dhti-cli 0.6.0 → 0.7.0

package/README.md

@@ -13,7 +13,7 @@
 
 - 🚀 *Dhanvantari rose out of the water with his four hands, holding a pot full of elixirs!*
 
-#### TL; DR: 🏥 DHTI enables rapid prototyping, sharing, and testing of GenAI applications within an Electronic Health Record (EHR), facilitating the seamless transition of your experiments to clinical practice.
+### TL; DR: 🏥 DHTI enables rapid prototyping, sharing, and testing of GenAI healthcare applications within an EHR, facilitating the seamless transition of your experiments to practice!
 👉 [Try it out today!](#try-it-out) and give us a star ⭐️ if you like it!
 
 ### About
@@ -62,8 +62,6 @@ The essence of DHTI is *modularity* with an emphasis on *configuration!* It is n
   <img src="https://github.com/dermatologist/dhti/blob/develop/notes/arch-1.drawio.svg" />
 </p>
 
-🔥 **Coming soon!:** We are currently working on expanding the DHTI architecture to support traditional machine learning models, such as *EEG sleep stage classification* and *trichogram analysis*, exposing inference pipelines as agentic tools!
-
 ## ✨ Features
 * **Modular**: Supports installable Gen AI routines and UI elements.
 * **Quick prototyping**: CLI helps in quick prototyping and testing of Gen AI routines and UI elements.
@@ -71,7 +69,7 @@ The essence of DHTI is *modularity* with an emphasis on *configuration!* It is n
 * **Developer friendly**: Copy working files to running containers for testing.
 * **Dry-run mode**: Preview changes before execution with the `--dry-run` flag.
 * **Dependency Injection**: Dependency injection for models and hyperparameters for configuring elixirs.
-* **Generate synthetic data**: DHTI supports generating synthetic data for testing.
+* **Generate synthetic data**: [DHTI supports generating synthetic data for testing, using synthea.](/notes/SYNTHEA.md)
 * **CQL support**: [CQL for clinical decision support](https://nuchange.ca/2025/06/v-llm-in-the-loop-cql-execution-with-unstructured-data-and-fhir-terminology-support.html).
 * **FHIR**: Data exchange with FHIR schema.
 * **MCP**: Built in MCP server for pluggable tools.
@@ -81,6 +79,15 @@ The essence of DHTI is *modularity* with an emphasis on *configuration!* It is n
 * **Graph utilities**: Neo4j for graph utilities.
 * **LLM**: Ollama for self-hosting LLM models.
 
+## ✨ New
+* **MCPX integration**: DHTI now includes an [MCP integrator](https://docs.lunar.dev/mcpx/) that allows other MCP servers to be "installed" and exposed seamlessly to DHTI through the MCPX gateway.
+* **DOCKTOR module**: A new module, [DOCKTOR](/notes/DOCKTOR.md), support traditional machine learning model packaged as Docker containers, to be used as MCP tools, enabling the deployment of inference pipelines as agent-invokable tools. (in beta)
+* **MCP aware agent**: [dhti-elixir-template](https://github.com/dermatologist/dhti-elixir-template) used in the examples now includes an [MCP aware agent](https://github.com/dermatologist/dhti-elixir-template/blob/feature/agent-2/src/dhti_elixir_template/chain.py) that can autodiscover and invoke tools from the MCPX gateway. Install it using `npx dhti-cli elixir install -g https://github.com/dermatologist/dhti-elixir-template.git -n dhti-elixir-template -b feature/agent2`.
+* **Medplum integration**: [Medplum](https://www.medplum.com/) is now supported as an alternative FHIR server. Read more [here](/notes/medplum.md). This allows you to add FHIR subscriptions for real-time updates and much more.
+* **Synthea integration**: You can now generate synthetic FHIR data using [Synthea](https://synthetichealth.github.io/synthea/). Read more [here](/notes/SYNTHEA.md).
+* **MIMIC support**: You can now load [MIMIC Demo](https://physionet.org/content/mimic-iv-demo/2.2/) data using DHTI in [one command](https://nuchange.ca/2024/11/loading-mimic-dataset-onto-a-fhir-server-in-two-easy-steps.html).
+
+
 ## 🔧 For Gen AI Developers
 
 *Developers can build elixirs and conchs for DHTI.*
@@ -124,6 +131,7 @@ Tools to fine-tune language models for the stack are on our roadmap. We encourag
 ## :sparkles: Resources (in Alpha)
 * [cookiecutter for scaffolding elixirs](https://github.com/dermatologist/cookiecutter-uv)
 * [cds-hooks-sandbox for testing](https://github.com/dermatologist/cds-hooks-sandbox/tree/dhti-1)
+* [Medplum integration](/notes/medplum.md)
 
 ## :sunglasses: Coming soon
 

package/dist/commands/compose.js

@@ -62,19 +62,19 @@ export default class Compose extends Command {
         const medplum = ['medplum-server', 'medplum-app', 'postgres-db', 'redis', 'mpclient'];
         const _modules = {
             cqlFhir,
+            docktor,
             fhir,
             gateway,
             langfuse,
             langserve,
             mcpFhir,
             mcpx,
-            docktor,
+            medplum,
             neo4j,
             ollama,
             openmrs,
             redis,
             webui,
-            medplum,
         };
         try {
             const masterData = yaml.load(fs.readFileSync(path.join(RESOURCES_DIR, 'docker-compose-master.yml'), 'utf8'));

package/dist/commands/docktor.d.ts

@@ -13,6 +13,6 @@ export default class Docktor extends Command {
         'model-path': import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
         workdir: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
     };
-    private restartMcpxContainer;
     run(): Promise<void>;
+    private restartMcpxContainer;
 }

