@jbrowse/core 2.10.2 → 2.11.0

package/BaseFeatureWidget/BaseFeatureDetail/Attributes.js

@@ -42,7 +42,7 @@ function Attributes(props) {
         }
         else if ((0, is_object_1.default)(value)) {
             const { omitSingleLevel, ...rest } = props;
-            return (0, util_2.isUriLocation)(value) ? (hideUris ? null : (react_1.default.createElement(UriField_1.default, { key: key, name: key, prefix: prefix, value: value }))) : (react_1.default.createElement(Attributes, { ...rest, key: key, attributes: value, descriptions: descriptions, prefix: [...prefix, key] }));
+            return (0, util_2.isUriLocation)(value) ? (hideUris ? null : (react_1.default.createElement(UriField_1.default, { key: key, name: key, prefix: prefix, value: value }))) : (react_1.default.createElement(Attributes, { key: key, ...rest, attributes: value, descriptions: descriptions, prefix: [...prefix, key] }));
         }
         else {
             return (react_1.default.createElement(SimpleField_1.default, { key: key, name: key, value: formatter(value, key), description: description, prefix: prefix, width: Math.min(maxLabelWidth, MAX_FIELD_NAME_WIDTH) }));

package/BaseFeatureWidget/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("../configuration/configurationSchema").ConfigurationSchemaType<{}, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export { configSchema };

package/BaseFeatureWidget/configSchema.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+const configuration_1 = require("../configuration");
+const configSchema = (0, configuration_1.ConfigurationSchema)('BaseFeatureWidget', {});
+exports.configSchema = configSchema;

package/BaseFeatureWidget/index.d.ts

@@ -1,128 +1,2 @@
-import PluginManager from '../PluginManager';
-declare const configSchema: import("../configuration/configurationSchema").ConfigurationSchemaType<{}, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-/**
- * #stateModel BaseFeatureWidget
- * displays data about features, allowing configuration callbacks to modify the
- * contents of what is displayed
- *
- * see: formatDetails-\>feature,formatDetails-\>subfeatures
- */
-export default function stateModelFactory(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<"BaseFeatureWidget">;
-    /**
-     * #property
-     */
-    featureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-}, {
-    error: unknown;
-} & {
-    /**
-     * #action
-     */
-    setFeatureData(featureData: Record<string, unknown>): void;
-    /**
-     * #action
-     */
-    clearFeatureData(): void;
-    /**
-     * #action
-     */
-    setFormattedData(feat: Record<string, unknown>): void;
-    /**
-     * #action
-     */
-    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
-    /**
-     * #action
-     */
-    setError(e: unknown): void;
-} & {
-    afterCreate(): void;
-}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    /**
-     * #property
-     */
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    /**
-     * #property
-     */
-    featureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    /**
-     * #property
-     */
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    /**
-     * #property
-     */
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-}>>, {
-    type: "BaseFeatureWidget";
-    id: string;
-    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    trackId: string | undefined;
-    trackType: string | undefined;
-    maxDepth: number | undefined;
-    formattedFields: any;
-    finalizedFeatureData: any;
-}>;
-export { configSchema, stateModelFactory };
+export { configSchema } from './configSchema';
+export { stateModelFactory } from './stateModelFactory';

