@jbrowse/product-core 2.6.1 → 2.6.3

package/dist/RootModel/FormatAbout.d.ts

@@ -0,0 +1,22 @@
+/**
+ * #config FormatAbout
+ * generally exists on the config.json or root config as configuration.formatAbout
+ */
+export declare function FormatAboutConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot configuration.formatAbout.config
+     */
+    config: {
+        type: string;
+        description: string;
+        defaultValue: {};
+        contextVariable: string[];
+    };
+    /**
+     * #slot configuration.formatAbout.hideUris
+     */
+    hideUris: {
+        type: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/RootModel/FormatAbout.js

@@ -0,0 +1,29 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FormatAboutConfigSchemaFactory = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config FormatAbout
+ * generally exists on the config.json or root config as configuration.formatAbout
+ */
+function FormatAboutConfigSchemaFactory() {
+    return (0, configuration_1.ConfigurationSchema)('FormatAbout', {
+        /**
+         * #slot configuration.formatAbout.config
+         */
+        config: {
+            type: 'frozen',
+            description: 'formats configuration object in about dialog',
+            defaultValue: {},
+            contextVariable: ['config'],
+        },
+        /**
+         * #slot configuration.formatAbout.hideUris
+         */
+        hideUris: {
+            type: 'boolean',
+            defaultValue: false,
+        },
+    });
+}
+exports.FormatAboutConfigSchemaFactory = FormatAboutConfigSchemaFactory;

package/dist/RootModel/FormatDetails.d.ts

@@ -0,0 +1,32 @@
+/**
+ * #config FormatDetails
+ * generally exists on the config.json or root config as configuration.formatDetails
+ */
+export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot configuration.formatDetails.feature
+     */
+    feature: {
+        type: string;
+        description: string;
+        defaultValue: {};
+        contextVariable: string[];
+    };
+    /**
+     * #slot configuration.formatDetails.subfeatures
+     */
+    subfeatures: {
+        type: string;
+        description: string;
+        defaultValue: {};
+        contextVariable: string[];
+    };
+    /**
+     * #slot configuration.formatDetails.depth
+     */
+    depth: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/RootModel/FormatDetails.js

@@ -0,0 +1,39 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FormatDetailsConfigSchemaFactory = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config FormatDetails
+ * generally exists on the config.json or root config as configuration.formatDetails
+ */
+function FormatDetailsConfigSchemaFactory() {
+    return (0, configuration_1.ConfigurationSchema)('FormatDetails', {
+        /**
+         * #slot configuration.formatDetails.feature
+         */
+        feature: {
+            type: 'frozen',
+            description: 'adds extra fields to the feature details',
+            defaultValue: {},
+            contextVariable: ['feature'],
+        },
+        /**
+         * #slot configuration.formatDetails.subfeatures
+         */
+        subfeatures: {
+            type: 'frozen',
+            description: 'adds extra fields to the subfeatures of a feature',
+            defaultValue: {},
+            contextVariable: ['feature'],
+        },
+        /**
+         * #slot configuration.formatDetails.depth
+         */
+        depth: {
+            type: 'number',
+            defaultValue: 2,
+            description: 'depth to iterate on subfeatures',
+        },
+    });
+}
+exports.FormatDetailsConfigSchemaFactory = FormatDetailsConfigSchemaFactory;

package/dist/RootModel/HierarchicalConfig.d.ts

@@ -0,0 +1,45 @@
+/**
+ * #config HierarchicalConfigSchema
+ * generally exists on the config.json or root config as configuration.hierarchical
+ */
+export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot configuration.hierarchical.sort.trackNames
+         */
+        trackNames: {
+            type: string;
+            defaultValue: boolean;
+        };
+        /**
+         * #slot configuration.hierarchical.sort.categories
+         */
+        categories: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot configuration.hierarchical.defaultCollapse.categoryNames
+         */
+        categoryNames: {
+            type: string;
+            defaultValue: never[];
+        };
+        /**
+         * #slot configuration.hierarchical.defaultCollapse.topLevelCategories
+         */
+        topLevelCategories: {
+            type: string;
+            defaultValue: boolean;
+        };
+        /**
+         * #slot configuration.hierarchical.defaultCollapse.subCategories
+         */
+        subCategories: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/dist/RootModel/HierarchicalConfig.js

