dhti-cli 1.0.1 → 1.2.0

package/README.md

@@ -25,6 +25,8 @@ Generative AI features are built as [LangServe Apps](https://python.langchain.co
 
 🚀 You can test the elixir using a real EMR system, [OpenMRS](https://openmrs.org/), that communicates with the elixir using **CDS-Hooks** or use any other CDS-Hooks compatible EMR system. You can also use the [CDS-Hooks sandbox for testing](https://github.com/dermatologist/cds-hooks-sandbox/tree/dhti-1) without an EMR.
 
+🚀 Checkout **[Vidhi Recipes](/vidhi/README.md)** for chatbot, RAG, imaging (DICOM) and MCPX for dockerized calculators
+
 #### How (non‑technical / clinical)
 DHTI includes ready‑to‑use [skills](/.github/skills/) that can prompt agentic platforms (e.g., [AntiGravity](https://antigravity.google/), VSCode, or Claude) to generate the GenAI backends and UI components (elixirs and conches) you need. Test these components with synthetic data in OpenMRS or the CDS‑Hooks sandbox, then hand them off to production teams. Because DHTI follows open standards, that handoff (the “valley of death”) becomes smoother and more predictable. Try the [prompts](/.github/skills/start-dhti/examples/e2e-sample.md) in your preferred agentic platform after cloning this repo.
 
@@ -52,15 +54,16 @@ npx dhti-cli docker -u                    # start services from compose
 ```
 
 Notes:
-- Configure models and hyperparameters in `~/dhti/elixir/app/bootstrap.py` or install from a local directory using `-l`.
+- Install from a local directory using `-l`.
 - Stop and remove containers with `npx dhti-cli docker -d`.
 
 ✌️  Decide where to test the new elixir: OpenMRS a full EHR system, or CDS-Hooks sandbox for a lightweight testing without an EHR.
 
 💥  Test elixir in a  CDS-Hooks sandbox.
 
-* `npx dhti-cli conch start -n dhti-elixir-schat` and navigate to the Application URL displayed in the console. (Uses hapi.fhir.org).
-* In the **Rx View** tab, type in the contentString textbox and wait for the elixir to respond.
+* `npx dhti-cli elixir start -n dhti-elixir-schat` and navigate to the **Application URL displayed in the console** (scroll up to see this). Not the base URL listed at the bottom.
+* Uses hapi.fhir.org for data.
+* In the **Rx View** tab, type in the contentString textbox and wait for the elixir to respond (Submits automatically in 5 seconds).
 
 <p align="center">
   <img src="https://github.com/dermatologist/dhti/blob/develop/notes/cds-hook-sandbox.jpg" />
@@ -88,12 +91,17 @@ You will see the new **patient context aware chatbot** in the patient summary pa
 
 * `npx dhti-cli docker -d` to stop and delete all the docker containers.
 
+## Configuration
+
+* `npx dhti-cli docker bootstrap -f bootstrap.py` will create and sync bootstrap.py where you can configure default model and hyperparameters for LangServe. Run this command after changing bootstrap.py to apply the changes.
+
 ## Wiki & Documentation
 * [![Wiki](https://img.shields.io/badge/DHTI-wiki-demo)](https://github.com/dermatologist/dhti/wiki)
 * [Documentation](https://dermatologist.github.io/dhti/)
 * [CLI Reference](/notes/README.md)
 
 ## User contributions & examples
+* 🚀 **[Vidhi Recipes](/vidhi/README.md)** for chatbot, RAG, imaging (DICOM) and MCPX for dockerized calculators
 * [Elixirs](https://github.com/dermatologist/dhti-elixir)
 * [OpenMRS Conches / UI](https://github.com/dermatologist/openmrs-esm-dhti)
 * [CDS Hooks Sandbox for testing](https://github.com/dermatologist/cds-hooks-sandbox)
@@ -101,14 +109,16 @@ You will see the new **patient context aware chatbot** in the patient summary pa
 ## Presentations
 ⭐️ **Pitched at [Falling Walls Lab Illinois](https://falling-walls.com/falling-walls-lab-illinois) and released on 2025-09-12.**
 
-## What problems do DHTI solve?
+## 🔧 What problems do DHTI solve?
