@medplum/cli 2.0.21 → 2.0.23

package/dist/cjs/index.cjs

@@ -4,15 +4,17 @@
 var core = require('@medplum/core');
 var commander = require('commander');
 var dotenv = require('dotenv');
+var os = require('os');
+var child_process = require('child_process');
+var http = require('http');
+var fs = require('fs');
+var path = require('path');
 var clientCloudformation = require('@aws-sdk/client-cloudformation');
 var clientCloudfront = require('@aws-sdk/client-cloudfront');
 var clientEcs = require('@aws-sdk/client-ecs');
 var clientS3 = require('@aws-sdk/client-s3');
 var fastGlob = require('fast-glob');
-var fs = require('fs');
 var fetch$1 = require('node-fetch');
-var os = require('os');
-var path = require('path');
 var promises = require('stream/promises');
 var tar = require('tar');
 var clientAcm = require('@aws-sdk/client-acm');
@@ -20,22 +22,99 @@ var clientSsm = require('@aws-sdk/client-ssm');
 var clientSts = require('@aws-sdk/client-sts');
 var crypto = require('crypto');
 var readline = require('readline');
-var child_process = require('child_process');
-var http = require('http');
+
+function createMedplumCommand(name) {
+    return new commander.Command(name)
+        .option('--client-id <clientId>', 'FHIR server client id')
+        .option('--client-secret <clientSecret>', 'FHIR server client secret')
+        .option('--base-url <baseUrl>', 'FHIR server base url')
+        .option('--token-url <tokenUrl>', 'FHIR server token url')
+        .option('--authorize-url <authorizeUrl>', 'FHIR server authorize url')
+        .option('--fhir-url-path <fhirUrlPath>', 'FHIR server url path');
+}
+
+class FileSystemStorage extends core.ClientStorage {
+    constructor() {
+        super();
+        this.dirName = path.resolve(os.homedir(), '.medplum');
+        this.fileName = path.resolve(this.dirName, 'credentials');
+    }
+    clear() {
+        this.writeFile({});
+    }
+    getString(key) {
+        return this.readFile()?.[key];
+    }
+    setString(key, value) {
+        const data = this.readFile() || {};
+        if (value) {
+            data[key] = value;
+        }
+        else {
+            delete data[key];
+        }
+        this.writeFile(data);
+    }
+    readFile() {
+        if (fs.existsSync(this.fileName)) {
+            return JSON.parse(fs.readFileSync(this.fileName, 'utf8'));
+        }
+        return undefined;
+    }
+    writeFile(data) {
+        if (!fs.existsSync(this.dirName)) {
+            fs.mkdirSync(this.dirName);
+        }
+        fs.writeFileSync(this.fileName, JSON.stringify(data, null, 2), 'utf8');
+    }
+}
+
+async function createMedplumClient(options) {
+    const baseUrl = options.baseUrl ?? process.env['MEDPLUM_BASE_URL'] ?? 'https://api.medplum.com/';
+    const fhirUrlPath = options.fhirUrlPath ?? process.env['MEDPLUM_FHIR_URL_PATH'] ?? '';
+    const accessToken = options.accessToken ?? process.env['MEDPLUM_CLIENT_ACCESS_TOKEN'] ?? '';
+    const tokenUrl = options.tokenUrl ?? process.env['MEDPLUM_TOKEN_URL'] ?? '';
+    const authorizeUrl = options.authorizeUrl ?? process.env['MEDPLUM_AUTHORIZE_URL'] ?? '';
+    const fetchApi = options.fetch ?? fetch;
+    const medplumClient = new core.MedplumClient({
+        fetch: fetchApi,
+        baseUrl,
+        tokenUrl,
+        fhirUrlPath,
+        authorizeUrl,
+        storage: new FileSystemStorage(),
+        onUnauthenticated: onUnauthenticated,
+    });
+    if (accessToken) {
+        medplumClient.setAccessToken(accessToken);
+    }
+    const clientId = options.clientId || process.env['MEDPLUM_CLIENT_ID'];
+    const clientSecret = options.clientSecret || process.env['MEDPLUM_CLIENT_SECRET'];
+    if (clientId && clientSecret) {
+        medplumClient.setBasicAuth(clientId, clientSecret);
+        await medplumClient.startClientLogin(clientId, clientSecret);
+    }
+    return medplumClient;
+}
+function onUnauthenticated() {
+    console.log('Unauthenticated: run `npx medplum login` to sign in');
+}
 
 const clientId = 'medplum-cli';