@@ -0,0 +1,52 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.HierarchicalConfigSchemaFactory = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+/**
+ * #config HierarchicalConfigSchema
+ * generally exists on the config.json or root config as configuration.hierarchical
+ */
+function HierarchicalConfigSchemaFactory() {
+    return (0, configuration_1.ConfigurationSchema)('hierarchical', {
+        sort: (0, configuration_1.ConfigurationSchema)('hierarchicalSort', {
+            /**
+             * #slot configuration.hierarchical.sort.trackNames
+             */
+            trackNames: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+            /**
+             * #slot configuration.hierarchical.sort.categories
+             */
+            categories: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+        }),
+        defaultCollapsed: (0, configuration_1.ConfigurationSchema)('defaultCollapsed', {
+            /**
+             * #slot configuration.hierarchical.defaultCollapse.categoryNames
+             */
+            categoryNames: {
+                type: 'stringArray',
+                defaultValue: [],
+            },
+            /**
+             * #slot configuration.hierarchical.defaultCollapse.topLevelCategories
+             */
+            topLevelCategories: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+            /**
+             * #slot configuration.hierarchical.defaultCollapse.subCategories
+             */
+            subCategories: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+        }),
+    });
+}
+exports.HierarchicalConfigSchemaFactory = HierarchicalConfigSchemaFactory;

package/dist/RootModel/index.d.ts

@@ -1,2 +1,5 @@
 export * from './BaseRootModel';
 export * from './InternetAccounts';
+export * from './FormatAbout';
+export * from './FormatDetails';
+export * from './HierarchicalConfig';

package/dist/RootModel/index.js

@@ -16,3 +16,6 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
 Object.defineProperty(exports, "__esModule", { value: true });
 __exportStar(require("./BaseRootModel"), exports);
 __exportStar(require("./InternetAccounts"), exports);
+__exportStar(require("./FormatAbout"), exports);
+__exportStar(require("./FormatDetails"), exports);
+__exportStar(require("./HierarchicalConfig"), exports);

package/dist/index.d.ts

@@ -1,3 +1,4 @@
 export * from './RootModel';
 export * from './Session';
 export * from './ui';
+export * from './rpcWorker';

package/dist/index.js

@@ -17,3 +17,4 @@ Object.defineProperty(exports, "__esModule", { value: true });
 __exportStar(require("./RootModel"), exports);
 __exportStar(require("./Session"), exports);
 __exportStar(require("./ui"), exports);
+__exportStar(require("./rpcWorker"), exports);

package/dist/rpcWorker.d.ts

@@ -0,0 +1,6 @@
+import { LoadedPlugin } from '@jbrowse/core/PluginLoader';
+import { PluginConstructor } from '@jbrowse/core/Plugin';
+export declare function initializeWorker(corePlugins: PluginConstructor[], opts: {
+    fetchESM?: (url: string) => Promise<LoadedPlugin>;
+    fetchCJS?: (url: string) => Promise<LoadedPlugin>;
+}): Promise<void>;

package/dist/rpcWorker.js

@@ -0,0 +1,74 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.initializeWorker = void 0;
+/* eslint-disable no-restricted-globals */
+const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
+const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
+const remoteAbortSignals_1 = require("@jbrowse/core/rpc/remoteAbortSignals");
+const PluginLoader_1 = __importDefault(require("@jbrowse/core/PluginLoader"));
+const serialize_error_1 = require("serialize-error");
+// waits for a message from the main thread containing our configuration, which
+// must be sent on boot
+function receiveConfiguration() {
+    const configurationP = new Promise(resolve => {
+        function listener(e) {
+            if (e.data.message === 'config') {
+                resolve(e.data.config);
+                removeEventListener('message', listener);
+            }
+        }
+        self.addEventListener('message', listener);
+    });
+    postMessage({ message: 'readyForConfig' });
+    return configurationP;
+}
+async function getPluginManager(corePlugins, opts) {
+    // Load runtime plugins
+    const config = await receiveConfiguration();
+    const pluginLoader = new PluginLoader_1.default(config.plugins, opts);
+    pluginLoader.installGlobalReExports(self);
+    const runtimePlugins = await pluginLoader.load(config.windowHref);
+    const plugins = [...corePlugins.map(p => ({ plugin: p })), ...runtimePlugins];
+    const pluginManager = new PluginManager_1.default(plugins.map(P => new P.plugin()));
+    pluginManager.createPluggableElements();
+    pluginManager.configure();
+    return pluginManager;
+}
+function wrapForRpc(func) {
+    return (args) => {
+        const { channel, rpcDriverClassName } = args;
+        return func({
+            ...args,
+            statusCallback: (message) => {
+                // @ts-expect-error
+                self.rpcServer.emit(channel, message);
+            },
+        }, rpcDriverClassName);
+    };
+}
+async function initializeWorker(corePlugins, opts) {
+    try {
+        const pluginManager = await getPluginManager(corePlugins, opts);
+        const rpcConfig = Object.fromEntries(pluginManager
+            .getRpcElements()
+            .map(e => [e.name, wrapForRpc(e.execute.bind(e))]));
+        // @ts-expect-error
+        self.rpcServer = new librpc_web_mod_1.default.Server({
+            ...rpcConfig,
+            ...(0, remoteAbortSignals_1.remoteAbortRpcHandler)(),
+            ping: () => {
+                // the ping method is required by the worker driver for checking the
+                // health of the worker
+            },
+        });
+        postMessage({ message: 'ready' });
+    }
+    catch (e) {
+        postMessage({ message: 'error', error: (0, serialize_error_1.serializeError)(e) });
+    }
+    /* do nothing */
+}
+exports.initializeWorker = initializeWorker;