 
 | Why | How |
 | --- | --- |
+| I am a clinician! I have no idea how to build GenAI apps. | ✨ DHTI comes with batteries ([skills](/.github/skills/)) included! Use your preferred agentic platform (e.g., [AntiGravity](https://antigravity.google/), [VSCode with Copilot in agent mode](https://code.visualstudio.com/docs/copilot/overview), Claude, [Cursor](https://cursor.com/) and many other) to generate elixirs and conches from [problem-oriented prompts](/prompts/e2e-sample.md) (most of these platforms have a free tier). Test them using synthetic data in OpenMRS or the CDS-Hooks sandbox, then hand them off to production teams. |
 | I know LangChain, but I don’t know how to build a chain/agent based on data in our EHR. | [These sample elixirs](https://github.com/dermatologist/dhti-elixir) adopt FHIR and cds-hooks as standards for data retrieval and display. The [base class](https://github.com/dermatologist/dhti-elixir-base) provides reusable artifacts |
 | I need a simple platform for experimenting. | This repository provides  everything to start experimenting fast. The command-line tools help to virtualize and orchestrate your experiments using [Docker](https://www.docker.com/)|
 | I am a UI designer. I want to design helpful UI for real users. | See [these sample conches](https://github.com/dermatologist/openmrs-esm-dhti). It shows how to build interface components (conches) for [OpenMRS](https://openmrs.org/) an open-source EMR used by many. Read more about [OpenMRS UI](https://o3-docs.openmrs.org/) |
 | We use another EMR  |  Your EMR may support CDS-Hook for displaying components. In that case, you can use [cds-hooks-sandbox for testing](https://github.com/dermatologist/cds-hooks-sandbox/tree/dhti-1) |
+| We don't use an EMR. We use a web based health information system for ------ population with no FHIR support. | You can still use DHTI as a GenAI experimentation platform. ✨ We have a [browser extension](https://github.com/dermatologist/openmrs-esm-dhti/blob/develop/packages/dhti-screen-grabber/README.md) that can read any web page! |
 | Our IT team is often unable to take my experiments to production. | Use DHTI, follow the recommended patterns, and you will make their lives easier.|
 
 

package/dist/commands/compose.js

@@ -80,6 +80,7 @@ export default class Compose extends Command {
         const mcpx = ['mcpx'];
         const docktor = ['mcpx'];
         const medplum = ['medplum-server', 'medplum-app', 'postgres-db', 'redis', 'mpclient'];
+        const orthanc = ['orthanc', 'cors-proxy'];
         const _modules = {
             cqlFhir,
             docktor,
@@ -95,6 +96,7 @@ export default class Compose extends Command {
             openmrs,
             redis,
             webui,
+            orthanc,
         };
         try {
             const masterData = yaml.load(fs.readFileSync(path.join(RESOURCES_DIR, 'docker-compose-master.yml'), 'utf8'));

package/dist/commands/conch.d.ts

@@ -9,8 +9,9 @@ export default class Conch extends Command {
         branch: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
         'dry-run': import("@oclif/core/interfaces").BooleanFlag<boolean>;
         git: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
-        name: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
-        sources: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        local: import("@oclif/core/interfaces").OptionFlag<string | undefined, import("@oclif/core/interfaces").CustomOptions>;
+        name: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
+        sources: import("@oclif/core/interfaces").OptionFlag<string[] | undefined, import("@oclif/core/interfaces").CustomOptions>;
         workdir: import("@oclif/core/interfaces").OptionFlag<string, import("@oclif/core/interfaces").CustomOptions>;
     };
     run(): Promise<void>;

package/dist/commands/conch.js

@@ -8,13 +8,16 @@ import { promisify } from 'node:util';
 const execAsync = promisify(exec);
 export default class Conch extends Command {
     static args = {
-        op: Args.string({ description: 'Operation to perform (init, install, or start)' }),
+        op: Args.string({ description: 'Operation to perform (add, init, install, or start)' }),
     };
     static description = 'Initialize, install, or start OpenMRS frontend development';
     static examples = [
+        '<%= config.bin %> <%= command.id %> add -g my-repo/my-package -n my-package -w ~/projects',
+        '<%= config.bin %> <%= command.id %> add -g my-repo/my-package -b main -n my-package -w ~/projects',
         '<%= config.bin %> <%= command.id %> install -n my-app -w ~/projects',
         '<%= config.bin %> <%= command.id %> init -n my-app -w ~/projects',
         '<%= config.bin %> <%= command.id %> start -n my-app -w ~/projects',
+        '<%= config.bin %> <%= command.id %> start -n my-app -w ~/projects -s packages/chatbot -s packages/utils',
     ];
     static flags = {
         branch: Flags.string({
@@ -28,13 +31,18 @@ export default class Conch extends Command {
         }),
         git: Flags.string({
             char: 'g',
