@jbrowse/plugin-authentication 2.2.0

package/esm/GoogleDriveOAuthModel/model.js

@@ -0,0 +1,108 @@
+import React from 'react';
+import { ConfigurationReference } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+import { RemoteFileWithRangeCache } from '@jbrowse/core/util/io';
+import { SvgIcon } from '@mui/material';
+import baseModel from '../OAuthModel/model';
+import { configSchema as OAuthConfigSchema } from '../OAuthModel';
+export class GoogleDriveFile extends RemoteFileWithRangeCache {
+    constructor(source, opts) {
+        super(source, opts);
+        this.statsPromise = this.fetch(source, {
+            metadataOnly: true,
+        }).then((response) => response.json());
+    }
+    async fetch(input, opts) {
+        return super.fetch(input, opts);
+    }
+    async stat() {
+        return this.statsPromise;
+    }
+}
+function GoogleDriveIcon(props) {
+    return (React.createElement(SvgIcon, { ...props },
+        React.createElement("path", { d: "M7.71,3.5L1.15,15L4.58,21L11.13,9.5M9.73,15L6.3,21H19.42L22.85,15M22.28,14L15.42,2H8.58L8.57,2L15.43,14H22.28Z" })));
+}
+async function getDescriptiveErrorMessage(response) {
+    let errorMessage;
+    try {
+        errorMessage = await response.text();
+    }
+    catch (error) {
+        errorMessage = '';
+    }
+    if (errorMessage) {
+        let errorMessageParsed;
+        try {
+            errorMessageParsed = JSON.parse(errorMessage);
+        }
+        catch (error) {
+            errorMessageParsed = undefined;
+        }
+        if (errorMessageParsed) {
+            errorMessage = errorMessageParsed.error.message;
+        }
+    }
+    return `Network response failure — ${response.status} (${response.statusText})${errorMessage ? ` (${errorMessage})` : ''}`;
+}
+const stateModelFactory = (configSchema) => {
+    return baseModel(OAuthConfigSchema)
+        .named('GoogleDriveOAuthInternetAccount')
+        .props({
+        type: types.literal('GoogleDriveOAuthInternetAccount'),
+        configuration: ConfigurationReference(configSchema),
+    })
+        .views(() => ({
+        get toggleContents() {
+            return React.createElement(GoogleDriveIcon, null);
+        },
+        get selectorLabel() {
+            return 'Enter Google Drive share link';
+        },
+    }))
+        .actions(self => ({
+        getFetcher(location) {
+            return async (input, init) => {
+                const urlId = String(input).match(/[-\w]{25,}/);
+                const driveUrl = new URL(`https://www.googleapis.com/drive/v3/files/${urlId}`);
+                const searchParams = new URLSearchParams();
+                if (init === null || init === void 0 ? void 0 : init.metadataOnly) {
+                    searchParams.append('fields', 'size');
+                }
+                else {
+                    searchParams.append('alt', 'media');
+                }
+                driveUrl.search = searchParams.toString();
+                const authToken = await self.getToken(location);
+                const newInit = self.addAuthHeaderToInit({ ...init, method: 'GET', credentials: 'same-origin' }, authToken);
+                const response = await fetch(driveUrl.toString(), newInit);
+                if (!response.ok) {
+                    const message = await getDescriptiveErrorMessage(response);
+                    throw new Error(message);
+                }
+                return response;
+            };
+        },
+        openLocation(location) {
+            return new GoogleDriveFile(location.uri, {
+                fetch: this.getFetcher(location),
+            });
+        },
+        async validateToken(token, location) {
+            const urlId = location.uri.match(/[-\w]{25,}/);
+            const response = await fetch(`https://www.googleapis.com/drive/v3/files/${urlId}`, {
+                headers: {
+                    Authorization: `Bearer ${token}`,
+                    'Content-Type': 'application/x-www-form-urlencoded',
+                },
+            });
+            if (!response.ok) {
+                const message = await getDescriptiveErrorMessage(response);
+                throw new Error(`Token could not be validated. ${message}`);
+            }
+            return token;
+        },
+    }));
+};
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/GoogleDriveOAuthModel/model.js.map

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package/esm/HTTPBasicModel/HTTPBasicLoginForm.d.ts

