@jbrowse/core 2.8.0 → 2.10.0

package/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js

@@ -57,8 +57,8 @@ function DataGridDetails({ value, prefix, name, }) {
     const rows = Object.entries(value).map(([k, val]) => {
         const { id, ...rest } = val;
         return {
-            id: k,
-            identifier: id,
+            id: k, // used by material UI
+            identifier: id, // renamed from id to identifier
             ...rest,
         };
     });

package/BaseFeatureWidget/BaseFeatureDetail/index.js

@@ -125,6 +125,7 @@ const BaseAttributes = (props) => {
 exports.BaseAttributes = BaseAttributes;
 function FeatureDetails(props) {
     const { omit = [], model, feature, depth = 0 } = props;
+    const { maxDepth } = model;
     const { mate, name = '', id = '', type = '', subfeatures, uniqueId } = feature;
     const pm = (0, util_1.getEnv)(model).pluginManager;
     const session = (0, util_1.getSession)(model);
@@ -149,7 +150,7 @@ function FeatureDetails(props) {
             react_1.default.createElement(material_1.Divider, null),
             react_1.default.createElement(BaseCard, { title: ExtraPanel.name },
                 react_1.default.createElement(ExtraPanel.Component, { ...props })))) : null,
-        (subfeatures === null || subfeatures === void 0 ? void 0 : subfeatures.length) ? (react_1.default.createElement(BaseCard, { title: "Subfeatures", defaultExpanded: depth < 1 }, subfeatures.map((sub, idx) => (react_1.default.createElement(FeatureDetails, { key: JSON.stringify(sub), feature: { ...sub, uniqueId: `${uniqueId}_${idx}` }, model: model, depth: depth + 1 }))))) : null));
+        depth < maxDepth && (subfeatures === null || subfeatures === void 0 ? void 0 : subfeatures.length) ? (react_1.default.createElement(BaseCard, { title: "Subfeatures", defaultExpanded: depth < 1 }, subfeatures.map((sub, idx) => (react_1.default.createElement(FeatureDetails, { key: JSON.stringify(sub), feature: { ...sub, uniqueId: `${uniqueId}_${idx}` }, model: model, depth: depth + 1 }))))) : null));
 }
 exports.FeatureDetails = FeatureDetails;
 const BaseFeatureDetail = (0, mobx_react_1.observer)(function ({ model }) {

package/BaseFeatureWidget/index.d.ts

@@ -1,35 +1,119 @@
 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;
-    setExtra(type?: string, trackId?: string): 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;
@@ -37,6 +121,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;
     trackType: string | undefined;
+    maxDepth: number | undefined;
     formattedFields: any;
     finalizedFeatureData: any;
 }>;

package/BaseFeatureWidget/index.js

@@ -15,44 +15,97 @@ exports.configSchema = configSchema;
 function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
     var _a;
     if (depth <= currentDepth) {
-        return returnObj;
+        return;
     }
-    returnObj.subfeatures = (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
+    (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
         formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
-        return parse(sub);
+        parse(sub);
     });
-    return returnObj;
 }
+/**
+ * #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;
         },
-        setExtra(type, trackId) {
+        /**
+         * #action
+         */
+        setExtra(type, trackId, maxDepth) {
             self.trackId = trackId;
             self.trackType = type;
+            self.maxDepth = maxDepth;
         },
+        /**
+         * #action
+         */
         setError(e) {
             self.error = e;
         },
@@ -60,11 +113,12 @@ function stateModelFactory(pluginManager) {
         .actions(self => ({
         afterCreate() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                var _a, _b;
                 try {
-                    self.setExtra((_a = self.track) === null || _a === void 0 ? void 0 : _a.type, (_b = self.track) === null || _b === void 0 ? void 0 : _b.configuration.trackId);
                     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) => ({
@@ -74,8 +128,7 @@ function stateModelFactory(pluginManager) {
                         if (track) {
                             // eslint-disable-next-line no-underscore-dangle
                             feature.__jbrowsefmt = combine('feature', feature);
-                            const depth = (0, configuration_1.getConf)(track, ['formatDetails', 'depth']);
-                            formatSubfeatures(feature, depth, sub => {
+                            formatSubfeatures(feature, (0, configuration_1.getConf)(track, ['formatDetails', 'depth']), sub => {
                                 // eslint-disable-next-line no-underscore-dangle
                                 sub.__jbrowsefmt = combine('subfeatures', sub);
                             });

package/PluginManager.d.ts

@@ -60,7 +60,26 @@ export interface RuntimePluginLoadRecord extends PluginLoadRecord {
 }
 export default class PluginManager {
     plugins: Plugin[];
-    jexl: any;
+    jexl: {
+        addBinaryOp: (operator: string, precedence: number, fn: (left: any, right: any) => any) => void;
+        addUnaryOp: (operator: string, fn: (right: any) => any) => void;
+        addTransform: (name: string, fn: (value: any, ...args: any[]) => any) => void;
+        addTransforms: (map: {
+            [key: string]: (value: any, ...args: any[]) => any;
+        }) => void;
+        getTransform: (name: string) => (value: any, ...args: any[]) => any;
+        addFunction: (name: string, fn: (value: any, ...args: any[]) => any) => void;
+        addFunctions: (map: {
+            [key: string]: (value: any, ...args: any[]) => any;
+        }) => void;
+        getFunction: (name: string) => (value: any, ...args: any[]) => any;
+        eval: (expression: string, context?: import("jexl/Expression").Context | undefined) => Promise<any>;
+        evalSync: (expression: string, context?: import("jexl/Expression").Context | undefined) => any;
+        compile: (expression: string) => import("jexl/Expression").default;
+        createExpression: (expression: string) => import("jexl/Expression").default;
+        removeOp: (operator: string) => void;
+        _grammar: import("jexl/Grammar").default;
+    };
     pluginMetadata: Record<string, PluginMetadata>;
     runtimePluginDefinitions: PluginDefinition[];
     elementCreationSchedule: PhasedScheduler<PluggableElementTypeGroup> | undefined;

package/PluginManager.js

@@ -71,7 +71,6 @@ class TypeRecord {
 class PluginManager {
     constructor(initialPlugins = []) {
         this.plugins = [];
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         this.jexl = (0, jexl_1.default)();
         this.pluginMetadata = {};
         this.runtimePluginDefinitions = [];

package/assemblyManager/assembly.d.ts

@@ -3,6 +3,7 @@ import { BaseOptions } from '../data_adapters/BaseAdapter';
 import PluginManager from '../PluginManager';
 import { Region, Feature } from '../util';
 import RpcManager from '../rpc/RpcManager';
+type AdapterConf = Record<string, unknown>;
 type RefNameAliases = Record<string, string | undefined>;
 export interface RefNameMap {
     forwardMap: RefNameAliases;
@@ -145,17 +146,17 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pm: Plugin
     /**
      * #method
      */
-    getAdapterMapEntry(adapterConf: unknown, options: BaseOptions): Promise<RefNameMap>;
+    getAdapterMapEntry(adapterConf: AdapterConf, options: BaseOptions): Promise<RefNameMap>;
     /**
      * #method
      * get Map of `canonical-name -> adapter-specific-name`
      */
-    getRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions): Promise<RefNameAliases>;
+    getRefNameMapForAdapter(adapterConf: AdapterConf, opts: BaseOptions): Promise<RefNameAliases>;
     /**
      * #method
      * get Map of `adapter-specific-name -> canonical-name`
      */
-    getReverseRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions): Promise<RefNameAliases>;
+    getReverseRefNameMapForAdapter(adapterConf: AdapterConf, opts: BaseOptions): Promise<RefNameAliases>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type AssemblyModel = ReturnType<typeof assemblyFactory>;
 export type Assembly = Instance<AssemblyModel>;

package/assemblyManager/assembly.js

@@ -4,12 +4,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
-const json_stable_stringify_1 = __importDefault(require("json-stable-stringify"));
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
 // locals
 const configuration_1 = require("../configuration");
 const util_1 = require("../util");
 const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
+const dataAdapterCache_1 = require("../data_adapters/dataAdapterCache");
 const refNameRegex = new RegExp('[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*');
 // Based on the UCSC Genome Browser chromosome color palette:
 // https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h
@@ -22,25 +22,25 @@ const refNameColors = [
     'rgb(204, 0, 0)',
     'rgb(255, 0, 0)',
     'rgb(255, 0, 204)',
-    'rgb(165, 132, 132)',
-    'rgb(204, 122, 0)',
-    'rgb(178, 142, 0)',
-    'rgb(153, 153, 0)',
-    'rgb(122, 153, 0)',
-    'rgb(0, 165, 0)',
+    'rgb(165, 132, 132)', // originally 'rgb(255, 204, 204)'
+    'rgb(204, 122, 0)', // originally rgb(255, 153, 0)'
+    'rgb(178, 142, 0)', // originally 'rgb(255, 204, 0)'
+    'rgb(153, 153, 0)', // originally 'rgb(255, 255, 0)'
+    'rgb(122, 153, 0)', // originally 'rgb(204, 255, 0)'
+    'rgb(0, 165, 0)', // originally 'rgb(0, 255, 0)'
     'rgb(53, 128, 0)',
     'rgb(0, 0, 204)',
-    'rgb(96, 145, 242)',
-    'rgb(107, 142, 178)',
-    'rgb(0, 165, 165)',
-    'rgb(122, 153, 153)',
+    'rgb(96, 145, 242)', // originally 'rgb(102, 153, 255)'
+    'rgb(107, 142, 178)', // originally 'rgb(153, 204, 255)'
+    'rgb(0, 165, 165)', // originally 'rgb(0, 255, 255)'
+    'rgb(122, 153, 153)', // originally 'rgb(204, 255, 255)'
     'rgb(153, 0, 204)',
     'rgb(204, 51, 255)',
-    'rgb(173, 130, 216)',
+    'rgb(173, 130, 216)', // originally 'rgb(204, 153, 255)'
     'rgb(102, 102, 102)',
-    'rgb(145, 145, 145)',
-    'rgb(142, 142, 142)',
-    'rgb(142, 142, 107)',
+    'rgb(145, 145, 145)', // originally 'rgb(153, 153, 153)'
+    'rgb(142, 142, 142)', // originally 'rgb(204, 204, 204)'
+    'rgb(142, 142, 107)', // originally 'rgb(204, 204, 153)'
     'rgb(96, 163, 48)', // originally 'rgb(121, 204, 61)'
 ];
 async function loadRefNameMap(assembly, adapterConfig, options, signal) {
@@ -78,9 +78,6 @@ function checkRefName(refName) {
         throw new Error(`Encountered invalid refName: "${refName}"`);
     }
 }
-function getAdapterId(adapterConf) {
-    return (0, json_stable_stringify_1.default)(adapterConf);
-}
 /**
  * #stateModel Assembly
  */
@@ -348,8 +345,7 @@ function assemblyFactory(assemblyConfigType, pm) {
             if (!options.sessionId) {
                 throw new Error('sessionId is required');
             }
-            const adapterId = getAdapterId(adapterConf);
-            return adapterLoads.get(adapterId, {
+            return adapterLoads.get((0, dataAdapterCache_1.adapterConfigCacheKey)(adapterConf), {
                 adapterConf,
                 self: self,
                 options: rest,