@jbrowse/plugin-config 4.3.0 → 5.0.0-beta.10

package/esm/RefNameAliasAdapter/configSchema.d.ts

@@ -1,19 +1,77 @@
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export declare function normalizeSnapshot(snap: Record<string, unknown>): Record<string, unknown>;
+/**
+ * #config RefNameAliasAdapter
+ * can read "chromAliases" type files from UCSC or any tab separated file of
+ * refName aliases
+ *
+ * #example
+ * Goes on an ASSEMBLY, under `refNameAliases` — not on a track. Writing
+ * `refNameAliases: { uri: '...' }` is shorthand for exactly this adapter:
+ * ```js
+ * {
+ *   name: 'hg38',
+ *   sequence: {
+ *     type: 'ReferenceSequenceTrack',
+ *     trackId: 'hg38-ReferenceSequenceTrack',
+ *     adapter: {
+ *       type: 'BgzipFastaAdapter',
+ *       uri: 'https://example.com/hg38.fa.gz',
+ *     },
+ *   },
+ *   refNameAliases: {
+ *     adapter: {
+ *       type: 'RefNameAliasAdapter',
+ *       uri: 'https://example.com/hg38.chromAlias.txt',
+ *     },
+ *   },
+ * }
+ * ```
+ *
+ * #example named column
+ * When the primary column — the one whose values match your FASTA — is not the
+ * first, name it. `refNameColumnHeaderName` reads the last `#`-prefixed line as
+ * the header; `refNameColumn` takes a zero-based index instead.
+ * ```js
+ * {
+ *   name: 'hg38',
+ *   sequence: {
+ *     type: 'ReferenceSequenceTrack',
+ *     trackId: 'hg38-ReferenceSequenceTrack',
+ *     adapter: {
+ *       type: 'BgzipFastaAdapter',
+ *       uri: 'https://example.com/hg38.fa.gz',
+ *     },
+ *   },
+ *   refNameAliases: {
+ *     adapter: {
+ *       type: 'RefNameAliasAdapter',
+ *       uri: 'https://example.com/aliases.txt',
+ *       refNameColumnHeaderName: 'ucsc',
+ *     },
+ *   },
+ * }
+ * ```
+ */
 declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    location: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    readonly location: {
+        type: "maybeFileLocation";
     };
-    refNameColumn: {
-        type: string;
+    readonly refNameColumn: {
+        type: "number";
+    } & {
         defaultValue: number;
     };
-    refNameColumnHeaderName: {
-        type: string;
-        description: string;
+    readonly refNameColumnHeaderName: {
+        type: "string";
+    } & {
         defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+export type RefNameAliasAdapterConfig = Instance<typeof RefNameAliasAdapter>;
 export default RefNameAliasAdapter;

package/esm/RefNameAliasAdapter/configSchema.js

@@ -1,34 +1,105 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-function x() { }
+import { ConfigurationSchema, expandUriShorthand, } from '@jbrowse/core/configuration';
+export function normalizeSnapshot(snap) {
+    return expandUriShorthand(snap, 'location');
+}
+/**
+ * #config RefNameAliasAdapter
+ * can read "chromAliases" type files from UCSC or any tab separated file of
+ * refName aliases
+ *
+ * #example
+ * Goes on an ASSEMBLY, under `refNameAliases` — not on a track. Writing
+ * `refNameAliases: { uri: '...' }` is shorthand for exactly this adapter:
+ * ```js
+ * {
+ *   name: 'hg38',
+ *   sequence: {
+ *     type: 'ReferenceSequenceTrack',
+ *     trackId: 'hg38-ReferenceSequenceTrack',
+ *     adapter: {
+ *       type: 'BgzipFastaAdapter',
+ *       uri: 'https://example.com/hg38.fa.gz',
+ *     },
+ *   },
+ *   refNameAliases: {
+ *     adapter: {
+ *       type: 'RefNameAliasAdapter',
+ *       uri: 'https://example.com/hg38.chromAlias.txt',
+ *     },
+ *   },
+ * }
+ * ```
+ *
+ * #example named column
+ * When the primary column — the one whose values match your FASTA — is not the
+ * first, name it. `refNameColumnHeaderName` reads the last `#`-prefixed line as
+ * the header; `refNameColumn` takes a zero-based index instead.
+ * ```js
+ * {
+ *   name: 'hg38',
+ *   sequence: {
+ *     type: 'ReferenceSequenceTrack',
+ *     trackId: 'hg38-ReferenceSequenceTrack',
+ *     adapter: {
+ *       type: 'BgzipFastaAdapter',
+ *       uri: 'https://example.com/hg38.fa.gz',
+ *     },
+ *   },
+ *   refNameAliases: {
+ *     adapter: {
+ *       type: 'RefNameAliasAdapter',
+ *       uri: 'https://example.com/aliases.txt',
+ *       refNameColumnHeaderName: 'ucsc',
+ *     },
+ *   },
+ * }
+ * ```
+ */
 const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
+    /**
+     * #slot
+     * location of the alias table: a UCSC `chromAlias.txt`, or any
+     * tab-separated file whose rows each list the alternate names of one
+     * reference sequence (`chr1<TAB>1<TAB>NC_000001.11`). The table lets a
+     * `1`-named file load against a `chr1`-named assembly.
+     */
     location: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my/aliases.txt',
-            locationType: 'UriLocation',
-        },
+        type: 'maybeFileLocation',
     },
+    /**
+     * #slot
+     * by default, the "ref names that match the fasta" are assumed to be in the
+     * first column (0), change this variable if needed
+     */
     refNameColumn: {
         type: 'number',
         defaultValue: 0,
+        advanced: true,
     },
+    /**
+     * #slot
+     * refNameColumnHeaderName
+     */
     refNameColumnHeaderName: {
         type: 'string',
         description: 'alternative to refNameColumn, instead looks at header (starts with # and finds column name)',
         defaultValue: '',
+        advanced: true,
     },
 }, {
     explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                location: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
+    /**
+     * #preProcessSnapshot
+     *
+     *
+     * preprocessor to allow minimal config:
+     * ```json
+     * {
+     *   "type": "RefNameAliasAdapter",
+     *   "uri": "yourfile.chromAlias.txt"
+     * }
+     * ```
+     */
+    preProcessSnapshot: normalizeSnapshot,
 });
 export default RefNameAliasAdapter;

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 | undefined, pluginManager?: PluginManager, opts?: BaseOptions): Promise<string[][]>;

package/esm/aliasUtils.js

@@ -0,0 +1,19 @@
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+// 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 (!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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "4.3.0",
+  "version": "5.0.0-beta.10",
   "type": "module",
   "description": "JBrowse 2 config utilities",
   "keywords": [
@@ -21,18 +21,17 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^5.6.0",
-    "@mui/icons-material": "^7.3.11",
-    "@mui/material": "^7.3.11",
-    "mobx": "^6.15.3",
-    "mobx-react": "^9.2.1",
-    "pluralize": "^8.0.0",
+    "@jbrowse/mobx-state-tree": "^6.6.1",
+    "@mui/icons-material": "^9.4.0",
+    "@mui/material": "^9.4.0",
+    "mobx": "^7.0.5",
+    "mobx-react": "^10.0.2",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.3.0"
+    "@jbrowse/core": "^5.0.0-beta.10"
   },
   "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"
   }
 }