@jbrowse/plugin-data-management 2.18.0 → 3.0.0

package/dist/PluginStoreWidget/components/PluginStoreWidget.js

@@ -15,18 +15,29 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const Clear_1 = __importDefault(require("@mui/icons-material/Clear"));
@@ -65,52 +76,29 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 const PluginStoreWidget = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const { plugins, error } = (0, util_2.useFetchPlugins)();
+    const { filterText } = model;
     const session = (0, util_1.getSession)(model);
     const { adminMode } = session;
     const { pluginManager } = (0, mobx_state_tree_1.getEnv)(model);
-    return (react_1.default.createElement("div", null,
-        adminMode && (react_1.default.createElement(react_1.default.Fragment, null,
-            !util_1.isElectron && (react_1.default.createElement("div", { className: classes.adminBadge },
-                react_1.default.createElement(InfoOutlined_1.default, { className: classes.mr }),
-                react_1.default.createElement(material_1.Typography, null,
-                    "You are using the ",
-                    react_1.default.createElement("code", null, "admin-server"),
-                    ". Any changes you make will be saved to your configuration file. You also have the ability to add custom plugins that are not in the store."))),
-            react_1.default.createElement(material_1.Button, { className: classes.customPluginButton, variant: "contained", onClick: () => {
-                    session.queueDialog(onClose => [
-                        AddCustomPluginDialog,
-                        {
-                            model,
-                            onClose,
-                        },
-                    ]);
-                } }, "Add custom plugin"))),
-        react_1.default.createElement(material_1.TextField, { label: "Filter plugins", value: model.filterText, onChange: event => {
-                model.setFilterText(event.target.value);
-            }, fullWidth: true, slotProps: {
-                input: {
-                    endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
-                        react_1.default.createElement(material_1.IconButton, { onClick: () => {
-                                model.clearFilterText();
-                            } },
-                            react_1.default.createElement(Clear_1.default, null)))),
-                },
-            } }),
-        react_1.default.createElement(material_1.Accordion, { defaultExpanded: true },
-            react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
-                react_1.default.createElement(material_1.Typography, { variant: "h5" }, "Installed plugins")),
-            react_1.default.createElement("div", { className: classes.m },
-                react_1.default.createElement(InstalledPluginsList_1.default, { pluginManager: pluginManager, model: model }))),
-        react_1.default.createElement(material_1.Accordion, { defaultExpanded: true },
-            react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
-                react_1.default.createElement(material_1.Typography, { variant: "h5" }, "Available plugins")),
-            error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : plugins ? (plugins
-                .filter(plugin => {
-                return (!(util_1.isElectron && plugin.cjsUrl) &&
-                    plugin.name
-                        .toLowerCase()
-                        .includes(model.filterText.toLowerCase()));
-            })
-                .map(plugin => (react_1.default.createElement(PluginCard_1.default, { key: plugin.name, plugin: plugin, model: model })))) : (react_1.default.createElement(ui_1.LoadingEllipses, null)))));
+    return ((0, jsx_runtime_1.jsxs)("div", { children: [adminMode && ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [!util_1.isElectron && ((0, jsx_runtime_1.jsxs)("div", { className: classes.adminBadge, children: [(0, jsx_runtime_1.jsx)(InfoOutlined_1.default, { className: classes.mr }), (0, jsx_runtime_1.jsxs)(material_1.Typography, { children: ["You are using the ", (0, jsx_runtime_1.jsx)("code", { children: "admin-server" }), ". Any changes you make will be saved to your configuration file. You also have the ability to add custom plugins that are not in the store."] })] })), (0, jsx_runtime_1.jsx)(material_1.Button, { className: classes.customPluginButton, variant: "contained", onClick: () => {
+                            session.queueDialog(onClose => [
+                                AddCustomPluginDialog,
+                                {
+                                    model,
+                                    onClose,
+                                },
+                            ]);
+                        }, children: "Add custom plugin" })] })), (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Filter plugins", value: filterText, onChange: event => {
+                    model.setFilterText(event.target.value);
+                }, fullWidth: true, slotProps: {
+                    input: {
+                        endAdornment: ((0, jsx_runtime_1.jsx)(material_1.InputAdornment, { position: "end", children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { onClick: () => {
+                                    model.clearFilterText();
+                                }, children: (0, jsx_runtime_1.jsx)(Clear_1.default, {}) }) })),
+                    },
+                } }), (0, jsx_runtime_1.jsxs)(material_1.Accordion, { defaultExpanded: true, children: [(0, jsx_runtime_1.jsx)(material_1.AccordionSummary, { expandIcon: (0, jsx_runtime_1.jsx)(ExpandMore_1.default, { className: classes.expandIcon }), children: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h5", children: "Installed plugins" }) }), (0, jsx_runtime_1.jsx)("div", { className: classes.m, children: (0, jsx_runtime_1.jsx)(InstalledPluginsList_1.default, { pluginManager: pluginManager, model: model }) })] }), (0, jsx_runtime_1.jsxs)(material_1.Accordion, { defaultExpanded: true, children: [(0, jsx_runtime_1.jsx)(material_1.AccordionSummary, { expandIcon: (0, jsx_runtime_1.jsx)(ExpandMore_1.default, { className: classes.expandIcon }), children: (0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h5", children: "Available plugins" }) }), error ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` })) : plugins ? (plugins
+                        .filter(plugin => !(util_1.isElectron && plugin.cjsUrl) &&
+                        plugin.name.toLowerCase().includes(filterText.toLowerCase()))
+                        .map(plugin => ((0, jsx_runtime_1.jsx)(PluginCard_1.default, { plugin: plugin, model: model }, plugin.name)))) : ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {}))] })] }));
 });
 exports.default = PluginStoreWidget;

