@jbrowse/core 2.16.0 → 2.16.1

package/BaseFeatureWidget/BaseFeatureDetail/BaseCard.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+import { BaseCardProps } from '../types';
+export default function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/BaseCard.js

@@ -0,0 +1,27 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BaseCard;
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+// icons
+const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    expansionPanelDetails: {
+        display: 'block',
+        padding: theme.spacing(1),
+    },
+    icon: {
+        color: theme.palette.tertiary.contrastText || '#fff',
+    },
+}));
+function BaseCard({ children, title, defaultExpanded = true, }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement(material_1.Accordion, { defaultExpanded: defaultExpanded },
+        react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.icon }) },
+            react_1.default.createElement(material_1.Typography, { variant: "button" }, title)),
+        react_1.default.createElement(material_1.AccordionDetails, { className: classes.expansionPanelDetails }, children)));
+}

package/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+import { BaseProps } from '../types';
+export default function CoreDetails(props: BaseProps): React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/CoreDetails.js

@@ -0,0 +1,33 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = CoreDetails;
+const react_1 = __importDefault(require("react"));
+// locals
+const util_1 = require("../../util");
+const SimpleField_1 = __importDefault(require("./SimpleField"));
+const Position_1 = __importDefault(require("./Position"));
+function CoreDetails(props) {
+    const { feature } = props;
+    const obj = feature;
+    const formattedFeat = { ...obj, ...obj.__jbrowsefmt };
+    const { start, end } = formattedFeat;
+    const displayedDetails = {
+        ...formattedFeat,
+        length: (0, util_1.toLocale)(end - start),
+    };
+    const coreRenderedDetails = {
+        description: 'Description',
+        name: 'Name',
+        length: 'Length',
+        type: 'Type',
+    };
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(SimpleField_1.default, { name: "Position", value: react_1.default.createElement(Position_1.default, { ...props, feature: formattedFeat }) }),
+        Object.entries(coreRenderedDetails)
+            .map(([key, name]) => [name, displayedDetails[key]])
+            .filter(([, value]) => value != null)
+            .map(([name, value]) => (react_1.default.createElement(SimpleField_1.default, { key: name, name: name, value: value })))));
+}

package/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.d.ts

@@ -0,0 +1,11 @@
+import React from 'react';
+import { IAnyStateTreeNode } from 'mobx-state-tree';
+import { SimpleFeatureSerialized } from '../../util';
+export default function FeatureDetails(props: {
+    model: IAnyStateTreeNode;
+    feature: SimpleFeatureSerialized;
+    depth?: number;
+    omit?: string[];
+    descriptions?: Record<string, React.ReactNode>;
+    formatter?: (val: unknown, key: string) => React.ReactNode;
+}): React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails.js

@@ -0,0 +1,66 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = FeatureDetails;
+const react_1 = __importDefault(require("react"));
+const ErrorBoundary_1 = require("@jbrowse/core/ui/ErrorBoundary");
+const material_1 = require("@mui/material");
+// locals
+const util_1 = require("../../util");
+const ui_1 = require("../../ui");
+const util_2 = require("./util");
+const SequenceFeatureDetails_1 = __importDefault(require("../SequenceFeatureDetails"));
+const Attributes_1 = __importDefault(require("./Attributes"));
+const BaseCard_1 = __importDefault(require("./BaseCard"));
+const CoreDetails_1 = __importDefault(require("./CoreDetails"));
+// coreDetails are omitted in some circumstances
+const coreDetails = [
+    'name',
+    'start',
+    'end',
+    'strand',
+    'refName',
+    'description',
+    'type',
+];
+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);
+    const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, {
+        session,
+        feature,
+        model,
+    });
+    const m = mate;
+    return (react_1.default.createElement(BaseCard_1.default, { title: (0, util_2.generateTitle)(name, id, type) },
+        react_1.default.createElement(material_1.Typography, null, "Core details"),
+        react_1.default.createElement(CoreDetails_1.default, { ...props }),
+        m ? (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(material_1.Divider, null),
+            react_1.default.createElement(material_1.Typography, null, "Mate details"),
+            react_1.default.createElement(CoreDetails_1.default, { ...props, feature: {
+                    ...m,
+                    start: m.start,
+                    end: m.end,
+                    refName: m.refName,
+                    uniqueId: `${uniqueId}-mate`,
+                } }))) : null,
+        react_1.default.createElement(material_1.Divider, null),
+        react_1.default.createElement(material_1.Typography, null, "Attributes"),
+        react_1.default.createElement(Attributes_1.default, { attributes: feature, ...props, omit: omit, omitSingleLevel: coreDetails }),
+        react_1.default.createElement(ErrorBoundary_1.ErrorBoundary, { FallbackComponent: e => react_1.default.createElement(ui_1.ErrorMessage, { error: e.error }) },
+            react_1.default.createElement(SequenceFeatureDetails_1.default, { ...props })),
+        ExtraPanel ? (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(material_1.Divider, null),
+            react_1.default.createElement(BaseCard_1.default, { title: ExtraPanel.name },
+                react_1.default.createElement(ExtraPanel.Component, { ...props })))) : null,
+        depth < maxDepth && (subfeatures === null || subfeatures === void 0 ? void 0 : subfeatures.length) ? (react_1.default.createElement(BaseCard_1.default, { title: "Subfeatures", defaultExpanded: depth < 1 }, subfeatures.map((sub, idx) => (react_1.default.createElement(FeatureDetails, { key: JSON.stringify(sub), feature: {
+                ...sub,
+                uniqueId: `${uniqueId}_${idx}`,
+            }, model: model, depth: depth + 1 }))))) : null));
+}

