@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/esm/{ucsc-trackhub → UCSCTrackHub}/ucscTrackHub.d.ts

@@ -1,29 +1,11 @@
-import { FileLocation } from '@jbrowse/core/util';
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
-export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
-export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
-export declare function makeLoc(first: string, base: {
-    uri: string;
-    baseUri?: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLocAlt(first: string, alt: string, base: {
-    uri: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLoc2(first: string, alt?: string): {
-    uri: string | undefined;
-    locationType: string;
-};
-export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }: {
+import type { TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
+export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }: {
     trackDb: TrackDbFile;
     trackDbLoc: FileLocation;
     assemblyName: string;
     sequenceAdapter: any;
+    baseUrl: string;
 }): ({
     trackId: string;
     assemblyNames: string[];
@@ -31,13 +13,17 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     name: string;
     description: string;
     category: string[] | undefined;
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
-    name: string | undefined;
+    name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         bamLocation: {
@@ -53,18 +39,23 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         cramLocation: {
@@ -78,21 +69,26 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         sequenceAdapter: any;
         bamLocation?: undefined;
         index?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
-        bigBedLocation: {
+        bigWigLocation: {
             uri: string | undefined;
             locationType: string;
         };
@@ -101,20 +97,25 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
-        bigWigLocation: {
+        bigBedLocation: {
             uri: string | undefined;
             locationType: string;
         };
@@ -123,17 +124,22 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         vcfGzLocation: {
@@ -150,17 +156,22 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         hicLocation: {
@@ -172,9 +183,15 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 })[];
 export { default as ucscAssemblies } from './ucscAssemblies';

package/esm/UCSCTrackHub/ucscTrackHub.js

@@ -0,0 +1,162 @@
+import { isUriLocation, notEmpty, objectHash } from '@jbrowse/core/util';
+import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks';
+import { makeLoc2, makeLoc, makeLocAlt, resolve } from './util';
+export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }) {
+    const parentTrackKeys = new Set([
+        'superTrack',
+        'compositeTrack',
+        'container',
+        'view',
+    ]);
+    return Object.entries(trackDb.data)
+        .map(([trackName, track]) => {
+        var _a;
+        const { data } = track;
+        if (Object.keys(data).some(key => parentTrackKeys.has(key))) {
+            return undefined;
+        }
+        else {
+            const parentTracks = [];
+            let currentTrackName = trackName;
+            do {
+                currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
+                if (currentTrackName) {
+                    currentTrackName = currentTrackName.split(' ')[0];
+                    parentTracks.push(trackDb.data[currentTrackName]);
+                }
+            } while (currentTrackName);
+            parentTracks.reverse();
+            return {
+                metadata: {
+                    ucscConfig: {
+                        ...track.data,
+                        ...(track.data.html
+                            ? {
+                                html: `<a href="${resolve(track.data.html, baseUrl)}">${track.data.html}</a>`,
+                            }
+                            : {}),
+                    },
+                },
+                category: [
+                    track.data.group,
+                    ...parentTracks
+                        .map(p => p === null || p === void 0 ? void 0 : p.data.group)
+                        .filter((f) => !!f),
+                ].filter(f => !!f),
+                ...makeTrackConfig({
+                    track,
+                    trackDbLoc,
+                    trackDb,
+                    sequenceAdapter,
+                }),
+            };
+        }
+    })
+        .filter(notEmpty)
+        .map(r => ({
+        ...r,
+        trackId: `ucsc-trackhub-${objectHash(r)}`,
+        assemblyNames: [assemblyName],
+    }));
+}
+function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
+    var _a;
+    const { data } = track;
+    const parent = data.parent || '';
+    const bigDataUrl = data.bigDataUrl || '';
+    const bigDataIdx = data.bigDataIndex || '';
+    const trackType = data.type || ((_a = trackDb.data[parent]) === null || _a === void 0 ? void 0 : _a.data.type) || '';
+    const name = (data.shortLabel || '') + (bigDataUrl.includes('xeno') ? ' (xeno)' : '');
+    const isUri = isUriLocation(trackDbLoc);
+    let baseTrackType = trackType.split(' ')[0] || '';
+    if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
+        baseTrackType = 'cram';
+    }
+    const bigDataLocation = isUri
+        ? makeLoc(bigDataUrl, trackDbLoc)
+        : makeLoc2(bigDataUrl);
+    if (baseTrackType === 'bam') {
+        return {
+            type: 'AlignmentsTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BamAdapter',
+                bamLocation: bigDataLocation,
+                index: {
+                    location: isUri
+                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
+                        : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
+                },
+            },
+        };
+    }
+    else if (baseTrackType === 'cram') {
+        return {
+            type: 'AlignmentsTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'CramAdapter',
+                cramLocation: bigDataLocation,
+                craiLocation: isUri
+                    ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
+                    : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
+                sequenceAdapter,
+            },
+        };
+    }
+    else if (baseTrackType === 'bigWig') {
+        return {
+            type: 'QuantitativeTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BigWigAdapter',
+                bigWigLocation: bigDataLocation,
+            },
+        };
+    }
+    else if (baseTrackType.startsWith('big')) {
+        return {
+            type: 'FeatureTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BigBedAdapter',
+                bigBedLocation: bigDataLocation,
+            },
+        };
+    }
+    else if (baseTrackType === 'vcfTabix') {
+        return {
+            type: 'VariantTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'VcfTabixAdapter',
+                vcfGzLocation: bigDataLocation,
+                index: {
+                    location: isUri
+                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
+                        : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
+                },
+            },
+        };
+    }
+    else if (baseTrackType === 'hic') {
+        return {
+            type: 'HicTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'HicAdapter',
+                hicLocation: bigDataLocation,
+            },
+        };
+    }
+    else {
+        return generateUnknownTrackConf(name, baseTrackType);
+    }
+}
+export { default as ucscAssemblies } from './ucscAssemblies';

