@jbrowse/plugin-legacy-jbrowse 1.7.11 → 2.0.0

package/esm/JBrowse1Connection/types.d.ts

@@ -0,0 +1,91 @@
+export interface ProtoTrack {
+    backendVersion?: number;
+    baseUrl?: string;
+    category?: string;
+    config?: Track;
+    dataRoot?: string;
+    features?: Feature[];
+    histograms?: Track;
+    index?: number;
+    key?: string;
+    label?: string;
+    metadata?: Metadata;
+    store?: Store | string;
+    storeClass?: string;
+    type?: string;
+    urlTemplate?: string;
+    baiUrlTemplate?: string;
+    craiUrlTemplate?: string;
+    tbiUrlTemplate?: string;
+    csiUrlTemplate?: string;
+    faiUrlTemplate?: string;
+    gziUrlTemplate?: string;
+    useAsRefSeqStore?: boolean;
+}
+export interface Track extends ProtoTrack {
+    label: string;
+}
+export interface Metadata {
+    category?: string;
+    description?: string;
+    Description?: string;
+}
+export interface Feature {
+    seq_id: string;
+    start: number;
+    end: number;
+    name?: string;
+}
+export interface Source {
+    url: string;
+    name?: string;
+    type?: string;
+}
+export interface TrackMetadata {
+    sources?: string | Source | (string | Source)[] | Record<string, Source>;
+}
+export interface Store extends ProtoTrack {
+    name?: string;
+}
+export interface Names {
+    baseUrl?: string;
+}
+export interface RefSeq {
+    name: string;
+    length: number;
+    end: number;
+    start: number;
+}
+export interface RefSeqs {
+    url?: string;
+    data?: RefSeq[];
+}
+export interface Include {
+    url: string;
+    cacheBuster?: boolean;
+    format?: string;
+    version?: number;
+}
+export interface Config {
+    baseUrl?: string;
+    cacheBuster?: boolean;
+    dataRoot?: string;
+    include?: string[];
+    names?: Record<string, string>;
+    nameUrl?: string;
+    refSeqs?: string | RefSeqs;
+    sourceUrl?: string;
+    stores?: Record<string, Store>;
+    trackMetadata?: TrackMetadata;
+    tracks?: Track | Track[] | Record<string, Track | ProtoTrack>;
+}
+export interface UriLocation {
+    uri: string;
+    baseUri?: string;
+    locationType: 'UriLocation';
+}
+export interface LocalPathLocation {
+    localPath: string;
+    locationType: 'LocalPathLocation';
+}
+export declare type JBLocation = UriLocation | LocalPathLocation;

package/esm/JBrowse1Connection/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/esm/JBrowse1Connection/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/types.ts"],"names":[],"mappings":""}

package/esm/JBrowse1Connection/util.d.ts

@@ -0,0 +1,26 @@
+import { Track, Source } from './types';
+export declare function isTrack(arg: any): arg is Track;
+export declare function isSource(arg: any): arg is Source;
+/**
+ * updates a with values from b, recursively
+ */
+declare type Obj = Record<string, any>;
+export declare function deepUpdate(a: Obj, b: Obj): Obj;
+/**
+ * replace variables in a template string with values
+ * @param template - String with variable names in curly brackets
+ * e.g., `http://foo/{bar}?arg={baz.foo}`
+ * @param fillWith - object with attribute-value mappings
+ * e.g., `{ 'bar': 'someurl', 'baz': { 'foo': 42 } }`
+ * @returns the template string with variables in fillWith replaced
+ * e.g., 'htp://foo/someurl?arg=valueforbaz'
+ */
+export declare function fillTemplate(template: string, fillWith: Obj): string;
+/**
+ * Clones objects (including DOM nodes) and all children.
+ * Warning: do not clone cyclic structures
+ * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
+ * @param src - The object to clone
+ */
+export declare function clone(src: any): any;
+export {};