-            default: 'dermatologist/openmrs-esm-dhti-template',
+            default: 'dermatologist/openmrs-esm-dhti',
             description: 'GitHub repository to install (for install operation)',
         }),
-        name: Flags.string({ char: 'n', description: 'Name of the conch' }),
+        local: Flags.string({
+            char: 'l',
+            description: 'Local path to use instead of calculated workdir/name path (for start operation)',
+        }),
+        name: Flags.string({ char: 'n', default: 'esm-dhti', description: 'Name of the conch' }),
         sources: Flags.string({
             char: 's',
-            description: 'Additional sources to include when starting (e.g., packages/esm-chatbot-agent)',
+            description: 'Additional sources to include when starting (e.g., packages/esm-chatbot-agent, packages/esm-another-app)',
+            multiple: true,
         }),
         workdir: Flags.string({
             char: 'w',
@@ -44,6 +52,43 @@ export default class Conch extends Command {
     };
     async run() {
         const { args, flags } = await this.parse(Conch);
+        if (args.op === 'add') {
+            // Validate that git and name are overridden from defaults
+            const defaultGit = 'dermatologist/openmrs-esm-dhti';
+            const defaultName = 'esm-dhti';
+            const gitOverridden = flags.git !== defaultGit;
+            const nameOverridden = flags.name !== defaultName;
+            if (!gitOverridden || !nameOverridden) {
+                console.log(chalk.yellow('Note: The "add" operation requires non-default values for both --git and --name flags.'));
+                if (!gitOverridden) {
+                    console.log(chalk.yellow('  Current --git: (default)'));
+                }
+                if (!nameOverridden) {
+                    console.log(chalk.yellow('  Current --name: (default)'));
+                }
+                console.log(chalk.yellow('\nNo changes made. Please provide custom --git and --name values.'));
+                this.exit(0);
+            }
+            if (flags['dry-run']) {
+                console.log(chalk.yellow('[DRY RUN] Would execute add operation:'));
+                const targetPath = path.join(flags.workdir, 'esm-dhti', 'packages', flags.name);
+                console.log(chalk.cyan(`  npx degit ${flags.git}#${flags.branch} ${targetPath}`));
+                return;
+            }
+            try {
+                console.log(chalk.blue(`Adding package ${flags.name} from ${flags.git}#${flags.branch}...`));
+                const targetPath = path.join(flags.workdir, 'esm-dhti', 'packages', flags.name);
+                const degitCommand = `npx degit ${flags.git}#${flags.branch} ${targetPath}`;
+                await execAsync(degitCommand);
+                console.log(chalk.green('✓ Package added successfully'));
+                console.log(chalk.green(`\n✓ Package is ready at ${targetPath}`));
+            }
+            catch (error) {
+                console.error(chalk.red('Error during add operation:'), error);
+                this.exit(1);
+            }
+            return;
+        }
         if (args.op === 'init') {
             // Validate required flags
             if (!flags.workdir) {
@@ -91,21 +136,26 @@ export default class Conch extends Command {
         }
         if (args.op === 'start') {
             // Validate required flags
-            if (!flags.workdir) {
-                console.error(chalk.red('Error: workdir flag is required for start operation'));
-                this.exit(1);
-            }
-            if (!flags.name) {
-                console.error(chalk.red('Error: name flag is required for start operation'));
-                this.exit(1);
+            if (!flags.local) {
+                // If --local is not provided, require workdir and name
+                if (!flags.workdir) {
+                    console.error(chalk.red('Error: workdir flag is required for start operation (unless --local is provided)'));
+                    this.exit(1);
+                }
+                if (!flags.name) {
+                    console.error(chalk.red('Error: name flag is required for start operation (unless --local is provided)'));
+                    this.exit(1);
+                }
             }
-            const targetDir = path.join(flags.workdir, flags.name);
+            const targetDir = flags.local || path.join(flags.workdir, flags.name);
             if (flags['dry-run']) {
                 console.log(chalk.yellow('[DRY RUN] Would execute start operation:'));
                 console.log(chalk.cyan(`  cd ${targetDir}`));
                 let dryRunCommand = 'corepack enable && yarn install && yarn start';
-                if (flags.sources) {
-                    dryRunCommand += ` --sources '${flags.sources}'`;
+                if (flags.sources && flags.sources.length > 0) {
+                    for (const source of flags.sources) {
+                        dryRunCommand += ` --sources '${source}'`;
+                    }
                 }
                 console.log(chalk.cyan(`  ${dryRunCommand}`));
