@jbrowse/plugin-authentication 4.3.0 → 5.0.0-beta.1

package/esm/ExternalTokenModel/ExternalTokenEntryForm.d.ts

@@ -1,4 +1,4 @@
 export declare const ExternalTokenEntryForm: ({ internetAccountId, handleClose, }: {
     internetAccountId: string;
     handleClose: (token?: string) => void;
-}) => import("react/jsx-runtime").JSX.Element;
+}) => import("react").JSX.Element;

package/esm/ExternalTokenModel/ExternalTokenEntryForm.js

@@ -1,20 +1,16 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { jsx as _jsx } from "react/jsx-runtime";
 import { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { Button, DialogActions, DialogContent, TextField } from '@mui/material';
+import { SubmitDialog } from '@jbrowse/core/ui';
+import { TextField } from '@mui/material';
 export const ExternalTokenEntryForm = ({ internetAccountId, handleClose, }) => {
     const [token, setToken] = useState('');
-    return (_jsxs(Dialog, { open: true, maxWidth: "xl", "data-testid": "externalToken-form", onClose: () => {
+    return (_jsx(SubmitDialog, { open: true, maxWidth: "xl", "data-testid": "externalToken-form", title: `Enter token for ${internetAccountId}`, submitText: "Add", submitDisabled: !token, onCancel: () => {
             handleClose();
-        }, title: `Enter token for ${internetAccountId}`, children: [_jsx(DialogContent, { style: { display: 'flex', flexDirection: 'column' }, children: _jsx(TextField, { required: true, label: "Enter Token", variant: "outlined", onChange: event => {
-                        setToken(event.target.value);
-                    }, margin: "dense", slotProps: {
-                        htmlInput: { 'data-testid': 'entry-externalToken' },
-                    } }) }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", disabled: !token, onClick: () => {
-                            if (token) {
-                                handleClose(token);
-                            }
-                        }, children: "Add" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
+        }, onSubmit: () => {
+            handleClose(token);
+        }, children: _jsx(TextField, { required: true, label: "Enter Token", variant: "outlined", onChange: event => {
+                setToken(event.target.value);
+            }, margin: "dense", slotProps: {
+                htmlInput: { 'data-testid': 'entry-externalToken' },
+            } }) }));
 };

package/esm/ExternalTokenModel/configSchema.d.ts

@@ -1,35 +1,54 @@
 import type { Instance } from '@jbrowse/mobx-state-tree';
+/**
+ * #config ExternalTokenInternetAccount
+ *
+ * #example
+ * For a token the user pastes in, or that an embedding portal hands over.
+ * JBrowse does not obtain the token itself — it prompts for one, then sends it
+ * on every request to a matching domain.
+ * ```js
+ * {
+ *   type: 'ExternalTokenInternetAccount',
+ *   internetAccountId: 'portalToken',
+ *   name: 'Data portal token',
+ *   domains: ['api.myportal.org'],
+ * }
+ * ```
+ */
 declare const ExternalTokenConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    validateWithHEAD: {
-        description: string;
-        type: string;
-        defaultValue: boolean;
+    /**
+     * #slot
+     */
+    readonly validateWithHEAD: {
+        readonly description: "validate the token with a HEAD request before using it";
+        readonly type: "boolean";
+        readonly defaultValue: true;
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    name: {
-        description: string;
-        type: string;
-        defaultValue: string;
+    readonly name: {
+        readonly description: "descriptive name of the internet account";
+        readonly type: "string";
+        readonly defaultValue: "";
     };
-    description: {
-        description: string;
-        type: string;
-        defaultValue: string;
+    readonly description: {
+        readonly description: "a description of the internet account";
+        readonly type: "string";
+        readonly defaultValue: "";
     };
-    authHeader: {
-        description: string;
-        type: string;
-        defaultValue: string;
+    readonly authHeader: {
+        readonly description: "request header for credentials";
+        readonly type: "string";
+        readonly defaultValue: "Authorization";
     };
-    tokenType: {
-        description: string;
-        type: string;
-        defaultValue: string;
+    readonly tokenType: {
+        readonly description: "a custom name for a token to include in the header";
+        readonly type: "string";
+        readonly defaultValue: "";
     };
-    domains: {
-        description: string;
-        type: string;
-        defaultValue: never[];
+    readonly domains: {
+        readonly description: "array of valid domains the url can contain to use this account";
+        readonly type: "stringArray";
+        readonly defaultValue: readonly [];
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "internetAccountId">>, undefined>>;
 export type ExternalTokenInternetAccountConfigModel = typeof ExternalTokenConfigSchema;