package/BaseFeatureWidget/BaseFeatureDetail/Position.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+import { BaseProps } from '../types';
+export default function Position(props: BaseProps): React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/Position.js

@@ -0,0 +1,20 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = Position;
+const react_1 = __importDefault(require("react"));
+const util_1 = require("../../util");
+function Position(props) {
+    const { feature } = props;
+    const strand = feature.strand;
+    const strandMap = {
+        '-1': '-',
+        '0': '',
+        '1': '+',
+    };
+    const str = strandMap[strand] ? `(${strandMap[strand]})` : '';
+    const loc = (0, util_1.assembleLocString)(feature);
+    return react_1.default.createElement(react_1.default.Fragment, null, `${loc} ${str}`);
+}

package/BaseFeatureWidget/BaseFeatureDetail/index.d.ts

@@ -1,8 +1,7 @@
 import React from 'react';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { SimpleFeatureSerialized } from '../../util';
 import { BaseCardProps, BaseProps } from '../types';
-export declare function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): React.JSX.Element;
+import BaseCard from './BaseCard';
+import FeatureDetails from './FeatureDetails';
 export declare const BaseCoreDetails: (props: BaseProps) => React.JSX.Element;
 export declare const BaseAttributes: (props: BaseProps) => React.JSX.Element;
 export interface BaseInputProps extends BaseCardProps {
@@ -11,14 +10,6 @@ export interface BaseInputProps extends BaseCardProps {
     descriptions?: Record<string, React.ReactNode>;
     formatter?: (val: unknown, key: string) => React.ReactNode;
 }
-export declare function FeatureDetails(props: {
-    model: IAnyStateTreeNode;
-    feature: SimpleFeatureSerialized;
-    depth?: number;
-    omit?: string[];
-    descriptions?: Record<string, React.ReactNode>;
-    formatter?: (val: unknown, key: string) => React.ReactNode;
-}): React.JSX.Element;
 declare const BaseFeatureDetail: ({ model }: BaseInputProps) => React.JSX.Element | null;
 export default BaseFeatureDetail;
-export { default as Attributes } from './Attributes';
+export { BaseCard, FeatureDetails };

