@jbrowse/plugin-data-management 2.7.2 → 2.9.0

package/dist/ucsc-trackhub/doConnect.js

@@ -0,0 +1,131 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.doConnect = void 0;
+const ucsc_hub_1 = require("@gmod/ucsc-hub");
+const ucscTrackHub_1 = require("./ucscTrackHub");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
+const nanoid_1 = require("@jbrowse/core/util/nanoid");
+function resolve(uri, baseUri) {
+    return new URL(uri, baseUri).href;
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+async function doConnect(self) {
+    var _a;
+    const session = (0, util_1.getSession)(self);
+    const notLoadedAssemblies = [];
+    try {
+        const hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
+        const hubFileText = await (0, io_1.openLocation)(hubFileLocation).readFile('utf8');
+        // @ts-expect-error
+        const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
+        const { assemblyManager } = session;
+        if (hubFileText.includes('useOneFile on')) {
+            const hub = new ucsc_hub_1.SingleFileHub(hubFileText);
+            const { genome, tracks } = hub;
+            const genomeName = genome.name;
+            const asm = assemblyManager.get(genomeName);
+            if (!asm) {
+                // @ts-expect-error
+                session.addSessionAssembly({
+                    name: genomeName,
+                    sequence: {
+                        type: 'ReferenceSequenceTrack',
+                        trackId: `${genomeName}-${(0, nanoid_1.nanoid)()}`,
+                        adapter: {
+                            type: 'TwoBitAdapter',
+                            twoBitLocation: {
+                                uri: resolve(genome.data.twoBitPath, hubUri),
+                            },
+                            chromSizesLocation: {
+                                uri: resolve(genome.data.chromSizes, hubUri),
+                            },
+                        },
+                    },
+                });
+            }
+            const asm2 = assemblyManager.get(genomeName);
+            const sequenceAdapter = (0, configuration_1.getConf)(asm2, ['sequence', 'adapter']);
+            const tracksNew = (0, ucscTrackHub_1.generateTracks)({
+                trackDb: tracks,
+                trackDbLoc: hubFileLocation,
+                assemblyName: genomeName,
+                sequenceAdapter,
+            });
+            self.addTrackConfs(tracksNew);
+        }
+        else {
+            const hubFile = new ucsc_hub_1.HubFile(hubFileText);
+            const genomeFile = hubFile.data.genomesFile;
+            if (!genomeFile) {
+                throw new Error('genomesFile not found on hub');
+            }
+            // @ts-expect-error
+            const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
+            const genomesFileLocation = hubUri
+                ? {
+                    uri: resolve(genomeFile, hubUri),
+                    locationType: 'UriLocation',
+                }
+                : {
+                    localPath: genomeFile,
+                    locationType: 'LocalPathLocation',
+                };
+            const genomesFile = await (0, ucscTrackHub_1.fetchGenomesFile)(genomesFileLocation);
+            const map = {};
+            for (const [genomeName, genome] of Object.entries(genomesFile.data)) {
+                const assemblyNames = (0, configuration_1.getConf)(self, 'assemblyNames');
+                if (assemblyNames.length > 0 && !assemblyNames.includes(genomeName)) {
+                    continue;
+                }
+                const asm = assemblyManager.get(genomeName);
+                if (!asm) {
+                    notLoadedAssemblies.push(genomeName);
+                    continue;
+                }
+                // @ts-expect-error
+                const db = genome.data.trackDb;
+                if (!db) {
+                    throw new Error('genomesFile not found on hub');
+                }
+                const base = new URL(genomeFile, hubUri);
+                const loc = hubUri
+                    ? {
+                        uri: new URL(db, base).href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        localPath: db,
+                        locationType: 'LocalPathLocation',
+                    };
+                const trackDb = await (0, ucscTrackHub_1.fetchTrackDbFile)(loc);
+                const sequenceAdapter = (0, configuration_1.getConf)(asm, ['sequence', 'adapter']);
+                const tracks = (0, ucscTrackHub_1.generateTracks)({
+                    trackDb,
+                    trackDbLoc: loc,
+                    assemblyName: genomeName,
+                    sequenceAdapter,
+                });
+                self.addTrackConfs(tracks);
+                map[genomeName] = tracks.length;
+            }
+            const loadedAssemblies = Object.entries(map);
+            const str1 = loadedAssemblies.length
+                ? `Loaded data from these assemblies: ${loadedAssemblies
+                    .map(([key, val]) => `${key} (${val} tracks)`)
+                    .join(', ')}`
+                : '';
+            const str2 = notLoadedAssemblies.length
+                ? `Skipped data from these assemblies: ${notLoadedAssemblies.join(', ')}`
+                : '';
+            session.notify([str1, str2].filter(f => !!f).join('. '), 'success');
+        }
+    }
+    catch (e) {
+        console.error(e);
+        session.notify(`${(0, configuration_1.getConf)(self, 'name')}: "${e}"`, 'error');
+        (_a = session.breakConnection) === null || _a === void 0 ? void 0 : _a.call(session, self.configuration);
+    }
+}
+exports.doConnect = doConnect;