package/esm/JBrowse1Connection/util.js

@@ -0,0 +1,136 @@
+import getValue from 'get-value';
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export function isTrack(arg) {
+    return arg && arg.label && typeof arg.label === 'string';
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export function isSource(arg) {
+    return arg && arg.url && typeof arg.url === 'string';
+}
+export function deepUpdate(a, b) {
+    for (const prop of Object.keys(b)) {
+        if (prop in a &&
+            typeof b[prop] === 'object' &&
+            typeof a[prop] === 'object') {
+            deepUpdate(a[prop], b[prop]);
+        }
+        else if (typeof a[prop] === 'undefined' ||
+            typeof b[prop] !== 'undefined') {
+            a[prop] = b[prop];
+        }
+    }
+    return a;
+}
+/**
+ * replace variables in a template string with values
+ * @param template - String with variable names in curly brackets
+ * e.g., `http://foo/{bar}?arg={baz.foo}`
+ * @param fillWith - object with attribute-value mappings
+ * e.g., `{ 'bar': 'someurl', 'baz': { 'foo': 42 } }`
+ * @returns the template string with variables in fillWith replaced
+ * e.g., 'htp://foo/someurl?arg=valueforbaz'
+ */
+export function fillTemplate(template, fillWith) {
+    return template.replace(/\{([\w\s.]+)\}/g, (match, varName) => {
+        varName = varName.replace(/\s+/g, ''); // remove all whitespace
+        const fill = getValue(fillWith, varName);
+        if (fill !== undefined) {
+            if (typeof fill === 'function') {
+                return fill(varName);
+            }
+            return fill;
+        }
+        if (fillWith.callback) {
+            // @ts-ignore
+            const v = fillWith.callback.call(this, varName);
+            if (v !== undefined) {
+                return v;
+            }
+        }
+        return match;
+    });
+}
+/**
+ * Clones objects (including DOM nodes) and all children.
+ * Warning: do not clone cyclic structures
+ * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
+ * @param src - The object to clone
+ */
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export function clone(src) {
+    if (!src ||
+        typeof src !== 'object' ||
+        Object.prototype.toString.call(src) === '[object Function]') {
+        // null, undefined, any non-object, or function
+        return src; // anything
+    }
+    if (src.nodeType && 'cloneNode' in src) {
+        // DOM Node
+        return src.cloneNode(true); // Node
+    }
+    if (src instanceof Date) {
+        // Date
+        return new Date(src.getTime()); // Date
+    }
+    if (src instanceof RegExp) {
+        // RegExp
+        return new RegExp(src); // RegExp
+    }
+    let r;
+    let i;
+    let l;
+    if (Array.isArray(src)) {
+        // array
+        r = [];
+        for (i = 0, l = src.length; i < l; ++i) {
+            if (i in src) {
+                r[i] = clone(src[i]);
+            }
+        }
+        // we don't clone functions for performance reasons
+        //    }else if(d.isFunction(src)){
+        //      // function
+        //      r = function(){ return src.apply(this, arguments); };
+    }
+    else {
+        // generic objects
+        r = src.constructor ? new src.constructor() : {};
+    }
+    return mixin(r, src, clone);
+}
+/**
+ * Copies/adds all properties of source to dest; returns dest.
+ * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
+ *
+ * All properties, including functions (sometimes termed "methods"), excluding
+ * any non-standard extensions found in Object.prototype, are copied/added to
+ * dest. Copying/adding each particular property is delegated to copyFunc
+ * (if any); copyFunc defaults to the Javascript assignment operator if not
+ * provided. Notice that by default, mixin executes a so-called "shallow copy"
+ * and aggregate types are copied/added by reference.
+ * @param dest - The object to which to copy/add all properties contained in
+ * source.
+ * @param source - The object from which to draw all properties to copy into dest.
+ * @param copyFunc - The process used to copy/add a property in source; defaults
+ * to the Javascript assignment operator.
+ * @returns dest, as modified
+ */
+function mixin(dest, source, copyFunc) {
+    let name;
+    let s;
+    const empty = {};
+    for (name in source) {
+        // the (!(name in empty) || empty[name] !== s) condition avoids copying
+        // properties in "source" inherited from Object.prototype.	 For example,
+        // if dest has a custom toString() method, don't overwrite it with the
+        // toString() method that source inherited from Object.prototype
+        s = source[name];
+        if (!(name in dest) ||
+            // @ts-ignore
+            (dest[name] !== s && (!(name in empty) || empty[name] !== s))) {
+            dest[name] = copyFunc ? copyFunc(s) : s;
+        }
+    }
+    return dest; // Object
+}
+//# sourceMappingURL=util.js.map

package/esm/JBrowse1Connection/util.js.map

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package/esm/JBrowse1TextSeachAdapter/HttpMap.d.ts

