@jbrowse/plugin-data-management 3.6.2 → 3.6.4

package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -57,7 +57,7 @@ const DefaultAddTrackWorkflow = (0, mobx_react_1.observer)(function ({ model, })
     }
     return ((0, jsx_runtime_1.jsx)("div", { className: classes.root, children: (0, jsx_runtime_1.jsx)(material_1.Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical", children: steps.map((label, idx) => ((0, jsx_runtime_1.jsxs)(material_1.Step, { children: [(0, jsx_runtime_1.jsx)(material_1.StepLabel, { children: label }), (0, jsx_runtime_1.jsxs)(material_1.StepContent, { children: [getStepContent(idx), (0, jsx_runtime_1.jsxs)("div", { className: classes.actionsContainer, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: activeStep === 0, className: classes.button, onClick: () => {
                                             setActiveStep(activeStep - 1);
-                                        }, children: "Back" }), (0, jsx_runtime_1.jsx)(material_1.Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: () => {
+                                        }, "data-testid": "addTrackBackButton", children: "Back" }), (0, jsx_runtime_1.jsx)(material_1.Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: () => {
                                             if (activeStep !== steps.length - 1) {
                                                 setActiveStep(activeStep + 1);
                                             }

package/dist/AddTrackWidget/model.js

@@ -56,6 +56,7 @@ function f(pluginManager) {
         },
         setTrackData(obj) {
             self.trackData = obj;
+            self.adapterHint = '';
         },
         setIndexTrackData(obj) {
             self.indexTrackData = obj;

package/dist/HierarchicalTrackSelectorWidget/filterTracks.js

@@ -11,16 +11,16 @@ function filterTracks(tracks, self) {
     if (!view) {
         return [];
     }
-    const trackListAssemblies = self.assemblyNames
-        .map(a => assemblyManager.get(a))
+    const viewAssemblyNames = self.assemblyNames
+        .map(a => assemblyManager.getCanonicalAssemblyName(a))
         .filter(util_1.notEmpty);
     return tracks
         .filter(c => {
-        const trackAssemblyNames = (0, configuration_1.readConfObject)(c, 'assemblyNames');
-        const trackAssemblies = trackAssemblyNames === null || trackAssemblyNames === void 0 ? void 0 : trackAssemblyNames.map(name => assemblyManager.get(name)).filter(util_1.notEmpty);
+        const trackConfigAssemblyNames = (0, configuration_1.readConfObject)(c, 'assemblyNames');
+        const trackCanonicalAssemblyNames = trackConfigAssemblyNames === null || trackConfigAssemblyNames === void 0 ? void 0 : trackConfigAssemblyNames.map(name => assemblyManager.getCanonicalAssemblyName(name)).filter(util_1.notEmpty);
         return view.trackSelectorAnyOverlap
-            ? (0, util_2.hasAnyOverlap)(trackAssemblies, trackListAssemblies)
-            : (0, util_2.hasAllOverlap)(trackAssemblies, trackListAssemblies);
+            ? (0, util_2.hasAnyOverlap)(trackCanonicalAssemblyNames, viewAssemblyNames)
+            : (0, util_2.hasAllOverlap)(trackCanonicalAssemblyNames, viewAssemblyNames);
     })
         .filter(c => {
         const { displayTypes } = pluginManager.getViewType(view.type);

package/dist/JB2TrackHubConnection/addRelativeUris.d.ts

@@ -0,0 +1 @@
+export declare function addRelativeUris(config: Record<string, unknown> | null, base: URL): void;

package/dist/JB2TrackHubConnection/addRelativeUris.js

@@ -0,0 +1,15 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.addRelativeUris = addRelativeUris;
+function addRelativeUris(config, base) {
+    if (typeof config === 'object' && config !== null) {
+        for (const key of Object.keys(config)) {
+            if (typeof config[key] === 'object' && config[key] !== null) {
+                addRelativeUris(config[key], base);
+            }
+            else if (key === 'uri') {
+                config.baseUri = base.href;
+            }
+        }
+    }
+}

package/dist/JB2TrackHubConnection/configSchema.d.ts

@@ -0,0 +1,27 @@
+declare const JB2TrackHubConnection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    configJsonLocation: {
+        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 JB2TrackHubConnection;

package/dist/JB2TrackHubConnection/configSchema.js

@@ -0,0 +1,34 @@
+"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 JB2TrackHubConnection = (0, configuration_1.ConfigurationSchema)('JB2TrackHubConnection', {
+    configJsonLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: 'http://mysite.com/path/to/config.json',
+            locationType: 'UriLocation',
+        },
+        description: 'location of the jb2 config file (usually called config.json)',
+    },
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'optional list of genomes to import from this config.json, if empty all genomes will be imported',
+    },
+}, {
+    baseConfiguration: models_1.baseConnectionConfig,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                configJsonLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
+exports.default = JB2TrackHubConnection;