package/esm/ExternalTokenModel/configSchema.js

@@ -1,13 +1,34 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { BaseInternetAccountConfig } from '@jbrowse/core/pluggableElementTypes/models';
-function x() { }
+/**
+ * #config ExternalTokenInternetAccount
+ *
+ * #example
+ * For a token the user pastes in, or that an embedding portal hands over.
+ * JBrowse does not obtain the token itself — it prompts for one, then sends it
+ * on every request to a matching domain.
+ * ```js
+ * {
+ *   type: 'ExternalTokenInternetAccount',
+ *   internetAccountId: 'portalToken',
+ *   name: 'Data portal token',
+ *   domains: ['api.myportal.org'],
+ * }
+ * ```
+ */
 const ExternalTokenConfigSchema = ConfigurationSchema('ExternalTokenInternetAccount', {
+    /**
+     * #slot
+     */
     validateWithHEAD: {
         description: 'validate the token with a HEAD request before using it',
         type: 'boolean',
         defaultValue: true,
     },
 }, {
+    /**
+     * #baseConfiguration
+     */
     baseConfiguration: BaseInternetAccountConfig,
     explicitlyTyped: true,
 });

package/esm/ExternalTokenModel/index.js

@@ -1,2 +1,2 @@
-export { default as configSchema } from "./configSchema.js";
-export { default as modelFactory } from "./model.js";
+export { default as configSchema } from './configSchema.js';
+export { default as modelFactory } from './model.js';