                 return;
@@ -113,7 +163,9 @@ export default class Conch extends Command {
             // Check if directory exists (not in dry-run mode)
             if (!fs.existsSync(targetDir)) {
                 console.error(chalk.red(`Error: Directory does not exist: ${targetDir}`));
-                console.log(chalk.yellow(`Run 'dhti-cli conch init -n ${flags.name} -w ${flags.workdir}' first`));
+                if (!flags.local) {
+                    console.log(chalk.yellow(`Run 'dhti-cli conch init -n ${flags.name} -w ${flags.workdir}' first`));
+                }
                 this.exit(1);
             }
             try {
@@ -121,8 +173,10 @@ export default class Conch extends Command {
                 console.log(chalk.yellow('Press Ctrl-C to stop\n'));
                 // Build the start command with sources flag if provided
                 let startCommand = 'corepack enable && yarn install && yarn start';
-                if (flags.sources) {
-                    startCommand += ` --sources '${flags.sources}'`;
+                if (flags.sources && flags.sources.length > 0) {
+                    for (const source of flags.sources) {
+                        startCommand += ` --sources '${source}'`;
+                    }
                 }
                 // Spawn corepack enable && yarn install && yarn start with stdio inheritance to show output and allow Ctrl-C
                 const child = spawn(startCommand, {
@@ -166,7 +220,7 @@ export default class Conch extends Command {
                 this.exit(1);
             }
             // Warn if sources flag is used with install (not applicable)
-            if (flags.sources) {
+            if (flags.sources && flags.sources.length > 0) {
                 console.warn(chalk.yellow('Warning: --sources flag is not applicable for install operation. It will be ignored.'));
                 console.warn(chalk.yellow('Use --sources with the start operation instead.'));
             }
@@ -185,8 +239,10 @@ export default class Conch extends Command {
                 console.log(chalk.green(`\n✓ Installation complete! Your app is ready at ${targetDir}`));
                 console.log(chalk.blue(`\nTo start development, run:`));
                 let startCmd = `dhti-cli conch start -n ${flags.name} -w ${flags.workdir}`;
-                if (flags.sources) {
-                    startCmd += ` -s '${flags.sources}'`;
+                if (flags.sources && flags.sources.length > 0) {
+                    for (const source of flags.sources) {
+                        startCmd += ` -s '${source}'`;
+                    }
                 }
                 console.log(chalk.cyan(`  ${startCmd}`));
             }
@@ -197,7 +253,7 @@ export default class Conch extends Command {
             return;
         }
         // If no valid operation is provided
-        console.error(chalk.red('Error: Invalid operation. Use "install", "init", or "start"'));
+        console.error(chalk.red('Error: Invalid operation. Use "add", "install", "init", or "start"'));
         this.exit(1);
     }
 }

package/dist/commands/docker.js

@@ -110,15 +110,20 @@ export default class Docker extends Command {
                 console.log('Please provide a valid path to bootstrap.py file');
                 this.exit(1);
             }
-            const copyCommand = `docker cp ${flags.file} ${flags.container}:/app/app/bootstrap.py`;
+            // Determine copy direction based on whether local file exists
+            const fileExists = fs.existsSync(flags.file);
+            const copyCommand = fileExists
+                ? `docker cp ${flags.file} ${flags.container}:/app/app/bootstrap.py`
+                : `docker cp ${flags.container}:/app/app/bootstrap.py ${flags.file}`;
             const restartCommand = `docker restart ${flags.container}`;
             if (flags['dry-run']) {
                 console.log(chalk.yellow('[DRY RUN] Would execute:'));
-                console.log(chalk.cyan(`  ${copyCommand}`));
+                const direction = fileExists ? 'to container' : 'from container';
+                console.log(chalk.cyan(`  ${copyCommand} (copy ${direction})`));
                 console.log(chalk.cyan(`  ${restartCommand}`));
                 return;
             }
-            // copy -f to container:/app/app/ and only restart after copy completes
+            // copy file and only restart after copy completes
             exec(copyCommand, (error, stdout, stderr) => {
                 if (error) {
                     console.error(`exec error: ${error}`);

package/dist/commands/elixir.js

@@ -299,43 +299,46 @@ export default class Elixir extends Command {
             }
             return;
         }
-        // Create a directory to install the elixir
-        if (!fs.existsSync(`${flags.workdir}/elixir`)) {
+        // Create a directory to install the elixir (only on first install)
+        const elixirDir = `${flags.workdir}/elixir`;
+        const isFirstInstall = !fs.existsSync(elixirDir);
+        if (isFirstInstall) {
             if (flags['dry-run']) {
