@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/dist/AddTrackWidget/components/doSubmit.js

@@ -0,0 +1,50 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.doSubmit = doSubmit;
+const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function doTextIndexTrack({ model }) {
+    const { textIndexingConf, trackConfig, trackName, assembly } = model;
+    const { jobsManager } = (0, mobx_state_tree_1.getRoot)(model);
+    const attr = textIndexingConf || {
+        attributes: ['Name', 'ID'],
+        exclude: ['CDS', 'exon'],
+    };
+    const indexName = `${trackName}-index`;
+    jobsManager.queueJob({
+        indexingParams: {
+            ...attr,
+            assemblies: [assembly],
+            tracks: [trackConfig.trackId],
+            indexType: 'perTrack',
+            name: indexName,
+            timestamp: new Date().toISOString(),
+        },
+        name: indexName,
+        cancelCallback: () => jobsManager.abortJob(),
+    });
+}
+function doSubmit({ model }) {
+    var _a;
+    const { textIndexTrack, trackConfig, trackAdapter, view } = model;
+    const session = (0, util_1.getSession)(model);
+    if (!(0, util_1.isSessionWithAddTracks)(session)) {
+        throw new Error("Can't add tracks to this session");
+    }
+    else if (trackConfig && trackAdapter) {
+        session.addTrackConf(trackConfig);
+        (_a = view === null || view === void 0 ? void 0 : view.showTrack) === null || _a === void 0 ? void 0 : _a.call(view, trackConfig.trackId);
+        if (util_1.isElectron &&
+            textIndexTrack &&
+            (0, util_1.isSupportedIndexingAdapter)(trackAdapter.type)) {
+            doTextIndexTrack({ model });
+        }
+        model.clearData();
+        if ((0, util_1.isSessionModelWithWidgets)(session)) {
+            session.hideWidget(model);
+        }
+    }
+    else {
+        throw new Error('Failed to add track.\nThe configuration of this file is not currently supported.');
+    }
+}

package/dist/AddTrackWidget/components/util.d.ts

@@ -0,0 +1,2 @@
+import type { AdapterType } from '@jbrowse/core/pluggableElementTypes';
+export declare function categorizeAdapters(adaptersList: AdapterType[]): Record<string, AdapterType[]>;

package/dist/AddTrackWidget/components/util.js

@@ -0,0 +1,15 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.categorizeAdapters = categorizeAdapters;
+function categorizeAdapters(adaptersList) {
+    var _a;
+    const map = {};
+    for (const adapter of adaptersList) {
+        const key = ((_a = adapter.adapterMetadata) === null || _a === void 0 ? void 0 : _a.category) || 'Default';
+        if (!map[key]) {
+            map[key] = [];
+        }
+        map[key].push(adapter);
+    }
+    return map;
+}

package/dist/AddTrackWidget/index.d.ts

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

package/dist/AddTrackWidget/index.js

@@ -15,21 +15,31 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 = AddTrackWidgetF;
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const configSchema = (0, configuration_1.ConfigurationSchema)('AddTrackWidget', {});
 function AddTrackWidgetF(pluginManager) {