package/esm/ExternalTokenModel/model.d.ts

@@ -1,71 +1,46 @@
 import type { ExternalTokenInternetAccountConfigModel } from './configSchema.ts';
-import type { UriLocation } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
-declare const stateModelFactory: (configSchema: ExternalTokenInternetAccountConfigModel) => import("@jbrowse/mobx-state-tree").IModelType<{
+/**
+ * #stateModel ExternalTokenInternetAccount
+ * Internet account that authenticates requests with a user-supplied external
+ * token, prompting for the token via a dialog and optionally validating it with
+ * a HEAD request. See
+ * [TokenEntryInternetAccount](../tokenentryinternetaccount) for the shared
+ * behavior.
+ */
+declare const stateModelFactory: (configSchema: ExternalTokenInternetAccountConfigModel) => import("@jbrowse/mobx-state-tree").IModelType<Omit<{
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            description: string;
-            type: string;
-            defaultValue: string;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly name: {
+            readonly description: "descriptive name of the internet account";
+            readonly type: "string";
+            readonly defaultValue: "";
         };
-        description: {
-            description: string;
-            type: string;
-            defaultValue: string;
+        readonly description: {
+            readonly description: "a description of the internet account";
+            readonly type: "string";
+            readonly defaultValue: "";
         };
-        authHeader: {
-            description: string;
-            type: string;
-            defaultValue: string;
+        readonly authHeader: {
+            readonly description: "request header for credentials";
+            readonly type: "string";
+            readonly defaultValue: "Authorization";
         };
-        tokenType: {
-            description: string;
-            type: string;
-            defaultValue: string;
+        readonly tokenType: {
+            readonly description: "a custom name for a token to include in the header";
+            readonly type: "string";
+            readonly defaultValue: "";
         };
-        domains: {
-            description: string;
-            type: string;
-            defaultValue: never[];
+        readonly domains: {
+            readonly description: "array of valid domains the url can contain to use this account";
+            readonly type: "stringArray";
+            readonly defaultValue: readonly [];
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "internetAccountId">>;
-} & {
-    type: import("@jbrowse/mobx-state-tree").ISimpleType<"ExternalTokenInternetAccount">;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        validateWithHEAD: {
-            description: string;
-            type: string;
-            defaultValue: boolean;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            description: string;
-            type: string;
-            defaultValue: string;
-        };
-        description: {
-            description: string;
-            type: string;
-            defaultValue: string;
-        };
-        authHeader: {
-            description: string;
-            type: string;
-            defaultValue: string;
-        };
-        tokenType: {
-            description: string;
-            type: string;
-            defaultValue: string;
-        };
-        domains: {
-            description: string;
-            type: string;
-            defaultValue: never[];
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "internetAccountId">>, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "internetAccountId">>>;
+}, "configuration" | "type"> & {
+    type: import("@jbrowse/mobx-state-tree").ILiteralType<"ExternalTokenInternetAccount">;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").IConfigurationReference<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
 }, {
     readonly name: string;
     readonly description: string;
@@ -74,22 +49,21 @@ declare const stateModelFactory: (configSchema: ExternalTokenInternetAccountConf
     readonly tokenType: string;
     readonly domains: string[];
     readonly toggleContents: React.ReactNode;
-    readonly SelectorComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
     readonly selectorLabel: string | undefined;
+    readonly showInFileSelector: boolean;
 } & {
-    handlesLocation(location: UriLocation): boolean;
+    handlesLocation(location: import("@jbrowse/core/util").UriLocation): boolean;
     readonly tokenKey: string;
 } & {
     getTokenFromUser(_resolve: (token: string) => void, _reject: (error: Error) => void): void;
     storeToken(token: string): void;
-    removeToken(): void;
-    retrieveToken(): string | null;
-    validateToken(token: string, _loc: UriLocation): Promise<string>;
+    retrieveToken(): string | undefined;
+    validateToken(token: string, _loc: import("@jbrowse/core/util").UriLocation): Promise<string>;
 } & {
-    getToken(location?: UriLocation): Promise<string>;
+    removeToken(): void;
+    getToken(location?: import("@jbrowse/core/util").UriLocation): Promise<string>;
 } & {
     addAuthHeaderToInit(init?: RequestInit, token?: string): {
-        headers: Headers;
         body?: BodyInit | null;
         cache?: RequestCache;
         credentials?: RequestCredentials;
@@ -103,23 +77,25 @@ declare const stateModelFactory: (configSchema: ExternalTokenInternetAccountConf
         referrerPolicy?: ReferrerPolicy;
         signal?: AbortSignal | null;
         window?: null;
+        headers: Headers;
     };
-    getPreAuthorizationInformation(location: UriLocation): Promise<{
+    fetchWithToken(loc: import("@jbrowse/core/util").UriLocation | undefined, run: (token: string) => Promise<Response>): Promise<Response>;
+    getPreAuthorizationInformation(location: import("@jbrowse/core/util").UriLocation): Promise<{
         internetAccountType: string;
         authInfo: {
             token: string;
-            configuration: any;
+            configuration: import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>;
         };
     }>;
 } & {
-    getFetcher(loc?: UriLocation): (input: RequestInfo, init?: RequestInit) => Promise<Response>;
+    getFetcher(loc?: import("@jbrowse/core/util").UriLocation): (input: RequestInfo, init?: RequestInit) => Promise<Response>;
 } & {
-    openLocation(location: UriLocation): import("@jbrowse/core/util/io").RemoteFileWithRangeCache;
+    openLocation(location: import("@jbrowse/core/util").UriLocation): import("@gmod/range-cache-filehandle").RemoteFileWithRangeCache;
 } & {
     readonly validateWithHEAD: boolean;
 } & {
     getTokenFromUser(resolve: (token: string) => void, reject: (error: Error) => void): void;
-    validateToken(token: string, location: UriLocation): Promise<string>;
+    validateToken(token: string, location: import("@jbrowse/core/util").UriLocation): Promise<string>;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;
 export type ExternalTokenStateModel = ReturnType<typeof stateModelFactory>;

package/esm/ExternalTokenModel/model.js

@@ -1,55 +1,12 @@
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
-import { InternetAccount } from '@jbrowse/core/pluggableElementTypes/models';
-import { getRoot, types } from '@jbrowse/mobx-state-tree';
-import { ExternalTokenEntryForm } from "./ExternalTokenEntryForm.js";
-const stateModelFactory = (configSchema) => {
-    return InternetAccount.named('ExternalTokenInternetAccount')
-        .props({
-        type: types.literal('ExternalTokenInternetAccount'),
-        configuration: ConfigurationReference(configSchema),
-    })
-        .views(self => ({
-        get validateWithHEAD() {
-            return getConf(self, 'validateWithHEAD');
-        },
-    }))
-        .actions(self => ({
-        getTokenFromUser(resolve, reject) {
-            const { session } = getRoot(self);
-            session.queueDialog((doneCallback) => [
-                ExternalTokenEntryForm,
-                {
-                    internetAccountId: self.internetAccountId,
-                    handleClose: (token) => {
-                        if (token) {
-                            resolve(token);
-                        }
-                        else {
-                            reject(new Error('user cancelled entry'));
-                        }
-                        doneCallback();
-                    },
-                },
-            ]);
-        },
-        async validateToken(token, location) {
-            if (!self.validateWithHEAD) {
-                return token;
-            }
-            const newInit = self.addAuthHeaderToInit({ method: 'HEAD' }, token);
-            const response = await fetch(location.uri, newInit);
-            if (!response.ok) {
-                let errorMessage;
-                try {
-                    errorMessage = await response.text();
-                }
-                catch (error) {
-                    errorMessage = '';
-                }
-                throw new Error(`Token could not be validated — ${response.status} ${errorMessage ? ` (${errorMessage})` : ''}`);
-            }
-            return token;
-        },
-    }));
-};
+import { ExternalTokenEntryForm } from '../lazyLoginForms.js';
+import { tokenEntryModelFactory } from '../tokenEntryModelFactory.js';
+/**
+ * #stateModel ExternalTokenInternetAccount
+ * Internet account that authenticates requests with a user-supplied external
+ * token, prompting for the token via a dialog and optionally validating it with
+ * a HEAD request. See
+ * [TokenEntryInternetAccount](../tokenentryinternetaccount) for the shared
+ * behavior.
+ */
+const stateModelFactory = (configSchema) => tokenEntryModelFactory('ExternalTokenInternetAccount', 'ExternalTokenInternetAccount', configSchema, ExternalTokenEntryForm);
 export default stateModelFactory;