package/esm/RootModel/FormatAbout.d.ts

@@ -0,0 +1,22 @@
+/**
+ * #config FormatAbout
+ * generally exists on the config.json or root config as configuration.formatAbout
+ */
+export declare function FormatAboutConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot configuration.formatAbout.config
+     */
+    config: {
+        type: string;
+        description: string;
+        defaultValue: {};
+        contextVariable: string[];
+    };
+    /**
+     * #slot configuration.formatAbout.hideUris
+     */
+    hideUris: {
+        type: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/RootModel/FormatAbout.js

@@ -0,0 +1,25 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config FormatAbout
+ * generally exists on the config.json or root config as configuration.formatAbout
+ */
+export function FormatAboutConfigSchemaFactory() {
+    return ConfigurationSchema('FormatAbout', {
+        /**
+         * #slot configuration.formatAbout.config
+         */
+        config: {
+            type: 'frozen',
+            description: 'formats configuration object in about dialog',
+            defaultValue: {},
+            contextVariable: ['config'],
+        },
+        /**
+         * #slot configuration.formatAbout.hideUris
+         */
+        hideUris: {
+            type: 'boolean',
+            defaultValue: false,
+        },
+    });
+}

package/esm/RootModel/FormatDetails.d.ts

@@ -0,0 +1,32 @@
+/**
+ * #config FormatDetails
+ * generally exists on the config.json or root config as configuration.formatDetails
+ */
+export declare function FormatDetailsConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot configuration.formatDetails.feature
+     */
+    feature: {
+        type: string;
+        description: string;
+        defaultValue: {};
+        contextVariable: string[];
+    };
+    /**
+     * #slot configuration.formatDetails.subfeatures
+     */
+    subfeatures: {
+        type: string;
+        description: string;
+        defaultValue: {};
+        contextVariable: string[];
+    };
+    /**
+     * #slot configuration.formatDetails.depth
+     */
+    depth: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/RootModel/FormatDetails.js

@@ -0,0 +1,35 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config FormatDetails
+ * generally exists on the config.json or root config as configuration.formatDetails
+ */
+export function FormatDetailsConfigSchemaFactory() {
+    return ConfigurationSchema('FormatDetails', {
+        /**
+         * #slot configuration.formatDetails.feature
+         */
+        feature: {
+            type: 'frozen',
+            description: 'adds extra fields to the feature details',
+            defaultValue: {},
+            contextVariable: ['feature'],
+        },
+        /**
+         * #slot configuration.formatDetails.subfeatures
+         */
+        subfeatures: {
+            type: 'frozen',
+            description: 'adds extra fields to the subfeatures of a feature',
+            defaultValue: {},
+            contextVariable: ['feature'],
+        },
+        /**
+         * #slot configuration.formatDetails.depth
+         */
+        depth: {
+            type: 'number',
+            defaultValue: 2,
+            description: 'depth to iterate on subfeatures',
+        },
+    });
+}

package/esm/RootModel/HierarchicalConfig.d.ts

@@ -0,0 +1,45 @@
+/**
+ * #config HierarchicalConfigSchema
+ * generally exists on the config.json or root config as configuration.hierarchical
+ */
+export declare function HierarchicalConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    sort: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot configuration.hierarchical.sort.trackNames
+         */
+        trackNames: {
+            type: string;
+            defaultValue: boolean;
+        };
+        /**
+         * #slot configuration.hierarchical.sort.categories
+         */
+        categories: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    defaultCollapsed: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot configuration.hierarchical.defaultCollapse.categoryNames
+         */
+        categoryNames: {
+            type: string;
+            defaultValue: never[];
+        };
+        /**
+         * #slot configuration.hierarchical.defaultCollapse.topLevelCategories
+         */
+        topLevelCategories: {
+            type: string;
+            defaultValue: boolean;
+        };
+        /**
+         * #slot configuration.hierarchical.defaultCollapse.subCategories
+         */
+        subCategories: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/RootModel/HierarchicalConfig.js