 const redirectUri = 'http://localhost:9615';
-const login = new commander.Command('login');
-const whoami = new commander.Command('whoami');
-login.action(async () => {
-    await startLogin(exports.medplum);
+const login = createMedplumCommand('login');
+const whoami = createMedplumCommand('whoami');
+login.action(async (options) => {
+    const medplum = await createMedplumClient(options);
+    await startLogin(medplum);
 });
-whoami.action(() => {
-    printMe(exports.medplum);
+whoami.action(async (options) => {
+    const medplum = await createMedplumClient(options);
+    printMe(medplum);
 });
 async function startLogin(medplum) {
     await startWebServer(medplum);
-    const loginUrl = new URL('/oauth2/authorize', medplum.getBaseUrl());
+    const loginUrl = new URL(medplum.getAuthorizeUrl());
     loginUrl.searchParams.set('client_id', clientId);
     loginUrl.searchParams.set('redirect_uri', redirectUri);
     loginUrl.searchParams.set('scope', 'openid');
@@ -204,7 +283,6 @@ function getEcsServiceName(resource) {
 
 /**
  * The AWS "describe" command prints details about a Medplum CloudFormation stack.
- *
  * @param tag The Medplum stack tag.
  */
 async function describeStacksCommand(tag) {
@@ -343,7 +421,6 @@ function escapeRegex(str) {
  * Expanding archive files without controlling resource consumption is security-sensitive
  *
  * See: https://sonarcloud.io/organizations/medplum/rules?open=typescript%3AS5042&rule_key=typescript%3AS5042
- *
  * @param destinationDir The destination directory where all files will be extracted.
  * @returns A tar file extractor.
  */
@@ -409,6 +486,8 @@ async function updateAppCommand(tag) {
  * Returns NPM package metadata for a given package name.
  * See: https://github.com/npm/registry/blob/master/docs/REGISTRY-API.md#getpackageversion
  * @param packageName The npm package name.
+ * @param version The npm package version string.
+ * @returns The package.json metadata content.
  */
 async function getNpmPackageMetadata(packageName, version) {
     const url = `https://registry.npmjs.org/${packageName}/${version}`;
@@ -508,6 +587,11 @@ async function uploadAppToS3(tmpDir, bucketName) {
 /**
  * Uploads a directory of files to S3.
  * @param options The upload options such as bucket name, content type, and cache control.
+ * @param options.rootDir The root directory of the upload.
+ * @param options.bucketName The destination bucket name.
+ * @param options.fileNamePattern The glob file pattern to upload.
+ * @param options.contentType The content type MIME type.
+ * @param options.cached True to mark as public and cached forever.
  */
 async function uploadFolderToS3(options) {
     const items = fastGlob.sync(options.fileNamePattern, { cwd: options.rootDir });
@@ -519,6 +603,10 @@ async function uploadFolderToS3(options) {
  * Uploads a file to S3.
  * @param filePath The file path.
  * @param options The upload options such as bucket name, content type, and cache control.
+ * @param options.rootDir The root directory of the upload.
+ * @param options.bucketName The destination bucket name.
+ * @param options.contentType The content type MIME type.
+ * @param options.cached True to mark as public and cached forever.
  */
 async function uploadFileToS3(filePath, options) {
     const fileStream = fs.createReadStream(filePath);
@@ -561,7 +649,6 @@ async function createInvalidation(distributionId) {
 /**
  * The AWS "update-server" command updates the Medplum server in a Medplum CloudFormation stack.
  * @param tag The Medplum stack tag.
- * @returns
  */
 async function updateServerCommand(tag) {
     const details = await getStackByTag(tag);
@@ -800,15 +887,26 @@ async function initStackCommand() {
     print('    https://www.medplum.com/docs/self-hosting/install-on-aws');
     print('');
 }
-/** Prints to stdout. */
+/**
+ * Prints to stdout.
+ * @param text The text to print.
+ */
 function print(text) {
     terminal.write(text + '\n');
 }
-/** Prints a header with extra line spacing. */
+/**
+ * Prints a header with extra line spacing.
