@atomic-ehr/fhir-canonical-manager 0.0.7 → 0.0.8

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@atomic-ehr/fhir-canonical-manager",
-  "version": "0.0.7",
+  "version": "0.0.8",
   "type": "module",
   "main": "./dist/index.js",
   "types": "./dist/index.d.ts",
@@ -39,6 +39,6 @@
       "search",
       "pat"
     ],
-    "registry": "https://fs.get-ig.org/pkgs"
+    "registry": "https://fs.get-ig.org/pkgs/"
   }
 }

package/src/cli/index.ts

@@ -1,29 +1,29 @@
 #!/usr/bin/env node
 
-import * as fs from 'fs';
-import * as path from 'path';
-import { fileURLToPath } from 'url';
-import { CanonicalManager } from '../index.js';
-import type { Config, IndexEntry, PackageInfo } from '../index.js';
+import * as fs from "fs";
+import * as path from "path";
+import { fileURLToPath } from "url";
+import { CanonicalManager } from "../index.js";
+import type { Config, IndexEntry, PackageInfo } from "../index.js";
 
 // Command handlers
-import { initCommand } from './init.js';
-import { listCommand } from './list.js';
-import { searchCommand } from './search.js';
-import { resolveCommand } from './resolve.js';
+import { initCommand } from "./init.js";
+import { listCommand } from "./list.js";
+import { searchCommand } from "./search.js";
+import { resolveCommand } from "./resolve.js";
 
 // Get version from package.json
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const packageJsonPath = path.join(__dirname, '..', '..', 'package.json');
+const packageJsonPath = path.join(__dirname, "..", "..", "package.json");
 
-let VERSION = 'unknown';
+let VERSION = "unknown";
 try {
-  const packageJson = JSON.parse(fs.readFileSync(packageJsonPath, 'utf-8'));
+  const packageJson = JSON.parse(fs.readFileSync(packageJsonPath, "utf-8"));
   VERSION = packageJson.version;
 } catch (error) {
   // Fallback version if package.json can't be read
-  VERSION = '0.0.3';
+  VERSION = "0.0.3";
 }
 
 function showHelp() {
@@ -34,7 +34,7 @@ Usage: fcm <command> [options]
 
 Commands:
   init       Initialize FHIR packages in current directory
-  list       List packages or resources  
+  list       List packages or resources
   search     Search for resources
   resolve    Get a resource by canonical URL
 
@@ -54,13 +54,19 @@ async function main() {
   const args = process.argv.slice(2);
   const command = args[0];
 
-  if (!command || command === '--help' || command === '-h') {
+  if (!command || command === "--help" || command === "-h") {
     showHelp();
+    if (process.env.NODE_ENV === 'test') {
+      return;
+    }
     process.exit(0);
   }
 
-  if (command === '--version' || command === '-v') {
+  if (command === "--version" || command === "-v") {
     console.log(VERSION);
+    if (process.env.NODE_ENV === 'test') {
+      return;
+    }
     process.exit(0);
   }
 
@@ -68,56 +74,67 @@ async function main() {
     init: initCommand,
     list: listCommand,
     search: searchCommand,
-    resolve: resolveCommand
+    resolve: resolveCommand,
   };
 
   if (!commands[command]) {
     console.error(`Error: Unknown command '${command}'`);
     console.error(`Run 'fcm --help' for usage information`);
+    if (process.env.NODE_ENV === 'test') {
+      throw new Error(`Unknown command '${command}'`);
+    }
     process.exit(1);
   }
 
   try {
     await commands[command](args.slice(1));
   } catch (error) {
-    console.error(`Error: ${error instanceof Error ? error.message : String(error)}`);
+    console.error(
+      `Error: ${error instanceof Error ? error.message : String(error)}`,
+    );
+    if (process.env.NODE_ENV === 'test') {
+      throw error;
+    }
     process.exit(1);
   }
 }
 