-                console.log(chalk.yellow(`[DRY RUN] Would create directory: ${flags.workdir}/elixir`));
+                console.log(chalk.yellow(`[DRY RUN] Would create directory: ${elixirDir}`));
+                console.log(chalk.yellow(`[DRY RUN] Would copy resources from ${RESOURCES_DIR}/genai to ${elixirDir}`));
             }
             else {
-                fs.mkdirSync(`${flags.workdir}/elixir`);
+                fs.mkdirSync(elixirDir);
+                fs.cpSync(path.join(RESOURCES_DIR, 'genai'), elixirDir, { recursive: true });
+                console.log(chalk.blue(`✓ Initialized elixir directory at ${elixirDir}`));
             }
         }
-        if (flags['dry-run']) {
-            console.log(chalk.yellow(`[DRY RUN] Would copy resources from ${RESOURCES_DIR}/genai to ${flags.workdir}/elixir`));
+        else if (args.op === 'install') {
+            console.log(chalk.blue(`Using existing elixir directory at ${elixirDir}`));
         }
-        else {
-            fs.cpSync(path.join(RESOURCES_DIR, 'genai'), `${flags.workdir}/elixir`, { recursive: true });
-        }
-        // if whl is not none, copy the whl file to thee whl directory
+        // if whl is not none, copy the whl file to the whl directory
         if (flags.whl !== 'none') {
-            if (!fs.existsSync(`${flags.workdir}/elixir/whl/`)) {
+            const whlDir = `${elixirDir}/whl/`;
+            if (!fs.existsSync(whlDir)) {
                 if (flags['dry-run']) {
-                    console.log(chalk.yellow(`[DRY RUN] Would create directory: ${flags.workdir}/whl/`));
+                    console.log(chalk.yellow(`[DRY RUN] Would create directory: ${whlDir}`));
                 }
                 else {
-                    fs.mkdirSync(`${flags.workdir}/whl/`);
+                    fs.mkdirSync(whlDir);
                 }
             }
             if (flags['dry-run']) {
-                console.log(chalk.yellow(`[DRY RUN] Would copy ${flags.whl} to ${flags.workdir}/elixir/whl/${path.basename(flags.whl)}`));
-                console.log(chalk.cyan('[DRY RUN] Installing elixir from whl file. Please modify boostrap.py file if needed'));
+                console.log(chalk.yellow(`[DRY RUN] Would copy ${flags.whl} to ${whlDir}${path.basename(flags.whl)}`));
+                console.log(chalk.cyan('[DRY RUN] Installing elixir from whl file. Please modify bootstrap.py file if needed'));
             }
             else {
-                fs.cpSync(flags.whl, `${flags.workdir}/elixir/whl/${path.basename(flags.whl)}`);
-                console.log('Installing elixir from whl file. Please modify boostrap.py file if needed');
+                fs.cpSync(flags.whl, `${whlDir}${path.basename(flags.whl)}`);
+                console.log('Installing elixir from whl file. Please modify bootstrap.py file if needed');
             }
         }
         // Install the elixir from git adding to the pyproject.toml file
-        let pyproject = flags['dry-run'] ? '' : fs.readFileSync(`${flags.workdir}/elixir/pyproject.toml`, 'utf8');
-        const originalServer = flags['dry-run'] ? '' : fs.readFileSync(`${flags.workdir}/elixir/app/server.py`, 'utf8');
+        // Always read from the current state, not the template
+        let pyproject = flags['dry-run'] ? '' : fs.readFileSync(`${elixirDir}/pyproject.toml`, 'utf8');
         let lineToAdd = '';
         if (flags.whl !== 'none') {
             lineToAdd = `${flags.name} = { file = "whl/${path.basename(flags.whl)}" }`;
@@ -366,11 +369,49 @@ export default class Elixir extends Command {
             }
             lineToAdd = `${flags.name} = { path = "${absolutePath}" }`;
         }
+        // Helper function to add dependency to pyproject.toml
+        const addDependencyToPyproject = (content, depName) => {
+            // Check if dependency already exists
+            if (content.includes(`"${depName}"`)) {
+                return content;
+            }
+            // Add to dependencies array
+            return content.replace('dependencies = [', `dependencies = [\n"${depName}",`);
+        };
+        // Helper function to add source to pyproject.toml
+        const addSourceToPyproject = (content, source) => {
+            // Check if source already exists (by checking for the package name)
+            if (content.includes(`${flags.name} =`)) {
+                return content;
+            }
+            // Add to [tool.uv.sources] section
+            return content.replace('[tool.uv.sources]', `[tool.uv.sources]\n${source}\n`);
+        };
+        // Helper function to remove dependency from pyproject.toml
+        const removeDependencyFromPyproject = (content, depName) => {
+            // Remove from dependencies array - handle both formats: "depName", or "depName",\n
+            let result = content.replace(`"${depName}",`, '').replace(`"${depName}"`, '');
+            // Also try to remove with newline variations
+            result = result.replace(`\n"${depName}",`, '').replace(`"${depName}",\n`, '');
+            return result;
+        };