package/dist/commands/docktor.js

@@ -22,8 +22,8 @@ export default class Docktor extends Command {
         }),
         environment: Flags.string({
             char: 'e',
-            multiple: true,
             description: 'Environment variables to pass to docker (format: VAR=value)',
+            multiple: true,
         }),
         image: Flags.string({ char: 'i', description: 'Docker image for the inference pipeline (required for install)' }),
         'model-path': Flags.string({
@@ -37,18 +37,6 @@ export default class Docktor extends Command {
             description: 'Working directory for MCPX config',
         }),
     };
-    async restartMcpxContainer(mcpxConfigPath, containerName) {
-        try {
-            const { execSync } = await import('node:child_process');
-            execSync(`docker cp ${mcpxConfigPath} ${containerName}:/lunar/packages/mcpx-server/`);
-            this.log(chalk.green('Copied mcp.json to container: /lunar/packages/mcpx-server/config/mcp.json'));
-            execSync(`docker restart ${containerName}`);
-            this.log(chalk.green(`Restarted ${containerName} container.`));
-        }
-        catch (err) {
-            this.log(chalk.red(`Failed to copy config or restart container '${containerName}'. Please check Docker status and container name.`));
-        }
-    }
     async run() {
         const { args, flags } = await this.parse(Docktor);
         const mcpxConfigPath = path.join(flags.workdir, 'config');
@@ -61,83 +49,105 @@ export default class Docktor extends Command {
         if (!fs.existsSync(mcpJsonPath)) {
             fs.writeFileSync(mcpJsonPath, JSON.stringify({ mcpServers: {} }, null, 2));
         }
-        let mcpConfig = JSON.parse(fs.readFileSync(mcpJsonPath, 'utf8'));
+        const mcpConfig = JSON.parse(fs.readFileSync(mcpJsonPath, 'utf8'));
         // Ensure mcpServers exists
         if (!mcpConfig.mcpServers) {
             mcpConfig.mcpServers = {};
         }
-        if (args.op === 'install') {
-            if (!args.name) {
-                this.error('Name is required for install operation');
-            }
-            if (!flags.image) {
-                this.error('Image is required for install operation');
-            }
-            const binds = [];
-            const envVars = [];
-            if (flags['model-path']) {
-                const absModelPath = path.resolve(flags['model-path']);
-                binds.push(`${absModelPath}:/model`);
+        switch (args.op) {
+            case 'install': {
+                if (!args.name) {
+                    this.error('Name is required for install operation');
+                }
+                if (!flags.image) {
+                    this.error('Image is required for install operation');
+                }
+                const binds = [];
+                const envVars = [];
+                if (flags['model-path']) {
+                    const absModelPath = path.resolve(flags['model-path']);
+                    binds.push(`${absModelPath}:/model`);
+                }
+                if (flags.environment && flags.environment.length > 0) {
+                    const invalidEnvVars = flags.environment.filter((e) => {
+                        const idx = e.indexOf('=');
+                        return idx <= 0 || idx === e.length - 1;
+                    });
+                    if (invalidEnvVars.length > 0) {
+                        this.error(`Invalid environment variable format. Expected 'NAME=value'. Invalid entries: ${invalidEnvVars.join(', ')}`);
+                    }
+                    envVars.push(...flags.environment);
+                }
+                // Add socket mounting for docker tools if needed, but primarily we want the container to run as a server
+                // MCPX handles the running of the docker container.
+                // We need to configure it in mcp.json so MCPX picks it up.
+                // Based on MCP std, docker servers are defined with `docker` command.
+                // Add (merge) new server into existing mcpServers
+                mcpConfig.mcpServers[args.name] = {
+                    args: [
+                        'run',
+                        '-i',
+                        '--rm',
+                        ...binds.flatMap((b) => ['-v', b]),
+                        ...envVars.flatMap((e) => ['-e', e]),
+                        flags.image,
+                    ],
+                    command: 'docker',
+                };
+                // Write back the updated config (preserving all other properties and existing servers)
+                fs.writeFileSync(mcpJsonPath, JSON.stringify(mcpConfig, null, 2));
+                this.log(chalk.green(`Inference pipeline '${args.name}' added`));
+                // Copy only mcp.json to container and restart (non-fatal if it fails)
+                try {
+                    await this.restartMcpxContainer(mcpxConfigPath, flags.container);
+                }
+                catch {
+                    this.log(chalk.yellow('Note: Could not restart container. Please restart manually if needed.'));
+                }
+                break;
             }
-            if (flags.environment && flags.environment.length > 0) {
-                const invalidEnvVars = flags.environment.filter((e) => {
-                    const idx = e.indexOf('=');
-                    return idx <= 0 || idx === e.length - 1;
-                });
-                if (invalidEnvVars.length > 0) {
-                    this.error(`Invalid environment variable format. Expected 'NAME=value'. Invalid entries: ${invalidEnvVars.join(', ')}`);
+            case 'remove': {
+                if (!args.name) {
+                    this.error('Name is required for remove operation');
+                }
+                if (mcpConfig.mcpServers && mcpConfig.mcpServers[args.name]) {
+                    delete mcpConfig.mcpServers[args.name];
+                    // Write back the updated config (preserving all other properties and remaining servers)
+                    fs.writeFileSync(mcpJsonPath, JSON.stringify(mcpConfig, null, 2));
+                    this.log(chalk.green(`Inference pipeline '${args.name}' removed`));
+                }
+                else {
+                    this.log(chalk.yellow(`Inference pipeline '${args.name}' not found.`));
                 }
-                envVars.push(...flags.environment);
+                break;
             }
-            // Add socket mounting for docker tools if needed, but primarily we want the container to run as a server
-            // MCPX handles the running of the docker container.
-            // We need to configure it in mcp.json so MCPX picks it up.
-            // Based on MCP std, docker servers are defined with `docker` command.
-            // Add (merge) new server into existing mcpServers
-            mcpConfig.mcpServers[args.name] = {
-                command: 'docker',
-                args: [
-                    'run',
-                    '-i',
-                    '--rm',
-                    ...binds.flatMap((b) => ['-v', b]),
-                    ...envVars.flatMap((e) => ['-e', e]),
-                    flags.image,
-                ],
-            };
-            // Write back the updated config (preserving all other properties and existing servers)
-            fs.writeFileSync(mcpJsonPath, JSON.stringify(mcpConfig, null, 2));
-            this.log(chalk.green(`Inference pipeline '${args.name}' added to MCPX config.`));
-            // Copy only mcp.json to container and restart
-            await this.restartMcpxContainer(mcpxConfigPath, flags.container);
-        }
-        else if (args.op === 'remove') {
-            if (!args.name) {
-                this.error('Name is required for remove operation');
+            case 'restart': {
+                await this.restartMcpxContainer(mcpxConfigPath, flags.container);
+                break;
             }
-            if (mcpConfig.mcpServers && mcpConfig.mcpServers[args.name]) {
-                delete mcpConfig.mcpServers[args.name];
-                // Write back the updated config (preserving all other properties and remaining servers)
-                fs.writeFileSync(mcpJsonPath, JSON.stringify(mcpConfig, null, 2));
-                this.log(chalk.green(`Inference pipeline '${args.name}' removed from MCPX config.`));
-                this.log(chalk.yellow('Please restart the MCPX container to apply changes: dhti-cli docktor restart'));
+            case 'list': {
+                this.log(chalk.blue('Installed Inference Pipelines:'));
+                for (const [name, config] of Object.entries(mcpConfig.mcpServers)) {
+                    const argsList = Array.isArray(config.args) ? config.args.join(' ') : '';
+                    this.log(`- ${name}: ${argsList}`);
+                }
+                break;
             }
-            else {
-                this.log(chalk.yellow(`Inference pipeline '${args.name}' not found.`));
+            default: {
+                this.error(`Unknown operation: ${args.op}`);
             }
         }
-        else if (args.op === 'restart') {
-            await this.restartMcpxContainer(mcpxConfigPath, flags.container);
-        }
-        else if (args.op === 'list') {
-            this.log(chalk.blue('Installed Inference Pipelines:'));
-            for (const [name, config] of Object.entries(mcpConfig.mcpServers)) {
-                const argsList = Array.isArray(config.args) ? config.args.join(' ') : '';
-                this.log(`- ${name}: ${argsList}`);
-            }
+    }
+    async restartMcpxContainer(mcpxConfigPath, containerName) {
+        try {
+            const { execSync } = await import('node:child_process');
+            execSync(`docker cp ${mcpxConfigPath} ${containerName}:/lunar/packages/mcpx-server/`);
+            this.log(chalk.green('Copied mcp.json to container: /lunar/packages/mcpx-server/config/mcp.json'));
+            execSync(`docker restart ${containerName}`);
+            this.log(chalk.green(`Restarted ${containerName} container.`));
         }
-        else {
-            this.error(`Unknown operation: ${args.op}`);
+        catch {
+            this.log(chalk.red(`Failed to copy config or restart container '${containerName}'. Please check Docker status and container name.`));
         }
     }
 }

