@jbrowse/plugin-data-management 3.7.0 → 4.0.1

package/dist/PluginStoreWidget/model.d.ts

@@ -1,13 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { Instance } from 'mobx-state-tree';
-export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"PluginStoreWidget">;
-    filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-}, {
-    clearFilterText(): void;
-    setFilterText(newText: string): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type PluginStoreStateModel = ReturnType<typeof stateModelFactory>;
-export type PluginStoreModel = Instance<PluginStoreStateModel>;

package/dist/PluginStoreWidget/model.js

@@ -1,22 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = stateModelFactory;
-const mst_1 = require("@jbrowse/core/util/types/mst");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function stateModelFactory(pluginManager) {
-    return mobx_state_tree_1.types
-        .model('PluginStoreModel', {
-        id: mst_1.ElementId,
-        type: mobx_state_tree_1.types.literal('PluginStoreWidget'),
-        filterText: '',
-        view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
-    })
-        .actions(self => ({
-        clearFilterText() {
-            self.filterText = '';
-        },
-        setFilterText(newText) {
-            self.filterText = newText;
-        },
-    }));
-}

package/dist/UCSCTrackHubConnection/configSchema.d.ts

@@ -1,27 +0,0 @@
-declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    hubTxtLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-        description: string;
-    };
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    name: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-export default UCSCTrackHubConnection;

package/dist/UCSCTrackHubConnection/configSchema.js

@@ -1,34 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-function x() { }
-const UCSCTrackHubConnection = (0, configuration_1.ConfigurationSchema)('UCSCTrackHubConnection', {
-    hubTxtLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: 'http://mysite.com/path/to/hub.txt',
-            locationType: 'UriLocation',
-        },
-        description: 'location of the hub file (usually called hub.txt)',
-    },
-    assemblyNames: {
-        type: 'stringArray',
-        defaultValue: [],
-        description: 'optional list of genomes to import from this track hub, if empty all genomes will be imported',
-    },
-}, {
-    baseConfiguration: models_1.baseConnectionConfig,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                hubTxtLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = UCSCTrackHubConnection;

package/dist/UCSCTrackHubConnection/doConnect.d.ts

@@ -1,5 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export declare function doConnect(self: {
-    configuration: AnyConfigurationModel;
-    addTrackConfs: (arg: Record<string, unknown>[]) => void;
-}): Promise<void>;

package/dist/UCSCTrackHubConnection/doConnect.js

@@ -1,152 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.doConnect = doConnect;
-const ucsc_hub_1 = require("@gmod/ucsc-hub");
-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");
-const ucscTrackHub_1 = require("./ucscTrackHub");
-const util_2 = require("./util");
-async function doConnect(self) {
-    var _a;
-    const { pluginManager } = (0, util_1.getEnv)(self);
-    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');
-        const hubUri = (0, util_2.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 shortLabel = genome.data.description;
-            const asm = assemblyManager.get(genomeName);
-            if (!asm) {
-                session.addSessionAssembly({
-                    name: genomeName,
-                    displayName: shortLabel,
-                    sequence: {
-                        type: 'ReferenceSequenceTrack',
-                        metadata: {
-                            ...genome.data,
-                            ...(genome.data.htmlPath
-                                ? {
-                                    htmlPath: `<a href="${(0, util_2.resolve)(genome.data.htmlPath, hubUri)}">${genome.data.htmlPath}</a>`,
-                                }
-                                : {}),
-                        },
-                        trackId: `${genomeName}-${(0, nanoid_1.nanoid)()}`,
-                        adapter: {
-                            type: 'TwoBitAdapter',
-                            twoBitLocation: {
-                                uri: (0, util_2.resolve)(genome.data.twoBitPath, hubUri),
-                            },
-                            chromSizesLocation: {
-                                uri: (0, util_2.resolve)(genome.data.chromSizes, hubUri),
-                            },
-                        },
-                    },
-                    ...(genome.data.chromAliasBb
-                        ? {
-                            refNameAliases: {
-                                adapter: {
-                                    type: 'BigBedAdapter',
-                                    uri: (0, util_2.resolve)(genome.data.chromAliasBb, 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,
-                baseUrl: hubUri,
-            });
-            self.addTrackConfs(tracksNew);
-            pluginManager.evaluateExtensionPoint('LaunchView-LinearGenomeView', {
-                session,
-                assembly: genomeName,
-                tracklist: true,
-                loc: genome.data.defaultPos,
-            });
-        }
-        else {
-            const hubFile = new ucsc_hub_1.HubFile(hubFileText);
-            const genomeFile = hubFile.data.genomesFile;
-            if (!genomeFile) {
-                throw new Error('genomesFile not found on hub');
-            }
-            const hubUri = (0, util_2.resolve)(hubFileLocation.uri, hubFileLocation.baseUri);
-            const genomesFileLocation = hubUri
-                ? {
-                    uri: (0, util_2.resolve)(genomeFile, hubUri),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    localPath: genomeFile,
-                    locationType: 'LocalPathLocation',
-                };
-            const genomesFile = await (0, util_2.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;
-                }
-                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, util_2.fetchTrackDbFile)(loc);
-                const sequenceAdapter = (0, configuration_1.getConf)(asm, ['sequence', 'adapter']);
-                const tracks = (0, ucscTrackHub_1.generateTracks)({
-                    trackDb,
-                    trackDbLoc: loc,
-                    assemblyName: genomeName,
-                    sequenceAdapter,
-                    baseUrl: hubUri,
-                });
-                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: ${notLoadedAssemblies.join(', ')}`
-                : '';
-            session.notify([str1, str2].filter(f => !!f).join('. '), 'success');
-        }
-    }
-    catch (e) {
-        console.error(e);
-        session.notifyError(`${(0, configuration_1.getConf)(self, 'name')}: "${e}"`, e);
-        (_a = session.breakConnection) === null || _a === void 0 ? void 0 : _a.call(session, self.configuration);
-    }
-}

