@jbrowse/plugin-data-management 2.7.2 → 2.9.0

package/esm/ucsc-trackhub/ucscTrackHub.d.ts

@@ -1,10 +1,10 @@
-import { TrackDbFile } from '@gmod/ucsc-hub';
 import { FileLocation } from '@jbrowse/core/util';
-export declare function fetchHubFile(hubLocation: FileLocation): Promise<import("@gmod/ucsc-hub").HubFile>;
-export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<import("@gmod/ucsc-hub").GenomesFile>;
+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;
@@ -19,5 +19,162 @@ export declare function makeLoc2(first: string, alt?: string): {
     uri: string | undefined;
     locationType: string;
 };
-export declare function generateTracks(trackDb: TrackDbFile, trackDbLoc: FileLocation, assemblyName: string, sequenceAdapter: any): any;
+export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }: {
+    trackDb: TrackDbFile;
+    trackDbLoc: FileLocation;
+    assemblyName: string;
+    sequenceAdapter: any;
+}): ({
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[] | undefined;
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        bamLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        index: {
+            location: {
+                uri: string | undefined;
+                locationType: string;
+            };
+        };
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        cramLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        craiLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        sequenceAdapter: any;
+        bamLocation?: undefined;
+        index?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        bigBedLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        bigWigLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        vcfGzLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        vcfGzLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        index: {
+            location: {
+                uri: string | undefined;
+                locationType: string;
+            };
+        };
+        bamLocation?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        hicLocation?: undefined;
+    };
+} | {
+    trackId: string;
+    assemblyNames: string[];
+    type: string;
+    name: string;
+    description: string;
+    category: string[];
+    adapter: {
+        type: string;
+        hicLocation: {
+            uri: string | undefined;
+            locationType: string;
+        };
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        sequenceAdapter?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        vcfGzLocation?: undefined;
+    };
+})[];
 export { default as ucscAssemblies } from './ucscAssemblies';

package/esm/ucsc-trackhub/ucscTrackHub.js

@@ -1,29 +1,19 @@
-import { isUriLocation, objectHash } from '@jbrowse/core/util';
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import { isUriLocation, notEmpty, objectHash, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
-import { generateUnsupportedTrackConf, generateUnknownTrackConf, } from '@jbrowse/core/util/tracks';
-export async function fetchHubFile(hubLocation) {
-    try {
-        const hubFileText = await openLocation(hubLocation).readFile('utf8');
-        const { HubFile } = await import('@gmod/ucsc-hub');
-        return new HubFile(hubFileText);
-    }
-    catch (error) {
-        throw new Error(`Not a valid hub.txt file, got error: '${error}'`);
-    }
-}
+import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks';
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
 export async function fetchGenomesFile(genomesLoc) {
     const genomesFileText = await openLocation(genomesLoc).readFile('utf8');
-    const { GenomesFile } = await import('@gmod/ucsc-hub');
     return new GenomesFile(genomesFileText);
 }
 export async function fetchTrackDbFile(trackDbLoc) {
     const text = await openLocation(trackDbLoc).readFile('utf8');
-    const { TrackDbFile } = await import('@gmod/ucsc-hub');
     return new TrackDbFile(text);
 }
 export function makeLoc(first, base) {
     return {
-        uri: new URL(first, base.uri).href,
+        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
         locationType: 'UriLocation',
     };
 }
@@ -41,11 +31,11 @@ export function makeLoc2(first, alt) {
             locationType: 'UriLocation',
         };
 }
-export function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapter) {
-    var _a;
-    const tracks = [];
-    for (const [trackName, track] of trackDb.entries()) {
-        const trackKeys = [...track.keys()];
+export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }) {
+    return Object.entries(trackDb.data)
+        .map(([trackName, track]) => {
+        var _a;
+        const trackKeys = Object.keys(track);
         const parentTrackKeys = new Set([
             'superTrack',
             'compositeTrack',
@@ -53,41 +43,44 @@ export function generateTracks(trackDb, trackDbLoc, assemblyName, sequenceAdapte
             'view',
         ]);
         if (trackKeys.some(key => parentTrackKeys.has(key))) {
-            continue;
+            return undefined;
         }
         const parentTracks = [];
         let currentTrackName = trackName;
         do {
-            currentTrackName = ((_a = trackDb.get(currentTrackName)) === null || _a === void 0 ? void 0 : _a.get('parent')) || '';
+            currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
             if (currentTrackName) {
                 ;
                 [currentTrackName] = currentTrackName.split(' ');
-                parentTracks.push(trackDb.get(currentTrackName));
+                parentTracks.push(trackDb.data[currentTrackName]);
             }
         } while (currentTrackName);
         parentTracks.reverse();
         const categories = parentTracks
-            .map(p => p === null || p === void 0 ? void 0 : p.get('shortLabel'))
+            .map(p => p === null || p === void 0 ? void 0 : p.data.shortLabel)
             .filter((f) => !!f);
-        const res = makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter);
-        tracks.push({
+        const res = makeTrackConfig({
+            track: track,
+            categories,
+            trackDbLoc,
+            trackDb,
+            sequenceAdapter,
+        });
+        return {
             ...res,
             trackId: `ucsc-trackhub-${objectHash(res)}`,
             assemblyNames: [assemblyName],
-        });
-    }
-    return tracks;
+        };
+    })
+        .filter(notEmpty);
 }
-function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter) {
+function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapter, }) {
     var _a;
-    let trackType = track.get('type');
-    const name = track.get('shortLabel') || '';
-    const bigDataUrl = track.get('bigDataUrl') || '';
-    const bigDataIdx = track.get('bigDataIndex') || '';
+    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 isUri = isUriLocation(trackDbLoc);
-    if (!trackType) {
-        trackType = (_a = trackDb.get(track.get('parent') || '')) === null || _a === void 0 ? void 0 : _a.get('type');
-    }
     let baseTrackType = (trackType === null || trackType === void 0 ? void 0 : trackType.split(' ')[0]) || '';
     if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
         baseTrackType = 'cram';
@@ -99,8 +92,8 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
         case 'bam':
             return {
                 type: 'AlignmentsTrack',
-                name: track.get('shortLabel'),
-                description: track.get('longLabel'),
+                name: track.data.longLabel,
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'BamAdapter',
@@ -112,142 +105,55 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
                     },
                 },
             };
-        case 'bigBarChart':
+        case 'cram':
             return {
-                type: 'FeatureTrack',
+                type: 'AlignmentsTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
+                    type: 'CramAdapter',
+                    cramLocation: bigDataLocation,
+                    craiLocation: isUri
+                        ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
+                        : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
+                    sequenceAdapter,
                 },
             };
+        case 'bigBarChart':
         case 'bigBed':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
         case 'bigGenePred':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
         case 'bigChain':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
-            };
         case 'bigInteract':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
-            };
         case 'bigMaf':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
-            };
+        case 'bigNarrowPeak':
         case 'bigPsl':
             return {
                 type: 'FeatureTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'BigBedAdapter',
                     bigBedLocation: bigDataLocation,
                 },
-                renderer: {
-                    type: 'SvgFeatureRenderer',
-                },
             };
         case 'bigWig':
             return {
                 type: 'QuantitativeTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'BigWigAdapter',
                     bigWigLocation: bigDataLocation,
                 },
             };
-        case 'cram':
-            return {
-                type: 'AlignmentsTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'CramAdapter',
-                    cramLocation: bigDataLocation,
-                    craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
-                        : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
-                    sequenceAdapter,
-                },
-            };
-        case 'bigNarrowPeak':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.get('longLabel'),
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
-        case 'peptideMapping':
-            return generateUnsupportedTrackConf(name, baseTrackType, categories);
         case 'vcfTabix':
             return {
                 type: 'VariantTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'VcfTabixAdapter',
@@ -263,7 +169,7 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
             return {
                 type: 'HicTrack',
                 name,
-                description: track.get('longLabel'),
+                description: track.data.longLabel,
                 category: categories,
                 adapter: {
                     type: 'HicAdapter',
@@ -271,6 +177,7 @@ function makeTrackConfig(track, categories, trackDbLoc, trackDb, sequenceAdapter
                 },
             };
         // unsupported types
+        //     case 'peptideMapping':
         //     case 'gvf':
         //     case 'ld2':
         //     case 'narrowPeak':

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.7.2",
+  "version": "2.9.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/ucsc-hub": "^0.1.6",
+    "@gmod/ucsc-hub": "^0.3.0",
     "@mui/icons-material": "^5.0.1",
     "@mui/x-data-grid": "^6.0.1",
     "clsx": "^2.0.0",
@@ -61,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "9052b295f2d322e729254457ed9fe2231fb22cce"
+  "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
 }

package/dist/HierarchicalTrackSelectorWidget/components/faceted/util.d.ts

@@ -1 +0,0 @@
-export declare function getRootKeys(obj: Record<string, unknown>): string[];

package/esm/HierarchicalTrackSelectorWidget/components/faceted/util.d.ts

@@ -1 +0,0 @@
-export declare function getRootKeys(obj: Record<string, unknown>): string[];