+        // Helper function to remove source from pyproject.toml
+        const removeSourceFromPyproject = (content, pkgName) => {
+            // Remove source line for this package
+            const sourceRegex = new RegExp(`${pkgName}\\s*=\\s*\\{[^}]*\\}\n?`, 'g');
+            return content.replace(sourceRegex, '');
+        };
+        let newPyproject = pyproject;
         if (!flags['dry-run']) {
-            pyproject = pyproject.replace('dependencies = [', `dependencies = [\n"${flags.name}",`);
-            pyproject = pyproject.replace('[tool.uv.sources]', `[tool.uv.sources]\n${lineToAdd}\n`);
+            if (args.op === 'install') {
+                newPyproject = addDependencyToPyproject(pyproject, flags.name);
+                newPyproject = addSourceToPyproject(newPyproject, lineToAdd);
+            }
+            else if (args.op === 'uninstall') {
+                newPyproject = removeDependencyFromPyproject(pyproject, flags.name);
+                newPyproject = removeSourceFromPyproject(newPyproject, flags.name);
+            }
         }
-        const newPyproject = pyproject;
         // Add the elixir import and bootstrap to the server.py file
         let CliImport = `from ${expoName}.bootstrap import bootstrap as ${expoName}_bootstrap\n`;
         CliImport += `${expoName}_bootstrap()\n`;
@@ -380,54 +421,99 @@ ${expoName}_chain = ${expoName}_chain_class().get_chain_as_langchain_tool()
 ${expoName}_mcp_tool = ${expoName}_chain_class().get_chain_as_mcp_tool
 mcp_server.add_tool(${expoName}_mcp_tool) # type: ignore
     `;
-        let newCliImport = '';
-        if (!flags['dry-run']) {
-            newCliImport = fs
-                .readFileSync(`${flags.workdir}/elixir/app/server.py`, 'utf8')
-                .replace('# DHTI_CLI_IMPORT', `#DHTI_CLI_IMPORT\n${CliImport}`);
-        }
         const langfuseRoute = `add_routes(app, ${expoName}_chain.with_config(config), path="/langserve/${expoName}")`;
-        const newLangfuseRoute = flags['dry-run']
-            ? ''
-            : newCliImport.replace('# DHTI_LANGFUSE_ROUTE', `#DHTI_LANGFUSE_ROUTE\n    ${langfuseRoute}`);
         const normalRoute = `add_routes(app, ${expoName}_chain, path="/langserve/${expoName}")`;
-        const newNormalRoute = flags['dry-run']
-            ? ''
-            : newLangfuseRoute.replace('# DHTI_NORMAL_ROUTE', `#DHTI_NORMAL_ROUTE\n    ${normalRoute}`);
         const commonRoutes = `\nadd_invokes(app, path="/langserve/${expoName}")\nadd_services(app, path="/langserve/${expoName}")`;
-        const finalRoute = flags['dry-run']
-            ? ''
-            : newNormalRoute.replace('# DHTI_COMMON_ROUTE', `#DHTI_COMMON_ROUTES${commonRoutes}`);
-        // if args.op === install, add the line to the pyproject.toml file
+        // Helper function to add elixir to server.py
+        // The strategy is to append imports BEFORE the 'import uvicorn' line
+        // and append routes AFTER the route marker comments
+        const addElixirToServer = (elixirName) => {
+            // Read fresh file content each time to get the current state
+            const content = flags['dry-run'] ? '' : fs.readFileSync(`${elixirDir}/app/server.py`, 'utf8');
+            if (flags['dry-run'] || content === '') {
+                return '';
+            }
+            // Check if elixir already installed
+            if (content.includes(`${elixirName}_bootstrap`)) {
+                return content;
+            }
+            let result = content;
+            // Find where to insert the import - look for 'import uvicorn' and insert before it
+            // This way, all imports are together before uvicorn import
+            if (!result.includes('import uvicorn')) {
+                console.error(chalk.red('Error: Could not find "import uvicorn" marker in server.py'));
+                return content;
+            }
+            result = result.replace('import uvicorn', `${CliImport}\nimport uvicorn`);
+            // For routes, we need to insert into both langfuse and normal route sections
+            // But only if they exist
+            // Find the langfuse try block and insert before 'except'
+            if (result.includes('except:')) {
+                // Insert langfuse route before except with proper indentation
+                result = result.replace('except:', `    ${langfuseRoute}\n\nexcept:`);
+                // Insert normal route in the except block, after the '# DHTI_NORMAL_ROUTE' marker
+                result = result.replace('# DHTI_NORMAL_ROUTE\n', `# DHTI_NORMAL_ROUTE\n    ${normalRoute}\n`);
+            }
+            // For common routes, look for the marker and append with proper indentation
+            const commonRoutesMarker = '# DHTI_COMMON_ROUTE';
+            if (result.includes(commonRoutesMarker)) {
+                // Get the exact indentation by checking what comes after the marker
+                const markerIndex = result.indexOf(commonRoutesMarker);
+                const afterMarker = result.substring(markerIndex + commonRoutesMarker.length);
+                const newlineAndIndent = afterMarker.match(/\n[ \t]*/)?.[0] || '\n';