package/BaseFeatureWidget/BaseFeatureDetail/index.js

@@ -3,149 +3,47 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Attributes = exports.BaseAttributes = exports.BaseCoreDetails = void 0;
-exports.BaseCard = BaseCard;
-exports.FeatureDetails = FeatureDetails;
+exports.FeatureDetails = exports.BaseCard = exports.BaseAttributes = exports.BaseCoreDetails = void 0;
 const react_1 = __importDefault(require("react"));
-const ErrorBoundary_1 = require("@jbrowse/core/ui/ErrorBoundary");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
-// icons
-const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
-// locals
-const util_1 = require("../../util");
+// utils
 const ui_1 = require("../../ui");
-const SequenceFeatureDetails_1 = __importDefault(require("../SequenceFeatureDetails"));
-const SimpleField_1 = __importDefault(require("./SimpleField"));
+const util_1 = require("./util");
+const util_2 = require("../util");
+// locals
 const Attributes_1 = __importDefault(require("./Attributes"));
-const util_2 = require("./util");
-// coreDetails are omitted in some circumstances
-const coreDetails = [
-    'name',
-    'start',
-    'end',
-    'strand',
-    'refName',
-    'description',
-    'type',
-];
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    expansionPanelDetails: {
-        display: 'block',
-        padding: theme.spacing(1),
-    },
-    icon: {
-        color: theme.palette.tertiary.contrastText || '#fff',
-    },
-}));
-function BaseCard({ children, title, defaultExpanded = true, }) {
-    const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Accordion, { defaultExpanded: defaultExpanded },
-        react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.icon }) },
-            react_1.default.createElement(material_1.Typography, { variant: "button" }, title)),
-        react_1.default.createElement(material_1.AccordionDetails, { className: classes.expansionPanelDetails }, children)));
-}
-function Position(props) {
-    const { feature } = props;
-    const strand = feature.strand;
-    const strandMap = {
-        '-1': '-',
-        '0': '',
-        '1': '+',
-    };
-    const str = strandMap[strand] ? `(${strandMap[strand]})` : '';
-    const loc = (0, util_1.assembleLocString)(feature);
-    return react_1.default.createElement(react_1.default.Fragment, null, `${loc} ${str}`);
-}
-function CoreDetails(props) {
-    const { feature } = props;
-    const obj = feature;
-    const formattedFeat = { ...obj, ...obj.__jbrowsefmt };
-    const { start, end } = formattedFeat;
-    const displayedDetails = {
-        ...formattedFeat,
-        length: (0, util_1.toLocale)(end - start),
-    };
-    const coreRenderedDetails = {
-        description: 'Description',
-        name: 'Name',
-        length: 'Length',
-        type: 'Type',
-    };
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(SimpleField_1.default, { name: "Position", value: react_1.default.createElement(Position, { ...props, feature: formattedFeat }) }),
-        Object.entries(coreRenderedDetails)
-            .map(([key, name]) => [name, displayedDetails[key]])
-            .filter(([, value]) => value != null)
-            .map(([name, value]) => (react_1.default.createElement(SimpleField_1.default, { key: name, name: name, value: value })))));
-}
+const BaseCard_1 = __importDefault(require("./BaseCard"));
+exports.BaseCard = BaseCard_1.default;
+const CoreDetails_1 = __importDefault(require("./CoreDetails"));
+const FeatureDetails_1 = __importDefault(require("./FeatureDetails"));
+exports.FeatureDetails = FeatureDetails_1.default;
 const BaseCoreDetails = (props) => {
     const { title = 'Primary data' } = props;
-    return (react_1.default.createElement(BaseCard, { ...props, title: title },
-        react_1.default.createElement(CoreDetails, { ...props })));
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: title },
+        react_1.default.createElement(CoreDetails_1.default, { ...props })));
 };
 exports.BaseCoreDetails = BaseCoreDetails;
 const BaseAttributes = (props) => {
     const { feature } = props;
-    return (react_1.default.createElement(BaseCard, { ...props, title: "Attributes" },
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Attributes" },
         react_1.default.createElement(Attributes_1.default, { ...props, attributes: feature })));
 };
 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);
-    const ExtraPanel = pm.evaluateExtensionPoint('Core-extraFeaturePanel', null, {
-        session,
-        feature,
-        model,
-    });
-    const m = mate;
-    return (react_1.default.createElement(BaseCard, { title: (0, util_2.generateTitle)(name, id, type) },
-        react_1.default.createElement(material_1.Typography, null, "Core details"),
-        react_1.default.createElement(CoreDetails, { ...props }),
-        m ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Divider, null),
-            react_1.default.createElement(material_1.Typography, null, "Mate details"),
-            react_1.default.createElement(CoreDetails, { ...props, feature: {
-                    ...m,
-                    start: m.start,
-                    end: m.end,
-                    refName: m.refName,
-                    uniqueId: `${uniqueId}-mate`,
-                } }))) : null,
-        react_1.default.createElement(material_1.Divider, null),
-        react_1.default.createElement(material_1.Typography, null, "Attributes"),
-        react_1.default.createElement(Attributes_1.default, { attributes: feature, ...props, omit: omit, omitSingleLevel: coreDetails }),
-        react_1.default.createElement(ErrorBoundary_1.ErrorBoundary, { FallbackComponent: e => react_1.default.createElement(ui_1.ErrorMessage, { error: e.error }) },
-            react_1.default.createElement(SequenceFeatureDetails_1.default, { ...props })),
-        ExtraPanel ? (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Divider, null),
-            react_1.default.createElement(BaseCard, { title: ExtraPanel.name },
-                react_1.default.createElement(ExtraPanel.Component, { ...props })))) : 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));
-}
 const BaseFeatureDetail = (0, mobx_react_1.observer)(function ({ model }) {
     const { error, featureData } = model;
     if (error) {
         return react_1.default.createElement(ui_1.ErrorMessage, { error: error });
     }
-    if (!featureData) {
+    else if (!featureData) {
         return null;
     }
-    // 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 snapshotting the
-    // featureData
-    const g = JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v)));
-    return (0, util_2.isEmpty)(g) ? null : react_1.default.createElement(FeatureDetails, { model: model, feature: g });
+    else {
+        // 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
+        // snapshotting the featureData
+        const featureData2 = (0, util_2.replaceUndefinedWithNull)(featureData);
+        return (0, util_1.isEmpty)(featureData2) ? null : (react_1.default.createElement(FeatureDetails_1.default, { model: model, feature: featureData2 }));
+    }
 });
 exports.default = BaseFeatureDetail;
-var Attributes_2 = require("./Attributes");
-Object.defineProperty(exports, "Attributes", { enumerable: true, get: function () { return __importDefault(Attributes_2).default; } });

