version", "getGenArkConfigUrl", "accession", "base", "rest", "match", "b1", "b2", "b3", "getConfigUrl", "assemblyName", "HubsViewerPlugin", "Plugin", "version", "pluginManager", "_defaultResult", "args", "
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"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"],
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"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 { 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) => 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 const anchor = document.createElement('a')\n anchor.href = URL.createObjectURL(\n new Blob([JSON.stringify(snap, null, 2)], { type: 'application/json' }),\n )\n anchor.download = 'session.jbrowse'\n anchor.click()\n URL.revokeObjectURL(anchor.href)\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 if (assemblyName.startsWith('GCA_') || assemblyName.startsWith('GCF_')) {\n return getGenArkConfigUrl(assemblyName)\n }\n return `https://jbrowse.org/ucsc/${assemblyName}/config.json`\n}\n\nexport default class HubsViewerPlugin extends Plugin {\n name = 'HubsViewerPlugin'\n version = version\n\n install(pluginManager: PluginManager) {\n pluginManager.addToExtensionPoint(\n 'Core-handleUnrecognizedAssembly',\n (_defaultResult, args) => {\n const session = args.session as Session | undefined\n const assemblyName = args.assemblyName as string | undefined\n if (!session || !assemblyName) {\n return\n }\n const uri = getConfigUrl(assemblyName)\n if (!uri) {\n return\n }\n const connectionId = `jb2hub-${assemblyName}`\n if (!session.connections.find(f => f.connectionId === connectionId)) {\n const conf = {\n type: 'JB2TrackHubConnection',\n uri,\n name: `conn_${assemblyName}`,\n assemblyNames: [assemblyName],\n connectionId,\n }\n session.addConnectionConf(conf)\n session.makeConnection(conf)\n }\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 pluginManager.rootModel.appendToMenu('File', {\n label: 'Download desktop session (.jbrowse)',\n onClick: (session: AbstractSessionModel) => {\n downloadDesktopSession(session)\n },\n })\n }\n }\n}\n", "export async function textfetch(url: string, arg?: RequestInit) {\n const res = await fetch(url, arg)\n if (!res.ok) {\n throw new Error(`HTTP ${res.status} from ${url}`)\n }\n return res.text()\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\": \"1.0.9\",\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\"\n },\n \"devDependencies\": {\n \"@eslint/js\": \"^10.0.1\",\n \"@fal-works/esbuild-plugin-global-externals\": \"^2.1.2\",\n \"@jbrowse/core\": \"^4.1.3\",\n \"@jbrowse/mobx-state-tree\": \"^5.0.2\",\n \"@mui/material\": \"^7.3.7\",\n \"@mui/system\": \"^7.3.7\",\n \"@mui/x-data-grid\": \"^8.26.0\",\n \"@types/node\": \"^25.1.0\",\n \"@types/react\": \"^19.2.10\",\n \"@typescript-eslint/eslint-plugin\": \"^8.59.1\",\n \"@typescript-eslint/parser\": \"^8.59.1\",\n \"esbuild\": \"^0.27.2\",\n \"eslint\": \"^10.2.1\",\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\": \"^6.0.0\",\n \"mobx-react\": \"^9.0.1\",\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\": \"^8.59.1\"\n },\n \"publishConfig\": {\n \"access\": \"public\"\n }\n}\n"],
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+
"mappings": "gpBAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,sBAAsB,ICAtD,IAAAC,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,oBAAoB,ICApD,IAAAC,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,iBAAiB,ICAjD,IAAAC,EAAA,GAAAC,EAAAD,EAAA,aAAAE,IAAA,IAAAC,EAAmB,OACnBC,EAAkD,OAClDC,EAAqC,OCMrC,SAASC,EAAWC,EAA2C,CAC7D,OAAO,MAAM,QAAQA,CAAK,EAAKA,EAAsC,CAAC,CACxE,CAKA,SAASC,EACPC,EACAC,EACAC,EAC2B,CAC3B,IAAMC,EAAS,IAAI,IACnB,QAAWC,IAAQ,CAAC,GAAGJ,EAAM,GAAGC,CAAS,EACvCE,EAAO,IAAIC,EAAKF,CAAG,EAAGE,CAAI,EAE5B,MAAO,CAAC,GAAGD,EAAO,OAAO,CAAC,CAC5B,CAOO,SAASE,EACdC,EACAC,EACyB,CACzB,GAAM,CAAE,cAAAC,EAAe,kBAAAC,EAAmB,GAAGC,CAAe,EAAIH,EAChE,MAAO,CACL,GAAGD,EACH,OAAQP,EACNF,EAAWS,EAAQ,MAAM,EACzBT,EAAWW,CAAa,EACxB,SACF,EACA,WAAYT,EACVF,EAAWS,EAAQ,UAAU,EAC7BT,EAAWY,CAAiB,EAC5B,MACF,EACA,eAAAC,CACF,CACF,CClDE,IAAAC,EAAW,QFmBb,SAASC,EAAuBC,EAA+B,CAC7D,GAAM,CAAE,QAAAC,CAAQ,KAAI,WAAwCD,CAAO,EAC7DE,EAAOC,KACX,eAAqCF,CAAO,KAC5C,eAAqCD,CAAO,CAC9C,EACMI,EAAS,SAAS,cAAc,GAAG,EACzCA,EAAO,KAAO,IAAI,gBAChB,IAAI,KAAK,CAAC,KAAK,UAAUF,EAAM,KAAM,CAAC,CAAC,EAAG,CAAE,KAAM,kBAAmB,CAAC,CACxE,EACAE,EAAO,SAAW,kBAClBA,EAAO,MAAM,EACb,IAAI,gBAAgBA,EAAO,IAAI,CACjC,CAEA,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,CAC1C,OAAIA,EAAa,WAAW,MAAM,GAAKA,EAAa,WAAW,MAAM,EAC5DT,EAAmBS,CAAY,EAEjC,4BAA4BA,CAAY,cACjD,CAEA,IAAqBC,EAArB,cAA8C,EAAAC,OAAO,CACnD,KAAO,mBACP,QAAUC,EAEV,QAAQC,EAA8B,CACpCA,EAAc,oBACZ,kCACA,CAACC,EAAgBC,IAAS,CACxB,IAAMpB,EAAUoB,EAAK,QACfN,EAAeM,EAAK,aAC1B,GAAI,CAACpB,GAAW,CAACc,EACf,OAEF,IAAMO,EAAMR,EAAaC,CAAY,EACrC,GAAI,CAACO,EACH,OAEF,IAAMC,EAAe,UAAUR,CAAY,GAC3C,GAAI,CAACd,EAAQ,YAAY,KAAKuB,GAAKA,EAAE,eAAiBD,CAAY,EAAG,CACnE,IAAME,EAAO,CACX,KAAM,wBACN,IAAAH,EACA,KAAM,QAAQP,CAAY,GAC1B,cAAe,CAACA,CAAY,EAC5B,aAAAQ,CACF,EACAtB,EAAQ,kBAAkBwB,CAAI,EAC9BxB,EAAQ,eAAewB,CAAI,CAC7B,CACF,CACF,CACF,CAEA,UAAUN,EAA8B,CAIlC,CAAC,iBAAc,yBAAsBA,EAAc,SAAS,GAC9DA,EAAc,UAAU,aAAa,OAAQ,CAC3C,MAAO,sCACP,QAAUlB,GAAkC,CAC1CD,EAAuBC,CAAO,CAChC,CACF,CAAC,CAEL,CACF",
|
|
6
|
+
"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", "asObjArray", "value", "mergeById", "base", "overrides", "key", "merged", "item", "toDesktopSnapshot", "jbrowse", "session", "sessionTracks", "sessionAssemblies", "defaultSession", "version", "downloadDesktopSession", "session", "jbrowse", "snap", "toDesktopSnapshot", "anchor", "getGenArkConfigUrl", "accession", "base", "rest", "match", "b1", "b2", "b3", "getConfigUrl", "assemblyName", "HubsViewerPlugin", "Plugin", "version", "pluginManager", "_defaultResult", "args", "uri", "connectionId", "f", "conf"]
|
|
7
7
|
}
|
package/dist/util.d.ts
CHANGED
package/dist/util.js
CHANGED
|
@@ -5,4 +5,31 @@ export async function textfetch(url, arg) {
|
|
|
5
5
|
}
|
|
6
6
|
return res.text();
|
|
7
7
|
}
|
|
8
|
+
function asObjArray(value) {
|
|
9
|
+
return Array.isArray(value) ? value : [];
|
|
10
|
+
}
|
|
11
|
+
// Merges two lists of config objects by an id key, with `overrides` winning so
|
|
12
|
+
// a session-scoped track/assembly that shadows a config one (same id) replaces
|
|
13
|
+
// it rather than duplicating.
