dhti-cli 0.5.0 → 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

@@ -59,15 +59,17 @@ export default class Compose extends Command {
         const mcpFhir = ['mcp-fhir', 'fhir', 'postgres-db'];
         const mcpx = ['mcpx'];
         const docktor = ['mcpx'];
+        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,

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/mimic.d.ts

@@ -7,6 +7,7 @@ export default class Mimic extends Command {
     static examples: string[];
     static flags: {
         'dry-run': import("@oclif/core/interfaces").BooleanFlag<boolean>;
+        token: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;
 }

package/dist/commands/mimic.js

@@ -11,9 +11,18 @@ export default class Mimic extends Command {
             default: false,
             description: 'Show what changes would be made without actually making them',
         }),
+        token: Flags.string({
+            char: 't',
+            description: 'Bearer token for authentication (optional)',
+        }),
     };
     async run() {
         const { args, flags } = await this.parse(Mimic);
+        // Ensure server URL ends with /$import
+        let serverUrl = args.server;
+        if (!serverUrl.endsWith('/$import')) {
+            serverUrl = serverUrl.replace(/\/$/, '') + '/$import';
+        }
         const mimic_request = `{
 
   "resourceType": "Parameters",
@@ -148,25 +157,34 @@ export default class Mimic extends Command {
 
 }`;
         if (flags['dry-run']) {
-            console.log(chalk.yellow(`[DRY RUN] Would send POST request to: ${args.server}`));
+            console.log(chalk.yellow(`[DRY RUN] Would send POST request to: ${serverUrl}`));
             console.log(chalk.cyan('[DRY RUN] Request headers:'));
             console.log(chalk.green('  Content-Type: application/fhir+json'));
             console.log(chalk.green('  Prefer: respond-async'));
+            if (flags.token) {
+                console.log(chalk.green('  Authorization: Bearer <token>'));
+            }
             console.log(chalk.cyan('[DRY RUN] Request body:'));
             console.log(mimic_request);
             return;
         }
+        // Build request headers
+        const headers = {
+            'Content-Type': 'application/fhir+json',
+            Prefer: 'respond-async',
+        };
+        if (flags.token) {
+            headers.Authorization = `Bearer ${flags.token}`;
+        }
         // send a POST request to the server with the mimic_request body
-        const response = await fetch(args.server, {
+        const response = await fetch(serverUrl, {
             body: mimic_request,
-            headers: {
-                'Content-Type': 'application/fhir+json',
-                Prefer: 'respond-async',
-            },
+            headers,
             method: 'POST',
         });
         if (!response.ok) {
             console.error(`Error: ${response.status} ${response.statusText}`);
+            this.exit(1);
         }
     }
 }

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;
+}