@jbrowse/plugin-data-management 2.18.0 → 3.0.1

package/esm/UCSCTrackHub/ucscTrackHub.d.ts

@@ -1,29 +1,11 @@
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { 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 generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }: {
+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

@@ -1,83 +1,72 @@
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
 import { isUriLocation, notEmpty, objectHash } from '@jbrowse/core/util';
-import { openLocation } from '@jbrowse/core/util/io';
 import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks';
-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 generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }) {
+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 trackKeys = Object.keys(track);
-        const parentTrackKeys = new Set([
-            'superTrack',
-            'compositeTrack',
-            'container',
-            'view',
-        ]);
-        if (trackKeys.some(key => parentTrackKeys.has(key))) {
+        const { data } = track;
+        if (Object.keys(data).some(key => parentTrackKeys.has(key))) {
             return undefined;
         }
-        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();
-        const categories = parentTracks
-            .map(p => p === null || p === void 0 ? void 0 : p.data.shortLabel)
-            .filter((f) => !!f);
-        const res = makeTrackConfig({
-            track: track,
-            categories,
-            trackDbLoc,
-            trackDb,
-            sequenceAdapter,
-        });
-        return {
-            ...res,
-            trackId: `ucsc-trackhub-${objectHash(res)}`,
-            assemblyNames: [assemblyName],
-        };
+        else {
+            const parentTracks = [];
+            let currentTrackName = trackName;
+            do {
+                currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
+                if (currentTrackName) {
+                    currentTrackName = currentTrackName.split(' ')[0];
+                    parentTracks.push(trackDb.data[currentTrackName]);
+                }
+            } while (currentTrackName);
+            parentTracks.reverse();
+            return {
+                metadata: {
+                    ucscConfig: {
+                        ...track.data,
+                        ...(track.data.html
+                            ? {
+                                html: `<a href="${resolve(track.data.html, baseUrl)}">${track.data.html}</a>`,
+                            }
+                            : {}),
+                    },
+                },
+                category: [
+                    track.data.group,
+                    ...parentTracks
+                        .map(p => p === null || p === void 0 ? void 0 : p.data.group)
+                        .filter((f) => !!f),
+                ].filter(f => !!f),
+                ...makeTrackConfig({
+                    track,
+                    trackDbLoc,
+                    trackDb,
+                    sequenceAdapter,
+                }),
+            };
+        }
     })
-        .filter(notEmpty);
+        .filter(notEmpty)
+        .map(r => ({
+        ...r,
+        trackId: `ucsc-trackhub-${objectHash(r)}`,
+        assemblyNames: [assemblyName],
+    }));
 }
-function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapter, }) {
+function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
     var _a;
-    const trackType = track.data.type || ((_a = trackDb.data[track.data.parent || '']) === null || _a === void 0 ? void 0 : _a.data.type) || '';
-    const name = track.data.shortLabel || '';
-    const bigDataUrl = track.data.bigDataUrl || '';
-    const bigDataIdx = track.data.bigDataIndex || '';
+    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')) {
@@ -86,96 +75,88 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
     const bigDataLocation = isUri
         ? makeLoc(bigDataUrl, trackDbLoc)
         : makeLoc2(bigDataUrl);
-    switch (baseTrackType) {
-        case 'bam':
-            return {
-                type: 'AlignmentsTrack',
-                name: track.data.longLabel,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BamAdapter',
-                    bamLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
-                    },
-                },
-            };
-        case 'cram':
-            return {
-                type: 'AlignmentsTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'CramAdapter',
-                    cramLocation: bigDataLocation,
-                    craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
-                        : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
-                    sequenceAdapter,
-                },
-            };
-        case 'bigBarChart':
-        case 'bigBed':
-        case 'bigGenePred':
-        case 'bigChain':
-        case 'bigInteract':
-        case 'bigMaf':
-        case 'bigNarrowPeak':
-        case 'bigPsl':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
-        case 'bigWig':
-            return {
-                type: 'QuantitativeTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigWigAdapter',
-                    bigWigLocation: bigDataLocation,
-                },
-            };
-        case 'vcfTabix':
-            return {
-                type: 'VariantTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'VcfTabixAdapter',
-                    vcfGzLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
-                    },
+    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`),
                 },
-            };
-        case 'hic':
-            return {
-                type: 'HicTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'HicAdapter',
-                    hicLocation: bigDataLocation,
+            },
+        };
+    }
+    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`),
                 },
-            };
-        default:
-            return generateUnknownTrackConf(name, baseTrackType, categories);
+            },
+        };
+    }
+    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

@@ -3,14 +3,14 @@ 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.Element>;
+}) => import("react/jsx-runtime").JSX.Element>;
 export default class DataManagementPlugin extends Plugin {
     name: string;
     exports: {
         AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
             session: import("@jbrowse/core/util").AbstractSessionModel;
             onClose: () => void;
-        }) => import("react").JSX.Element>;
+        }) => import("react/jsx-runtime").JSX.Element>;
     };
     install(pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.18.0",
+  "version": "3.0.1",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -36,29 +36,30 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/ucsc-hub": "^0.3.0",
+    "@gmod/ucsc-hub": "^1.0.0",
+    "@jbrowse/core": "^3.0.1",
+    "@jbrowse/plugin-config": "^3.0.1",
+    "@jbrowse/product-core": "^3.0.1",
     "@mui/icons-material": "^6.0.0",
-    "@mui/x-data-grid": "^7.0.0",
-    "react-virtualized-auto-sizer": "^1.0.2",
-    "react-vtree": "^3.0.0-beta.1",
-    "react-window": "^1.8.6"
-  },
-  "peerDependencies": {
-    "@jbrowse/core": "^2.0.0",
-    "@jbrowse/plugin-config": "^2.0.0",
-    "@jbrowse/product-core": "^2.0.0",
     "@mui/material": "^6.0.0",
+    "@mui/x-data-grid": "^7.0.0",
+    "deepmerge": "^4.3.1",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "react": ">=16.8.0",
+    "react-virtualized-auto-sizer": "^1.0.2",
+    "react-vtree": "^3.0.0-beta.1",
+    "react-window": "^1.8.6",
     "tss-react": "^4.0.0"
   },
+  "peerDependencies": {
+    "react": ">=18.0.0"
+  },
   "publishConfig": {
     "access": "public"
   },
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
+  "gitHead": "aa2f1d1a89d2361c7fd1a93fe29506fa4554f5cc"
 }