|
|
14
|
+
function mergeById(base, overrides, key) {
|
|
15
|
+
const merged = new Map();
|
|
16
|
+
for (const item of [...base, ...overrides]) {
|
|
17
|
+
merged.set(item[key], item);
|
|
18
|
+
}
|
|
19
|
+
return [...merged.values()];
|
|
20
|
+
}
|
|
21
|
+
// Builds a desktop `.jbrowse` snapshot (a config plus a defaultSession) from a
|
|
22
|
+
// web root config and its live session. Session-scoped tracks/assemblies are
|
|
23
|
+
// hoisted into the config arrays so they open as first-class config entries in
|
|
24
|
+
// desktop; the rest of the session becomes the defaultSession. Web sessions are
|
|
25
|
+
// always UriLocation-based, so the result is fully portable to desktop.
|
|
26
|
+
export function toDesktopSnapshot(jbrowse, session) {
|
|
27
|
+
const { sessionTracks, sessionAssemblies, ...defaultSession } = session;
|
|
28
|
+
return {
|
|
29
|
+
...jbrowse,
|
|
30
|
+
tracks: mergeById(asObjArray(jbrowse.tracks), asObjArray(sessionTracks), 'trackId'),
|
|
31
|
+
assemblies: mergeById(asObjArray(jbrowse.assemblies), asObjArray(sessionAssemblies), 'name'),
|
|
32
|
+
defaultSession,
|
|
33
|
+
};
|
|
34
|
+
}
|
|
8
35
|
//# sourceMappingURL=util.js.map
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
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"}
|
|
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;AAED,SAAS,UAAU,CAAC,KAAc;IAChC,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAE,KAAmC,CAAC,CAAC,CAAC,EAAE,CAAA;AACzE,CAAC;AAED,+EAA+E;AAC/E,+EAA+E;AAC/E,8BAA8B;AAC9B,SAAS,SAAS,CAChB,IAA+B,EAC/B,SAAoC,EACpC,GAAW;IAEX,MAAM,MAAM,GAAG,IAAI,GAAG,EAAoC,CAAA;IAC1D,KAAK,MAAM,IAAI,IAAI,CAAC,GAAG,IAAI,EAAE,GAAG,SAAS,CAAC,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,IAAI,CAAC,CAAA;IAC7B,CAAC;IACD,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;AAC7B,CAAC;AAED,+EAA+E;AAC/E,6EAA6E;AAC7E,+EAA+E;AAC/E,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,UAAU,iBAAiB,CAC/B,OAAgC,EAChC,OAAgC;IAEhC,MAAM,EAAE,aAAa,EAAE,iBAAiB,EAAE,GAAG,cAAc,EAAE,GAAG,OAAO,CAAA;IACvE,OAAO;QACL,GAAG,OAAO;QACV,MAAM,EAAE,SAAS,CACf,UAAU,CAAC,OAAO,CAAC,MAAM,CAAC,EAC1B,UAAU,CAAC,aAAa,CAAC,EACzB,SAAS,CACV;QACD,UAAU,EAAE,SAAS,CACnB,UAAU,CAAC,OAAO,CAAC,UAAU,CAAC,EAC9B,UAAU,CAAC,iBAAiB,CAAC,EAC7B,MAAM,CACP;QACD,cAAc;KACf,CAAA;AACH,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,7 +1,11 @@
|
|
|
1
1
|
{
|
|
2
|
-
"version": "1.0.