@@ -0,0 +1,39 @@
+export default class HttpMap {
+    url: string;
+    constructor(args: {
+        url: string;
+    });
+    /**
+     * loads meta.json file from names directory and reads number of hash_bits used
+     */
+    readMeta(): Promise<{
+        hashHexCharacters: number;
+        compress: any;
+        tracks: any;
+    }>;
+    getHashHexCharacters(): Promise<number>;
+    getCompress(): Promise<any>;
+    getTrackNames(): Promise<any>;
+    /**
+     * Returns contents of a bucket given a key
+     * @param key - string
+     */
+    get(key: string): Promise<any>;
+    /**
+     * Returns a bucket given a key
+     * @param key - string
+     */
+    getBucket(key: string): Promise<any>;
+    /**
+     * Loads a file using the url and provided id.
+     * Returns response object with contents of the file
+     * @param id - string
+     */
+    loadFile(id: string): Promise<any>;
+    /**
+     * Returns the corresponding path of the file given a hex string
+     * @param hex - hex string
+     */
+    hexToDirPath(hex: string): Promise<string>;
+    hash(data: string): string;
+}

package/esm/JBrowse1TextSeachAdapter/HttpMap.js

@@ -0,0 +1,89 @@
+/*
+ * Helper class allows reading names index generated in JBrowse1
+ * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
+ */
+import crc32 from 'buffer-crc32';
+export default class HttpMap {
+    constructor(args) {
+        // make sure url has a trailing slash
+        this.url = /\/$/.test(args.url) ? args.url : `${args.url}/`;
+    }
+    /**
+     * loads meta.json file from names directory and reads number of hash_bits used
+     */
+    async readMeta() {
+        const meta = await this.loadFile('meta.json');
+        const { compress, track_names: tracks } = meta;
+        const hashHexCharacters = Math.ceil(meta.hash_bits / 4);
+        return { hashHexCharacters, compress, tracks };
+    }
+    async getHashHexCharacters() {
+        const meta = await this.readMeta();
+        return meta.hashHexCharacters;
+    }
+    async getCompress() {
+        const meta = await this.readMeta();
+        return meta.compress;
+    }
+    async getTrackNames() {
+        const meta = await this.readMeta();
+        return meta.tracks;
+    }
+    /**
+     * Returns contents of a bucket given a key
+     * @param key - string
+     */
+    async get(key) {
+        const bucket = await this.getBucket(key);
+        return bucket[key];
+    }
+    /**
+     * Returns a bucket given a key
+     * @param key - string
+     */
+    async getBucket(key) {
+        const bucketIdent = this.hash(key);
+        const hexToDirPath = await this.hexToDirPath(bucketIdent);
+        return this.loadFile(hexToDirPath);
+    }
+    /**
+     * Loads a file using the url and provided id.
+     * Returns response object with contents of the file
+     * @param id - string
+     */
+    async loadFile(id) {
+        const response = await fetch(`${this.url}${id}`);
+        if (!response.ok) {
+            throw new Error(`HTTP ${response.status} ${response.statusText}`);
+        }
+        return response.json();
+    }
+    /**
+     * Returns the corresponding path of the file given a hex string
+     * @param hex - hex string
+     */
+    async hexToDirPath(hex) {
+        // zero-pad the hex string to be 8 chars if necessary
+        const hashHexCharacters = await this.getHashHexCharacters();
+        if (hashHexCharacters) {
+            const compress = await this.getCompress();
+            while (hex.length < 8) {
+                hex = `0${hex}`;
+            }
+            hex = hex.substr(8 - hashHexCharacters);
+            const dirpath = [];
+            for (let i = 0; i < hex.length; i += 3) {
+                dirpath.push(hex.substring(i, i + 3));
+            }
+            return `${dirpath.join('/')}.json${compress ? 'z' : ''}`;
+        }
+        return '';
+    }
+    hash(data) {
+        return crc32(Buffer.from(data))
+            .toString('hex')
+            .toLowerCase()
+            .replace('-', 'n');
+    }
+}
+//# sourceMappingURL=HttpMap.js.map