package/dist/commands/synthea.d.ts

@@ -0,0 +1,73 @@
+import { Command } from '@oclif/core';
+/**
+ * Synthea command for managing synthetic FHIR data generation
+ *
+ * This command provides subcommands to:
+ * - install: Download and install Synthea JAR file
+ * - generate: Generate synthetic FHIR data using Synthea
+ * - upload: Upload generated FHIR resources to a FHIR server
+ * - delete: Clean up generated synthetic data
+ * - download: Download pre-generated Synthea datasets
+ */
+export default class Synthea extends Command {
+    static args: {
+        subcommand: import("@oclif/core/interfaces").Arg<string, Record<string, unknown>>;
+    };
+    static description: string;
+    static examples: string[];
+    static flags: {
+        age: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        city: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        covid19: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        covid19_10k: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        covid19_csv: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        covid19_csv_10k: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        'dry-run': import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        endpoint: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        gender: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        population: import("@oclif/core/interfaces").OptionFlag<number, import("@oclif/core/interfaces").CustomOptions>;
+        seed: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        state: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        synthea_sample_data_csv_latest: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        synthea_sample_data_fhir_latest: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        synthea_sample_data_fhir_stu3_latest: import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        token: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        workdir: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+    };
+    /**
+     * Main command execution
+     * Dispatches to appropriate subcommand handler
+     * @returns Promise that resolves when subcommand completes
+     */
+    run(): Promise<void>;
+    /**
+     * Delete synthetic data
+     * @param flags Command flags including workdir and dry-run
+     * @returns Promise that resolves when deletion completes
+     */
+    private delete;
+    /**
+     * Download pre-generated Synthea datasets
+     * @param flags Command flags including workdir, dataset selections, and dry-run
+     * @returns Promise that resolves when download completes
+     */
+    private download;
+    /**
+     * Generate synthetic FHIR data
+     * @param flags Command flags including population, state, city, gender, age, seed, workdir, and dry-run
+     * @returns Promise that resolves when generation completes
+     */
+    private generate;
+    /**
+     * Install Synthea JAR file
+     * @param flags Command flags including workdir and dry-run
+     * @returns Promise that resolves when installation completes
+     */
+    private install;
+    /**
+     * Upload FHIR resources to server
+     * @param flags Command flags including endpoint, token, workdir, and dry-run
+     * @returns Promise that resolves when upload completes
+     */
+    private upload;
+}