package/dist/ucsc-trackhub/model.d.ts

@@ -1,4 +1,8 @@
 import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #stateModel UCSCTrackHubConnection
+ * extends BaseConnectionModel
+ */
 export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
@@ -10,11 +14,16 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
         };
         assemblyNames: {
             type: string;
-            defaultValue: never[];
+            defaultValue: never[]; /**
+             * #action
+             */
             description: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
+    /**
+     * #property
+     */
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         hubTxtLocation: {
             type: string;
@@ -25,7 +34,9 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
             description: string;
         };
         assemblyNames: {
-            type: string;
+            type: string; /**
+             * #property
+             */
             defaultValue: never[];
             description: string;
         };
@@ -41,6 +52,9 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
             description: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
+    /**
+     * #property
+     */
     type: import("mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
 }, {
     connect(_arg: {
@@ -67,5 +81,8 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
     clear(): void;
 } & {
+    /**
+     * #action
+     */
     connect(): Promise<void>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/ucsc-trackhub/model.js

@@ -28,88 +28,33 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
 const mobx_state_tree_1 = require("mobx-state-tree");
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
+/**
+ * #stateModel UCSCTrackHubConnection
+ * extends BaseConnectionModel
+ */
 function UCSCTrackHubConnection(pluginManager) {
     return mobx_state_tree_1.types
         .compose('UCSCTrackHubConnection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
+        /**
+         * #property
+         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
+        /**
+         * #property
+         */
         type: mobx_state_tree_1.types.literal('UCSCTrackHubConnection'),
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
         async connect() {
-            var _a, _b;
-            const session = (0, util_1.getSession)(self);
-            const notLoadedAssemblies = [];
-            try {
-                const hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
-                const { generateTracks, fetchGenomesFile, fetchTrackDbFile, fetchHubFile, } = await Promise.resolve().then(() => __importStar(require('./ucscTrackHub')));
-                const hubFile = await fetchHubFile(hubFileLocation);
-                const genomeFile = hubFile.get('genomesFile');
-                if (!genomeFile) {
-                    throw new Error('genomesFile not found on hub');
-                }
-                const hubUri = new URL(hubFileLocation.uri, hubFileLocation.baseUri);
-                const genomesFileLocation = hubUri
-                    ? {
-                        uri: new URL(genomeFile, hubUri).href,
-                        locationType: 'UriLocation',
-                    }
-                    : {
-                        localPath: genomeFile,
-                        locationType: 'LocalPathLocation',
-                    };
-                const genomesFile = await fetchGenomesFile(genomesFileLocation);
-                const map = {};
-                for (const [genomeName, genome] of genomesFile) {
-                    const assemblyNames = (0, configuration_1.getConf)(self, 'assemblyNames');
-                    if (assemblyNames.length > 0 &&
-                        !assemblyNames.includes(genomeName)) {
-                        continue;
-                    }
-                    const conf = (_a = session.assemblyManager.get(genomeName)) === null || _a === void 0 ? void 0 : _a.configuration;
-                    if (!conf) {
-                        notLoadedAssemblies.push(genomeName);
-                        continue;
-                    }
-                    const db = genome.get('trackDb');
-                    if (!db) {
-                        throw new Error('genomesFile not found on hub');
-                    }
-                    const base = new URL(genomeFile, hubUri);
-                    const loc = hubUri
-                        ? {
-                            uri: new URL(db, base).href,
-                            locationType: 'UriLocation',
-                        }
-                        : {
-                            localPath: db,
-                            locationType: 'LocalPathLocation',
-                        };
-                    const trackDb = await fetchTrackDbFile(loc);
-                    const seqAdapter = (0, configuration_1.readConfObject)(conf, ['sequence', 'adapter']);
-                    const tracks = generateTracks(trackDb, loc, genomeName, seqAdapter);
-                    self.addTrackConfs(tracks);
-                    map[genomeName] = tracks.length;
-                }
-                const loadedAssemblies = Object.entries(map);
-                const str1 = loadedAssemblies.length
-                    ? `Loaded data from these assemblies: ${loadedAssemblies
-                        .map(([key, val]) => `${key} (${val} tracks)`)
-                        .join(', ')}`
-                    : '';
-                const str2 = notLoadedAssemblies.length
-                    ? `Skipped data from these assemblies: ${notLoadedAssemblies.join(', ')}`
-                    : '';
-                session.notify([str1, str2].filter(f => !!f).join('. '), 'success');
-            }
-            catch (e) {
-                console.error(e);
-                session.notify(`There was a problem connecting to the UCSC Track Hub "${self.configuration.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${e}"`, 'error');
-                (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
-            }
+            const { doConnect } = await Promise.resolve().then(() => __importStar(require('./doConnect')));
+            // eslint-disable-next-line @typescript-eslint/no-floating-promises
+            doConnect(self);
         },
     }));
 }

package/dist/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';