@jbrowse/plugin-config 4.2.1 → 5.0.0-beta.1

package/esm/RefNameAliasAdapter/index.js

@@ -1,10 +1,11 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from "./configSchema.js";
+import configSchema, { normalizeSnapshot } from './configSchema.js';
 export default function RefNameAliasAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'RefNameAliasAdapter',
+        normalizeSnapshot,
         configSchema,
-        getAdapterClass: () => import("./RefNameAliasAdapter.js").then(r => r.default),
+        getAdapterClass: () => import('./RefNameAliasAdapter.js').then(r => r.default),
         adapterMetadata: {
             hiddenFromGUI: true,
         },

package/esm/aliasUtils.d.ts

@@ -0,0 +1,4 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { FileLocation } from '@jbrowse/core/util/types';
+export declare function readAliasRows(loc: FileLocation, pluginManager?: PluginManager, opts?: BaseOptions): Promise<string[][]>;

package/esm/aliasUtils.js

@@ -0,0 +1,26 @@
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { isUriLocation } from '@jbrowse/core/util/types';
+// The alias adapters' `location` slots default to a "/path/to/my/..."
+// placeholder; that (and a blank uri) means "no file configured", so the
+// adapter yields no aliases rather than trying to fetch the placeholder path.
+function isUnconfiguredLocation(loc) {
+    return isUriLocation(loc) && (!loc.uri || loc.uri.startsWith('/path/to/my/'));
+}
+// Reads a tab-separated alias file into rows of columns, dropping blank lines.
+// Returns [] when no file is configured.
+export async function readAliasRows(loc, pluginManager, opts) {
+    if (isUnconfiguredLocation(loc)) {
+        return [];
+    }
+    // fetchAndMaybeUnzipText rather than readFile('utf8') so the read reports byte
+    // progress (readFile's utf8 path takes res.text(), which can't) and so a
+    // gzipped chromAlias works. UCSC's chromAlias files are the slowest of the
+    // four parallel assembly loads on a big assembly, so this is the one whose
+    // progress the spinner most often ends up showing
+    const text = await fetchAndMaybeUnzipText(openLocation(loc, pluginManager), opts, 'Downloading chromosome aliases');
+    return text
+        .split(/\n|\r\n|\r/)
+        .filter(line => !!line.trim())
+        .map(line => line.split('\t'));
+}

package/esm/index.d.ts

@@ -3,9 +3,9 @@ import type PluginManager from '@jbrowse/core/PluginManager';
 declare const LazyConfigurationEditorComponent: import("react").LazyExoticComponent<({ model, }: {
     model: {
         target?: import("@jbrowse/core/configuration").AnyConfigurationModel;
+        expandedDisplayId?: string;
     };
-    session?: import("@jbrowse/core/util").AbstractSessionModel;
-}) => import("react/jsx-runtime").JSX.Element>;
+}) => import("react").JSX.Element>;
 export default class ConfigurationPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,12 +1,12 @@
 import { lazy } from 'react';
 import Plugin from '@jbrowse/core/Plugin';
-import ConfigurationEditorWidgetF from "./ConfigurationEditorWidget/index.js";
-import FromConfigAdapterF from "./FromConfigAdapter/index.js";
-import FromConfigRegionsAdapterF from "./FromConfigRegionsAdapter/index.js";
-import FromConfigSequenceAdapterF from "./FromConfigSequenceAdapter/index.js";
-import NcbiSequenceReportAliasAdapterF from "./NcbiSequenceReportAliasAdapter/index.js";
-import RefNameAliasAdapterF from "./RefNameAliasAdapter/index.js";
-const LazyConfigurationEditorComponent = lazy(() => import("./ConfigurationEditorWidget/components/ConfigurationEditor.js"));
+import ConfigurationEditorWidgetF from './ConfigurationEditorWidget/index.js';
+import FromConfigAdapterF from './FromConfigAdapter/index.js';
+import FromConfigRegionsAdapterF from './FromConfigRegionsAdapter/index.js';
+import FromConfigSequenceAdapterF from './FromConfigSequenceAdapter/index.js';
+import NcbiSequenceReportAliasAdapterF from './NcbiSequenceReportAliasAdapter/index.js';
+import RefNameAliasAdapterF from './RefNameAliasAdapter/index.js';
+const LazyConfigurationEditorComponent = lazy(() => import('./ConfigurationEditorWidget/components/ConfigurationEditor.js'));
 export default class ConfigurationPlugin extends Plugin {
     name = 'ConfigurationPlugin';
     install(pluginManager) {

package/esm/normalizeUriSnapshot.d.ts

@@ -0,0 +1 @@
+export declare function normalizeUriSnapshot(snap: Record<string, unknown>): Record<string, unknown>;

package/esm/normalizeUriSnapshot.js

@@ -0,0 +1,13 @@
+// allows a minimal config of `{ uri: "..." }` by lifting `uri`/`baseUri` into
+// a proper `location` fileLocation slot. Shared by the alias adapters.
+export function normalizeUriSnapshot(snap) {
+    return snap.uri
+        ? {
+            ...snap,
+            location: {
+                uri: snap.uri,
+                baseUri: snap.baseUri,
+            },
+        }
+        : snap;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "4.2.1",
+  "version": "5.0.0-beta.1",
   "type": "module",
   "description": "JBrowse 2 config utilities",
   "keywords": [
@@ -21,18 +21,17 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^5.6.0",
-    "@mui/icons-material": "^7.3.10",
-    "@mui/material": "^7.3.10",
-    "mobx": "^6.15.0",
-    "mobx-react": "^9.2.1",
-    "pluralize": "^8.0.0",
+    "@jbrowse/mobx-state-tree": "^6.5.1",
+    "@mui/icons-material": "^9.3.1",
+    "@mui/material": "^9.3.1",
+    "mobx": "^7.0.3",
+    "mobx-react": "^10.0.2",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.2.1"
+    "@jbrowse/core": "^5.0.0-beta.1"
   },
   "peerDependencies": {
-    "react": ">=18.0.0",
-    "react-dom": ">=18.0.0"
+    "react": ">=19.0.0",
+    "react-dom": ">=19.0.0"
   },
   "publishConfig": {
     "access": "public"
@@ -42,14 +41,11 @@
     "build": "pnpm run /^build:/",
     "test": "cd ../..; jest --passWithNoTests plugins/config",
     "prebuild": "pnpm clean",
-    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "build:esm": "node ../../node_modules/typescript7/bin/tsc --build tsconfig.build.esm.json",
     "clean": "rimraf esm *.tsbuildinfo"
   },
   "types": "esm/index.d.ts",
   "exports": {
-    ".": {
-      "types": "./esm/index.d.ts",
-      "import": "./esm/index.js"
-    }
+    ".": "./esm/index.js"
   }
 }