package/dist/commands/synthea.js

@@ -0,0 +1,579 @@
+import { Args, Command, Flags } from '@oclif/core';
+import chalk from 'chalk';
+import { exec } from 'node:child_process';
+import { createWriteStream, existsSync, mkdirSync, readFileSync, readdirSync, rmSync, statSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { join } from 'node:path';
+import { createInterface } from 'node:readline';
+import { promisify } from 'node:util';
+const execAsync = promisify(exec);
+/**
+ * Synthea command for managing synthetic FHIR data generation
+ *
+ * This command provides subcommands to:
+ * - install: Download and install Synthea JAR file
+ * - generate: Generate synthetic FHIR data using Synthea
+ * - upload: Upload generated FHIR resources to a FHIR server
+ * - delete: Clean up generated synthetic data
+ * - download: Download pre-generated Synthea datasets
+ */
+export default class Synthea extends Command {
+    static args = {
+        subcommand: Args.string({
+            description: 'Subcommand to execute: install, generate, upload, delete, download',
+            options: ['install', 'generate', 'upload', 'delete', 'download'],
+            required: true,
+        }),
+    };
+    static description = 'Manage Synthea synthetic FHIR data generation';
+    static examples = [
+        '<%= config.bin %> <%= command.id %> install',
+        '<%= config.bin %> <%= command.id %> generate -p 10',
+        '<%= config.bin %> <%= command.id %> upload -e http://fhir:8005/baseR4',
+        '<%= config.bin %> <%= command.id %> delete',
+        '<%= config.bin %> <%= command.id %> download --covid19',
+    ];
+    static flags = {
+        // Generate flags
+        age: Flags.string({
+            char: 'a',
+            description: 'Generate patients with specific age range (e.g., "0-18" for pediatric)',
+        }),
+        city: Flags.string({
+            char: 'c',
+            description: 'City for patient generation',
+        }),
+        // Download flags - various datasets from synthea.mitre.org
+        covid19: Flags.boolean({
+            description: 'Download COVID-19 dataset (1k patients)',
+        }),
+        // eslint-disable-next-line camelcase
+        covid19_10k: Flags.boolean({
+            description: 'Download COVID-19 dataset (10k patients)',
+        }),
+        // eslint-disable-next-line camelcase
+        covid19_csv: Flags.boolean({
+            description: 'Download COVID-19 CSV dataset (1k patients)',
+        }),
+        // eslint-disable-next-line camelcase
+        covid19_csv_10k: Flags.boolean({
+            description: 'Download COVID-19 CSV dataset (10k patients)',
+        }),
+        // Common flags
+        'dry-run': Flags.boolean({
+            default: false,
+            description: 'Show what changes would be made without actually making them',
+        }),
+        // Upload flags
+        endpoint: Flags.string({
+            char: 'e',
+            default: 'http://fhir:8005/baseR4',
+            description: 'FHIR server endpoint URL',
+        }),
+        gender: Flags.string({
+            char: 'g',
+            description: 'Generate patients of specific gender (M or F)',
+            options: ['M', 'F'],
+        }),
+        population: Flags.integer({
+            char: 'p',
+            default: 1,
+            description: 'Number of patients to generate',
+        }),
+        seed: Flags.string({
+            char: 's',
+            description: 'Random seed for reproducible generation',
+        }),
+        state: Flags.string({
+            description: 'State for patient generation (default: Massachusetts)',
+        }),
+        // eslint-disable-next-line camelcase
+        synthea_sample_data_csv_latest: Flags.boolean({
+            description: 'Download latest CSV sample data',
+        }),
+        // eslint-disable-next-line camelcase
+        synthea_sample_data_fhir_latest: Flags.boolean({
+            description: 'Download latest FHIR sample data',
+        }),
+        // eslint-disable-next-line camelcase
+        synthea_sample_data_fhir_stu3_latest: Flags.boolean({
+            description: 'Download latest FHIR STU3 sample data',
+        }),
+        token: Flags.string({
+            char: 't',
+            description: 'Bearer token for FHIR server authentication',
+        }),
+        workdir: Flags.string({
+            char: 'w',
+            default: join(homedir(), 'dhti'),
+            description: 'Working directory for Synthea files',
+        }),
+    };
+    /**
+     * Main command execution
+     * Dispatches to appropriate subcommand handler
+     * @returns Promise that resolves when subcommand completes
+     */
+    async run() {
+        const { args, flags } = await this.parse(Synthea);
+        // Execute appropriate subcommand
+        switch (args.subcommand) {
+            case 'install': {
+                await this.install(flags);
+                break;
+            }
+            case 'generate': {
+                await this.generate(flags);
+                break;
+            }
+            case 'upload': {
+                await this.upload(flags);
+                break;
+            }
+            case 'delete': {
+                await this.delete(flags);
+                break;
+            }
+            case 'download': {
+                await this.download(flags);
+                break;
+            }
+            default: {
+                this.error(`Unknown subcommand: ${args.subcommand}`);
+            }
+        }
+    }
+    /**
+     * Delete synthetic data
+     * @param flags Command flags including workdir and dry-run
+     * @returns Promise that resolves when deletion completes
+     */
+    async delete(flags) {
+        const dataDir = join(flags.workdir, 'synthea_data');
+        if (flags['dry-run']) {
+            console.log(chalk.yellow('[DRY RUN] Data deletion simulation'));
+            console.log(chalk.cyan(`  Data directory: ${dataDir}`));
+            console.log(chalk.green('[DRY RUN] Would delete all files in synthea_data directory'));
+            return;
+        }
+        // Check if directory exists
+        if (!existsSync(dataDir)) {
+            console.log(chalk.yellow(`⚠ Directory does not exist: ${dataDir}`));
+            return;
+        }
+        // Count files
+        let fileCount = 0;
+        const countFiles = (dir) => {
+            const items = readdirSync(dir);
+            for (const item of items) {
+                const fullPath = join(dir, item);
+                const stat = statSync(fullPath);
+                if (stat.isDirectory()) {
+                    countFiles(fullPath);
+                }
+                else {
+                    fileCount++;
+                }
+            }
+        };
+        countFiles(dataDir);
+        console.log(chalk.yellow(`⚠ About to delete ${fileCount} files from: ${dataDir}`));
+        // Confirmation prompt
+        const rl = createInterface({
+            input: process.stdin,
+            output: process.stdout,
+        });
+        const answer = await new Promise((resolve) => {
+            rl.question(chalk.red('Are you sure you want to delete all data? (yes/N): '), resolve);
+        });
+        rl.close();
+        if (answer.toLowerCase() !== 'yes') {
+            console.log(chalk.blue('Deletion cancelled.'));
+            return;
+        }
+        // Delete directory
+        try {
+            rmSync(dataDir, { force: true, recursive: true });
+            console.log(chalk.green(`✓ Deleted: ${dataDir}`));
+        }
+        catch (error) {
+            this.error(`Failed to delete directory: ${error instanceof Error ? error.message : String(error)}`);
+        }
+    }
+    /**
+     * Download pre-generated Synthea datasets
+     * @param flags Command flags including workdir, dataset selections, and dry-run
+     * @returns Promise that resolves when download completes
+     */
+    async download(flags) {
+        const tmpDir = '/tmp/synthea_downloads';
+        const outputDir = join(flags.workdir, 'synthea_data');
+        // Map of dataset flags to download URLs
+        // eslint-disable-next-line camelcase
+        const datasets = {
+            covid19: {
+                file: 'covid19.zip',
+                url: 'https://synthea.mitre.org/downloads/covid19_1k.zip',
+            },
+            // eslint-disable-next-line camelcase
+            covid19_10k: {
+                file: 'covid19_10k.zip',
+                url: 'https://synthea.mitre.org/downloads/covid19_10k.zip',
+            },
+            // eslint-disable-next-line camelcase
+            covid19_csv: {
+                file: 'covid19_csv.zip',