@@ -0,0 +1,5 @@
+/// <reference types="react" />
+export declare const HTTPBasicLoginForm: ({ internetAccountId, handleClose, }: {
+    internetAccountId: string;
+    handleClose: (arg?: string) => void;
+}) => JSX.Element;

package/esm/HTTPBasicModel/HTTPBasicLoginForm.js

@@ -0,0 +1,28 @@
+import React, { useState } from 'react';
+import { Button, Dialog, DialogContent, DialogTitle, DialogActions, TextField, } from '@mui/material';
+export const HTTPBasicLoginForm = ({ internetAccountId, handleClose, }) => {
+    const [username, setUsername] = useState('');
+    const [password, setPassword] = useState('');
+    function onSubmit(event) {
+        if (username && password) {
+            handleClose(btoa(`${username}:${password}`));
+        }
+        else {
+            handleClose();
+        }
+        event.preventDefault();
+    }
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Dialog, { open: true, maxWidth: "xl", "data-testid": "login-httpbasic" },
+            React.createElement(DialogTitle, null,
+                "Log In for ",
+                internetAccountId),
+            React.createElement("form", { onSubmit: onSubmit },
+                React.createElement(DialogContent, { style: { display: 'flex', flexDirection: 'column' } },
+                    React.createElement(TextField, { required: true, label: "Username", variant: "outlined", inputProps: { 'data-testid': 'login-httpbasic-username' }, onChange: event => setUsername(event.target.value), margin: "dense" }),
+                    React.createElement(TextField, { required: true, label: "Password", type: "password", autoComplete: "current-password", variant: "outlined", inputProps: { 'data-testid': 'login-httpbasic-password' }, onChange: event => setPassword(event.target.value), margin: "dense" })),
+                React.createElement(DialogActions, null,
+                    React.createElement(Button, { variant: "contained", color: "primary", type: "submit" }, "Submit"),
+                    React.createElement(Button, { variant: "contained", type: "submit", onClick: () => handleClose() }, "Cancel"))))));
+};
+//# sourceMappingURL=HTTPBasicLoginForm.js.map

package/esm/HTTPBasicModel/HTTPBasicLoginForm.js.map

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package/esm/HTTPBasicModel/configSchema.d.ts

@@ -0,0 +1,5 @@
+import { Instance } from 'mobx-state-tree';
+declare const HTTPBasicConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare type HTTPBasicInternetAccountConfigModel = typeof HTTPBasicConfigSchema;
+export declare type HTTPBasicInternetAccountConfig = Instance<HTTPBasicInternetAccountConfigModel>;
+export default HTTPBasicConfigSchema;

package/esm/HTTPBasicModel/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { BaseInternetAccountConfig } from '@jbrowse/core/pluggableElementTypes/models';
+/**
+ * #config HTTPBasicInternetAccount
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const HTTPBasicConfigSchema = ConfigurationSchema('HTTPBasicInternetAccount', {
+    /**
+     * #slot
+     */
+    tokenType: {
+        description: 'a custom name for a token to include in the header',
+        type: 'string',
+        defaultValue: 'Basic',
+    },
+    /**
+     * #slot
+     */
+    validateWithHEAD: {
+        description: 'validate the token with a HEAD request before using it',
+        type: 'boolean',
+        defaultValue: true,
+    },
+}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: BaseInternetAccountConfig,
+    explicitlyTyped: true,
+});
+export default HTTPBasicConfigSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/HTTPBasicModel/configSchema.js.map

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package/esm/HTTPBasicModel/index.d.ts

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+export { default as modelFactory } from './model';

package/esm/HTTPBasicModel/index.js

@@ -0,0 +1,3 @@
+export { default as configSchema } from './configSchema';
+export { default as modelFactory } from './model';
+//# sourceMappingURL=index.js.map

package/esm/HTTPBasicModel/index.js.map

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package/esm/HTTPBasicModel/model.d.ts