package/dist/AddTrackWidget/model.d.ts

@@ -1,25 +1,13 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { FileLocation } from '@jbrowse/core/util/types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { FileLocation } from '@jbrowse/core/util/types';
+import type { Instance } from 'mobx-state-tree';
 interface IndexingAttr {
     attributes: string[];
     exclude: string[];
 }
-/**
- * #stateModel AddTrackModel
- */
 export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"AddTrackWidget">;
-    /**
-     * #property
-     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     trackSource: string;
@@ -31,100 +19,44 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     adapterHint: string;
     textIndexTrack: boolean;
     textIndexingConf: IndexingAttr | undefined;
+    mixinData: {};
 } & {
-    /**
-     * #action
-     */
+    setMixinData(arg: Record<string, unknown>): void;
     setAdapterHint(obj: string): void;
-    /**
-     * #action
-     */
     setTrackSource(str: string): void;
-    /**
-     * #action
-     */
     setTextIndexingConf(conf: IndexingAttr): void;
-    /**
-     * #action
-     */
     setTextIndexTrack(flag: boolean): void;
-    /**
-     * #action
-     */
     setTrackData(obj: FileLocation): void;
-    /**
-     * #action
-     */
     setIndexTrackData(obj: FileLocation): void;
-    /**
-     * #action
-     */
     setAssembly(str: string): void;
-    /**
-     * #action
-     */
     setTrackName(str: string): void;
-    /**
-     * #action
-     */
     setTrackType(str: string): void;
-    /**
-     * #action
-     */
     clearData(): void;
 } & {
-    /**
-     * #getter
-     */
     readonly trackAdapter: import("@jbrowse/core/util/tracks").AdapterConfig | undefined;
-    /**
-     * #getter
-     */
     readonly trackName: string;
-    /**
-     * #getter
-     */
     readonly isFtp: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeTrackUrl: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeIndexUrl: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeUrl: boolean;
-    /**
-     * #getter
-     */
     readonly trackHttp: any;
-    /**
-     * #getter
-     */
     readonly indexHttp: any;
-    /**
-     * #getter
-     */
     readonly wrongProtocol: any;
-    /**
-     * #getter
-     */
     readonly unsupported: boolean;
-    /**
-     * #getter
-     */
     readonly assembly: any;
-    /**
-     * #getter
-     */
+    readonly trackAdapterType: string | undefined;
     readonly trackType: string;
 } & {
-    /**
-     * #getter
-     */
+    readonly trackConfig: {
+        trackId: string;
+        type: string;
+        name: string;
+        assemblyNames: any[];
+        adapter: {
+            sequenceAdapter: any;
+            type: string;
+        };
+    } | undefined;
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type AddTrackStateModel = ReturnType<typeof f>;