+                url: 'https://synthea.mitre.org/downloads/covid19_csv_1k.zip',
+            },
+            // eslint-disable-next-line camelcase
+            covid19_csv_10k: {
+                file: 'covid19_csv_10k.zip',
+                url: 'https://synthea.mitre.org/downloads/covid19_csv_10k.zip',
+            },
+            // eslint-disable-next-line camelcase
+            synthea_sample_data_csv_latest: {
+                file: 'synthea_sample_data_csv_latest.zip',
+                url: 'https://synthea.mitre.org/downloads/synthea_sample_data_csv_latest.zip',
+            },
+            // eslint-disable-next-line camelcase
+            synthea_sample_data_fhir_latest: {
+                file: 'synthea_sample_data_fhir_latest.zip',
+                url: 'https://synthea.mitre.org/downloads/synthea_sample_data_fhir_latest.zip',
+            },
+            // eslint-disable-next-line camelcase
+            synthea_sample_data_fhir_stu3_latest: {
+                file: 'synthea_sample_data_fhir_stu3_latest.zip',
+                url: 'https://synthea.mitre.org/downloads/synthea_sample_data_fhir_stu3_latest.zip',
+            },
+        };
+        // Find which dataset to download
+        const selectedDatasets = Object.keys(datasets).filter((key) => flags[key]);
+        if (selectedDatasets.length === 0) {
+            if (flags['dry-run']) {
+                console.log(chalk.yellow('[DRY RUN] Dataset download simulation'));
+                console.log(chalk.yellow('⚠ No dataset selected. Use one of the following flags:'));
+            }
+            else {
+                console.log(chalk.yellow('⚠ No dataset selected. Use one of the following flags:'));
+            }
+            for (const [key] of Object.entries(datasets)) {
+                console.log(chalk.cyan(`  --${key}`));
+            }
+            return;
+        }
+        if (flags['dry-run']) {
+            console.log(chalk.yellow('[DRY RUN] Dataset download simulation'));
+            console.log(chalk.cyan(`  Temporary directory: ${tmpDir}`));
+            console.log(chalk.cyan(`  Output directory: ${outputDir}`));
+            for (const dataset of selectedDatasets) {
+                console.log(chalk.cyan(`  Dataset: ${dataset}`));
+                console.log(chalk.cyan(`    URL: ${datasets[dataset].url}`));
+            }
+            console.log(chalk.green('[DRY RUN] Would download and extract selected datasets'));
+            return;
+        }
+        // Create directories
+        if (!existsSync(tmpDir)) {
+            mkdirSync(tmpDir, { recursive: true });
+        }
+        if (!existsSync(outputDir)) {
+            mkdirSync(outputDir, { recursive: true });
+        }
+        // Download and extract each selected dataset
+        // Note: Sequential processing is intentional to avoid overwhelming the server
+        // eslint-disable-next-line no-await-in-loop
+        for (const datasetKey of selectedDatasets) {
+            const dataset = datasets[datasetKey];
+            const downloadPath = join(tmpDir, dataset.file);
+            console.log(chalk.blue(`\nDownloading ${datasetKey}...`));
+            console.log(chalk.gray(`URL: ${dataset.url}`));
+            try {
+                // Download file
+                // eslint-disable-next-line no-await-in-loop
+                const response = await fetch(dataset.url);
+                if (!response.ok) {
+                    throw new Error(`Failed to download: ${response.statusText}`);
+                }
+                const fileStream = createWriteStream(downloadPath);
+                // @ts-expect-error - ReadableStream types from fetch
+                const reader = response.body.getReader();
+                let downloadedBytes = 0;
+                const contentLength = Number.parseInt(response.headers.get('content-length') || '0', 10);
+                // eslint-disable-next-line no-constant-condition
+                while (true) {
+                    // eslint-disable-next-line no-await-in-loop
+                    const { done, value } = await reader.read();
+                    if (done)
+                        break;
+                    downloadedBytes += value.length;
+                    fileStream.write(value);
+                    if (contentLength > 0) {
+                        const progress = Math.round((downloadedBytes / contentLength) * 100);
+                        process.stdout.write(`\rDownloading: ${progress}%`);
+                    }
+                }
+                fileStream.end();
+                console.log('\n' + chalk.green(`✓ Downloaded ${dataset.file}`));
+                // Extract ZIP file
+                console.log(chalk.blue('Extracting...'));
+                // eslint-disable-next-line no-await-in-loop
+                await execAsync(`unzip -o "${downloadPath}" -d "${outputDir}"`);
+                console.log(chalk.green(`✓ Extracted to ${outputDir}`));
+            }
+            catch (error) {
+                console.log(chalk.red(`✗ Failed to download ${datasetKey}: ${error instanceof Error ? error.message : String(error)}`));
+            }
+        }
+        console.log(chalk.green(`\n✓ Download complete. Data available at: ${outputDir}`));
+    }
+    /**
+     * Generate synthetic FHIR data
+     * @param flags Command flags including population, state, city, gender, age, seed, workdir, and dry-run
+     * @returns Promise that resolves when generation completes
+     */
+    async generate(flags) {
+        const syntheaDir = join(flags.workdir, 'synthea');
+        const jarPath = join(syntheaDir, 'synthea-with-dependencies.jar');
+        const outputDir = join(flags.workdir, 'synthea_data');
+        if (flags['dry-run']) {
+            console.log(chalk.yellow('[DRY RUN] Synthetic data generation simulation'));
+            console.log(chalk.cyan(`  Synthea JAR: ${jarPath}`));
+            console.log(chalk.cyan(`  Output directory: ${outputDir}`));
+            console.log(chalk.cyan(`  Population: ${flags.population} patients`));
+            if (flags.state)
+                console.log(chalk.cyan(`  State: ${flags.state}`));
+            if (flags.city)
+                console.log(chalk.cyan(`  City: ${flags.city}`));
+            if (flags.gender)
+                console.log(chalk.cyan(`  Gender: ${flags.gender}`));
+            if (flags.age)
+                console.log(chalk.cyan(`  Age range: ${flags.age}`));
+            if (flags.seed)
+                console.log(chalk.cyan(`  Random seed: ${flags.seed}`));
+            console.log(chalk.green('[DRY RUN] Would create output directory'));
+            console.log(chalk.green('[DRY RUN] Would execute Synthea JAR to generate data'));
+            return;
+        }
+        // Check if JAR exists
+        if (!existsSync(jarPath)) {
+            console.log(chalk.red(`✗ Synthea JAR not found at: ${jarPath}\nRun 'dhti-cli synthea install' first.`));
+            this.exit(1);
+        }
+        // Create output directory
+        if (!existsSync(outputDir)) {
+            mkdirSync(outputDir, { recursive: true });
+            console.log(chalk.green(`✓ Created output directory: ${outputDir}`));
+        }
+        // Build Synthea command
+        const javaArgs = ['-jar', jarPath];
+        // Add optional flags
+        if (flags.population)
+            javaArgs.push('-p', String(flags.population));
+        if (flags.state)
+            javaArgs.push('-s', flags.state);
+        if (flags.city)
+            javaArgs.push('-c', flags.city);
+        if (flags.gender)
+            javaArgs.push('-g', flags.gender);
+        if (flags.age)
+            javaArgs.push('-a', flags.age);
+        if (flags.seed)
+            javaArgs.push('--seed', flags.seed);
+        // Set output directory
+        javaArgs.push('--exporter.baseDirectory', outputDir);
+        console.log(chalk.blue('Generating synthetic data...'));
+        console.log(chalk.gray(`Command: java ${javaArgs.join(' ')}`));
+        try {
+            const { stderr, stdout } = await execAsync(`java ${javaArgs.join(' ')}`, {
+                cwd: syntheaDir,
+                maxBuffer: 10 * 1024 * 1024, // 10MB buffer
+            });
+            if (stdout)
+                console.log(stdout);
+            if (stderr)
+                console.error(chalk.yellow(stderr));
+            console.log(chalk.green(`✓ Generated synthetic data in: ${outputDir}`));
+            // Show FHIR output location
+            const fhirDir = join(outputDir, 'fhir');
+            if (existsSync(fhirDir)) {
+                const files = readdirSync(fhirDir);
+                console.log(chalk.cyan(`\nGenerated ${files.length} FHIR resource files`));
+                console.log(chalk.white(`FHIR files location: ${fhirDir}`));
+            }
+        }
+        catch (error) {
+            this.error(`Failed to generate synthetic data: ${error instanceof Error ? error.message : String(error)}`);
+        }
+    }
+    /**
+     * Install Synthea JAR file
+     * @param flags Command flags including workdir and dry-run
+     * @returns Promise that resolves when installation completes
+     */
+    async install(flags) {
+        const syntheaDir = join(flags.workdir, 'synthea');
+        const jarPath = join(syntheaDir, 'synthea-with-dependencies.jar');
+        if (flags['dry-run']) {
+            console.log(chalk.yellow('[DRY RUN] Synthea installation simulation'));
+            console.log(chalk.cyan(`  Working directory: ${flags.workdir}`));
+            console.log(chalk.cyan(`  Synthea directory: ${syntheaDir}`));
+            console.log(chalk.cyan(`  JAR path: ${jarPath}`));
+            console.log(chalk.green('[DRY RUN] Would create synthea directory'));
+            console.log(chalk.green('[DRY RUN] Would download synthea-with-dependencies.jar'));
+            console.log(chalk.green('[DRY RUN] Would display usage instructions'));
+            return;
+        }
+        // Create synthea directory
+        if (!existsSync(syntheaDir)) {
+            mkdirSync(syntheaDir, { recursive: true });
+            console.log(chalk.green(`✓ Created directory: ${syntheaDir}`));
+        }
+        // Check if JAR already exists
+        if (existsSync(jarPath)) {
+            console.log(chalk.yellow(`⚠ Synthea JAR already exists at: ${jarPath}`));
+            const rl = createInterface({
+                input: process.stdin,
+                output: process.stdout,
+            });
+            const answer = await new Promise((resolve) => {
+                rl.question('Overwrite existing file? (y/N): ', resolve);
+            });
+            rl.close();
+            if (answer.toLowerCase() !== 'y') {
+                console.log(chalk.blue('Installation cancelled.'));
+                return;
+            }
+        }
+        // Download synthea-with-dependencies.jar
+        console.log(chalk.blue('Downloading synthea-with-dependencies.jar...'));
+        const downloadUrl = 'https://github.com/synthetichealth/synthea/releases/download/master-branch-latest/synthea-with-dependencies.jar';
+        try {
+            const response = await fetch(downloadUrl);
+            if (!response.ok) {
+                throw new Error(`Failed to download: ${response.statusText}`);
+            }
+            const fileStream = createWriteStream(jarPath);
+            // @ts-expect-error - ReadableStream types from fetch
+            const reader = response.body.getReader();
+            let downloadedBytes = 0;
+            const contentLength = Number.parseInt(response.headers.get('content-length') || '0', 10);
+            // eslint-disable-next-line no-constant-condition
+            while (true) {
+                // eslint-disable-next-line no-await-in-loop
+                const { done, value } = await reader.read();
+                if (done)
+                    break;
+                downloadedBytes += value.length;
+                fileStream.write(value);
+                if (contentLength > 0) {
+                    const progress = Math.round((downloadedBytes / contentLength) * 100);
+                    process.stdout.write(`\rDownloading: ${progress}%`);
+                }
+            }
+            fileStream.end();
+            console.log('\n' + chalk.green(`✓ Downloaded synthea-with-dependencies.jar to ${jarPath}`));
+        }
+        catch (error) {
+            this.error(`Failed to download Synthea JAR: ${error instanceof Error ? error.message : String(error)}`);
+        }
+        // Display usage instructions
+        console.log(chalk.cyan('\n' + '='.repeat(60)));
+        console.log(chalk.bold.green('Synthea Installation Complete!'));
+        console.log(chalk.cyan('='.repeat(60)));
+        console.log(chalk.white('\nUsage Instructions:'));
+        console.log(chalk.white('-------------------'));
+        console.log(chalk.white('To generate synthetic data:'));
+        console.log(chalk.yellow(`  ${this.config.bin} synthea generate -p 10`));
+        console.log(chalk.white('\nTo upload data to FHIR server:'));
+        console.log(chalk.yellow(`  ${this.config.bin} synthea upload -e http://fhir:8005/baseR4`));
+        console.log(chalk.white('\nManual usage:'));
+        console.log(chalk.yellow(`  cd ${syntheaDir}`));
+        console.log(chalk.yellow('  java -jar synthea-with-dependencies.jar -p 10'));
+        console.log(chalk.white('\nFor more options, see:'));
+        console.log(chalk.blue('  https://github.com/synthetichealth/synthea/wiki/Basic-Setup-and-Running'));
+        console.log(chalk.cyan('='.repeat(60) + '\n'));
+    }
+    /**
+     * Upload FHIR resources to server
+     * @param flags Command flags including endpoint, token, workdir, and dry-run
+     * @returns Promise that resolves when upload completes
+     */
+    async upload(flags) {
+        const fhirDir = join(flags.workdir, 'synthea_data', 'fhir');
+        if (flags['dry-run']) {
+            console.log(chalk.yellow('[DRY RUN] FHIR upload simulation'));
+            console.log(chalk.cyan(`  FHIR directory: ${fhirDir}`));
+            console.log(chalk.cyan(`  Endpoint: ${flags.endpoint}`));
+            if (flags.token)
+                console.log(chalk.cyan('  Authentication: Bearer token'));
+            console.log(chalk.green('[DRY RUN] Would read FHIR resources from directory'));
+            console.log(chalk.green('[DRY RUN] Would upload each resource to FHIR server'));
+            return;
+        }
+        // Check if FHIR directory exists
+        if (!existsSync(fhirDir)) {
+            console.log(chalk.red(`✗ FHIR data directory not found: ${fhirDir}\nRun 'dhti-cli synthea generate' first.`));
+            this.exit(1);
+        }
+        // Read all JSON files from FHIR directory
+        const files = readdirSync(fhirDir).filter((f) => f.endsWith('.json'));
+        if (files.length === 0) {
+            console.log(chalk.yellow('⚠ No FHIR JSON files found in directory'));
+            return;
+        }
+        console.log(chalk.blue(`Found ${files.length} FHIR resource files`));
+        // Prepare headers
+        const headers = {
+            'Content-Type': 'application/fhir+json',
+        };
+        if (flags.token) {
+            headers.Authorization = `Bearer ${flags.token}`;
+        }
+        let successCount = 0;
+        let failCount = 0;
+        // Upload each file
+        // Note: Sequential processing is intentional to maintain order and avoid overwhelming server
+        // eslint-disable-next-line no-await-in-loop
+        for (const [index, file] of files.entries()) {
+            const filePath = join(fhirDir, file);
+            console.log(chalk.gray(`[${index + 1}/${files.length}] Uploading ${file}...`));
+            try {
+                const content = readFileSync(filePath, 'utf8');
+                const resource = JSON.parse(content);
+                // Determine resource type and construct URL
+                const { resourceType } = resource;
+                if (!resourceType) {
+                    console.log(chalk.yellow(`  ⚠ Skipping ${file} - no resourceType`));
+                    continue;
+                }
+                const url = `${flags.endpoint}/${resourceType}`;
+                // eslint-disable-next-line no-await-in-loop
+                const response = await fetch(url, {
+                    body: content,
+                    headers,
+                    method: 'POST',
+                });
+                if (response.ok) {
+                    successCount++;
+                    console.log(chalk.green(`  ✓ Uploaded ${file}`));
+                }
+                else {
+                    failCount++;
+                    console.log(chalk.red(`  ✗ Failed to upload ${file}: ${response.status} ${response.statusText}`));
+                }
+            }
+            catch (error) {
+                failCount++;
+                console.log(chalk.red(`  ✗ Error uploading ${file}: ${error instanceof Error ? error.message : String(error)}`));
+            }
+        }
+        // Summary
+        console.log(chalk.cyan('\n' + '='.repeat(60)));
+        console.log(chalk.bold.white('Upload Summary'));
+        console.log(chalk.cyan('='.repeat(60)));
+        console.log(chalk.green(`  ✓ Successful: ${successCount}`));
+        console.log(chalk.red(`  ✗ Failed: ${failCount}`));
+        console.log(chalk.white(`  Total: ${files.length}`));
+        console.log(chalk.cyan('='.repeat(60) + '\n'));
+    }
+}

package/dist/resources/docker-compose-master.yml

@@ -12,7 +12,6 @@ services:
       - "80:80"
       - "9001:80"
 
-
   frontend:
     image: openmrs/openmrs-reference-application-3-frontend:3.0.0-beta.17
     # image: openmrs/openmrs-reference-application-3-frontend:${TAG:-3.0.0-beta.17} # dev3, qa, demo, 3.0.0-beta.18
@@ -59,7 +58,7 @@ services:
     restart: "unless-stopped"
     command: "mysqld --character-set-server=utf8 --collation-server=utf8_general_ci"
     healthcheck:
-      test: "mysql --user=${OMRS_DB_USER:-openmrs} --password=${OMRS_DB_PASSWORD:-openmrs} --execute \"SHOW DATABASES;\""
+      test: 'mysql --user=${OMRS_DB_USER:-openmrs} --password=${OMRS_DB_PASSWORD:-openmrs} --execute "SHOW DATABASES;"'
       interval: 3s
       timeout: 1s
       retries: 5
@@ -78,11 +77,15 @@ services:
       - "8001:8001"
     restart: "unless-stopped"
     environment:
-      - OLLAMA_SERVER_URL==http://ollama:11434
+      - OLLAMA_SERVER_URL=http://ollama:11434
       - OLLAMA_WEBUI=http://ollama-webui:8080
       - LANGFUSE_HOST=http://langfuse:3000
-      - LANGFUSE_PUBLIC_KEY=pk-lf-abcd
-      - LANGFUSE_SECRET_KEY=sk-lf-abcd
+      - LANGFUSE_PUBLIC_KEY=${LANGFUSE_PUBLIC_KEY:-pk-lf-abcd}
+      - LANGFUSE_SECRET_KEY=${LANGFUSE_SECRET_KEY:-sk-lf-abcd}
+      - GOOGLE_API_KEY=${GOOGLE_API_KEY:-google-api-key}
+      - OPENAI_API_KEY=${OPENAI_API_KEY:-openai-api-key}
+      - OPENAI_API_BASE=${OPENAI_API_BASE:-https://openrouter.ai/api/v1}
+      - OPENROUTER_API_KEY=${OPENROUTER_API_KEY:-openrouter-api-key}
 
   ollama:
     image: ollama/ollama:latest
@@ -105,7 +108,7 @@ services:
     ports:
       - 8080:8080
     environment:
-      - '/ollama/api=http://ollama:11434/api'
+      - "/ollama/api=http://ollama:11434/api"
     extra_hosts:
       - host.docker.internal:host-gateway
     restart: unless-stopped
@@ -118,19 +121,19 @@ services:
     depends_on:
       - postgres-db
     environment:
-        - "spring.datasource.url=jdbc:postgresql://postgres-db:5432/postgres"
-        - "spring.datasource.username=postgres"
-        - "spring.datasource.password=postgres"
-        - "spring.datasource.driverClassName=org.postgresql.Driver"
-        - "spring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect"
-        - "hapi.fhir.fhir_version=R4"
-        - "hapi.fhir.cors.allowed-origins=*"
-        - "hapi.fhir.cors.allowCredentials=true"
-        - "hapi.fhir.bulkdata.enabled=true"
-        - "hapi.fhir.bulk_export_enabled=true"
-        - "hapi.fhir.bulk_import_enabled=true"
-        - "hapi.fhir.enforce_referential_integrity_on_write=false"
-        - "hapi.fhir.enforce_referential_integrity_on_delete=false"
+      - "spring.datasource.url=jdbc:postgresql://postgres-db:5432/postgres"
+      - "spring.datasource.username=postgres"
+      - "spring.datasource.password=postgres"
+      - "spring.datasource.driverClassName=org.postgresql.Driver"
+      - "spring.jpa.properties.hibernate.dialect=ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect"
+      - "hapi.fhir.fhir_version=R4"
+      - "hapi.fhir.cors.allowed-origins=*"
+      - "hapi.fhir.cors.allowCredentials=true"
+      - "hapi.fhir.bulkdata.enabled=true"
+      - "hapi.fhir.bulk_export_enabled=true"
+      - "hapi.fhir.bulk_import_enabled=true"
+      - "hapi.fhir.enforce_referential_integrity_on_write=false"
+      - "hapi.fhir.enforce_referential_integrity_on_delete=false"
 
   mcp-fhir:
     image: beapen/fhir-mcp-server:4.0
@@ -264,7 +267,7 @@ services:
       redis:
         condition: service_healthy
     ports:
-      - '8103:8103'
+      - "8103:8103"
     volumes:
       # Conditionally define a volume for a `medplum.config.json` if one is specified by the MEDPLUM_CONFIG_PATH env var
       - ${MEDPLUM_CONFIG_PATH:-./medplum.config.json}:/usr/src/medplum/packages/server/medplum.config.json
@@ -280,43 +283,43 @@ services:
       "
     environment:
       MEDPLUM_PORT: 8103
-      MEDPLUM_BASE_URL: 'http://localhost:8103/'
-      MEDPLUM_APP_BASE_URL: 'http://localhost:3103/'
-      MEDPLUM_STORAGE_BASE_URL: 'http://localhost:8103/storage/'
+      MEDPLUM_BASE_URL: "http://localhost:8103/"
+      MEDPLUM_APP_BASE_URL: "http://localhost:3103/"
+      MEDPLUM_STORAGE_BASE_URL: "http://localhost:8103/storage/"
 
-      MEDPLUM_DATABASE_HOST: 'postgres-db'
+      MEDPLUM_DATABASE_HOST: "postgres-db"
       MEDPLUM_DATABASE_PORT: 5432
-      MEDPLUM_DATABASE_DBNAME: 'postgres'
-      MEDPLUM_DATABASE_USERNAME: 'postgres'
-      MEDPLUM_DATABASE_PASSWORD: 'postgres'
+      MEDPLUM_DATABASE_DBNAME: "postgres"
+      MEDPLUM_DATABASE_USERNAME: "postgres"
+      MEDPLUM_DATABASE_PASSWORD: "postgres"
 
-      MEDPLUM_REDIS_HOST: 'redis'
+      MEDPLUM_REDIS_HOST: "redis"
       MEDPLUM_REDIS_PORT: 6379
       # MEDPLUM_REDIS_PASSWORD: 'medplum'
 