@@ -0,0 +1,67 @@
+/// <reference types="react" />
+import { UriLocation } from '@jbrowse/core/util/types';
+import { HTTPBasicInternetAccountConfigModel } from './configSchema';
+import { Instance } from 'mobx-state-tree';
+declare const stateModelFactory: (configSchema: HTTPBasicInternetAccountConfigModel) => import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"HTTPBasicInternetAccount">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+}, {
+    readonly name: string;
+    readonly description: string;
+    readonly internetAccountId: string;
+    readonly authHeader: string;
+    readonly tokenType: string;
+    readonly domains: string[];
+    readonly toggleContents: import("react").ReactNode;
+    readonly SelectorComponent: import("@jbrowse/core/util/types").AnyReactComponentType | undefined;
+    readonly selectorLabel: string | undefined;
+} & {
+    handlesLocation(location: 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, location: UriLocation): Promise<string>;
+} & {
+    getToken(location?: UriLocation | undefined): Promise<string>;
+} & {
+    addAuthHeaderToInit(init: RequestInit | undefined, token: string): {
+        headers: Headers;
+        body?: BodyInit | null | undefined;
+        cache?: RequestCache | undefined;
+        credentials?: RequestCredentials | undefined;
+        integrity?: string | undefined;
+        keepalive?: boolean | undefined;
+        method?: string | undefined;
+        mode?: RequestMode | undefined;
+        redirect?: RequestRedirect | undefined;
+        referrer?: string | undefined;
+        referrerPolicy?: ReferrerPolicy | undefined;
+        signal?: AbortSignal | null | undefined;
+        window?: null | undefined;
+    };
+    getPreAuthorizationInformation(location: UriLocation): Promise<{
+        internetAccountType: string;
+        authInfo: {
+            token: string;
+            configuration: any;
+        };
+    }>;
+} & {
+    getFetcher(location?: UriLocation | undefined): (input: RequestInfo, init?: RequestInit | undefined) => Promise<Response>;
+} & {
+    openLocation(location: UriLocation): import("@jbrowse/core/util/io").RemoteFileWithRangeCache;
+} & {
+    readonly validateWithHEAD: boolean;
+} & {
+    getTokenFromUser(resolve: (token: string) => void, reject: (error: Error) => void): void;
+    validateToken(token: string, location: UriLocation): Promise<string>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default stateModelFactory;
+export declare type HTTPBasicStateModel = ReturnType<typeof stateModelFactory>;
+export declare type HTTPBasicModel = Instance<HTTPBasicStateModel>;

package/esm/HTTPBasicModel/model.js

@@ -0,0 +1,57 @@
+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
+import { InternetAccount } from '@jbrowse/core/pluggableElementTypes/models';
+import { types, getRoot } from 'mobx-state-tree';
+import { HTTPBasicLoginForm } from './HTTPBasicLoginForm';
+const stateModelFactory = (configSchema) => {
+    return InternetAccount.named('HTTPBasicInternetAccount')
+        .props({
+        type: types.literal('HTTPBasicInternetAccount'),
+        configuration: ConfigurationReference(configSchema),
+    })
+        .views(self => ({
+        get validateWithHEAD() {
+            return getConf(self, 'validateWithHEAD');
+        },
+    }))
+        .actions(self => ({
+        getTokenFromUser(resolve, reject) {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            const { session } = getRoot(self);
+            session.queueDialog((doneCallback) => [
+                HTTPBasicLoginForm,
+                {
+                    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(`Error validating token — ${response.status} (${response.statusText})${errorMessage ? ` (${errorMessage})` : ''}`);
+            }
+            return token;
+        },
+    }));
+};
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/HTTPBasicModel/model.js.map

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package/esm/OAuthModel/configSchema.d.ts

@@ -0,0 +1,5 @@
+import { Instance } from 'mobx-state-tree';
+declare const OAuthConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare type OAuthInternetAccountConfigModel = typeof OAuthConfigSchema;
+export declare type OAuthInternetAccountConfig = Instance<OAuthInternetAccountConfigModel>;
+export default OAuthConfigSchema;

package/esm/OAuthModel/configSchema.js

@@ -0,0 +1,88 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { BaseInternetAccountConfig } from '@jbrowse/core/pluggableElementTypes/models';
+/**
+ * #config OAuthInternetAccount
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const OAuthConfigSchema = ConfigurationSchema('OAuthInternetAccount', {
+    /**
+     * #slot
+     */
+    tokenType: {
+        description: 'a custom name for a token to include in the header',
+        type: 'string',
+        defaultValue: 'Bearer',
+    },
+    /**
+     * #slot
+     */
+    authEndpoint: {
+        description: 'the authorization code endpoint of the internet account',
+        type: 'string',
+        defaultValue: '',
+    },
+    /**
+     * #slot
+     */
+    tokenEndpoint: {
+        description: 'the token endpoint of the internet account',
+        type: 'string',
+        defaultValue: '',
+    },
+    /**
+     * #slot
+     */
+    needsPKCE: {
+        description: 'boolean to indicate if the endpoint needs a PKCE code',
+        type: 'boolean',
+        defaultValue: false,
+    },
+    /**
+     * #slot
+     */
+    clientId: {
+        description: 'id for the OAuth application',
+        type: 'string',
+        defaultValue: '',
+    },
+    /**
+     * #slot
+     */
+    scopes: {
+        description: 'optional scopes for the authorization call',
+        type: 'string',
+        defaultValue: '',
+    },
+    /**
+     * #slot
+     */
+    state: {
+        description: 'optional state for the authorization call',
+        type: 'string',
+        defaultValue: '',
+    },
+    /**
+     * #slot
+     */
+    responseType: {
+        description: 'the type of response from the authorization endpoint',
+        type: 'string',
+        defaultValue: 'code',
+    },
+    /**
+     * #slot
+     */
+    hasRefreshToken: {
+        description: 'true if the endpoint can supply a refresh token',
+        type: 'boolean',
+        defaultValue: false,
+    },
+}, {
+    /**
+     * #baseConfiguration
+     */
+    baseConfiguration: BaseInternetAccountConfig,
+    explicitlyTyped: true,
+});
+export default OAuthConfigSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/OAuthModel/configSchema.js.map