|
|
2
|
+
"version": "1.0.9",
|
|
3
3
|
"license": "MIT",
|
|
4
4
|
"name": "@cmdcolin/jbrowse-plugin-hubs",
|
|
5
|
+
"repository": {
|
|
6
|
+
"type": "git",
|
|
7
|
+
"url": "git+https://github.com/GMOD/jbrowse-plugin-hubs.git"
|
|
8
|
+
},
|
|
5
9
|
"keywords": [
|
|
6
10
|
"jbrowse",
|
|
7
11
|
"jbrowse2"
|
|
@@ -17,15 +21,16 @@
|
|
|
17
21
|
"clean": "rimraf dist",
|
|
18
22
|
"start": "node esbuild.mjs --watch",
|
|
19
23
|
"test": "echo 'no tests'",
|
|
20
|
-
"format": "prettier --write .",
|
|
21
|
-
"prebuild": "
|
|
24
|
+
"format": "pnpm prettier --write .",
|
|
25
|
+
"prebuild": "pnpm clean",
|
|
22
26
|
"build": "tsc && NODE_ENV=production node esbuild.mjs",
|
|
23
|
-
"lint": "eslint --report-unused-disable-directives --max-warnings 0",
|
|
24
|
-
"prepack": "
|
|
25
|
-
"postversion": "git push --follow-tags"
|
|
27
|
+
"lint": "eslint src --report-unused-disable-directives --max-warnings 0",
|
|
28
|
+
"prepack": "pnpm build",
|
|
29
|
+
"postversion": "git push --follow-tags",
|
|
30
|
+
"preversion": "pnpm lint"
|
|
26
31
|
},
|
|
27
32
|
"devDependencies": {
|
|
28
|
-
"@eslint/js": "^
|
|
33
|
+
"@eslint/js": "^10.0.1",
|
|
29
34
|
"@fal-works/esbuild-plugin-global-externals": "^2.1.2",
|
|
30
35
|
"@jbrowse/core": "^4.1.3",
|
|
31
36
|
"@jbrowse/mobx-state-tree": "^5.0.2",
|
|
@@ -34,10 +39,14 @@
|
|
|
34
39
|
"@mui/x-data-grid": "^8.26.0",
|
|
35
40
|
"@types/node": "^25.1.0",
|
|
36
41
|
"@types/react": "^19.2.10",
|
|
42
|
+
"@typescript-eslint/eslint-plugin": "^8.59.1",
|
|
43
|
+
"@typescript-eslint/parser": "^8.59.1",
|
|
37
44
|
"esbuild": "^0.27.2",
|
|
38
|
-
"eslint": "^
|
|
39
|
-
"eslint-plugin-import": "^
|
|
40
|
-
"eslint-plugin-
|
|
45
|
+
"eslint": "^10.2.1",
|
|
46
|
+
"eslint-plugin-import-x": "^4.16.2",
|
|
47
|
+
"eslint-plugin-react": "^7.37.5",
|
|
48
|
+
"eslint-plugin-react-hooks": "^7.1.1",
|
|
49
|
+
"eslint-plugin-unicorn": "^64.0.0",
|
|
41
50
|
"mobx": "^6.0.0",
|
|
42
51
|
"mobx-react": "^9.0.1",
|
|
43
52
|
"prettier": "^3.8.1",
|
|
@@ -48,7 +57,7 @@
|
|
|
48
57
|
"rxjs": "^7.8.1",
|
|
49
58
|
"serve": "^14.2.0",
|
|
50
59
|
"typescript": "^5.1.6",
|
|
51
|
-
"typescript-eslint": "^8.
|
|
60
|
+
"typescript-eslint": "^8.59.1"
|
|
52
61
|
},
|
|
53
62
|
"publishConfig": {
|
|
54
63
|
"access": "public"
|
package/src/index.ts
CHANGED
|
@@ -1,14 +1,38 @@
|
|
|
1
1
|
import Plugin from '@jbrowse/core/Plugin'
|
|
2
|
-
import
|
|
2
|
+
import { isAbstractMenuManager, isElectron } from '@jbrowse/core/util'
|
|
3
|
+
import { getRoot, getSnapshot } from '@jbrowse/mobx-state-tree'
|
|
3
4
|
|
|
5
|
+
import { toDesktopSnapshot } from './util'
|
|
4
6
|
import { version } from '../package.json'
|
|
5
7
|
|
|
8
|
+
import type PluginManager from '@jbrowse/core/PluginManager'
|
|
9
|
+
import type { AbstractSessionModel } from '@jbrowse/core/util'
|
|
10
|
+
import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree'
|
|
11
|
+
|
|
6
12
|
interface Session {
|
|
7
13
|
makeConnection: (conf: unknown) => void
|
|
8
14
|
addConnectionConf: (conf: unknown) => void
|
|
9
15
|
connections: { connectionId: string }[]
|
|
10
16
|
}
|
|
11
17
|
|
|
18
|
+
// Serializes the current web session as a desktop `.jbrowse` file. genomes
|
|
19
|
+
// sessions are config-shaped already, so this just folds the live session into
|
|
20
|
+
// a defaultSession and downloads it; desktop opens it via File > Open session.