+ * @param text The text to print.
+ */
 function header(text) {
     print('\n' + text + '\n');
 }
-/** Prints a question and waits for user input. */
+/**
+ * Prints a question and waits for user input.
+ * @param text The question text to print.
+ * @param defaultValue Optional default value.
+ * @returns The selected value, or default value on empty selection.
+ */
 function ask(text, defaultValue = '') {
     return new Promise((resolve) => {
         terminal.question(text + (defaultValue ? ' (' + defaultValue + ')' : '') + ' ', (answer) => {
@@ -816,7 +914,13 @@ function ask(text, defaultValue = '') {
         });
     });
 }
-/** Prints a question and waits for user to choose one of the provided options. */
+/**
+ * Prints a question and waits for user to choose one of the provided options.
+ * @param text The prompt text to print.
+ * @param options The list of options that the user can select.
+ * @param defaultValue Optional default value.
+ * @returns The selected value, or default value on empty selection.
+ */
 async function choose(text, options, defaultValue = '') {
     const str = text + ' [' + options.map((o) => (o === defaultValue ? '(' + o + ')' : o)).join('|') + ']';
     // eslint-disable-next-line no-constant-condition
@@ -828,15 +932,28 @@ async function choose(text, options, defaultValue = '') {
         print('Please choose one of the following options: ' + options.join(', '));
     }
 }
-/** Prints a question and waits for the user to choose a valid integer option. */
+/**
+ * Prints a question and waits for the user to choose a valid integer option.
+ * @param text The prompt text to print.
+ * @param options The list of options that the user can select.
+ * @param defaultValue Optional default value.
+ * @returns The selected value, or default value on empty selection.
+ */
 async function chooseInt(text, options, defaultValue = 0) {
     return parseInt(await choose(text, options.map((o) => o.toString()), defaultValue.toString()));
 }
-/** Prints a question and waits for the user to choose yes or no. */
+/**
+ * Prints a question and waits for the user to choose yes or no.
+ * @param text The question to print.
+ * @returns true on accept or false on reject.
+ */
 async function yesOrNo(text) {
     return (await choose(text, ['y', 'n'])).toLowerCase() === 'y';
 }
-/** Prints a question and waits for the user to confirm yes. Throws error on no, and exits the program. */
+/**
+ * Prints a question and waits for the user to confirm yes. Throws error on no, and exits the program.
+ * @param text The prompt text to print.
+ */
 async function checkOk(text) {
     if (!(await yesOrNo(text))) {
         print('Exiting...');
@@ -908,7 +1025,6 @@ async function listCertificates(region) {
  * 1. If the certificate already exists, return the ARN.
  * 2. If the certificate does not exist, and the user wants to create a new certificate, create it and return the ARN.
  * 3. If the certificate does not exist, and the user does not want to create a new certificate, return a placeholder.
- *
  * @param config In-progress config settings.
  * @param allCerts List of all existing certificates.
  * @param region The AWS region where the certificate is needed.
@@ -963,7 +1079,6 @@ async function requestCert(region, domain) {
  *   3. It must be a 2048-bit key pair.
  *
  * See: https://docs.aws.amazon.com/AmazonCloudFront/latest/DeveloperGuide/private-content-trusted-signers.html#private-content-creating-cloudfront-key-pairs
- *
  * @returns A new signing key.