package/dist/PluginStoreWidget/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/UCSCTrackHub/doConnect.js

@@ -7,9 +7,7 @@ const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const nanoid_1 = require("@jbrowse/core/util/nanoid");
 const ucscTrackHub_1 = require("./ucscTrackHub");
-function resolve(uri, baseUri) {
-    return new URL(uri, baseUri).href;
-}
+const util_2 = require("./util");
 async function doConnect(self) {
     var _a;
     const session = (0, util_1.getSession)(self);
@@ -17,7 +15,7 @@ async function doConnect(self) {
     try {
         const hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
         const hubFileText = await (0, io_1.openLocation)(hubFileLocation).readFile('utf8');
-        const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
+        const hubUri = (0, util_2.resolve)(hubFileLocation.uri, hubFileLocation.baseUri);
         const { assemblyManager } = session;
         if (hubFileText.includes('useOneFile on')) {
             const hub = new ucsc_hub_1.SingleFileHub(hubFileText);
@@ -29,14 +27,22 @@ async function doConnect(self) {
                     name: genomeName,
                     sequence: {
                         type: 'ReferenceSequenceTrack',
+                        metadata: {
+                            ...genome,
+                            ...(genome.data.htmlPath
+                                ? {
+                                    htmlPath: `<a href="${(0, util_2.resolve)(genome.data.htmlPath, hubUri)}">${genome.data.htmlPath}</a>`,
+                                }
+                                : {}),
+                        },
                         trackId: `${genomeName}-${(0, nanoid_1.nanoid)()}`,
                         adapter: {
                             type: 'TwoBitAdapter',
                             twoBitLocation: {
-                                uri: resolve(genome.data.twoBitPath, hubUri),
+                                uri: (0, util_2.resolve)(genome.data.twoBitPath, hubUri),
                             },
                             chromSizesLocation: {
-                                uri: resolve(genome.data.chromSizes, hubUri),
+                                uri: (0, util_2.resolve)(genome.data.chromSizes, hubUri),
                             },
                         },
                     },
@@ -49,6 +55,7 @@ async function doConnect(self) {
                 trackDbLoc: hubFileLocation,
                 assemblyName: genomeName,
                 sequenceAdapter,
+                baseUrl: hubUri,
             });
             self.addTrackConfs(tracksNew);
         }
@@ -58,17 +65,17 @@ async function doConnect(self) {
             if (!genomeFile) {
                 throw new Error('genomesFile not found on hub');
             }
-            const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
+            const hubUri = (0, util_2.resolve)(hubFileLocation.uri, hubFileLocation.baseUri);
             const genomesFileLocation = hubUri
                 ? {
-                    uri: resolve(genomeFile, hubUri),
+                    uri: (0, util_2.resolve)(genomeFile, hubUri),
                     locationType: 'UriLocation',
                 }
                 : {
                     localPath: genomeFile,
                     locationType: 'LocalPathLocation',
                 };
-            const genomesFile = await (0, ucscTrackHub_1.fetchGenomesFile)(genomesFileLocation);
+            const genomesFile = await (0, util_2.fetchGenomesFile)(genomesFileLocation);
             const map = {};
             for (const [genomeName, genome] of Object.entries(genomesFile.data)) {
                 const assemblyNames = (0, configuration_1.getConf)(self, 'assemblyNames');
@@ -94,13 +101,14 @@ async function doConnect(self) {
                         localPath: db,
                         locationType: 'LocalPathLocation',
                     };
-                const trackDb = await (0, ucscTrackHub_1.fetchTrackDbFile)(loc);
+                const trackDb = await (0, util_2.fetchTrackDbFile)(loc);
                 const sequenceAdapter = (0, configuration_1.getConf)(asm, ['sequence', 'adapter']);
                 const tracks = (0, ucscTrackHub_1.generateTracks)({
                     trackDb,
                     trackDbLoc: loc,
                     assemblyName: genomeName,
                     sequenceAdapter,
+                    baseUrl: hubUri,
                 });
                 self.addTrackConfs(tracks);
                 map[genomeName] = tracks.length;