package/dist/JB2TrackHubConnection/doConnect.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.doConnect = doConnect;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
+const addRelativeUris_1 = require("./addRelativeUris");
+const util_2 = require("./util");
+async function doConnect(self) {
+    var _a;
+    const session = (0, util_1.getSession)(self);
+    try {
+        const configJsonLocation = (0, configuration_1.getConf)(self, 'configJsonLocation');
+        const configJson = JSON.parse(await (0, io_1.openLocation)(configJsonLocation).readFile('utf8'));
+        const configUri = (0, util_2.resolve)(configJsonLocation.uri, configJsonLocation.baseUri);
+        (0, addRelativeUris_1.addRelativeUris)(configJson, new URL(configUri));
+        if (configJson.assemblies) {
+            for (const assembly of configJson.assemblies) {
+                if (!session.assemblyManager.get(assembly.name)) {
+                    session.addSessionAssembly(assembly);
+                }
+            }
+        }
+        if (configJson.tracks) {
+            self.addTrackConfs(configJson.tracks);
+        }
+        session.notify('Successfully loaded', '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/JB2TrackHubConnection/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function JB2TrackHubConnectionF(pluginManager: PluginManager): void;

package/dist/JB2TrackHubConnection/index.js

@@ -0,0 +1,21 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = JB2TrackHubConnectionF;
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
+function JB2TrackHubConnectionF(pluginManager) {
+    pluginManager.addConnectionType(() => {
+        return new pluggableElementTypes_1.ConnectionType({
+            name: 'JB2TrackHubConnection',
+            configSchema: configSchema_1.default,
+            stateModel: (0, model_1.default)(pluginManager),
+            displayName: 'JB2 Track Hub',
+            description: 'A JBrowse 2 config file based trackhub',
+            url: 'https://jbrowse.org/jb2/',
+        });
+    });
+}

package/dist/JB2TrackHubConnection/model.d.ts

@@ -0,0 +1,75 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function JB2TrackHubConnection(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<{
+        configJsonLocation: {
+            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<"JB2TrackHubConnection">;
+}, {
+    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/JB2TrackHubConnection/model.js

@@ -0,0 +1,56 @@
+"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 = JB2TrackHubConnection;
+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 JB2TrackHubConnection(pluginManager) {
+    return mobx_state_tree_1.types
+        .compose('JB2TrackHubConnection', (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('JB2TrackHubConnection'),
+    }))
+        .actions(self => ({
+        async connect() {
+            const { doConnect } = await Promise.resolve().then(() => __importStar(require('./doConnect')));
+            doConnect(self);
+        },
+    }));
+}

package/dist/{UCSCTrackHub → UCSCTrackHubConnection}/ucscTrackHub.d.ts

@@ -180,4 +180,3 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     };
     category: (string | undefined)[];
 })[];
-export { default as ucscAssemblies } from './ucscAssemblies';

package/dist/{UCSCTrackHub → UCSCTrackHubConnection}/ucscTrackHub.js

@@ -1,9 +1,5 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ucscAssemblies = void 0;
 exports.generateTracks = generateTracks;
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
@@ -164,5 +160,3 @@ function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
         return (0, tracks_1.generateUnknownTrackConf)(name, baseTrackType);
     }
 }
-var ucscAssemblies_1 = require("./ucscAssemblies");
-Object.defineProperty(exports, "ucscAssemblies", { enumerable: true, get: function () { return __importDefault(ucscAssemblies_1).default; } });

package/dist/UCSCTrackHubConnection/util.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fetchGenomesFile = fetchGenomesFile;
+exports.fetchTrackDbFile = fetchTrackDbFile;
+exports.makeLoc = makeLoc;
+exports.makeLocAlt = makeLocAlt;
+exports.makeLoc2 = makeLoc2;
+exports.resolve = resolve;
+const ucsc_hub_1 = require("@gmod/ucsc-hub");
+const io_1 = require("@jbrowse/core/util/io");
+async function fetchGenomesFile(genomesLoc) {
+    const genomesFileText = await (0, io_1.openLocation)(genomesLoc).readFile('utf8');
+    return new ucsc_hub_1.GenomesFile(genomesFileText);
+}
+async function fetchTrackDbFile(trackDbLoc) {
+    const text = await (0, io_1.openLocation)(trackDbLoc).readFile('utf8');
+    return new ucsc_hub_1.TrackDbFile(text);
+}
+function makeLoc(first, base) {
+    return {
+        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
+        locationType: 'UriLocation',
+    };
+}
+function makeLocAlt(first, alt, base) {
+    return first ? makeLoc(first, base) : makeLoc(alt, base);
+}
+function makeLoc2(first, alt) {
+    return first
+        ? {
+            uri: first,
+            locationType: 'LocalPath',
+        }
+        : {
+            uri: alt,
+            locationType: 'UriLocation',
+        };
+}
+function resolve(uri, baseUri) {
+    return new URL(uri, baseUri).href;
+}