  */
 function generateSigningKey() {
@@ -1029,31 +1144,37 @@ aws
 aws.command('update-server').description('Update the server image').argument('<tag>').action(updateServerCommand);
 aws.command('update-app').description('Update the app site').argument('<tag>').action(updateAppCommand);
 
-const bot = new commander.Command('bot');
+const botSaveCommand = createMedplumCommand('save');
+const botDeployCommand = createMedplumCommand('deploy');
+const botCreateCommand = createMedplumCommand('create');
+const bot = new commander.Command('bot')
+    .addCommand(botSaveCommand)
+    .addCommand(botDeployCommand)
+    .addCommand(botCreateCommand);
 // Commands to deprecate
-const saveBotDeprecate = new commander.Command('save-bot');
-const deployBotDeprecate = new commander.Command('deploy-bot');
-const createBotDeprecate = new commander.Command('create-bot');
-bot
-    .command('save')
+const saveBotDeprecate = createMedplumCommand('save-bot');
+const deployBotDeprecate = createMedplumCommand('deploy-bot');
+const createBotDeprecate = createMedplumCommand('create-bot');
+botSaveCommand
     .description('Saving the bot')
     .argument('<botName>')
-    .action(async (botName) => {
-    await botWrapper(exports.medplum, botName);
+    .action(async (botName, options) => {
+    const medplum = await createMedplumClient(options);
+    await botWrapper(medplum, botName);
 });
-bot
-    .command('deploy')
+botDeployCommand
     .description('Deploy the app to AWS')
     .argument('<botName>')
-    .action(async (botName) => {
-    await botWrapper(exports.medplum, botName, true);
+    .action(async (botName, options) => {
+    const medplum = await createMedplumClient(options);
+    await botWrapper(medplum, botName, true);
 });
-bot
-    .command('create')
+botCreateCommand
     .arguments('<botName> <projectId> <sourceFile> <distFile>')
     .description('Creating a bot')
-    .action(async (botName, projectId, sourceFile, distFile) => {
-    await createBot(exports.medplum, [botName, projectId, sourceFile, distFile]);
+    .action(async (botName, projectId, sourceFile, distFile, options) => {
+    const medplum = await createMedplumClient(options);
+    await createBot(medplum, [botName, projectId, sourceFile, distFile]);
 });
 async function botWrapper(medplum, botName, deploy = false) {
     const botConfigs = readBotConfigs(botName);
@@ -1070,55 +1191,63 @@ async function botWrapper(medplum, botName, deploy = false) {
 saveBotDeprecate
     .description('Saves the bot')
     .argument('<botName>')
-    .action(async (botName) => {
-    await botWrapper(exports.medplum, botName);
+    .action(async (botName, options) => {
+    const medplum = await createMedplumClient(options);
+    await botWrapper(medplum, botName);
 });
 deployBotDeprecate
     .description('Deploy the bot to AWS')
     .argument('<botName>')
-    .action(async (botName) => {
-    await botWrapper(exports.medplum, botName, true);
+    .action(async (botName, options) => {
+    const medplum = await createMedplumClient(options);
+    await botWrapper(medplum, botName, true);
 });
 createBotDeprecate
     .arguments('<botName> <projectId> <sourceFile> <distFile>')
     .description('Creates and saves the bot')
-    .action(async (botName, projectId, sourceFile, distFile) => {
-    await createBot(exports.medplum, [botName, projectId, sourceFile, distFile]);
+    .action(async (botName, projectId, sourceFile, distFile, options) => {
+    const medplum = await createMedplumClient(options);
+    await createBot(medplum, [botName, projectId, sourceFile, distFile]);
 });
 
-const bulk = new commander.Command('bulk');
-bulk
-    .command('export')
-    .option('-e, --exportLevel <exportLevel>', 'Optional export level. Defaults to system level export. "Group/:id" - Group of Patients, "Patient" - All Patients.')
+const bulkExportCommand = createMedplumCommand('export');
+const bulkImportCommand = createMedplumCommand('import');
+const bulk = new commander.Command('bulk').addCommand(bulkExportCommand).addCommand(bulkImportCommand);
+bulkExportCommand
+    .option('-e, --export-level <exportLevel>', 'Optional export level. Defaults to system level export. "Group/:id" - Group of Patients, "Patient" - All Patients.')
     .option('-t, --types <types>', 'optional resource types to export')
     .option('-s, --since <since>', 'optional Resources will be included in the response if their state has changed after the supplied time (e.g. if Resource.meta.lastUpdated is later than the supplied _since time).')