package/esm/JBrowse1TextSeachAdapter/HttpMap.js.map

@@ -0,0 +1 @@
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package/esm/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.d.ts

@@ -0,0 +1,33 @@
+import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { Instance } from 'mobx-state-tree';
+import MyConfigSchema from './configSchema';
+import HttpMap from './HttpMap';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export interface TooManyHits {
+    name: string;
+    hitLimit: number;
+}
+interface SearchResults {
+    prefix: ({
+        name: string;
+    } | string)[];
+    exact: [string, number, string, string, number, number][];
+}
+export declare type NamesIndexRecord = string | Array<string | number>;
+export default class JBrowse1TextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
+    httpMap: HttpMap;
+    tracksNames?: string[];
+    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    /**
+     * Returns the contents of the file containing the query if it exists
+     * else it returns empty
+     * @param query - string query
+     */
+    loadIndexFile(query: string): Promise<Record<string, SearchResults>>;
+    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
+    formatResults(results: SearchResults, tracks: string[], searchType?: string): BaseResult[];
+    freeResources(): void;
+}
+export {};

package/esm/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js

@@ -0,0 +1,67 @@
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { readConfObject } from '@jbrowse/core/configuration';
+import HttpMap from './HttpMap';
+//  Jbrowse1 text search adapter
+// Uses index built by generate-names.pl
+export default class JBrowse1TextSearchAdapter extends BaseAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const namesIndexLocation = readConfObject(config, 'namesIndexLocation');
+        if (!namesIndexLocation) {
+            throw new Error('must provide namesIndexLocation');
+        }
+        this.httpMap = new HttpMap({
+            url: namesIndexLocation.baseUri
+                ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href
+                : namesIndexLocation.uri,
+        });
+    }
+    /**
+     * Returns the contents of the file containing the query if it exists
+     * else it returns empty
+     * @param query - string query
+     */
+    async loadIndexFile(query) {
+        return this.httpMap.getBucket(query);
+    }
+    async searchIndex(args) {
+        const { searchType, queryString } = args;
+        const tracks = this.tracksNames || (await this.httpMap.getTrackNames());
+        const entries = await this.loadIndexFile(queryString.toLowerCase());
+        if (entries[queryString]) {
+            return this.formatResults(entries[queryString], tracks, searchType);
+        }
+        return [];
+    }
+    formatResults(results, tracks, searchType) {
+        return [
+            ...(searchType === 'exact'
+                ? []
+                : results.prefix.map(result => {
+                    return new BaseResult({
+                        label: typeof result === 'object' ? result.name : result,
+                        matchedAttribute: 'name',
+                        matchedObject: { result: result },
+                    });
+                })),
+            ...results.exact.map(result => {
+                const name = result[0];
+                const trackIndex = result[1];
+                const refName = result[3];
+                const start = result[4];
+                const end = result[5];
+                const locstring = `${refName || name}:${start}-${end}`;
+                return new BaseResult({
+                    locString: locstring,
+                    label: name,
+                    matchedAttribute: 'name',
+                    matchedObject: result,
+                    trackId: tracks[trackIndex],
+                });
+            }),
+        ].filter(result => result.getLabel() !== 'too many matches');
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=JBrowse1TextSearchAdapter.js.map

package/esm/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js.map

@@ -0,0 +1 @@
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package/esm/JBrowse1TextSeachAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/JBrowse1TextSeachAdapter/configSchema.js