@@ -0,0 +1 @@
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package/esm/OAuthModel/index.d.ts

@@ -0,0 +1,2 @@
+export { default as configSchema } from './configSchema';
+export { default as modelFactory } from './model';

package/esm/OAuthModel/index.js

@@ -0,0 +1,3 @@
+export { default as configSchema } from './configSchema';
+export { default as modelFactory } from './model';
+//# sourceMappingURL=index.js.map

package/esm/OAuthModel/index.js.map

@@ -0,0 +1 @@
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package/esm/OAuthModel/model.d.ts

@@ -0,0 +1,91 @@
+/// <reference types="react" />
+import { UriLocation } from '@jbrowse/core/util';
+import { Instance } from 'mobx-state-tree';
+import { OAuthInternetAccountConfigModel } from './configSchema';
+declare const stateModelFactory: (configSchema: OAuthInternetAccountConfigModel) => import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"OAuthInternetAccount">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+}, {
+    readonly name: string;
+    readonly description: string;
+    readonly internetAccountId: string;
+    readonly authHeader: string;
+    readonly tokenType: string;
+    readonly domains: string[];
+    readonly toggleContents: import("react").ReactNode;
+    readonly SelectorComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
+    readonly selectorLabel: string | undefined;
+} & {
+    handlesLocation(location: 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, location: UriLocation): Promise<string>;
+} & {
+    getToken(location?: UriLocation | undefined): Promise<string>;
+} & {
+    addAuthHeaderToInit(init: RequestInit | undefined, token: string): {
+        headers: Headers;
+        body?: BodyInit | null | undefined;
+        cache?: RequestCache | undefined;
+        credentials?: RequestCredentials | undefined;
+        integrity?: string | undefined;
+        keepalive?: boolean | undefined;
+        method?: string | undefined;
+        mode?: RequestMode | undefined;
+        redirect?: RequestRedirect | undefined;
+        referrer?: string | undefined;
+        referrerPolicy?: ReferrerPolicy | undefined;
+        signal?: AbortSignal | null | undefined;
+        window?: null | undefined;
+    };
+    getPreAuthorizationInformation(location: UriLocation): Promise<{
+        internetAccountType: string;
+        authInfo: {
+            token: string;
+            configuration: any;
+        };
+    }>;
+} & {
+    getFetcher(location?: UriLocation | undefined): (input: RequestInfo, init?: RequestInit | undefined) => Promise<Response>;
+} & {
+    openLocation(location: UriLocation): import("@jbrowse/core/util/io").RemoteFileWithRangeCache;
+} & {
+    readonly codeVerifierPKCE: string;
+} & {
+    readonly authEndpoint: string;
+    readonly tokenEndpoint: string;
+    readonly needsPKCE: boolean;
+    readonly clientId: string;
+    readonly scopes: string;
+    /**
+     * OAuth state parameter: https://www.rfc-editor.org/rfc/rfc6749#section-4.1.1
+     * Can override or extend if dynamic state is needed.
+     */
+    state(): string | undefined;
+    readonly responseType: "code" | "token";
+    readonly hasRefreshToken: boolean;
+    readonly refreshTokenKey: string;
+} & {
+    storeRefreshToken(refreshToken: string): void;
+    removeRefreshToken(): void;
+    retrieveRefreshToken(): string | null;
+    exchangeAuthorizationForAccessToken(token: string, redirectUri: string): Promise<string>;
+    exchangeRefreshForAccessToken(refreshToken: string): Promise<string>;
+} & {
+    addMessageChannel(resolve: (token: string) => void, reject: (error: Error) => void): void;
+    deleteMessageChannel(): void;
+    finishOAuthWindow(event: MessageEvent, resolve: (token: string) => void, reject: (error: Error) => void): Promise<void>;
+    useEndpointForAuthorization(resolve: (token: string) => void, reject: (error: Error) => void): Promise<void>;
+    getTokenFromUser(resolve: (token: string) => void, reject: (error: Error) => void): Promise<void>;
+    validateToken(token: string, location: UriLocation): Promise<string>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default stateModelFactory;
+export declare type OAuthStateModel = ReturnType<typeof stateModelFactory>;
+export declare type OAuthModel = Instance<OAuthStateModel>;