 // Export utility functions for commands
-export function parseArgs(args: string[]): { positional: string[], options: Record<string, string | boolean> } {
+export function parseArgs(args: string[]): {
+  positional: string[];
+  options: Record<string, string | boolean>;
+} {
   const positional: string[] = [];
   const options: Record<string, string | boolean> = {};
 
   for (let i = 0; i < args.length; i++) {
     const arg = args[i];
-    if (arg && arg.startsWith('--')) {
+    if (arg && arg.startsWith("--")) {
       const key = arg.slice(2);
       const nextArg = args[i + 1];
-      if (nextArg && !nextArg.startsWith('--')) {
+      if (nextArg && !nextArg.startsWith("--")) {
         options[key] = nextArg;
         i++;
       } else {
         options[key] = true;
       }
-    } else if (arg && arg.startsWith('-')) {
+    } else if (arg && arg.startsWith("-")) {
       // Handle short aliases
       switch (arg) {
-        case '-sd':
-          options.resourceType = 'StructureDefinition';
+        case "-sd":
+          options.resourceType = "StructureDefinition";
           break;
-        case '-cs':
-          options.resourceType = 'CodeSystem';
+        case "-cs":
+          options.resourceType = "CodeSystem";
           break;
-        case '-vs':
-          options.resourceType = 'ValueSet';
+        case "-vs":
+          options.resourceType = "ValueSet";
           break;
         default:
           // Handle other single-letter flags
           const key = arg.slice(1);
           const nextArg = args[i + 1];
-          if (nextArg && !nextArg.startsWith('-')) {
+          if (nextArg && !nextArg.startsWith("-")) {
             options[key] = nextArg;
             i++;
           } else {
@@ -133,10 +150,10 @@ export function parseArgs(args: string[]): { positional: string[], options: Reco
 }
 
 export async function loadPackageJson(): Promise<any> {
-  const packagePath = path.join(process.cwd(), 'package.json');
+  const packagePath = path.join(process.cwd(), "package.json");
   try {
     if (fs.existsSync(packagePath)) {
-      const content = fs.readFileSync(packagePath, 'utf-8');
+      const content = fs.readFileSync(packagePath, "utf-8");
       return JSON.parse(content);
     }
   } catch (error) {
@@ -146,8 +163,8 @@ export async function loadPackageJson(): Promise<any> {
 }
 
 export async function savePackageJson(data: any): Promise<void> {
-  const packagePath = path.join(process.cwd(), 'package.json');
-  fs.writeFileSync(packagePath, JSON.stringify(data, null, 2) + '\n');
+  const packagePath = path.join(process.cwd(), "package.json");
+  fs.writeFileSync(packagePath, JSON.stringify(data, null, 2) + "\n");
 }
 
 export function getConfigFromPackageJson(packageJson: any): Partial<Config> {
@@ -155,15 +172,8 @@ export function getConfigFromPackageJson(packageJson: any): Partial<Config> {
   return {
     packages: fcm.packages || [],
     registry: fcm.registry,
-    workingDir: process.cwd()
+    workingDir: process.cwd(),
   };
 }
 
-// Run CLI
-// Check if this file is being run directly
-const isMain = import.meta.url === `file://${process.argv[1]}` || 
-                (typeof Bun !== 'undefined' && import.meta.main);
-
-if (isMain) {
-  main();
-}
+main();

package/src/cli/init.ts

@@ -1,9 +1,9 @@
-import * as fs from 'fs';
-import * as path from 'path';
-import { exec } from 'child_process';
-import { promisify } from 'util';
-import { parseArgs, loadPackageJson, savePackageJson } from './index.js';
-import { CanonicalManager } from '../index.js';
+import * as fs from "fs";
+import * as path from "path";
+import { exec } from "child_process";
+import { promisify } from "util";
+import { parseArgs, loadPackageJson, savePackageJson } from "./index.js";
+import { CanonicalManager } from "../index.js";
 
 const execAsync = promisify(exec);
 
@@ -15,13 +15,13 @@ export async function initCommand(args: string[]): Promise<void> {
   // Load or create package.json
   let packageJson = await loadPackageJson();
   const isNewPackageJson = !packageJson;
-  
+
   if (!packageJson) {
     // Create minimal package.json
     packageJson = {
       name: path.basename(process.cwd()),
       version: "1.0.0",
-      type: "module"
+      type: "module",
     };
   }
 
@@ -29,17 +29,23 @@ export async function initCommand(args: string[]): Promise<void> {
   if (!packageJson.fcm) {
     packageJson.fcm = {
       packages: [],
-      registry: registry || "https://fs.get-ig.org/pkgs"
+      registry: registry 
+        ? (registry.endsWith('/') ? registry : `${registry}/`)
+        : "https://fs.get-ig.org/pkgs/",
     };
   }
 
   // If no packages specified, use packages from config
-  const packagesToInstall = packages.length > 0 ? packages : packageJson.fcm.packages;
-  
+  const packagesToInstall =
+    packages.length > 0 ? packages : packageJson.fcm.packages;
+
   if (packagesToInstall.length === 0) {
     console.error("Error: No packages specified");
     console.error("Usage: fcm init [packages...]");
     console.error("Example: fcm init hl7.fhir.r4.core hl7.fhir.us.core@5.0.1");
+    if (process.env.NODE_ENV === 'test') {
+      throw new Error("No packages specified");
+    }
     process.exit(1);
   }
 
@@ -50,9 +56,9 @@ export async function initCommand(args: string[]): Promise<void> {
   });
   packageJson.fcm.packages = Array.from(existingPackages);
 
-  // Update registry if provided
+  // Update registry if provided, ensuring it ends with /
   if (registry) {
-    packageJson.fcm.registry = registry;
+    packageJson.fcm.registry = registry.endsWith('/') ? registry : `${registry}/`;
   }
 
   // Initialize dependencies if not present
@@ -62,24 +68,24 @@ export async function initCommand(args: string[]): Promise<void> {
 
   // Save package.json
   await savePackageJson(packageJson);
-  
+
   if (isNewPackageJson) {
     console.log("Created package.json");
   }
 
   // Install packages using npm
   console.log("Installing FHIR packages...");
-  
+
   for (const pkg of packagesToInstall) {
     console.log(`Installing ${pkg}...`);
     try {
-      const command = packageJson.fcm.registry 
+      const command = packageJson.fcm.registry
         ? `npm install ${pkg} --registry ${packageJson.fcm.registry}`
         : `npm install ${pkg}`;
-      
-      await execAsync(command, { 
+
+      await execAsync(command, {
         cwd: process.cwd(),
-        maxBuffer: 10 * 1024 * 1024 // 10MB buffer
+        maxBuffer: 10 * 1024 * 1024, // 10MB buffer
       });
     } catch (error) {
       console.error(`Failed to install ${pkg}`);
@@ -89,21 +95,22 @@ export async function initCommand(args: string[]): Promise<void> {
 
   // Initialize CanonicalManager to build cache
   console.log("Building package index...");
+  console.log("Registry", packageJson?.fcm?.registry);
   const manager = CanonicalManager({
     packages: packageJson.fcm.packages,
     workingDir: process.cwd(),
-    registry: packageJson.fcm.registry
+    registry: packageJson.fcm.registry,
   });
 
   await manager.init();
-  
+
   // Show summary
   const installedPackages = await manager.packages();
   console.log("\nInstalled packages:");
-  installedPackages.forEach(pkg => {
+  installedPackages.forEach((pkg) => {
     console.log(`  ${pkg.name}@${pkg.version}`);
   });
 
   await manager.destroy();
   console.log("\nInitialization complete!");
-}
+}

package/src/cli/list.ts

@@ -12,6 +12,9 @@ export async function listCommand(args: string[]): Promise<void> {
   if (!packageJson?.fcm?.packages || packageJson.fcm.packages.length === 0) {
     console.error("Error: No FHIR packages configured");
     console.error("Run 'fcm init' first to initialize packages");
+    if (process.env.NODE_ENV === 'test') {
+      throw new Error("No FHIR packages configured");
+    }
     process.exit(1);
   }
 
@@ -41,6 +44,9 @@ export async function listCommand(args: string[]): Promise<void> {
         console.error(`Error: Package '${packageName}' not found`);
         console.error("Available packages:");
         packages.forEach(p => console.error(`  - ${p.name}`));
+        if (process.env.NODE_ENV === 'test') {
+          throw new Error(`Package '${packageName}' not found`);
+        }
         process.exit(1);
       }
 

package/src/cli/resolve.ts

@@ -10,6 +10,9 @@ export async function resolveCommand(args: string[]): Promise<void> {
     console.error("Error: Canonical URL required");
     console.error("Usage: fcm resolve <canonical-url> [--fields field1,field2]");
     console.error("Example: fcm resolve http://hl7.org/fhir/StructureDefinition/Patient");
+    if (process.env.NODE_ENV === 'test') {
+      throw new Error("Canonical URL required");
+    }
     process.exit(1);
   }
 