-    .action(async ({ exportLevel, types, since }) => {
-    const response = await exports.medplum.bulkExport(exportLevel, types, since);
+    .action(async (options) => {
+    const { exportLevel, types, since } = options;
+    const medplum = await createMedplumClient(options);
+    const response = await medplum.bulkExport(exportLevel, types, since);
     response.output?.forEach(async ({ type, url }) => {
-        const data = await exports.medplum.download(url);
-        const fileName = `${type}.ndjson`;
+        const fileUrl = new URL(url);
+        const data = await medplum.download(url);
+        const fileName = `${type}_${fileUrl.pathname}`.replace(/[^a-zA-Z0-9]+/g, '_') + '.ndjson';
         fs.writeFile(`${fileName}`, await data.text(), () => {
             console.log(`${fileName} is created`);
         });
     });
 });
-bulk
-    .command('import')
+bulkImportCommand
     .argument('<filename>', 'File Name')
-    .option('--numResourcesPerRequest <numResourcesPerRequest>', 'optional number of resources to import per batch request. Defaults to 25.', '25')
+    .option('--num-resources-per-request <numResourcesPerRequest>', 'optional number of resources to import per batch request. Defaults to 25.', '25')
+    .option('--add-extensions-for-missing-values', 'optional flag to add extensions for missing values in a resource', false)
     .action(async (fileName, options) => {
     const path$1 = path.resolve(process.cwd(), fileName);
-    const { numResourcesPerRequest } = options;
-    await importFile(path$1, parseInt(numResourcesPerRequest));
+    const { numResourcesPerRequest, addExtensionsForMissingValues } = options;
+    const medplum = await createMedplumClient(options);
+    await importFile(path$1, parseInt(numResourcesPerRequest), medplum, addExtensionsForMissingValues);
 });
-async function importFile(path, numResourcesPerRequest) {
+async function importFile(path, numResourcesPerRequest, medplum, addExtensionsForMissingValues) {
     let entries = [];
     const fileStream = fs.createReadStream(path);
     const rl = readline.createInterface({
         input: fileStream,
     });
     for await (const line of rl) {
-        const resource = JSON.parse(line);
+        const resource = parseResource(line, addExtensionsForMissingValues);
         entries.push({
             resource: resource,
             request: {
@@ -1127,16 +1256,16 @@ async function importFile(path, numResourcesPerRequest) {
             },
         });
         if (entries.length % numResourcesPerRequest === 0) {
-            await sendBatchEntries(entries);
+            await sendBatchEntries(entries, medplum);
             entries = [];
         }
     }
     if (entries.length > 0) {
-        await sendBatchEntries(entries);
+        await sendBatchEntries(entries, medplum);
     }
 }
-async function sendBatchEntries(entries) {
-    const result = await exports.medplum.executeBatch({
+async function sendBatchEntries(entries, medplum) {
+    const result = await medplum.executeBatch({
         resourceType: 'Bundle',
         type: 'transaction',
         entry: entries,
@@ -1145,13 +1274,53 @@ async function sendBatchEntries(entries) {
         prettyPrint(resultEntry.response);
     });
 }
+function parseResource(jsonString, addExtensionsForMissingValues) {
+    const resource = JSON.parse(jsonString);
+    if (addExtensionsForMissingValues) {
+        return addExtensionsForMissingValuesResource(resource);
+    }
+    return resource;
+}
+function addExtensionsForMissingValuesResource(resource) {
+    if (resource.resourceType === 'ExplanationOfBenefit') {
+        return addExtensionsForMissingValuesExplanationOfBenefits(resource);
+    }
+    return resource;
+}
+function addExtensionsForMissingValuesExplanationOfBenefits(resource) {
+    if (!resource.provider) {
+        resource.provider = getUnmappedExtension();
+    }
+    resource.item?.forEach((item) => {
+        if (!item?.productOrService) {
+            item.productOrService = getUnmappedExtension();
+        }
+    });
+    return resource;
+}
+function getUnmappedExtension() {
+    return {
+        extension: [
+            {
+                url: 'https://g.co/unmapped-by-bcda',
+                valueString: 'This is a required FHIR R4 Field, but not mapped by BCDA, which is why we expect it to be empty.',
+            },
+        ],
+    };
+}
 
-const project = new commander.Command('project');
-project
-    .command('list')