+                result = result.replace(commonRoutesMarker, `${commonRoutesMarker}${newlineAndIndent}${commonRoutes}`);
+            }
+            return result;
+        };
+        // Helper function to remove elixir from server.py
+        const removeElixirFromServer = () => {
+            // Read fresh file content each time to get the current state
+            const content = flags['dry-run'] ? '' : fs.readFileSync(`${elixirDir}/app/server.py`, 'utf8');
+            if (flags['dry-run'] || content === '') {
+                return '';
+            }
+            let result = content;
+            result = result.replace(CliImport, '');
+            result = result.replace(langfuseRoute, '');
+            result = result.replace(normalRoute, '');
+            result = result.replace(commonRoutes, '');
+            return result;
+        };
+        let finalRoute = '';
+        if (!flags['dry-run'] && args.op === 'install') {
+            finalRoute = addElixirToServer(expoName);
+        }
+        else if (!flags['dry-run'] && args.op === 'uninstall') {
+            finalRoute = removeElixirFromServer();
+        }
         if (args.op === 'install') {
             if (flags['dry-run']) {
                 console.log(chalk.yellow('[DRY RUN] Would update files:'));
-                console.log(chalk.cyan(`  - ${flags.workdir}/elixir/pyproject.toml`));
+                console.log(chalk.cyan(`  - ${elixirDir}/pyproject.toml`));
                 console.log(chalk.green(`    Add dependency: "${flags.name}"`));
                 console.log(chalk.green(`    Add source: ${lineToAdd}`));
-                console.log(chalk.cyan(`  - ${flags.workdir}/elixir/app/server.py`));
+                console.log(chalk.cyan(`  - ${elixirDir}/app/server.py`));
                 console.log(chalk.green(`    Add import and routes for ${expoName}`));
             }
             else {
-                fs.writeFileSync(`${flags.workdir}/elixir/pyproject.toml`, newPyproject);
-                fs.writeFileSync(`${flags.workdir}/elixir/app/server.py`, finalRoute);
+                fs.writeFileSync(`${elixirDir}/pyproject.toml`, newPyproject);
+                fs.writeFileSync(`${elixirDir}/app/server.py`, finalRoute);
+                console.log(chalk.green(`✓ Elixir '${flags.name}' installed successfully`));
             }
         }
         if (args.op === 'uninstall') {
             if (flags['dry-run']) {
                 console.log(chalk.yellow('[DRY RUN] Would update files:'));
-                console.log(chalk.cyan(`  - ${flags.workdir}/elixir/pyproject.toml`));
+                console.log(chalk.cyan(`  - ${elixirDir}/pyproject.toml`));
+                console.log(chalk.green(`    Remove dependency: "${flags.name}"`));
                 console.log(chalk.green(`    Remove source: ${lineToAdd}`));
-                console.log(chalk.cyan(`  - ${flags.workdir}/elixir/app/server.py`));
+                console.log(chalk.cyan(`  - ${elixirDir}/app/server.py`));
                 console.log(chalk.green(`    Remove import and routes for ${expoName}`));
             }
             else {
-                // if args.op === uninstall, remove the line from the pyproject.toml file
-                fs.writeFileSync(`${flags.workdir}/elixir/pyproject.toml`, pyproject.replace(lineToAdd, ''));
-                let newServer = originalServer.replace(CliImport, '');
-                newServer = newServer.replace(langfuseRoute, '');
-                newServer = newServer.replace(normalRoute, '');
-                fs.writeFileSync(`${flags.workdir}/elixir/app/server.py`, newServer);
+                fs.writeFileSync(`${elixirDir}/pyproject.toml`, newPyproject);
+                fs.writeFileSync(`${elixirDir}/app/server.py`, finalRoute);
+                console.log(chalk.green(`✓ Elixir '${flags.name}' uninstalled successfully`));
             }
         }
     }

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

@@ -1,4 +1,3 @@
-
 services:
   gateway:
     image: beapen/dhti-gateway:latest
@@ -88,7 +87,6 @@ services:
       - OPENROUTER_API_KEY=${OPENROUTER_API_KEY:-openrouter-api-key}
       - FHIR_BASE_URL=${FHIR_BASE_URL:-http://localhost:8080/openmrs/ws/fhir2/R4}
 
-
   ollama:
     image: ollama/ollama:latest
     ports:
@@ -215,7 +213,7 @@ services:
     environment:
       - REDIS_HOSTS=local:redis:6379
     ports:
-      - "8081:8081"
+      - "8181:8081"
 
   neo4j:
     image: neo4j:5.1-enterprise
@@ -357,6 +355,28 @@ services:
     depends_on:
       - medplum-server
 
+  orthanc:
+    image: orthancteam/orthanc:latest
+    ports:
+      # Orthanc web interface and DICOMweb port
+      - "8042:8042"
+      # DICOM store SCU/SCP port (default 4242 in container, 104 is standard, 8104 used in some examples)
+      - "8104:4242"
+    environment:
+      # Enable the web interface and remote access
+      - ORTHANC_JSON={"RemoteAccessAllowed":true,"AuthenticationEnabled":false,"HttpHeaders":{"Access-Control-Allow-Origin":"*","Access-Control-Allow-Methods":"GET, POST, PUT, DELETE, OPTIONS","Access-Control-Allow-Headers":"Content-Type"},"HttpRequestTimeout":60}