@@ -0,0 +1,20 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('JBrowse1TextSearchAdapter', {
+    // metadata about tracks and assemblies covered by text search adapter
+    namesIndexLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },
+        description: 'the location of the JBrowse1 names index data directory',
+    },
+    tracks: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'List of tracks covered by text search adapter',
+    },
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'List of assemblies covered by text search adapter',
+    },
+}, { explicitlyTyped: true, explicitIdentifier: 'textSearchAdapterId' });
+//# sourceMappingURL=configSchema.js.map

package/esm/JBrowse1TextSeachAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/JBrowse1TextSeachAdapter/index.d.ts

@@ -0,0 +1,2 @@
+export { default as AdapterClass } from './JBrowse1TextSearchAdapter';
+export { default as configSchema } from './configSchema';

package/esm/JBrowse1TextSeachAdapter/index.js

@@ -0,0 +1,3 @@
+export { default as AdapterClass } from './JBrowse1TextSearchAdapter';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/JBrowse1TextSeachAdapter/index.js.map

@@ -0,0 +1 @@
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package/esm/NCListAdapter/NCListAdapter.d.ts

@@ -0,0 +1,31 @@
+import { Region } from '@jbrowse/core/util/types';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Instance } from 'mobx-state-tree';
+import NCListFeature from './NCListFeature';
+import MyConfigSchema from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class NCListAdapter extends BaseFeatureDataAdapter {
+    private nclist;
+    private configRefNames?;
+    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    /**
+     * Fetch features for a certain region. Use getFeaturesInRegion() if you also
+     * want to verify that the store has features for the given reference sequence
+     * before fetching.
+     * @param region -
+     * @param opts - [signal] optional signalling object for aborting the fetch
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    wrapFeature(ncFeature: any): NCListFeature;
+    hasDataForRefName(refName: string): Promise<boolean>;
+    getRefNames(): Promise<string[]>;
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources(): void;
+}

package/esm/NCListAdapter/NCListAdapter.js

@@ -0,0 +1,62 @@
+import NCListStore from '@gmod/nclist';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { checkAbortSignal } from '@jbrowse/core/util';
+import { RemoteFile } from 'generic-filehandle';
+import { readConfObject } from '@jbrowse/core/configuration';
+import NCListFeature from './NCListFeature';
+export default class NCListAdapter extends BaseFeatureDataAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const refNames = readConfObject(config, 'refNames');
+        const rootUrlTemplate = readConfObject(config, 'rootUrlTemplate');
+        this.configRefNames = refNames;
+        this.nclist = new NCListStore({
+            baseUrl: '',
+            urlTemplate: rootUrlTemplate.uri,
+            readFile: (url) => new RemoteFile(String(rootUrlTemplate.baseUri
+                ? new URL(url, rootUrlTemplate.baseUri).toString()
+                : url)).readFile(),
+        });
+    }
+    /**
+     * Fetch features for a certain region. Use getFeaturesInRegion() if you also
+     * want to verify that the store has features for the given reference sequence
+     * before fetching.
+     * @param region -
+     * @param opts - [signal] optional signalling object for aborting the fetch
+     * @returns Observable of Feature objects in the region
+     */
+    getFeatures(region, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { signal } = opts;
+            for await (const feature of this.nclist.getFeatures(region, opts)) {
+                checkAbortSignal(signal);
+                observer.next(this.wrapFeature(feature));
+            }
+            observer.complete();
+        });
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    wrapFeature(ncFeature) {
+        return new NCListFeature(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
+    }
+    async hasDataForRefName(refName) {
+        const root = await this.nclist.getDataRoot(refName);
+        return !!(root && root.stats && root.stats.featureCount);
+    }
+    /*
+     * NCList is unable to get list of ref names so returns empty
+     * @return Promise<string[]> of empty list
+     */
+    getRefNames() {
+        return Promise.resolve(this.configRefNames || []);
+    }
+    /**
+     * called to provide a hint that data tied to a certain region
+     * will not be needed for the forseeable future and can be purged
+     * from caches, etc
+     */
+    freeResources() { }
+}
+//# sourceMappingURL=NCListAdapter.js.map

package/esm/NCListAdapter/NCListAdapter.js.map

@@ -0,0 +1 @@
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