-    .description('List of current projects')
-    .action(async () => {
-    projectList(exports.medplum);
+const projectListCommand = createMedplumCommand('list');
+const projectCurrentCommand = createMedplumCommand('current');
+const projectSwitchCommand = createMedplumCommand('switch');
+const projectInviteCommand = createMedplumCommand('invite');
+const project = new commander.Command('project')
+    .addCommand(projectListCommand)
+    .addCommand(projectCurrentCommand)
+    .addCommand(projectSwitchCommand)
+    .addCommand(projectInviteCommand);
+projectListCommand.description('List of current projects').action(async (options) => {
+    const medplum = await createMedplumClient(options);
+    projectList(medplum);
 });
 function projectList(medplum) {
     const logins = medplum.getLogins();
@@ -1160,25 +1329,22 @@ function projectList(medplum) {
         .join('\n\n');
     console.log(projects);
 }
-project
-    .command('current')
-    .description('Project you are currently on')
-    .action(() => {
-    const login = exports.medplum.getActiveLogin();
+projectCurrentCommand.description('Project you are currently on').action(async (options) => {
+    const medplum = await createMedplumClient(options);
+    const login = medplum.getActiveLogin();
     if (!login) {
         throw new Error('Unauthenticated: run `npx medplum login` to login');
     }
     console.log(`${login.project.display} (${login.project.reference})`);
 });
-project
-    .command('switch')
+projectSwitchCommand
     .description('Switching to another project from the current one')
     .argument('<projectId>')
-    .action(async (projectId) => {
-    await switchProject(exports.medplum, projectId);
+    .action(async (projectId, options) => {
+    const medplum = await createMedplumClient(options);
+    await switchProject(medplum, projectId);
 });
-project
-    .command('invite')
+projectInviteCommand
     .description('Invite a member to your current project (run npx medplum project current to confirm)')
     .arguments('<firstName> <lastName> <email>')
     .option('--send-email', 'If you want to send the email when inviting the user')
@@ -1187,7 +1353,8 @@ project
     .choices(['Practitioner', 'Patient', 'RelatedPerson'])
     .default('Practitioner'))
     .action(async (firstName, lastName, email, options) => {
-    const login = exports.medplum.getActiveLogin();
+    const medplum = await createMedplumClient(options);
+    const login = medplum.getActiveLogin();
     if (!login) {
         throw new Error('Unauthenticated: run `npx medplum login` to login');
     }
@@ -1203,7 +1370,7 @@ project
         sendEmail: !!options.sendEmail,
         admin: !!options.admin,
     };
-    await inviteUser(projectId, inviteBody);
+    await inviteUser(projectId, inviteBody, medplum);
 });
 async function switchProject(medplum, projectId) {
     const logins = medplum.getLogins();
@@ -1216,9 +1383,9 @@ async function switchProject(medplum, projectId) {
         console.log(`Switched to project ${projectId}\n`);
     }
 }
-async function inviteUser(projectId, inviteBody) {
+async function inviteUser(projectId, inviteBody, medplum) {
     try {
-        await exports.medplum.invite(projectId, inviteBody);
+        await medplum.invite(projectId, inviteBody);
         if (inviteBody.sendEmail) {
             console.log('Email sent');
         }
@@ -1229,19 +1396,21 @@ async function inviteUser(projectId, inviteBody) {
     }
 }
 
-const deleteObject = new commander.Command('delete');
-const get = new commander.Command('get');
-const patch = new commander.Command('patch');
-const post = new commander.Command('post');
-const put = new commander.Command('put');
-deleteObject.argument('<url>', 'Resource/$id').action(async (url) => {
-    prettyPrint(await exports.medplum.delete(cleanUrl(url)));
+const deleteObject = createMedplumCommand('delete');
+const get = createMedplumCommand('get');
+const patch = createMedplumCommand('patch');
+const post = createMedplumCommand('post');
+const put = createMedplumCommand('put');
+deleteObject.argument('<url>', 'Resource/$id').action(async (url, options) => {
+    const medplum = await createMedplumClient(options);
+    prettyPrint(await medplum.delete(cleanUrl(url)));
 });
 get
     .argument('<url>', 'Resource/$id')
     .option('--as-transaction', 'Print out the bundle as a transaction type')
     .action(async (url, options) => {
-    const response = await exports.medplum.get(cleanUrl(url));