package/BaseFeatureWidget/index.js

@@ -1,171 +1,7 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = exports.configSchema = void 0;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
-const clone_1 = __importDefault(require("clone"));
-const configuration_1 = require("../configuration");
-const util_1 = require("../util");
-const mst_1 = require("../util/types/mst");
-const configSchema = (0, configuration_1.ConfigurationSchema)('BaseFeatureWidget', {});
-exports.configSchema = configSchema;
-function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
-    var _a;
-    if (depth <= currentDepth) {
-        return;
-    }
-    (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
-        formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
-        parse(sub);
-    });
-}
-/**
- * #stateModel BaseFeatureWidget
- * displays data about features, allowing configuration callbacks to modify the
- * contents of what is displayed
- *
- * see: formatDetails-\>feature,formatDetails-\>subfeatures
- */
-function stateModelFactory(pluginManager) {
-    return mobx_state_tree_1.types
-        .model('BaseFeatureWidget', {
-        /**
-         * #property
-         */
-        id: mst_1.ElementId,
-        /**
-         * #property
-         */
-        type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
-        /**
-         * #property
-         */
-        featureData: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
-        formattedFields: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
-        unformattedFeatureData: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
-        view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
-        /**
-         * #property
-         */
-        track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
-        /**
-         * #property
-         */
-        trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        /**
-         * #property
-         */
-        maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-    })
-        .volatile(() => ({
-        error: undefined,
-    }))
-        .actions(self => ({
-        /**
-         * #action
-         */
-        setFeatureData(featureData) {
-            self.unformattedFeatureData = featureData;
-        },
-        /**
-         * #action
-         */
-        clearFeatureData() {
-            self.featureData = undefined;
-        },
-        /**
-         * #action
-         */
-        setFormattedData(feat) {
-            self.featureData = feat;
-        },
-        /**
-         * #action
-         */
-        setExtra(type, trackId, maxDepth) {
-            self.trackId = trackId;
-            self.trackType = type;
-            self.maxDepth = maxDepth;
-        },
-        /**
-         * #action
-         */
-        setError(e) {
-            self.error = e;
-        },
-    }))
-        .actions(self => ({
-        afterCreate() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                try {
-                    const { unformattedFeatureData, track } = self;
-                    const session = (0, util_1.getSession)(self);
-                    if (track) {
-                        self.setExtra(track.type, track.configuration.trackId, (0, configuration_1.getConf)(track, ['formatDetails', 'maxDepth']));
-                    }
-                    if (unformattedFeatureData) {
-                        const feature = (0, clone_1.default)(unformattedFeatureData);
-                        const combine = (arg2, feature) => ({
-                            ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
-                            ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
-                        });
-                        if (track) {
-                            // eslint-disable-next-line no-underscore-dangle
-                            feature.__jbrowsefmt = combine('feature', feature);
-                            formatSubfeatures(feature, (0, configuration_1.getConf)(track, ['formatDetails', 'depth']), sub => {
-                                // eslint-disable-next-line no-underscore-dangle
-                                sub.__jbrowsefmt = combine('subfeatures', sub);
-                            });
-                        }
-                        self.setFormattedData(feature);
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            }));
-        },
-    }))
-        .preProcessSnapshot(snap => {
-        // @ts-expect-error
-        const { featureData, finalizedFeatureData, ...rest } = snap;
-        return {
-            unformattedFeatureData: featureData,
-            featureData: finalizedFeatureData,
-            ...rest,
-        };
-    })
-        .postProcessSnapshot(snap => {
-        // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
-        const { unformattedFeatureData, featureData, ...rest } = snap;
-        // finalizedFeatureData avoids running formatter twice if loading from
-        // snapshot
-        return {
-            // replacing undefined with null helps with allowing fields to be
-            // hidden, setting null is not allowed by jexl so we set it to
-            // undefined to hide. see config guide. this replacement happens both
-            // here and when displaying the featureData in base feature widget
-            finalizedFeatureData: JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v))),
-            ...rest,
-        };
-    });
-}
-exports.default = stateModelFactory;
-exports.stateModelFactory = stateModelFactory;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return configSchema_1.configSchema; } });
+var stateModelFactory_1 = require("./stateModelFactory");
+Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return stateModelFactory_1.stateModelFactory; } });

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -0,0 +1,126 @@
+import PluginManager from '../PluginManager';
+/**
+ * #stateModel BaseFeatureWidget
+ * displays data about features, allowing configuration callbacks to modify the
+ * contents of what is displayed
+ *
+ * see: formatDetails-\>feature,formatDetails-\>subfeatures
+ */
+export declare function stateModelFactory(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<"BaseFeatureWidget">;
+    /**
+     * #property
+     */
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}, {
+    error: unknown;
+} & {
+    /**
+     * #action
+     */
+    setFeatureData(featureData: Record<string, unknown>): void;
+    /**
+     * #action
+     */
+    clearFeatureData(): void;
+    /**
+     * #action
+     */
+    setFormattedData(feat: Record<string, unknown>): void;
+    /**
+     * #action
+     */
+    setExtra(type?: string, trackId?: string, maxDepth?: number): void;
+    /**
+     * #action
+     */
+    setError(e: unknown): void;
+} & {
+    afterCreate(): void;
+}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    /**
+     * #property
+     */
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    /**
+     * #property
+     */
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    /**
+     * #property
+     */
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    /**
+     * #property
+     */
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    /**
+     * #property
+     */
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>>, {
+    id: string;
+    type: "BaseFeatureWidget";
+    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    trackId: string | undefined;
+    trackType: string | undefined;
+    maxDepth: number | undefined;
+    formattedFields: any;
+    finalizedFeatureData: any;
+}>;