+    volumes:
+      # Persist the data (DICOM files and database)
+      - orthanc-data:/var/lib/orthanc/
+    restart: unless-stopped
+
+  cors-proxy:
+    image: redocly/cors-anywhere:latest
+    ports:
+      - "8010:8080"
+    restart: "unless-stopped"
+
+
 volumes:
   openmrs-data: ~
   openmrs-db: ~
@@ -368,3 +388,4 @@ volumes:
   ollama-root: ~
   ollama-webui: ~
   mcpx-config: ~
+  orthanc-data: ~

package/dist/resources/genai/app/bootstrap.py

@@ -1,19 +1,49 @@
 from kink import di
-from os import getenv
+import os
 from dotenv import load_dotenv
+from langchain.chat_models import init_chat_model
+from langchain_community.llms.fake import FakeListLLM
 from langchain_core.prompts import PromptTemplate
-from langchain_core.language_models.fake import FakeListLLM
+from langchain_google_genai import ChatGoogleGenerativeAI
+from langchain_openai import ChatOpenAI
 
 ## Override the default configuration of elixirs here if needed
 
 
 def bootstrap():
     load_dotenv()
-    fake_llm = FakeListLLM(responses=["Paris", "I don't know"])
+    di["fhir_access_token"] = os.environ.get(
+        "FHIR_ACCESS_TOKEN", "YWRtaW46QWRtaW4xMjM="
+    )  # admin:Admin123 in base64
+    di["fhir_base_url"] = os.environ.get(
+        "FHIR_BASE_URL", "http://backend:8080/openmrs/ws/fhir2/R4"
+    )
+    # Check if google api key is set in the environment
+    if os.environ.get("GOOGLE_API_KEY"):
+        llm = ChatGoogleGenerativeAI(model="gemini-2.5-flash")
+    # Check if openai api key is set in the environment
+    elif os.environ.get("OPENAI_API_KEY"):
+        llm = ChatOpenAI(model="gpt-4o", temperature=0)
+    else:
+        llm = FakeListLLM(responses=["I am a fake LLM", "I don't know"])
+    di["main_llm"] = llm
+
+    openrouter_api_key = os.environ.get("OPENROUTER_API_KEY")
+    if openrouter_api_key:
+        model = init_chat_model(
+            model="nvidia/nemotron-nano-9b-v2:free",
+            model_provider="openai",
+            base_url="https://openrouter.ai/api/v1",
+            api_key=openrouter_api_key,
+        )
+    else:
+        # Fallback to the main LLM if no OpenRouter API key is configured
+        model = llm
+
+    di["function_llm"] = model
     di["main_prompt"] = PromptTemplate.from_template(
         "Summarize the following in 100 words: {input}"
     )
-    di["main_llm"] = fake_llm
     di["cds_hook_discovery"] = {
         "services": [
             {

package/oclif.manifest.json

@@ -87,15 +87,18 @@
       "aliases": [],
       "args": {
         "op": {
-          "description": "Operation to perform (init, install, or start)",
+          "description": "Operation to perform (add, init, install, or start)",
           "name": "op"
         }
       },
       "description": "Initialize, install, or start OpenMRS frontend development",
       "examples": [
+        "<%= config.bin %> <%= command.id %> add -g my-repo/my-package -n my-package -w ~/projects",
+        "<%= config.bin %> <%= command.id %> add -g my-repo/my-package -b main -n my-package -w ~/projects",
         "<%= config.bin %> <%= command.id %> install -n my-app -w ~/projects",
         "<%= config.bin %> <%= command.id %> init -n my-app -w ~/projects",
-        "<%= config.bin %> <%= command.id %> start -n my-app -w ~/projects"
+        "<%= config.bin %> <%= command.id %> start -n my-app -w ~/projects",
+        "<%= config.bin %> <%= command.id %> start -n my-app -w ~/projects -s packages/chatbot -s packages/utils"
       ],
       "flags": {
         "branch": {
@@ -117,7 +120,15 @@
           "char": "g",
           "description": "GitHub repository to install (for install operation)",
           "name": "git",
-          "default": "dermatologist/openmrs-esm-dhti-template",
+          "default": "dermatologist/openmrs-esm-dhti",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "local": {
+          "char": "l",
+          "description": "Local path to use instead of calculated workdir/name path (for start operation)",
+          "name": "local",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
@@ -126,16 +137,17 @@
           "char": "n",
           "description": "Name of the conch",
           "name": "name",
+          "default": "esm-dhti",
           "hasDynamicHelp": false,
           "multiple": false,
           "type": "option"
         },
         "sources": {
           "char": "s",
-          "description": "Additional sources to include when starting (e.g., packages/esm-chatbot-agent)",
+          "description": "Additional sources to include when starting (e.g., packages/esm-chatbot-agent, packages/esm-another-app)",
           "name": "sources",
           "hasDynamicHelp": false,
-          "multiple": false,
+          "multiple": true,
           "type": "option"
         },
         "workdir": {
@@ -796,5 +808,5 @@
       ]
     }
   },
-  "version": "1.0.1"
+  "version": "1.2.0"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "dhti-cli",
   "description": "DHTI CLI",
-  "version": "1.0.1",
+  "version": "1.2.0",
   "author": "Bell Eapen",
   "bin": {
     "dhti-cli": "bin/run.js"