package/dist/UCSCTrackHub/model.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/UCSCTrackHub/ucscTrackHub.d.ts

@@ -1,29 +1,11 @@
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { TrackDbFile } from '@gmod/ucsc-hub';
 import type { FileLocation } from '@jbrowse/core/util';
-export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
-export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
-export declare function makeLoc(first: string, base: {
-    uri: string;
-    baseUri?: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLocAlt(first: string, alt: string, base: {
-    uri: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLoc2(first: string, alt?: string): {
-    uri: string | undefined;
-    locationType: string;
-};
-export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }: {
+export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }: {
     trackDb: TrackDbFile;
     trackDbLoc: FileLocation;
     assemblyName: string;
     sequenceAdapter: any;
+    baseUrl: string;
 }): ({
     trackId: string;
     assemblyNames: string[];
@@ -31,13 +13,17 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     name: string;
     description: string;
     category: string[] | undefined;
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
-    name: string | undefined;
+    name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         bamLocation: {
@@ -53,18 +39,23 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         cramLocation: {
@@ -78,21 +69,26 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         sequenceAdapter: any;
         bamLocation?: undefined;
         index?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
-        bigBedLocation: {
+        bigWigLocation: {
             uri: string | undefined;
             locationType: string;
         };
@@ -101,20 +97,25 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
-        bigWigLocation: {
+        bigBedLocation: {
             uri: string | undefined;
             locationType: string;
         };
@@ -123,17 +124,22 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         vcfGzLocation: {
@@ -150,17 +156,22 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         hicLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 } | {
     trackId: string;
     assemblyNames: string[];
     type: string;
     name: string;
     description: string | undefined;
-    category: string[];
     adapter: {
         type: string;
         hicLocation: {
@@ -172,9 +183,15 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         cramLocation?: undefined;
         craiLocation?: undefined;
         sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
         bigWigLocation?: undefined;
+        bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
     };
+    metadata: {
+        ucscConfig: {
+            html?: string | undefined;
+        };
+    };
+    category: (string | undefined)[];
 })[];
 export { default as ucscAssemblies } from './ucscAssemblies';