+    const medplum = await createMedplumClient(options);
+    const response = await medplum.get(cleanUrl(url));
     if (options.asTransaction) {
         prettyPrint(core.convertToTransactionBundle(response));
     }
@@ -1249,14 +1418,17 @@ get
         prettyPrint(response);
     }
 });
-patch.arguments('<url> <body>').action(async (url, body) => {
-    prettyPrint(await exports.medplum.patch(cleanUrl(url), parseBody(body)));
+patch.arguments('<url> <body>').action(async (url, body, options) => {
+    const medplum = await createMedplumClient(options);
+    prettyPrint(await medplum.patch(cleanUrl(url), parseBody(body)));
 });
-post.arguments('<url> <body>').action(async (url, body) => {
-    prettyPrint(await exports.medplum.post(cleanUrl(url), parseBody(body)));
+post.arguments('<url> <body>').action(async (url, body, options) => {
+    const medplum = await createMedplumClient(options);
+    prettyPrint(await medplum.post(cleanUrl(url), parseBody(body)));
 });
-put.arguments('<url> <body>').action(async (url, body) => {
-    prettyPrint(await exports.medplum.put(cleanUrl(url), parseBody(body)));
+put.arguments('<url> <body>').action(async (url, body, options) => {
+    const medplum = await createMedplumClient(options);
+    prettyPrint(await medplum.put(cleanUrl(url), parseBody(body)));
 });
 function parseBody(input) {
     if (!input) {
@@ -1279,51 +1451,7 @@ function cleanUrl(input) {
     return 'fhir/R4/' + input;
 }
 
-class FileSystemStorage extends core.ClientStorage {
-    constructor() {
-        super();
-        this.dirName = path.resolve(os.homedir(), '.medplum');
-        this.fileName = path.resolve(this.dirName, 'credentials');
-    }
-    clear() {
-        this.writeFile({});
-    }
-    getString(key) {
-        return this.readFile()?.[key];
-    }
-    setString(key, value) {
-        const data = this.readFile() || {};
-        if (value) {
-            data[key] = value;
-        }
-        else {
-            delete data[key];
-        }
-        this.writeFile(data);
-    }
-    readFile() {
-        if (fs.existsSync(this.fileName)) {
-            return JSON.parse(fs.readFileSync(this.fileName, 'utf8'));
-        }
-        return undefined;
-    }
-    writeFile(data) {
-        if (!fs.existsSync(this.dirName)) {
-            fs.mkdirSync(this.dirName);
-        }
-        fs.writeFileSync(this.fileName, JSON.stringify(data, null, 2), 'utf8');
-    }
-}
-
-exports.medplum = void 0;
-async function main(medplumClient, argv) {
-    exports.medplum = medplumClient;
-    // Legacy support for MEDPLUM_CLIENT_ID and MEDPLUM_CLIENT_SECRET environment variables
-    const clientId = process.env['MEDPLUM_CLIENT_ID'];
-    const clientSecret = process.env['MEDPLUM_CLIENT_SECRET'];
-    if (clientId && clientSecret) {
-        await exports.medplum.startClientLogin(clientId, clientSecret);
-    }
+async function main(argv) {
     try {
         const index = new commander.Command('medplum').description('Command to access Medplum CLI');
         index.version(core.MEDPLUM_VERSION);
@@ -1338,7 +1466,7 @@ async function main(medplumClient, argv) {
         index.addCommand(deleteObject);
         // Project
         index.addCommand(project);
-        // Export
+        // Bulk Commands
         index.addCommand(bulk);
         // Bot Commands
         index.addCommand(bot);
@@ -1354,28 +1482,12 @@ async function main(medplumClient, argv) {
         console.error('Error: ' + core.normalizeErrorString(err));
     }
 }
-function run() {
+async function run() {
     dotenv.config();
-    const baseUrl = process.env['MEDPLUM_BASE_URL'] || 'https://api.medplum.com/';
-    const fhirUrlPath = process.env['MEDPLUM_FHIR_URL_PATH'] || '';
-    const accessToken = process.env['MEDPLUM_CLIENT_ACCESS_TOKEN'] || '';
-    const medplumClient = new core.MedplumClient({
-        fetch,
-        baseUrl,
-        fhirUrlPath,
-        storage: new FileSystemStorage(),
-        onUnauthenticated: onUnauthenticated,
-    });
-    if (accessToken) {
-        medplumClient.setAccessToken(accessToken);
-    }
-    main(medplumClient, process.argv).catch((err) => console.error('Unhandled error:', err));
+    await main(process.argv);
 }
 if (require.main === module) {
-    run();
-}
-function onUnauthenticated() {
-    console.log('Unauthenticated: run `npx medplum login` to sign in');
+    run().catch((err) => console.error('Unhandled error:', err));
 }
 
 exports.main = main;