-      MEDPLUM_BINARY_STORAGE: 'file:./binary/'
+      MEDPLUM_BINARY_STORAGE: "file:./binary/"
       MEDPLUM_SUPPORT_EMAIL: '\"Medplum\" <support@medplum.com>'
-      MEDPLUM_GOOGLE_CLIENT_ID: '397236612778-c0b5tnjv98frbo1tfuuha5vkme3cmq4s.apps.googleusercontent.com'
-      MEDPLUM_GOOGLE_CLIENT_SECRET: ''
-      MEDPLUM_RECAPTCHA_SITE_KEY: '6LfHdsYdAAAAAC0uLnnRrDrhcXnziiUwKd8VtLNq'
-      MEDPLUM_RECAPTCHA_SECRET_KEY: '6LfHdsYdAAAAAH9dN154jbJ3zpQife3xaiTvPChL'
-      MEDPLUM_MAX_JSON_SIZE: '1mb'
-      MEDPLUM_MAX_BATCH_SIZE: '50mb'
-      MEDPLUM_BOT_LAMBDA_ROLE_ARN: ''
-      MEDPLUM_BOT_LAMBDA_LAYER_NAME: 'medplum-bot-layer'
-      MEDPLUM_VM_CONTEXT_BOTS_ENABLED: 'true'
-      MEDPLUM_DEFAULT_BOT_RUNTIME_VERSION: 'vmcontext'
-      MEDPLUM_ALLOWED_ORIGINS: '*'
-      MEDPLUM_INTROSPECTION_ENABLED: 'true'
+      MEDPLUM_GOOGLE_CLIENT_ID: "397236612778-c0b5tnjv98frbo1tfuuha5vkme3cmq4s.apps.googleusercontent.com"
+      MEDPLUM_GOOGLE_CLIENT_SECRET: ""
+      MEDPLUM_RECAPTCHA_SITE_KEY: "6LfHdsYdAAAAAC0uLnnRrDrhcXnziiUwKd8VtLNq"
+      MEDPLUM_RECAPTCHA_SECRET_KEY: "6LfHdsYdAAAAAH9dN154jbJ3zpQife3xaiTvPChL"
+      MEDPLUM_MAX_JSON_SIZE: "1mb"
+      MEDPLUM_MAX_BATCH_SIZE: "50mb"
+      MEDPLUM_BOT_LAMBDA_ROLE_ARN: ""
+      MEDPLUM_BOT_LAMBDA_LAYER_NAME: "medplum-bot-layer"
+      MEDPLUM_VM_CONTEXT_BOTS_ENABLED: "true"
+      MEDPLUM_DEFAULT_BOT_RUNTIME_VERSION: "vmcontext"
+      MEDPLUM_ALLOWED_ORIGINS: "*"
+      MEDPLUM_INTROSPECTION_ENABLED: "true"
       MEDPLUM_SHUTDOWN_TIMEOUT_MILLISECONDS: 30000
 
     healthcheck:
       test:
         # We use Node's fetch for healthcheck because this image doesn't have a curl or wget installed
         [
-          'CMD',
-          'node',
-          '-e',
+          "CMD",
+          "node",
+          "-e",
           'fetch("http://localhost:8103/healthcheck").then(r => r.json()).then(console.log).catch(() => { process.exit(1); })',
         ]
       interval: 30s
@@ -331,9 +334,9 @@ services:
     #   medplum-server:
     #     condition: service_healthy
     ports:
-      - '3103:3000'
+      - "3103:3000"
     healthcheck:
-      test: ['CMD', 'curl', '-f', 'http://localhost:3103']
+      test: ["CMD", "curl", "-f", "http://localhost:3103"]
       interval: 10s
       timeout: 5s
       retries: 5
@@ -362,4 +365,4 @@ volumes:
   ollama-code: ~
   ollama-root: ~
   ollama-webui: ~
-  mcpx-config: ~
+  mcpx-config: ~

package/oclif.manifest.json

@@ -482,6 +482,173 @@
         "mimic.js"
       ]
     },
+    "synthea": {
+      "aliases": [],
+      "args": {
+        "subcommand": {
+          "description": "Subcommand to execute: install, generate, upload, delete, download",
+          "name": "subcommand",
+          "options": [
+            "install",
+            "generate",
+            "upload",
+            "delete",
+            "download"
+          ],
+          "required": true
+        }
+      },
+      "description": "Manage Synthea synthetic FHIR data generation",
+      "examples": [
+        "<%= config.bin %> <%= command.id %> install",
+        "<%= config.bin %> <%= command.id %> generate -p 10",
+        "<%= config.bin %> <%= command.id %> upload -e http://fhir:8005/baseR4",
+        "<%= config.bin %> <%= command.id %> delete",
+        "<%= config.bin %> <%= command.id %> download --covid19"
+      ],
+      "flags": {
+        "age": {
+          "char": "a",
+          "description": "Generate patients with specific age range (e.g., \"0-18\" for pediatric)",
+          "name": "age",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "city": {
+          "char": "c",
+          "description": "City for patient generation",
+          "name": "city",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "covid19": {
+          "description": "Download COVID-19 dataset (1k patients)",
+          "name": "covid19",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "covid19_10k": {
+          "description": "Download COVID-19 dataset (10k patients)",
+          "name": "covid19_10k",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "covid19_csv": {
+          "description": "Download COVID-19 CSV dataset (1k patients)",
+          "name": "covid19_csv",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "covid19_csv_10k": {
+          "description": "Download COVID-19 CSV dataset (10k patients)",
+          "name": "covid19_csv_10k",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "dry-run": {
+          "description": "Show what changes would be made without actually making them",
+          "name": "dry-run",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "endpoint": {
+          "char": "e",
+          "description": "FHIR server endpoint URL",
+          "name": "endpoint",
+          "default": "http://fhir:8005/baseR4",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "gender": {
+          "char": "g",
+          "description": "Generate patients of specific gender (M or F)",
+          "name": "gender",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "options": [
+            "M",
+            "F"
+          ],
+          "type": "option"
+        },
+        "population": {
+          "char": "p",
+          "description": "Number of patients to generate",
+          "name": "population",
+          "default": 1,
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "seed": {
+          "char": "s",
+          "description": "Random seed for reproducible generation",
+          "name": "seed",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "state": {
+          "description": "State for patient generation (default: Massachusetts)",
+          "name": "state",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "synthea_sample_data_csv_latest": {
+          "description": "Download latest CSV sample data",
+          "name": "synthea_sample_data_csv_latest",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "synthea_sample_data_fhir_latest": {
+          "description": "Download latest FHIR sample data",
+          "name": "synthea_sample_data_fhir_latest",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "synthea_sample_data_fhir_stu3_latest": {
+          "description": "Download latest FHIR STU3 sample data",
+          "name": "synthea_sample_data_fhir_stu3_latest",
+          "allowNo": false,
+          "type": "boolean"
+        },
+        "token": {
+          "char": "t",
+          "description": "Bearer token for FHIR server authentication",
+          "name": "token",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "workdir": {
+          "char": "w",
+          "description": "Working directory for Synthea files",
+          "name": "workdir",
+          "default": "/home/runner/dhti",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "synthea",
+      "pluginAlias": "dhti-cli",
+      "pluginName": "dhti-cli",
+      "pluginType": "core",
+      "strict": true,
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "synthea.js"
+      ]
+    },
     "synthetic": {
       "aliases": [],
       "args": {
@@ -574,5 +741,5 @@
       ]
     }
   },
-  "version": "0.6.0"
+  "version": "0.7.0"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "dhti-cli",
   "description": "DHTI CLI",
-  "version": "0.6.0",
+  "version": "0.7.0",
   "author": "Bell Eapen",
   "bin": {
     "dhti-cli": "bin/run.js"
@@ -83,7 +83,8 @@
     "postpack": "shx rm -f oclif.manifest.json",
     "posttest": "echo 'npm run lint'",
     "prepack": "npx oclif manifest && npx oclif readme --readme-path notes/README.md",
-    "test": "mocha --forbid-only \"test/**/*.test.ts\"",
+    "test": "mocha --forbid-only \"test/**/*.test.ts\" --exclude \"test/e2e/**/*.test.ts\"",
+    "test-e2e": "mocha --forbid-only \"test/**/*.test.ts\"",
     "readme": "npx oclif readme --readme-path notes/README.md && git add notes/README.md",
     "docs": "typedoc --exclude src/tool.ts --html docs src"
   },