package/dist/index.js

@@ -42,8 +42,9 @@ const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const AddConnectionWidget_1 = __importDefault(require("./AddConnectionWidget"));
 const AddTrackWidget_1 = __importDefault(require("./AddTrackWidget"));
 const HierarchicalTrackSelectorWidget_1 = __importDefault(require("./HierarchicalTrackSelectorWidget"));
+const JB2TrackHubConnection_1 = __importDefault(require("./JB2TrackHubConnection"));
 const PluginStoreWidget_1 = __importDefault(require("./PluginStoreWidget"));
-const UCSCTrackHub_1 = __importDefault(require("./UCSCTrackHub"));
+const UCSCTrackHubConnection_1 = __importDefault(require("./UCSCTrackHubConnection"));
 const AssemblyManager = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AssemblyManager'))));
 exports.AssemblyManager = AssemblyManager;
 class DataManagementPlugin extends Plugin_1.default {
@@ -55,7 +56,8 @@ class DataManagementPlugin extends Plugin_1.default {
         };
     }
     install(pluginManager) {
-        (0, UCSCTrackHub_1.default)(pluginManager);
+        (0, UCSCTrackHubConnection_1.default)(pluginManager);
+        (0, JB2TrackHubConnection_1.default)(pluginManager);
         (0, AddTrackWidget_1.default)(pluginManager);
         (0, HierarchicalTrackSelectorWidget_1.default)(pluginManager);
         (0, AddConnectionWidget_1.default)(pluginManager);

package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -52,7 +52,7 @@ const DefaultAddTrackWorkflow = observer(function ({ model, }) {
     }
     return (_jsx("div", { className: classes.root, children: _jsx(Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical", children: steps.map((label, idx) => (_jsxs(Step, { children: [_jsx(StepLabel, { children: label }), _jsxs(StepContent, { children: [getStepContent(idx), _jsxs("div", { className: classes.actionsContainer, children: [_jsx(Button, { disabled: activeStep === 0, className: classes.button, onClick: () => {
                                             setActiveStep(activeStep - 1);
-                                        }, children: "Back" }), _jsx(Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: () => {
+                                        }, "data-testid": "addTrackBackButton", children: "Back" }), _jsx(Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: () => {
                                             if (activeStep !== steps.length - 1) {
                                                 setActiveStep(activeStep + 1);
                                             }

package/esm/AddTrackWidget/model.js

@@ -50,6 +50,7 @@ export default function f(pluginManager) {
         },
         setTrackData(obj) {
             self.trackData = obj;
+            self.adapterHint = '';
         },
         setIndexTrackData(obj) {
             self.indexTrackData = obj;

package/esm/HierarchicalTrackSelectorWidget/filterTracks.js

@@ -8,16 +8,16 @@ export function filterTracks(tracks, self) {
     if (!view) {
         return [];
     }
-    const trackListAssemblies = self.assemblyNames
-        .map(a => assemblyManager.get(a))
+    const viewAssemblyNames = self.assemblyNames
+        .map(a => assemblyManager.getCanonicalAssemblyName(a))
         .filter(notEmpty);
     return tracks
         .filter(c => {
-        const trackAssemblyNames = readConfObject(c, 'assemblyNames');
-        const trackAssemblies = trackAssemblyNames === null || trackAssemblyNames === void 0 ? void 0 : trackAssemblyNames.map(name => assemblyManager.get(name)).filter(notEmpty);
+        const trackConfigAssemblyNames = readConfObject(c, 'assemblyNames');
+        const trackCanonicalAssemblyNames = trackConfigAssemblyNames === null || trackConfigAssemblyNames === void 0 ? void 0 : trackConfigAssemblyNames.map(name => assemblyManager.getCanonicalAssemblyName(name)).filter(notEmpty);
         return view.trackSelectorAnyOverlap
-            ? hasAnyOverlap(trackAssemblies, trackListAssemblies)
-            : hasAllOverlap(trackAssemblies, trackListAssemblies);
+            ? hasAnyOverlap(trackCanonicalAssemblyNames, viewAssemblyNames)
+            : hasAllOverlap(trackCanonicalAssemblyNames, viewAssemblyNames);
     })
         .filter(c => {
         const { displayTypes } = pluginManager.getViewType(view.type);