package/BaseFeatureWidget/stateModelFactory.d.ts

@@ -76,6 +76,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
+    /**
+     * #volatile
+     */
     error: unknown;
 } & {
     /**

package/BaseFeatureWidget/stateModelFactory.js

@@ -11,6 +11,7 @@ const configuration_1 = require("../configuration");
 const util_1 = require("../util");
 const mst_1 = require("../util/types/mst");
 const model_1 = require("./SequenceFeatureDetails/model");
+const util_2 = require("./util");
 function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
     var _a;
     if (depth <= currentDepth) {
@@ -77,6 +78,9 @@ function stateModelFactory(pluginManager) {
         sequenceFeatureDetails: mobx_state_tree_1.types.optional((0, model_1.SequenceFeatureDetailsF)(), {}),
     })
         .volatile(() => ({
+        /**
+         * #volatile
+         */
         error: undefined,
     }))
         .actions(self => ({
@@ -163,7 +167,7 @@ function stateModelFactory(pluginManager) {
             // 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))),
+            finalizedFeatureData: (0, util_2.replaceUndefinedWithNull)(featureData),
             ...rest,
         };
     });

package/BaseFeatureWidget/util.d.ts

@@ -42,3 +42,4 @@ export declare function calculateUTRs2(cds: Feat[], parentFeat: Feat): {
     end: number;
 }[];
 export declare function ellipses(slug: string): string;
+export declare function replaceUndefinedWithNull(obj: Record<string, unknown>): any;

package/BaseFeatureWidget/util.js

@@ -6,6 +6,7 @@ exports.revlist = revlist;
 exports.calculateUTRs = calculateUTRs;
 exports.calculateUTRs2 = calculateUTRs2;
 exports.ellipses = ellipses;
+exports.replaceUndefinedWithNull = replaceUndefinedWithNull;
 function stitch(subfeats, sequence) {
     return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
 }
@@ -64,3 +65,6 @@ function calculateUTRs2(cds, parentFeat) {
 function ellipses(slug) {
     return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug;
 }
+function replaceUndefinedWithNull(obj) {
+    return JSON.parse(JSON.stringify(obj, (_, v) => (v === undefined ? null : v)));
+}

package/ReExports/modules.js

@@ -191,9 +191,9 @@ const MuiPrefixMUI = Object.fromEntries(Object.entries(LazyMUICore).map(([key, v
     `@mui/material/${key}`,
     value,
 ]));
-const Attributes = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./Attributes'))));
-const FeatureDetails = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./FeatureDetails'))));
-const BaseCard = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BaseCard'))));
+const Attributes = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../BaseFeatureWidget/BaseFeatureDetail/Attributes'))));
+const FeatureDetails = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../BaseFeatureWidget/BaseFeatureDetail/FeatureDetails'))));
+const BaseCard = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../BaseFeatureWidget/BaseFeatureDetail/BaseCard'))));
 const DataGridEntries = {
     DataGrid: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({ default: module.DataGrid }))),
     GridActionsCellItem: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.16.0",
+  "version": "2.16.1",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -72,5 +72,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
 }