|
|
21
|
+
function downloadDesktopSession(session: AbstractSessionModel) {
|
|
22
|
+
const { jbrowse } = getRoot<{ jbrowse: IAnyStateTreeNode }>(session)
|
|
23
|
+
const snap = toDesktopSnapshot(
|
|
24
|
+
getSnapshot<Record<string, unknown>>(jbrowse),
|
|
25
|
+
getSnapshot<Record<string, unknown>>(session),
|
|
26
|
+
)
|
|
27
|
+
const anchor = document.createElement('a')
|
|
28
|
+
anchor.href = URL.createObjectURL(
|
|
29
|
+
new Blob([JSON.stringify(snap, null, 2)], { type: 'application/json' }),
|
|
30
|
+
)
|
|
31
|
+
anchor.download = 'session.jbrowse'
|
|
32
|
+
anchor.click()
|
|
33
|
+
URL.revokeObjectURL(anchor.href)
|
|
34
|
+
}
|
|
35
|
+
|
|
12
36
|
function getGenArkConfigUrl(accession: string) {
|
|
13
37
|
const [base, rest] = accession.split('_')
|
|
14
38
|
if (!rest) {
|
|
@@ -62,5 +86,17 @@ export default class HubsViewerPlugin extends Plugin {
|
|
|
62
86
|
)
|
|
63
87
|
}
|
|
64
88
|
|
|
65
|
-
configure(
|
|
89
|
+
configure(pluginManager: PluginManager) {
|
|
90
|
+
// jbrowse-web only. In desktop you'd just save the session, and an exported
|
|
91
|
+
// .jbrowse file carries this plugin in its plugins list, so an older desktop
|
|
92
|
+
// would otherwise load and run this menu code when opening that file.
|
|
93
|
+
if (!isElectron && isAbstractMenuManager(pluginManager.rootModel)) {
|
|
94
|
+
pluginManager.rootModel.appendToMenu('File', {
|
|
95
|
+
label: 'Download desktop session (.jbrowse)',
|
|
96
|
+
onClick: (session: AbstractSessionModel) => {
|
|
97
|
+
downloadDesktopSession(session)
|
|
98
|
+
},
|
|
99
|
+
})
|
|
100
|
+
}
|
|
101
|
+
}
|
|
66
102
|
}
|
package/src/util.ts
CHANGED
|
@@ -5,3 +5,48 @@ export async function textfetch(url: string, arg?: RequestInit) {
|
|
|
5
5
|
}
|
|
6
6
|
return res.text()
|
|
7
7
|
}
|
|
8
|
+
|
|
9
|
+
function asObjArray(value: unknown): Record<string, unknown>[] {
|
|
10
|
+
return Array.isArray(value) ? (value as Record<string, unknown>[]) : []
|
|
11
|
+
}
|
|
12
|
+
|
|
13
|
+
// Merges two lists of config objects by an id key, with `overrides` winning so
|
|
14
|
+
// a session-scoped track/assembly that shadows a config one (same id) replaces
|
|
15
|
+
// it rather than duplicating.
|
|
16
|
+
function mergeById(
|
|
17
|
+
base: Record<string, unknown>[],
|
|
18
|
+
overrides: Record<string, unknown>[],
|
|
19
|
+
key: string,
|
|
20
|
+
): Record<string, unknown>[] {
|
|
21
|
+
const merged = new Map<unknown, Record<string, unknown>>()
|
|
22
|
+
for (const item of [...base, ...overrides]) {
|
|
23
|
+
merged.set(item[key], item)
|
|
24
|
+
}
|
|
25
|
+
return [...merged.values()]
|
|
26
|
+
}
|
|
27
|
+
|
|
28
|
+
// Builds a desktop `.jbrowse` snapshot (a config plus a defaultSession) from a
|
|
29
|
+
// web root config and its live session. Session-scoped tracks/assemblies are
|
|
30
|
+
// hoisted into the config arrays so they open as first-class config entries in
|
|
31
|
+
// desktop; the rest of the session becomes the defaultSession. Web sessions are
|
|
32
|
+
// always UriLocation-based, so the result is fully portable to desktop.
|
|
33
|
+
export function toDesktopSnapshot(
|
|
34
|
+
jbrowse: Record<string, unknown>,
|
|
35
|
+
session: Record<string, unknown>,
|
|
36
|
+
): Record<string, unknown> {
|
|
37
|
+
const { sessionTracks, sessionAssemblies, ...defaultSession } = session
|
|
38
|
+
return {
|
|
39
|
+
...jbrowse,
|
|
40
|
+
tracks: mergeById(
|
|
41
|
+
asObjArray(jbrowse.tracks),
|
|
42
|
+
asObjArray(sessionTracks),
|
|
43
|
+
'trackId',
|
|
44
|
+
),
|
|
45
|
+
assemblies: mergeById(
|
|
46
|
+
asObjArray(jbrowse.assemblies),
|
|
47
|
+
asObjArray(sessionAssemblies),
|
|
48
|
+
'name',
|
|
49
|
+
),
|
|
50
|
+
defaultSession,
|
|
51
|
+
}
|
|
52
|
+
}
|