package/esm/JB2TrackHubConnection/addRelativeUris.d.ts

@@ -0,0 +1 @@
+export declare function addRelativeUris(config: Record<string, unknown> | null, base: URL): void;

package/esm/JB2TrackHubConnection/addRelativeUris.js

@@ -0,0 +1,12 @@
+export function addRelativeUris(config, base) {
+    if (typeof config === 'object' && config !== null) {
+        for (const key of Object.keys(config)) {
+            if (typeof config[key] === 'object' && config[key] !== null) {
+                addRelativeUris(config[key], base);
+            }
+            else if (key === 'uri') {
+                config.baseUri = base.href;
+            }
+        }
+    }
+}

package/esm/JB2TrackHubConnection/configSchema.d.ts

@@ -0,0 +1,27 @@
+declare const JB2TrackHubConnection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    configJsonLocation: {
+        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 JB2TrackHubConnection;

package/esm/JB2TrackHubConnection/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
+function x() { }
+const JB2TrackHubConnection = ConfigurationSchema('JB2TrackHubConnection', {
+    configJsonLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: 'http://mysite.com/path/to/config.json',
+            locationType: 'UriLocation',
+        },
+        description: 'location of the jb2 config file (usually called config.json)',
+    },
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'optional list of genomes to import from this config.json, if empty all genomes will be imported',
+    },
+}, {
+    baseConfiguration: baseConnectionConfig,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                configJsonLocation: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
+export default JB2TrackHubConnection;

package/esm/JB2TrackHubConnection/doConnect.d.ts

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

package/esm/JB2TrackHubConnection/doConnect.js

@@ -0,0 +1,31 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { addRelativeUris } from './addRelativeUris';
+import { resolve } from './util';
+export async function doConnect(self) {
+    var _a;
+    const session = getSession(self);
+    try {
+        const configJsonLocation = getConf(self, 'configJsonLocation');
+        const configJson = JSON.parse(await openLocation(configJsonLocation).readFile('utf8'));
+        const configUri = resolve(configJsonLocation.uri, configJsonLocation.baseUri);
+        addRelativeUris(configJson, new URL(configUri));
+        if (configJson.assemblies) {
+            for (const assembly of configJson.assemblies) {
+                if (!session.assemblyManager.get(assembly.name)) {
+                    session.addSessionAssembly(assembly);
+                }
+            }
+        }
+        if (configJson.tracks) {
+            self.addTrackConfs(configJson.tracks);
+        }
+        session.notify('Successfully loaded', 'success');
+    }
+    catch (e) {
+        console.error(e);
+        session.notifyError(`${getConf(self, 'name')}: "${e}"`, e);
+        (_a = session.breakConnection) === null || _a === void 0 ? void 0 : _a.call(session, self.configuration);
+    }
+}

package/esm/JB2TrackHubConnection/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function JB2TrackHubConnectionF(pluginManager: PluginManager): void;

package/esm/JB2TrackHubConnection/index.js

@@ -0,0 +1,15 @@
+import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
+import configSchema from './configSchema';
+import stateModelFactory from './model';
+export default function JB2TrackHubConnectionF(pluginManager) {
+    pluginManager.addConnectionType(() => {
+        return new ConnectionType({
+            name: 'JB2TrackHubConnection',
+            configSchema,
+            stateModel: stateModelFactory(pluginManager),
+            displayName: 'JB2 Track Hub',
+            description: 'A JBrowse 2 config file based trackhub',
+            url: 'https://jbrowse.org/jb2/',
+        });
+    });
+}

package/esm/JB2TrackHubConnection/model.d.ts

@@ -0,0 +1,75 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function JB2TrackHubConnection(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<{
+        configJsonLocation: {
+            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<"JB2TrackHubConnection">;
+}, {
+    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/esm/JB2TrackHubConnection/model.js