package/dist/UCSCTrackHubConnection/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function UCSCTrackHubConnectionF(pluginManager: PluginManager): void;

package/dist/UCSCTrackHubConnection/index.js

@@ -1,21 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = UCSCTrackHubConnectionF;
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function UCSCTrackHubConnectionF(pluginManager) {
-    pluginManager.addConnectionType(() => {
-        return new pluggableElementTypes_1.ConnectionType({
-            name: 'UCSCTrackHubConnection',
-            configSchema: configSchema_1.default,
-            stateModel: (0, model_1.default)(pluginManager),
-            displayName: 'UCSC Track Hub',
-            description: 'A track or assembly hub in the Track Hub format',
-            url: 'https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
-        });
-    });
-}

package/dist/UCSCTrackHubConnection/model.d.ts

@@ -1,75 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-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>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-} & {
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        hubTxtLocation: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-    type: import("mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
-}, {
-    connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
-} & {
-    afterAttach(): void;
-    addTrackConf(trackConf: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-    addTrackConfs(trackConfs: (({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
-    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
-    clear(): void;
-} & {
-    connect(): Promise<void>;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/UCSCTrackHubConnection/model.js

@@ -1,56 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = UCSCTrackHubConnection;
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const configSchema_1 = __importDefault(require("./configSchema"));
-function UCSCTrackHubConnection(pluginManager) {
-    return mobx_state_tree_1.types
-        .compose('UCSCTrackHubConnection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
-        type: mobx_state_tree_1.types.literal('UCSCTrackHubConnection'),
-    }))
-        .actions(self => ({
-        async connect() {
-            const { doConnect } = await Promise.resolve().then(() => __importStar(require('./doConnect')));
-            doConnect(self);
-        },
-    }));
-}

package/dist/UCSCTrackHubConnection/ucscAssemblies.d.ts

@@ -1,2 +0,0 @@
-declare const _default: string[];
-export default _default;

package/dist/UCSCTrackHubConnection/ucscAssemblies.js

@@ -1,199 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = `ailMel1
-allMis1
-anoCar1
-anoCar2
-anoGam1
-anoGam3
-apiMel1
-apiMel2
-aplCal1
-aptMan1
-aquChr2
-balAcu1
-bisBis1
-bosTau2
-bosTau3
-bosTau4
-bosTau6
-bosTau7
-bosTau8
-braFlo1
-caeJap1
-caePb1
-caePb2
-caeRem2
-caeRem3
-calJac1
-calJac3
-calMil1
-canFam1
-canFam3
-cavPor3
-cb3
-ce10
-ce11
-ce2
-ce4
-ce6
-cerSim1
-chlSab2
-choHof1
-chrPic1
-ci1
-ci2
-ci3
-criGri1
-criGriChoV1
-danRer10
-danRer11
-danRer3
-danRer4
-danRer5
-danRer6
-danRer7
-dasNov3
-dipOrd1
-dm1
-dm2
-dm3
-dm6
-dp2
-dp3
-droAna1
-droAna2
-droEre1
-droGri1
-droMoj1
-droMoj2
-droPer1
-droSec1
-droSim1
-droVir1
-droVir2
-droYak1
-droYak2
-eboVir3
-echTel1
-echTel2
-equCab1
-equCab2
-eriEur1
-eriEur2
-felCat3
-felCat4
-felCat5
-felCat8
-fr1
-fr2
-fr3
-gadMor1
-galGal2
-galGal3
-galGal4
-galGal5
-galGal6
-galVar1
-gasAcu1
-geoFor1
-gorGor3
-gorGor4
-gorGor5
-hetGla1
-hetGla2
-hg16
-hg18
-hg19
-hg38
-latCha1
-loxAfr3
-macEug2
-macFas5
-manPen1
-melGal1
-melGal5
-melUnd1
-micMur1
-micMur2
-mm10
-mm7
-mm8
-mm9
-monDom2
-monDom4
-monDom5
-musFur1
-myoLuc2
-nanPar1
-nasLar1
-nomLeu1
-nomLeu2
-nomLeu3
-ochPri2
-ochPri3
-oreNil2
-ornAna1
-ornAna2
-oryCun2
-oryLat2
-otoGar3
-oviAri1
-oviAri3
-oviAri4
-panPan1
-panPan2
-panTro1
-panTro2
-panTro3
-panTro4
-panTro5
-panTro6
-papAnu2
-papHam1
-petMar1
-petMar2
-ponAbe2
-ponAbe3
-priPac1
-proCap1
-pteVam1
-rheMac2
-rheMac3
-rheMac8
-rhiRox1
-rn4
-rn5
-rn6
-sacCer1
-sacCer2
-sacCer3
-saiBol1
-sarHar1
-sorAra1
-sorAra2
-speTri2
-strPur1
-strPur2
-susScr11
-susScr2
-susScr3
-taeGut1
-taeGut2
-tarSyr1
-tarSyr2
-tetNig1
-tetNig2
-thaSir1
-triMan1
-tupBel1
-turTru2
-venter1
-vicPac1
-vicPac2
-xenLae2
-xenTro1
-xenTro2
-xenTro3
-xenTro7
-xenTro9`.split(/\r?\n/);