package/esm/GoogleDriveOAuthModel/GoogleDriveFilehandle.d.ts

@@ -1,15 +1,8 @@
 import { RemoteFileWithRangeCache } from '@jbrowse/core/util/io';
-import type { FilehandleOptions, Stats } from 'generic-filehandle2';
-export interface RequestInitWithMetadata extends RequestInit {
-    metadataOnly?: boolean;
-}
-interface GoogleDriveFilehandleOptions extends FilehandleOptions {
-    fetch(input: RequestInfo, opts?: RequestInitWithMetadata): Promise<Response>;
-}
+import type { RequestInitWithMetadata } from './model.tsx';
+import type { Stats } from 'generic-filehandle2';
 export declare class GoogleDriveFile extends RemoteFileWithRangeCache {
     private statsPromise;
-    constructor(source: string, opts: GoogleDriveFilehandleOptions);
     fetch(input: RequestInfo, opts?: RequestInitWithMetadata): Promise<Response>;
     stat(): Promise<Stats>;
 }
-export {};

package/esm/GoogleDriveOAuthModel/GoogleDriveFilehandle.js

@@ -1,16 +1,37 @@
 import { RemoteFileWithRangeCache } from '@jbrowse/core/util/io';
 export class GoogleDriveFile extends RemoteFileWithRangeCache {
     statsPromise;
-    constructor(source, opts) {
-        super(source, opts);
-        this.statsPromise = this.fetch(source, {
-            metadataOnly: true,
-        }).then(response => response.json());
-    }
+    // Override to widen opts type so metadataOnly can be passed through to getFetcher
     async fetch(input, opts) {
         return super.fetch(input, opts);
     }
+    // Fetched on demand rather than from the constructor: openLocation builds a
+    // filehandle for every file a track opens and most are read by byte range
+    // only, so an eager metadata request cost a round trip (and a token
+    // validation) per handle for a size nobody asked for.
     async stat() {
+        this.statsPromise ??= this.fetch(this.url, { metadataOnly: true })
+            .then(response => response.json())
+            // Drive serializes its int64 fields as JSON strings, so `size` arrives as
+            // "12345" — passed on untouched it satisfies `Stats` in name only, and
+            // the first caller to do arithmetic on it concatenates instead
+            .then(({ size }) => {
+            const stats = { size: Number(size) };
+            // This is the only place the size of a Drive file is ever observed: the
+            // metadata request carries no Content-Range, so the chunk cache's own
+            // way of learning it never fires here, and without it every bgzf
+            // reader's deliberate over-read of the final block goes to the network
+            // to be refused. Drive omits `size` for a file that has none, and
+            // recordSize drops the NaN that produces rather than caching it.
+            this.recordSize(stats.size);
+            return stats;
+        })
+            // a cached rejection is permanent, so one dropped request would take
+            // every later stat() of this file with it
+            .catch((error) => {
+            this.statsPromise = undefined;
+            throw error;
+        });
         return this.statsPromise;
     }
 }

package/esm/GoogleDriveOAuthModel/GoogleDriveIcon.d.ts

@@ -1,2 +1,2 @@
 import type { SvgIconProps } from '@mui/material';
-export default function GoogleDriveIcon(props: SvgIconProps): import("react/jsx-runtime").JSX.Element;
+export default function GoogleDriveIcon(props: SvgIconProps): import("react").JSX.Element;