package/dist/AddTrackWidget/model.js

@@ -1,9 +1,15 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = f;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mst_1 = require("@jbrowse/core/util/types/mst");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
+const mst_1 = require("@jbrowse/core/util/types/mst");
+const deepmerge_1 = __importDefault(require("deepmerge"));
+const mobx_state_tree_1 = require("mobx-state-tree");
 function isAbsoluteUrl(url = '') {
     try {
         new URL(url);
@@ -13,95 +19,56 @@ function isAbsoluteUrl(url = '') {
         return url.startsWith('/');
     }
 }
-/**
- * #stateModel AddTrackModel
- */
 function f(pluginManager) {
     return mobx_state_tree_1.types
         .model('AddTrackModel', {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('AddTrackWidget'),
-        /**
-         * #property
-         */
         view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .volatile(() => ({
         trackSource: 'fromFile',
         trackData: undefined,
         indexTrackData: undefined,
-        // alts
         altAssemblyName: '',
         altTrackName: '',
         altTrackType: '',
         adapterHint: '',
         textIndexTrack: true,
         textIndexingConf: undefined,
+        mixinData: {},
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
+        setMixinData(arg) {
+            self.mixinData = arg;
+        },
         setAdapterHint(obj) {
             self.adapterHint = obj;
         },
-        /**
-         * #action
-         */
         setTrackSource(str) {
             self.trackSource = str;
         },
-        /**
-         * #action
-         */
         setTextIndexingConf(conf) {
             self.textIndexingConf = conf;
         },
-        /**
-         * #action
-         */
         setTextIndexTrack(flag) {
             self.textIndexTrack = flag;
         },
-        /**
-         * #action
-         */
         setTrackData(obj) {
             self.trackData = obj;
         },
-        /**
-         * #action
-         */
         setIndexTrackData(obj) {
             self.indexTrackData = obj;
         },
-        /**
-         * #action
-         */
         setAssembly(str) {
             self.altAssemblyName = str;
         },
-        /**
-         * #action
-         */
         setTrackName(str) {
             self.altTrackName = str;
         },
-        /**
-         * #action
-         */
         setTrackType(str) {
             self.altTrackType = str;
         },
-        /**
-         * #action
-         */
         clearData() {
             self.trackSource = '';
             self.altTrackName = '';
@@ -115,107 +82,90 @@ function f(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get trackAdapter() {
             const { trackData, indexTrackData, adapterHint } = self;
             return trackData
                 ? (0, tracks_1.guessAdapter)(trackData, indexTrackData, adapterHint, self)
                 : undefined;
         },
-        /**
-         * #getter
-         */
         get trackName() {
             return (self.altTrackName ||
                 (self.trackData ? (0, tracks_1.getFileName)(self.trackData) : ''));
         },
-        /**
-         * #getter
-         */
         get isFtp() {
             var _a, _b;
             const { trackData: track, indexTrackData: index } = self;
-            return !!(
-            // @ts-expect-error
-            (((_a = index === null || index === void 0 ? void 0 : index.uri) === null || _a === void 0 ? void 0 : _a.startsWith('ftp://')) || ((_b = track === null || track === void 0 ? void 0 : track.uri) === null || _b === void 0 ? void 0 : _b.startsWith('ftp://'))));
+            return !!((((_a = index === null || index === void 0 ? void 0 : index.uri) === null || _a === void 0 ? void 0 : _a.startsWith('ftp://')) || ((_b = track === null || track === void 0 ? void 0 : track.uri) === null || _b === void 0 ? void 0 : _b.startsWith('ftp://'))));
         },
-        /**
-         * #getter
-         */
         get isRelativeTrackUrl() {
             var _a;
-            // @ts-expect-error
             const uri = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri;
             return uri ? !isAbsoluteUrl(uri) : false;
         },
-        /**
-         * #getter
-         */
         get isRelativeIndexUrl() {
             var _a;
-            // @ts-expect-error
             const uri = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri;
             return uri ? !isAbsoluteUrl(uri) : false;
         },
-        /**
-         * #getter
-         */
         get isRelativeUrl() {
             return this.isRelativeIndexUrl || this.isRelativeTrackUrl;
         },
-        /**
-         * #getter
-         */
         get trackHttp() {
             var _a, _b;
-            // @ts-expect-error
             return (_b = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
         },
-        /**
-         * #getter
-         */
         get indexHttp() {
             var _a, _b;
-            // @ts-expect-error
             return (_b = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
         },
-        /**
-         * #getter
-         */
         get wrongProtocol() {
             return (window.location.protocol === 'https:' &&
                 (this.trackHttp || this.indexHttp));
         },
-        /**
-         * #getter
-         */
         get unsupported() {
             var _a;
             return ((_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type) === tracks_1.UNSUPPORTED;
         },
-        /**
-         * #getter
-         */
         get assembly() {
             var _a;
             return self.altAssemblyName || ((_a = self.view.assemblyNames) === null || _a === void 0 ? void 0 : _a[0]);
         },
-        /**
-         * #getter
-         */
+        get trackAdapterType() {
+            var _a;
+            return (_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type;
+        },
         get trackType() {
             return (self.altTrackType ||
-                (this.trackAdapter
-                    ? (0, tracks_1.guessTrackType)(this.trackAdapter.type, self)
+                (this.trackAdapterType
+                    ? (0, tracks_1.guessTrackType)(this.trackAdapterType, self)
                     : ''));
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
+        get trackConfig() {
+            const session = (0, util_1.getSession)(self);
+            const assemblyInstance = session.assemblyManager.get(self.assembly);
+            return assemblyInstance &&
+                self.trackAdapter &&
+                self.trackAdapter.type !== 'UNKNOWN'
+                ? (0, deepmerge_1.default)({
+                    trackId: [
+                        `${self.trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+                        session.adminMode ? '' : '-sessionTrack',
+                    ].join(''),
+                    type: self.trackType,
+                    name: self.trackName,
+                    assemblyNames: [self.assembly],
+                    adapter: {
+                        ...self.trackAdapter,
+                        sequenceAdapter: (0, configuration_1.getConf)(assemblyInstance, [
+                            'sequence',
+                            'adapter',
+                        ]),
+                    },
+                }, self.mixinData)
+                : undefined;
+        },
         get warningMessage() {
             if (self.isFtp) {
                 return 'Warning: JBrowse cannot access files using the ftp protocol';
@@ -231,7 +181,9 @@ function f(pluginManager) {
           https URL for your track, or access the JBrowse app from the http
           protocol`;
             }
-            return '';
+            else {
+                return '';
+            }
         },
     }));
 }

package/dist/AssemblyManager/AssemblyAddForm.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
-import { AbstractRootModel } from '@jbrowse/core/util/types';
-declare const AssemblyAddForm: ({ rootModel, setFormOpen, }: {
-    rootModel: AbstractRootModel;
-    setFormOpen: (arg: boolean) => void;
-}) => React.JSX.Element;
+import type { AbstractSessionModel } from '@jbrowse/core/util/types';
+declare const AssemblyAddForm: ({ session, onClose, }: {
+    session: AbstractSessionModel;
+    onClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AssemblyAddForm;