@@ -0,0 +1,17 @@
+import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
+import { types } from 'mobx-state-tree';
+import configSchema from './configSchema';
+export default function JB2TrackHubConnection(pluginManager) {
+    return types
+        .compose('JB2TrackHubConnection', BaseConnectionModelFactory(pluginManager), types.model({
+        configuration: ConfigurationReference(configSchema),
+        type: types.literal('JB2TrackHubConnection'),
+    }))
+        .actions(self => ({
+        async connect() {
+            const { doConnect } = await import('./doConnect');
+            doConnect(self);
+        },
+    }));
+}

package/esm/JB2TrackHubConnection/util.d.ts

@@ -0,0 +1,22 @@
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
+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;
+};
+export declare function makeLocAlt(first: string, alt: string, base: {
+    uri: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLoc2(first: string, alt?: string): {
+    uri: string | undefined;
+    locationType: string;
+};
+export declare function resolve(uri: string, baseUri: string): string;

package/esm/UCSCTrackHubConnection/doConnect.d.ts

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

package/esm/{UCSCTrackHub → UCSCTrackHubConnection}/ucscTrackHub.d.ts

@@ -180,4 +180,3 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     };
     category: (string | undefined)[];
 })[];
-export { default as ucscAssemblies } from './ucscAssemblies';

package/esm/{UCSCTrackHub → UCSCTrackHubConnection}/ucscTrackHub.js

@@ -157,4 +157,3 @@ function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
         return generateUnknownTrackConf(name, baseTrackType);
     }
 }
-export { default as ucscAssemblies } from './ucscAssemblies';

package/esm/UCSCTrackHubConnection/util.d.ts

@@ -0,0 +1,22 @@
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
+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;
+};
+export declare function makeLocAlt(first: string, alt: string, base: {
+    uri: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLoc2(first: string, alt?: string): {
+    uri: string | undefined;
+    locationType: string;
+};
+export declare function resolve(uri: string, baseUri: string): string;

package/esm/UCSCTrackHubConnection/util.js

@@ -0,0 +1,33 @@
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import { openLocation } from '@jbrowse/core/util/io';
+export async function fetchGenomesFile(genomesLoc) {
+    const genomesFileText = await openLocation(genomesLoc).readFile('utf8');
+    return new GenomesFile(genomesFileText);
+}
+export async function fetchTrackDbFile(trackDbLoc) {
+    const text = await openLocation(trackDbLoc).readFile('utf8');
+    return new TrackDbFile(text);
+}
+export function makeLoc(first, base) {
+    return {
+        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
+        locationType: 'UriLocation',
+    };
+}
+export function makeLocAlt(first, alt, base) {
+    return first ? makeLoc(first, base) : makeLoc(alt, base);
+}
+export function makeLoc2(first, alt) {
+    return first
+        ? {
+            uri: first,
+            locationType: 'LocalPath',
+        }
+        : {
+            uri: alt,
+            locationType: 'UriLocation',
+        };
+}
+export function resolve(uri, baseUri) {
+    return new URL(uri, baseUri).href;
+}

package/esm/index.js

@@ -3,8 +3,9 @@ import Plugin from '@jbrowse/core/Plugin';
 import AddConnectionWidgetF from './AddConnectionWidget';
 import AddTrackWidgetF from './AddTrackWidget';
 import HierarchicalTrackSelectorWidgetF from './HierarchicalTrackSelectorWidget';
+import JB2TrackHubConnectionF from './JB2TrackHubConnection';
 import PluginStoreWidgetF from './PluginStoreWidget';
-import UCSCTrackHubConnectionF from './UCSCTrackHub';
+import UCSCTrackHubConnectionF from './UCSCTrackHubConnection';
 const AssemblyManager = lazy(() => import('./AssemblyManager'));
 export default class DataManagementPlugin extends Plugin {
     constructor() {
@@ -16,6 +17,7 @@ export default class DataManagementPlugin extends Plugin {
     }
     install(pluginManager) {
         UCSCTrackHubConnectionF(pluginManager);
+        JB2TrackHubConnectionF(pluginManager);
         AddTrackWidgetF(pluginManager);
         HierarchicalTrackSelectorWidgetF(pluginManager);
         AddConnectionWidgetF(pluginManager);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "3.6.2",
+  "version": "3.6.4",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -37,9 +37,9 @@
   },
   "dependencies": {
     "@gmod/ucsc-hub": "^2.0.1",
-    "@jbrowse/core": "^3.6.2",
-    "@jbrowse/plugin-config": "^3.6.2",
-    "@jbrowse/product-core": "^3.6.2",
+    "@jbrowse/core": "^3.6.4",
+    "@jbrowse/plugin-config": "^3.6.4",
+    "@jbrowse/product-core": "^3.6.4",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "@mui/x-data-grid": "^8.0.0",
@@ -61,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "2a2c52face5f1b8fe899f48d5903e5c5f06dba63"
+  "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
 }