@jbrowse/plugin-data-management 2.13.0 → 2.14.0

package/esm/PluginStoreWidget/components/InstalledPlugin.js

@@ -19,13 +19,12 @@ function LockedPlugin() {
         React.createElement(LockIcon, null)));
 }
 const InstalledPlugin = observer(function ({ plugin, model, }) {
-    var _a;
     const [dialogPlugin, setDialogPlugin] = useState();
     const { pluginManager } = getEnv(model);
     const session = getSession(model);
     const { jbrowse, adminMode } = session;
     const isSessionPlugin = isSessionWithSessionPlugins(session)
-        ? (_a = session.sessionPlugins) === null || _a === void 0 ? void 0 : _a.some(p => pluginManager.pluginMetadata[plugin.name].url === p.url)
+        ? session.sessionPlugins.some(p => { var _a; return ((_a = pluginManager.pluginMetadata[plugin.name]) === null || _a === void 0 ? void 0 : _a.url) === p.url; })
         : false;
     return (React.createElement(React.Fragment, null,
         dialogPlugin ? (React.createElement(Suspense, { fallback: null },
@@ -42,7 +41,9 @@ const InstalledPlugin = observer(function ({ plugin, model, }) {
                     setDialogPlugin(undefined);
                 } }))) : null,
         React.createElement(ListItem, { key: plugin.name },
-            adminMode || isSessionPlugin ? (React.createElement(IconButton, { "data-testid": `removePlugin-${plugin.name}`, onClick: () => setDialogPlugin(plugin.name) },
+            adminMode || isSessionPlugin ? (React.createElement(IconButton, { "data-testid": `removePlugin-${plugin.name}`, onClick: () => {
+                    setDialogPlugin(plugin.name);
+                } },
                 React.createElement(CloseIcon, null))) : (React.createElement(LockedPlugin, null)),
             React.createElement(Typography, null, plugin.name))));
 });

package/esm/PluginStoreWidget/components/PluginCard.js

@@ -30,10 +30,10 @@ const PluginCard = observer(function PluginCard({ plugin, model, adminMode, }) {
     const session = getSession(model);
     const { pluginManager } = getEnv(model);
     const { runtimePluginDefinitions } = pluginManager;
+    // @ts-expect-error
     const isInstalled = runtimePluginDefinitions.some(d => d.url === plugin.url);
     const [tempDisabled, setTempDisabled] = useState(false);
     const disableButton = isInstalled || tempDisabled;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const rootModel = getParent(model, 3);
     const { jbrowse } = rootModel;
     return (React.createElement(Card, { variant: "outlined", key: plugin.name, className: classes.card },

package/esm/PluginStoreWidget/components/PluginStoreWidget.js

@@ -45,12 +45,20 @@ const PluginStoreWidget = observer(function ({ model, }) {
                     "You are using the ",
                     React.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.createElement(Button, { className: classes.customPluginButton, variant: "contained", onClick: () => setOpen(true) }, "Add custom plugin"),
+            React.createElement(Button, { className: classes.customPluginButton, variant: "contained", onClick: () => {
+                    setOpen(true);
+                } }, "Add custom plugin"),
             open ? (React.createElement(Suspense, { fallback: null },
-                React.createElement(AddCustomPluginDialog, { onClose: () => setOpen(false), model: model }))) : null)),
-        React.createElement(TextField, { label: "Filter plugins", value: model.filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
+                React.createElement(AddCustomPluginDialog, { onClose: () => {
+                        setOpen(false);
+                    }, model: model }))) : null)),
+        React.createElement(TextField, { label: "Filter plugins", value: model.filterText, onChange: event => {
+                model.setFilterText(event.target.value);
+            }, fullWidth: true, InputProps: {
                 endAdornment: (React.createElement(InputAdornment, { position: "end" },
-                    React.createElement(IconButton, { onClick: () => model.clearFilterText() },
+                    React.createElement(IconButton, { onClick: () => {
+                            model.clearFilterText();
+                        } },
                         React.createElement(ClearIcon, null)))),
             } }),
         React.createElement(Accordion, { defaultExpanded: true },

package/esm/PluginStoreWidget/model.d.ts

@@ -6,7 +6,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
+    /**
+     * #action
+     */
     clearFilterText(): void;
+    /**
+     * #action
+     */
     setFilterText(newText: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type PluginStoreStateModel = ReturnType<typeof stateModelFactory>;