package/BaseFeatureWidget/stateModelFactory.js

@@ -0,0 +1,168 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.stateModelFactory = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
+const clone_1 = __importDefault(require("clone"));
+const configuration_1 = require("../configuration");
+const util_1 = require("../util");
+const mst_1 = require("../util/types/mst");
+function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
+    var _a;
+    if (depth <= currentDepth) {
+        return;
+    }
+    (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
+        formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
+        parse(sub);
+    });
+}
+/**
+ * #stateModel BaseFeatureWidget
+ * displays data about features, allowing configuration callbacks to modify the
+ * contents of what is displayed
+ *
+ * see: formatDetails-\>feature,formatDetails-\>subfeatures
+ */
+function stateModelFactory(pluginManager) {
+    return mobx_state_tree_1.types
+        .model('BaseFeatureWidget', {
+        /**
+         * #property
+         */
+        id: mst_1.ElementId,
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
+        /**
+         * #property
+         */
+        featureData: mobx_state_tree_1.types.frozen(),
+        /**
+         * #property
+         */
+        formattedFields: mobx_state_tree_1.types.frozen(),
+        /**
+         * #property
+         */
+        unformattedFeatureData: mobx_state_tree_1.types.frozen(),
+        /**
+         * #property
+         */
+        view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
+        /**
+         * #property
+         */
+        track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
+        /**
+         * #property
+         */
+        trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        /**
+         * #property
+         */
+        trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        /**
+         * #property
+         */
+        maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
+    })
+        .volatile(() => ({
+        error: undefined,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setFeatureData(featureData) {
+            self.unformattedFeatureData = featureData;
+        },
+        /**
+         * #action
+         */
+        clearFeatureData() {
+            self.featureData = undefined;
+        },
+        /**
+         * #action
+         */
+        setFormattedData(feat) {
+            self.featureData = feat;
+        },
+        /**
+         * #action
+         */
+        setExtra(type, trackId, maxDepth) {
+            self.trackId = trackId;
+            self.trackType = type;
+            self.maxDepth = maxDepth;
+        },
+        /**
+         * #action
+         */
+        setError(e) {
+            self.error = e;
+        },
+    }))
+        .actions(self => ({
+        afterCreate() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
+                try {
+                    const { unformattedFeatureData, track } = self;
+                    const session = (0, util_1.getSession)(self);
+                    if (track) {
+                        self.setExtra(track.type, track.configuration.trackId, (0, configuration_1.getConf)(track, ['formatDetails', 'maxDepth']));
+                    }
+                    if (unformattedFeatureData) {
+                        const feature = (0, clone_1.default)(unformattedFeatureData);
+                        const combine = (arg2, feature) => ({
+                            ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
+                            ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
+                        });
+                        if (track) {
+                            // eslint-disable-next-line no-underscore-dangle
+                            feature.__jbrowsefmt = combine('feature', feature);
+                            formatSubfeatures(feature, (0, configuration_1.getConf)(track, ['formatDetails', 'depth']), sub => {
+                                // eslint-disable-next-line no-underscore-dangle
+                                sub.__jbrowsefmt = combine('subfeatures', sub);
+                            });
+                        }
+                        self.setFormattedData(feature);
+                    }
+                }
+                catch (e) {
+                    console.error(e);
+                    self.setError(e);
+                }
+            }));
+        },
+    }))
+        .preProcessSnapshot(snap => {
+        // @ts-expect-error
+        const { featureData, finalizedFeatureData, ...rest } = snap;
+        return {
+            unformattedFeatureData: featureData,
+            featureData: finalizedFeatureData,
+            ...rest,
+        };
+    })
+        .postProcessSnapshot(snap => {
+        // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+        const { unformattedFeatureData, featureData, ...rest } = snap;
+        // finalizedFeatureData avoids running formatter twice if loading from
+        // snapshot
+        return {
+            // replacing undefined with null helps with allowing fields to be
+            // hidden, setting null is not allowed by jexl so we set it to
+            // undefined to hide. see config guide. this replacement happens both
+            // here and when displaying the featureData in base feature widget
+            finalizedFeatureData: JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v))),
+            ...rest,
+        };
+    });
+}
+exports.stateModelFactory = stateModelFactory;

package/Plugin.d.ts

@@ -9,6 +9,6 @@ export default abstract class Plugin {
     version?: string;
     install(_pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;
-    configurationSchema: AnyConfigurationSchemaType | undefined;
+    configurationSchema?: AnyConfigurationSchemaType;
 }
 export type PluginConstructor = new (...args: unknown[]) => Plugin;

package/Plugin.js

@@ -4,9 +4,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
  * base class for a JBrowse plugin
  */
 class Plugin {
-    constructor() {
-        this.configurationSchema = undefined;
-    }
     install(_pluginManager) { }
     configure(_pluginManager) { }
 }

package/PluginLoader.d.ts

@@ -55,7 +55,7 @@ export default class PluginLoader {
         default: PluginConstructor;
     }>;
     loadPlugin(def: PluginDefinition, baseUri?: string): Promise<PluginConstructor>;
-    installGlobalReExports(target: WindowOrWorkerGlobalScope): void;
+    installGlobalReExports(target: WindowOrWorkerGlobalScope): this;
     load(baseUri?: string): Promise<{
         plugin: PluginConstructor;
         definition: PluginDefinition;

package/PluginLoader.js

@@ -152,6 +152,7 @@ class PluginLoader {
         target.JBrowseExports = Object.fromEntries(Object.entries(ReExports_1.default).map(([moduleName, module]) => {
             return [moduleName, module];
         }));
+        return this;
     }
     async load(baseUri) {
         return Promise.all(this.definitions.map(async (definition) => ({