@@ -0,0 +1,48 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config HierarchicalConfigSchema
+ * generally exists on the config.json or root config as configuration.hierarchical
+ */
+export function HierarchicalConfigSchemaFactory() {
+    return ConfigurationSchema('hierarchical', {
+        sort: ConfigurationSchema('hierarchicalSort', {
+            /**
+             * #slot configuration.hierarchical.sort.trackNames
+             */
+            trackNames: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+            /**
+             * #slot configuration.hierarchical.sort.categories
+             */
+            categories: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+        }),
+        defaultCollapsed: ConfigurationSchema('defaultCollapsed', {
+            /**
+             * #slot configuration.hierarchical.defaultCollapse.categoryNames
+             */
+            categoryNames: {
+                type: 'stringArray',
+                defaultValue: [],
+            },
+            /**
+             * #slot configuration.hierarchical.defaultCollapse.topLevelCategories
+             */
+            topLevelCategories: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+            /**
+             * #slot configuration.hierarchical.defaultCollapse.subCategories
+             */
+            subCategories: {
+                type: 'boolean',
+                defaultValue: false,
+            },
+        }),
+    });
+}

package/esm/RootModel/index.d.ts

@@ -1,2 +1,5 @@
 export * from './BaseRootModel';
 export * from './InternetAccounts';
+export * from './FormatAbout';
+export * from './FormatDetails';
+export * from './HierarchicalConfig';

package/esm/RootModel/index.js

@@ -1,2 +1,5 @@
 export * from './BaseRootModel';
 export * from './InternetAccounts';
+export * from './FormatAbout';
+export * from './FormatDetails';
+export * from './HierarchicalConfig';

package/esm/index.d.ts

@@ -1,3 +1,4 @@
 export * from './RootModel';
 export * from './Session';
 export * from './ui';
+export * from './rpcWorker';

package/esm/index.js

@@ -1,3 +1,4 @@
 export * from './RootModel';
 export * from './Session';
 export * from './ui';
+export * from './rpcWorker';

package/esm/rpcWorker.d.ts

@@ -0,0 +1,6 @@
+import { LoadedPlugin } from '@jbrowse/core/PluginLoader';
+import { PluginConstructor } from '@jbrowse/core/Plugin';
+export declare function initializeWorker(corePlugins: PluginConstructor[], opts: {
+    fetchESM?: (url: string) => Promise<LoadedPlugin>;
+    fetchCJS?: (url: string) => Promise<LoadedPlugin>;
+}): Promise<void>;

package/esm/rpcWorker.js

@@ -0,0 +1,67 @@
+/* eslint-disable no-restricted-globals */
+import RpcServer from 'librpc-web-mod';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { remoteAbortRpcHandler } from '@jbrowse/core/rpc/remoteAbortSignals';
+import PluginLoader from '@jbrowse/core/PluginLoader';
+import { serializeError } from 'serialize-error';
+// waits for a message from the main thread containing our configuration, which
+// must be sent on boot
+function receiveConfiguration() {
+    const configurationP = new Promise(resolve => {
+        function listener(e) {
+            if (e.data.message === 'config') {
+                resolve(e.data.config);
+                removeEventListener('message', listener);
+            }
+        }
+        self.addEventListener('message', listener);
+    });
+    postMessage({ message: 'readyForConfig' });
+    return configurationP;
+}
+async function getPluginManager(corePlugins, opts) {
+    // Load runtime plugins
+    const config = await receiveConfiguration();
+    const pluginLoader = new PluginLoader(config.plugins, opts);
+    pluginLoader.installGlobalReExports(self);
+    const runtimePlugins = await pluginLoader.load(config.windowHref);
+    const plugins = [...corePlugins.map(p => ({ plugin: p })), ...runtimePlugins];
+    const pluginManager = new PluginManager(plugins.map(P => new P.plugin()));
+    pluginManager.createPluggableElements();
+    pluginManager.configure();
+    return pluginManager;
+}
+function wrapForRpc(func) {
+    return (args) => {
+        const { channel, rpcDriverClassName } = args;
+        return func({
+            ...args,
+            statusCallback: (message) => {
+                // @ts-expect-error
+                self.rpcServer.emit(channel, message);
+            },
+        }, rpcDriverClassName);
+    };
+}
+export async function initializeWorker(corePlugins, opts) {
+    try {
+        const pluginManager = await getPluginManager(corePlugins, opts);
+        const rpcConfig = Object.fromEntries(pluginManager
+            .getRpcElements()
+            .map(e => [e.name, wrapForRpc(e.execute.bind(e))]));
+        // @ts-expect-error
+        self.rpcServer = new RpcServer.Server({
+            ...rpcConfig,
+            ...remoteAbortRpcHandler(),
+            ping: () => {
+                // the ping method is required by the worker driver for checking the
+                // health of the worker
+            },
+        });
+        postMessage({ message: 'ready' });
+    }
+    catch (e) {
+        postMessage({ message: 'error', error: serializeError(e) });
+    }
+    /* do nothing */
+}