@@ -18,6 +21,9 @@ export async function resolveCommand(args: string[]): Promise<void> {
   if (!packageJson?.fcm?.packages || packageJson.fcm.packages.length === 0) {
     console.error("Error: No FHIR packages configured");
     console.error("Run 'fcm init' first to initialize packages");
+    if (process.env.NODE_ENV === 'test') {
+      throw new Error("No FHIR packages configured");
+    }
     process.exit(1);
   }
 
@@ -47,6 +53,9 @@ export async function resolveCommand(args: string[]): Promise<void> {
     }
   } catch (error) {
     console.error(`Error: Resource not found: ${url}`);
+    if (process.env.NODE_ENV === 'test') {
+      throw error;
+    }
     process.exit(1);
   } finally {
     await manager.destroy();

package/src/cli/search.ts

@@ -15,6 +15,9 @@ export async function searchCommand(args: string[]): Promise<void> {
   if (!packageJson?.fcm?.packages || packageJson.fcm.packages.length === 0) {
     console.error("Error: No FHIR packages configured");
     console.error("Run 'fcm init' first to initialize packages");
+    if (process.env.NODE_ENV === 'test' || process.env.BUN_TEST) {
+      throw new Error("No FHIR packages configured");
+    }
     process.exit(1);
   }
 
@@ -23,12 +26,19 @@ export async function searchCommand(args: string[]): Promise<void> {
   await manager.init();
 
   try {
-    // Build search criteria
-    const searchCriteria: any = {};
+    // Build filters for smart search
+    const filters: any = {};
+    
+    if (resourceTypeFilter) {
+      filters.resourceType = resourceTypeFilter;
+    }
+    
+    if (typeFilter) {
+      filters.type = typeFilter;
+    }
     
-    // Handle kind filter through search criteria
     if (kindFilter) {
-      searchCriteria.kind = kindFilter;
+      filters.kind = kindFilter;
     }
 
     if (packageFilter) {
@@ -36,42 +46,16 @@ export async function searchCommand(args: string[]): Promise<void> {
       const pkg = packages.find(p => p.name === packageFilter);
       if (!pkg) {
         console.error(`Error: Package '${packageFilter}' not found`);
+        if (process.env.NODE_ENV === 'test' || process.env.BUN_TEST) {
+          throw new Error(`Package '${packageFilter}' not found`);
+        }
         process.exit(1);
       }
-      searchCriteria.package = pkg;
+      filters.package = pkg;
     }
 
-    // Search for resources
-    let results = await manager.searchEntries(searchCriteria);
-
-    // Filter by resourceType if specified
-    if (resourceTypeFilter) {
-      results = results.filter(entry => entry.resourceType === resourceTypeFilter);
-    }
-
-    // Filter by type if specified (e.g., Extension, Patient, Observation)
-    if (typeFilter) {
-      results = results.filter(entry => entry.type === typeFilter);
-    }
-
-    // Filter by URL pattern if provided
-    if (searchTerms.length > 0) {
-      // Convert search terms to lowercase for case-insensitive matching
-      const terms = searchTerms.map(t => t.toLowerCase());
-      
-      results = results.filter(entry => {
-        if (!entry.url) return false;
-        const urlLower = entry.url.toLowerCase();
-        
-        // Check if all search terms match as prefixes in the URL
-        return terms.every(term => {
-          // Split the URL into parts (by /, -, _, .)
-          const urlParts = urlLower.split(/[\/\-_\.]+/);
-          // Check if any part starts with the search term
-          return urlParts.some(part => part.startsWith(term));
-        });
-      });
-    }
+    // Use the new smartSearch from core
+    const results = await manager.smartSearch(searchTerms, filters);
 
     if (isJson) {
       console.log(JSON.stringify(results, null, 2));