package/esm/PluginStoreWidget/model.js

@@ -3,15 +3,33 @@ import { ElementId } from '@jbrowse/core/util/types/mst';
 export default function stateModelFactory(pluginManager) {
     return types
         .model('PluginStoreModel', {
+        /**
+         * #property
+         */
         id: ElementId,
+        /**
+         * #property
+         */
         type: types.literal('PluginStoreWidget'),
+        /**
+         * #property
+         */
         filterText: '',
+        /**
+         * #property
+         */
         view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .actions(self => ({
+        /**
+         * #action
+         */
         clearFilterText() {
             self.filterText = '';
         },
+        /**
+         * #action
+         */
         setFilterText(newText) {
             self.filterText = newText;
         },

package/esm/ucsc-trackhub/doConnect.d.ts

@@ -1 +1,5 @@
-export declare function doConnect(self: any): Promise<void>;
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function doConnect(self: {
+    configuration: AnyConfigurationModel;
+    addTrackConfs: (arg: Record<string, unknown>[]) => void;
+}): Promise<void>;

package/esm/ucsc-trackhub/doConnect.js

@@ -7,7 +7,6 @@ import { nanoid } from '@jbrowse/core/util/nanoid';
 function resolve(uri, baseUri) {
     return new URL(uri, baseUri).href;
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 export async function doConnect(self) {
     var _a;
     const session = getSession(self);

package/esm/ucsc-trackhub/model.d.ts

@@ -56,9 +56,29 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
-    addTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): any[];
-    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
+    addTrackConf(trackConf: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
+    addTrackConfs(trackConfs: (({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
+    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {
     /**

package/esm/ucsc-trackhub/ucscTrackHub.d.ts

@@ -35,8 +35,8 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     trackId: string;
     assemblyNames: string[];
     type: string;
-    name: string;
-    description: string;
+    name: string | undefined;
+    description: string | undefined;
     category: string[];
     adapter: {
         type: string;
@@ -63,7 +63,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     assemblyNames: string[];
     type: string;
     name: string;
-    description: string;
+    description: string | undefined;
     category: string[];
     adapter: {
         type: string;
@@ -88,7 +88,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     assemblyNames: string[];
     type: string;
     name: string;
-    description: string;
+    description: string | undefined;
     category: string[];
     adapter: {
         type: string;
@@ -110,7 +110,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     assemblyNames: string[];
     type: string;
     name: string;
-    description: string;
+    description: string | undefined;
     category: string[];
     adapter: {
         type: string;
@@ -132,7 +132,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     assemblyNames: string[];
     type: string;
     name: string;
-    description: string;
+    description: string | undefined;
     category: string[];
     adapter: {
         type: string;
@@ -159,7 +159,7 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
     assemblyNames: string[];
     type: string;
     name: string;
-    description: string;
+    description: string | undefined;
     category: string[];
     adapter: {
         type: string;

package/esm/ucsc-trackhub/ucscTrackHub.js

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import { isUriLocation, notEmpty, objectHash, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks';
@@ -50,8 +49,7 @@ export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdap
         do {
             currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
             if (currentTrackName) {
-                ;
-                [currentTrackName] = currentTrackName.split(' ');
+                currentTrackName = currentTrackName.split(' ')[0];
                 parentTracks.push(trackDb.data[currentTrackName]);
             }
         } while (currentTrackName);
@@ -81,7 +79,7 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
     const bigDataUrl = track.data.bigDataUrl || '';
     const bigDataIdx = track.data.bigDataIndex || '';
     const isUri = isUriLocation(trackDbLoc);
-    let baseTrackType = (trackType === null || trackType === void 0 ? void 0 : trackType.split(' ')[0]) || '';
+    let baseTrackType = trackType.split(' ')[0] || '';
     if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
         baseTrackType = 'cram';
     }
@@ -100,8 +98,8 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
                     bamLocation: bigDataLocation,
                     index: {
                         location: isUri
-                            ? makeLocAlt(bigDataIdx, bigDataUrl + '.bai', trackDbLoc)
-                            : makeLoc2(bigDataIdx, bigDataUrl + '.bai'),
+                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
+                            : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
                     },
                 },
             };
@@ -115,8 +113,8 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
                     type: 'CramAdapter',
                     cramLocation: bigDataLocation,
                     craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
-                        : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
+                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
+                        : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
                     sequenceAdapter,
                 },
             };
@@ -160,8 +158,8 @@ function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapt
                     vcfGzLocation: bigDataLocation,
                     index: {
                         location: isUri
-                            ? makeLocAlt(bigDataIdx, bigDataUrl + '.tbi', trackDbLoc)
-                            : makeLoc2(bigDataIdx, bigDataUrl + '.tbi'),
+                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
+                            : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
                     },
                 },
             };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.13.0",
+  "version": "2.14.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/data-management",
+    "test": "cd ../..; jest --passWithNoTests plugins/data-management",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -60,5 +60,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }