@jbrowse/core 2.7.2 → 2.9.0

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

@@ -112,7 +112,8 @@ function CoreDetails(props) {
             .map(([name, value]) => (react_1.default.createElement(SimpleField_1.default, { key: name, name: name, value: value })))));
 }
 const BaseCoreDetails = (props) => {
-    return (react_1.default.createElement(BaseCard, { ...props, title: "Primary data" },
+    const { title = 'Primary data' } = props;
+    return (react_1.default.createElement(BaseCard, { ...props, title: title },
         react_1.default.createElement(CoreDetails, { ...props })));
 };
 exports.BaseCoreDetails = BaseCoreDetails;
@@ -124,6 +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);
@@ -148,7 +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/assemblyManager/assembly.js

@@ -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) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.7.2",
+  "version": "2.9.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -73,5 +73,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "9052b295f2d322e729254457ed9fe2231fb22cce"
+  "gitHead": "a50b6f67cf8c8f3c65a7b8cd858de2fcca1f2909"
 }

package/pluggableElementTypes/models/baseTrackConfig.d.ts

@@ -101,6 +101,14 @@ export declare function createBaseTrackConfig(pluginManager: PluginManager): imp
             defaultValue: number;
             description: string;
         };
+        /**
+         * #slot formatDetails.maxDepth
+         */
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
     }, import("../../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     formatAbout: import("../../configuration/configurationSchema").ConfigurationSchemaType<{
         /**

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -105,6 +105,14 @@ function createBaseTrackConfig(pluginManager) {
                 defaultValue: 2,
                 description: 'depth of subfeatures to iterate the formatter on formatDetails.subfeatures (e.g. you may not want to format the exon/cds subfeatures, so limited to 2',
             },
+            /**
+             * #slot formatDetails.maxDepth
+             */
+            maxDepth: {
+                type: 'number',
+                defaultValue: 99999,
+                description: 'Maximum depth to render subfeatures',
+            },
         }),
         formatAbout: (0, configuration_1.ConfigurationSchema)('FormatAbout', {
             /**

package/rpc/BaseRpcDriver.js

@@ -138,7 +138,7 @@ class BaseRpcDriver {
         // now actually call the worker
         const callP = worker
             .call(functionName, filteredAndSerializedArgs, {
-            timeout: 5 * 60 * 1000,
+            timeout: 5 * 60 * 1000, // 5 minutes
             statusCallback: args.statusCallback,
             rpcDriverClassName: this.name,
             ...options,

package/rpc/WebWorkerRpcDriver.d.ts

@@ -1,3 +1,4 @@
+/// <reference path="../../rpc/declaration.d.ts" />
 import Rpc from 'librpc-web-mod';
 import BaseRpcDriver, { RpcDriverConstructorArgs } from './BaseRpcDriver';
 import { PluginDefinition } from '../PluginLoader';