package/esm/UCSCTrackHub/util.d.ts

@@ -0,0 +1,22 @@
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
+export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
+export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
+export declare function makeLoc(first: string, base: {
+    uri: string;
+    baseUri?: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLocAlt(first: string, alt: string, base: {
+    uri: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLoc2(first: string, alt?: string): {
+    uri: string | undefined;
+    locationType: string;
+};
+export declare function resolve(uri: string, baseUri: string): string;

package/esm/UCSCTrackHub/util.js

@@ -0,0 +1,33 @@
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import { openLocation } from '@jbrowse/core/util/io';
+export async function fetchGenomesFile(genomesLoc) {
+    const genomesFileText = await openLocation(genomesLoc).readFile('utf8');
+    return new GenomesFile(genomesFileText);
+}
+export async function fetchTrackDbFile(trackDbLoc) {
+    const text = await openLocation(trackDbLoc).readFile('utf8');
+    return new TrackDbFile(text);
+}
+export function makeLoc(first, base) {
+    return {
+        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
+        locationType: 'UriLocation',
+    };
+}
+export function makeLocAlt(first, alt, base) {
+    return first ? makeLoc(first, base) : makeLoc(alt, base);
+}
+export function makeLoc2(first, alt) {
+    return first
+        ? {
+            uri: first,
+            locationType: 'LocalPath',
+        }
+        : {
+            uri: alt,
+            locationType: 'UriLocation',
+        };
+}
+export function resolve(uri, baseUri) {
+    return new URL(uri, baseUri).href;
+}

package/esm/index.d.ts

@@ -1,20 +1,20 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
-    rootModel: any;
-    onClose: (arg: boolean) => void;
-}) => import("react").JSX.Element>;
+import type PluginManager from '@jbrowse/core/PluginManager';
+declare const AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
+    session: import("@jbrowse/core/util").AbstractSessionModel;
+    onClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element>;
 export default class DataManagementPlugin extends Plugin {
     name: string;
     exports: {
-        AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
-            rootModel: any;
-            onClose: (arg: boolean) => void;
-        }) => import("react").JSX.Element>;
+        AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
+            session: import("@jbrowse/core/util").AbstractSessionModel;
+            onClose: () => void;
+        }) => import("react/jsx-runtime").JSX.Element>;
     };
     install(pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;
 }
 export { AssemblyManager };
-export { type AddTrackModel } from './AddTrackWidget/model';
-export { type HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
+export type { AddTrackModel } from './AddTrackWidget/model';
+export type { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';

package/esm/index.js

@@ -1,10 +1,10 @@
 import { lazy } from 'react';
 import Plugin from '@jbrowse/core/Plugin';
-import UCSCTrackHubConnectionF from './ucsc-trackhub';
-import AddTrackWidgetF from './AddTrackWidget';
 import AddConnectionWidgetF from './AddConnectionWidget';
-import PluginStoreWidgetF from './PluginStoreWidget';
+import AddTrackWidgetF from './AddTrackWidget';
 import HierarchicalTrackSelectorWidgetF from './HierarchicalTrackSelectorWidget';
+import PluginStoreWidgetF from './PluginStoreWidget';
+import UCSCTrackHubConnectionF from './UCSCTrackHub';
 const AssemblyManager = lazy(() => import('./AssemblyManager'));
 export default class DataManagementPlugin extends Plugin {
     constructor() {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -36,9 +36,10 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/ucsc-hub": "^0.3.0",
+    "@gmod/ucsc-hub": "^1.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
+    "deepmerge": "^4.3.1",
     "react-virtualized-auto-sizer": "^1.0.2",
     "react-vtree": "^3.0.0-beta.1",
     "react-window": "^1.8.6"
@@ -60,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }