@atomic-ehr/fhir-canonical-manager 0.0.14 → 0.0.16

package/src/cli/index.ts

@@ -1,181 +0,0 @@
-#!/usr/bin/env node
-
-import * as fs from "node:fs";
-import * as path from "node:path";
-import { fileURLToPath } from "node:url";
-import type { Config } from "../index.js";
-
-// Command handlers
-import { initCommand } from "./init.js";
-import { listCommand } from "./list.js";
-import { resolveCommand } from "./resolve.js";
-import { searchCommand } from "./search.js";
-import { searchParamCommand } from "./searchparam.js";
-
-// Get version from package.json
-const __filename = fileURLToPath(import.meta.url);
-const __dirname = path.dirname(__filename);
-const packageJsonPath = path.join(__dirname, "..", "..", "package.json");
-
-let VERSION = "unknown";
-try {
-    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";
-}
-
-function showHelp() {
-    console.log(`
-fcm - FHIR Canonical Manager CLI
-
-Usage: fcm <command> [options]
-
-Commands:
-  init         Initialize FHIR packages in current directory
-  list         List packages or resources
-  search       Search for resources
-  resolve      Get a resource by canonical URL
-  searchparam  Display search parameters for a resource type
-
-Options:
-  --help     Show help
-  --version  Show version
-
-Examples:
-  fcm init hl7.fhir.r4.core
-  fcm list
-  fcm search Patient
-  fcm resolve http://hl7.org/fhir/StructureDefinition/Patient
-  fcm searchparam Patient
-`);
-}
-
-async function main() {
-    const args = process.argv.slice(2);
-    const command = args[0];
-
-    if (!command || command === "--help" || command === "-h") {
-        showHelp();
-        if (process.env.NODE_ENV === "test") {
-            return;
-        }
-        process.exit(0);
-    }
-
-    if (command === "--version" || command === "-v") {
-        console.log(VERSION);
-        if (process.env.NODE_ENV === "test") {
-            return;
-        }
-        process.exit(0);
-    }
-
-    const commands: Record<string, (args: string[]) => Promise<void>> = {
-        init: initCommand,
-        list: listCommand,
-        search: searchCommand,
-        resolve: resolveCommand,
-        searchparam: searchParamCommand,
-    };
-
-    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)}`);
-        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>;
-} {
-    const positional: string[] = [];
-    const options: Record<string, string | boolean> = {};
-
-    for (let i = 0; i < args.length; i++) {
-        const arg = args[i];
-        if (arg?.startsWith("--")) {
-            const key = arg.slice(2);
-            const nextArg = args[i + 1];
-            if (nextArg && !nextArg.startsWith("--")) {
-                options[key] = nextArg;
-                i++;
-            } else {
-                options[key] = true;
-            }
-        } else if (arg?.startsWith("-")) {
-            // Handle short aliases
-            switch (arg) {
-                case "-sd":
-                    options.resourceType = "StructureDefinition";
-                    break;
-                case "-cs":
-                    options.resourceType = "CodeSystem";
-                    break;
-                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("-")) {
-                        options[key] = nextArg;
-                        i++;
-                    } else {
-                        options[key] = true;
-                    }
-                }
-            }
-        } else if (arg) {
-            positional.push(arg);
-        }
-    }
-
-    return { positional, options };
-}
-
-export async function loadPackageJson(): Promise<any> {
-    const packagePath = path.join(process.cwd(), "package.json");
-    try {
-        if (fs.existsSync(packagePath)) {
-            const content = fs.readFileSync(packagePath, "utf-8");
-            return JSON.parse(content);
-        }
-    } catch (_error) {
-        // Ignore parse errors
-    }
-    return null;
-}
-
-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`);
-}
-
-export function getConfigFromPackageJson(packageJson: any): Partial<Config> {
-    const fcm = packageJson?.fcm || {};
-    return {
-        packages: fcm.packages || [],
-        registry: fcm.registry,
-        workingDir: process.cwd(),
-    };
-}
-
-main();

package/src/cli/init.ts

@@ -1,112 +0,0 @@
-import { exec } from "node:child_process";
-import * as path from "node:path";
-import { promisify } from "node:util";
-import { CanonicalManager } from "../index.js";
-import { loadPackageJson, parseArgs, savePackageJson } from "./index.js";
-
-const execAsync = promisify(exec);
-
-export async function initCommand(args: string[]): Promise<void> {
-    const { positional, options } = parseArgs(args);
-    const packages = positional;
-    const registry = options.registry as string | undefined;
-
-    // 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",
-        };
-    }
-
-    // Initialize fcm config
-    if (!packageJson.fcm) {
-        packageJson.fcm = {
-            packages: [],
-            registry: registry ? (registry.endsWith("/") ? registry : `${registry}/`) : "https://fs.get-ig.org/pkgs/",
-        };
-    }
-
-    // If no packages specified, use packages from config
-    const packagesToInstall = packages.length > 0 ? packages : packageJson.fcm.packages;
-
-    if (packagesToInstall.length === 0) {
-        console.error("Error: No packages specified");
-        console.error("Usage: fcm init [packages...]");
-        console.error("Example: fcm init hl7.fhir.r4.core hl7.fhir.us.core@5.0.1");
-        if (process.env.NODE_ENV === "test") {
-            throw new Error("No packages specified");
-        }
-        process.exit(1);
-    }
-
-    // Update fcm packages list (merge with existing)
-    const existingPackages = new Set(packageJson.fcm.packages);
-    packagesToInstall.forEach((pkg: string) => {
-        existingPackages.add(pkg);
-    });
-    packageJson.fcm.packages = Array.from(existingPackages);
-
-    // Update registry if provided, ensuring it ends with /
-    if (registry) {
-        packageJson.fcm.registry = registry.endsWith("/") ? registry : `${registry}/`;
-    }
-
-    // Initialize dependencies if not present
-    if (!packageJson.dependencies) {
-        packageJson.dependencies = {};
-    }
-
-    // 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
-                ? `npm install ${pkg} --registry ${packageJson.fcm.registry}`
-                : `npm install ${pkg}`;
-
-            await execAsync(command, {
-                cwd: process.cwd(),
-                maxBuffer: 10 * 1024 * 1024, // 10MB buffer
-            });
-        } catch (error) {
-            console.error(`Failed to install ${pkg}`);
-            throw error;
-        }
-    }
-
-    // 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,
-    });
-
-    await manager.init();
-
-    // Show summary
-    const installedPackages = await manager.packages();
-    console.log("\nInstalled packages:");
-    installedPackages.forEach((pkg) => {
-        console.log(`  ${pkg.name}@${pkg.version}`);
-    });
-
-    await manager.destroy();
-    console.log("\nInitialization complete!");
-}

package/src/cli/list.ts

@@ -1,95 +0,0 @@
-import { CanonicalManager } from "../index.js";
-import { getConfigFromPackageJson, loadPackageJson, parseArgs } from "./index.js";
-
-export async function listCommand(args: string[]): Promise<void> {
-    const { positional, options } = parseArgs(args);
-    const packageName = positional[0];
-    const isJson = options.json === true;
-    const typeFilter = options.type as string | undefined;
-
-    // Load config from package.json
-    const packageJson = await loadPackageJson();
-    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);
-    }
-
-    const config = getConfigFromPackageJson(packageJson);
-    const manager = CanonicalManager(config as any);
-    await manager.init();
-
-    try {
-        if (!packageName) {
-            // List all packages
-            const packages = await manager.packages();
-
-            if (isJson) {
-                console.log(JSON.stringify(packages, null, 2));
-            } else {
-                console.log("Packages:");
-                packages.forEach((pkg) => {
-                    console.log(`  ${pkg.name}@${pkg.version}`);
-                });
-            }
-        } else {
-            // List resources in a specific package
-            const packages = await manager.packages();
-            const pkg = packages.find((p) => p.name === packageName);
-
-            if (!pkg) {
-                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);
-            }
-
-            let resources = await manager.searchEntries({ package: pkg });
-
-            // Apply type filter if specified
-            if (typeFilter) {
-                resources = resources.filter((r) => r.resourceType === typeFilter);
-            }
-
-            if (isJson) {
-                console.log(JSON.stringify(resources, null, 2));
-            } else {
-                console.log(`Resources in ${packageName}:`);
-
-                if (resources.length === 0) {
-                    console.log("  No resources found");
-                } else {
-                    // Group by type
-                    const byType = resources.reduce(
-                        (acc, resource) => {
-                            const type = resource.resourceType || resource.type || "Unknown";
-                            if (!acc[type]) acc[type] = 0;
-                            acc[type]++;
-                            return acc;
-                        },
-                        {} as Record<string, number>,
-                    );
-
-                    // Show summary
-                    Object.entries(byType)
-                        .sort()
-                        .forEach(([type, count]) => {
-                            console.log(`  ${type}: ${count}`);
-                        });
-
-                    console.log(`\nTotal: ${resources.length} resources`);
-                }
-            }
-        }
-    } finally {
-        await manager.destroy();
-    }
-}

package/src/cli/resolve.ts

@@ -1,63 +0,0 @@
-import { CanonicalManager } from "../index.js";
-import { getConfigFromPackageJson, loadPackageJson, parseArgs } from "./index.js";
-
-export async function resolveCommand(args: string[]): Promise<void> {
-    const { positional, options } = parseArgs(args);
-    const url = positional[0];
-    const fields = options.fields as string | undefined;
-
-    if (!url) {
-        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);
-    }
-
-    // Load config from package.json
-    const packageJson = await loadPackageJson();
-    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);
-    }
-
-    const config = getConfigFromPackageJson(packageJson);
-    const manager = CanonicalManager(config as any);
-    await manager.init();
-
-    try {
-        // Resolve the resource
-        const resource = await manager.resolve(url);
-
-        if (fields) {
-            // Extract only specified fields
-            const fieldList = fields.split(",").map((f) => f.trim());
-            const filtered: any = {};
-
-            fieldList.forEach((field) => {
-                if (field in resource) {
-                    filtered[field] = resource[field];
-                }
-            });
-
-            console.log(JSON.stringify(filtered, null, 2));
-        } else {
-            // Output full resource
-            console.log(JSON.stringify(resource, null, 2));
-        }
-    } 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

@@ -1,83 +0,0 @@
-import { CanonicalManager } from "../index.js";
-import { getConfigFromPackageJson, loadPackageJson, parseArgs } from "./index.js";
-
-export async function searchCommand(args: string[]): Promise<void> {
-    const { positional, options } = parseArgs(args);
-    const searchTerms = positional; // Now support multiple search terms
-    const isJson = options.json === true;
-    const resourceTypeFilter = (options.type || options.resourceType) as string | undefined;
-    const typeFilter = options.t as string | undefined;
-    const kindFilter = options.k as string | undefined;
-    const packageFilter = options.package as string | undefined;
-
-    // Load config from package.json
-    const packageJson = await loadPackageJson();
-    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);
-    }
-
-    const config = getConfigFromPackageJson(packageJson);
-    const manager = CanonicalManager(config as any);
-    await manager.init();
-
-    try {
-        // Build filters for smart search
-        const filters: any = {};
-
-        if (resourceTypeFilter) {
-            filters.resourceType = resourceTypeFilter;
-        }
-
-        if (typeFilter) {
-            filters.type = typeFilter;
-        }
-
-        if (kindFilter) {
-            filters.kind = kindFilter;
-        }
-
-        if (packageFilter) {
-            const packages = await manager.packages();
-            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);
-            }
-            filters.package = pkg;
-        }
-
-        // Use the new smartSearch from core
-        const results = await manager.smartSearch(searchTerms, filters);
-
-        if (isJson) {
-            console.log(JSON.stringify(results, null, 2));
-        } else {
-            if (results.length === 0) {
-                console.log("No resources found");
-            } else {
-                const searchInfo = searchTerms.length > 0 ? ` matching "${searchTerms.join(" ")}"` : "";
-                console.log(`Found ${results.length} resource${results.length === 1 ? "" : "s"}${searchInfo}:`);
-
-                results.forEach((resource) => {
-                    const info = {
-                        resourceType: resource.resourceType,
-                        kind: resource.kind,
-                        type: resource.type,
-                        package: resource.package?.name,
-                    };
-                    console.log(`${resource.url}, ${JSON.stringify(info)}`);
-                });
-            }
-        }
-    } finally {
-        await manager.destroy();
-    }
-}

package/src/cli/searchparam.ts

@@ -1,163 +0,0 @@
-/**
- * Search parameters command - displays search parameters for a resource type
- */
-
-import { CanonicalManager } from "../index.js";
-import type { SearchParameter } from "../types/index.js";
-import { getConfigFromPackageJson, loadPackageJson, parseArgs } from "./index.js";
-
-export async function searchParamCommand(args: string[]): Promise<void> {
-    const { positional, options } = parseArgs(args);
-
-    if (options.help || positional.length === 0) {
-        console.log(`
-Usage: fcm searchparam <resourceType> [options]
-
-Display search parameters for a specific FHIR resource type
-
-Arguments:
-  resourceType    The FHIR resource type (e.g., Patient, Observation)
-
-Options:
-  --format        Output format: table (default), json, csv
-  --help          Show this help message
-
-Examples:
-  fcm searchparam Patient
-  fcm searchparam Observation --format json
-  fcm searchparam Encounter --format csv
-`);
-        return;
-    }
-
-    const resourceType = positional[0];
-    if (!resourceType) {
-        console.error("Error: Resource type is required");
-        process.exit(1);
-    }
-    const format = (options.format as string) || "table";
-
-    // Load config from package.json
-    const packageJson = await loadPackageJson();
-    if (!packageJson) {
-        throw new Error("No package.json found. Run 'fcm init' to initialize a project.");
-    }
-
-    const config = getConfigFromPackageJson(packageJson);
-    const manager = CanonicalManager({
-        packages: config.packages || [],
-        registry: config.registry,
-        workingDir: config.workingDir || process.cwd(),
-    });
-
-    await manager.init();
-
-    try {
-        const searchParams = await manager.getSearchParametersForResource(resourceType);
-
-        if (searchParams.length === 0) {
-            console.log(`No search parameters found for resource type '${resourceType}'`);
-            return;
-        }
-
-        // Format output based on requested format
-        switch (format) {
-            case "json":
-                outputJson(searchParams);
-                break;
-            case "csv":
-                outputCsv(searchParams);
-                break;
-            default:
-                outputTable(searchParams);
-                break;
-        }
-    } finally {
-        await manager.destroy();
-    }
-}
-
-function outputTable(searchParams: SearchParameter[]): void {
-    console.log("");
-
-    // Display each parameter as a multiline block
-    for (const param of searchParams) {
-        const code = param.code || "";
-        const type = param.type || "";
-        const expression = param.expression || "";
-        const url = param.url || "";
-
-        console.log(`Code:       ${code}`);
-        console.log(`Type:       ${type}`);
-        if (expression) {
-            // Wrap long expressions
-            if (expression.length > 60) {
-                console.log(`Expression: ${wrapText(expression, 60, "            ")}`);
-            } else {
-                console.log(`Expression: ${expression}`);
-            }
-        } else {
-            console.log(`Expression: (none)`);
-        }
-        console.log(`URL:        ${url}`);
-        console.log("---");
-    }
-
-    console.log(`Total: ${searchParams.length} search parameters`);
-}
-
-// Helper function to wrap text at specified width
-function wrapText(text: string, width: number, indent: string): string {
-    const words = text.split(" ");
-    const lines: string[] = [];
-    let currentLine = "";
-
-    for (const word of words) {
-        if (currentLine.length + word.length + 1 <= width) {
-            currentLine += (currentLine ? " " : "") + word;
-        } else {
-            if (currentLine) {
-                lines.push(currentLine);
-            }
-            currentLine = word;
-        }
-    }
-
-    if (currentLine) {
-        lines.push(currentLine);
-    }
-
-    return lines.join(`\n${indent}`);
-}
-
-function outputJson(searchParams: SearchParameter[]): void {
-    const output = searchParams.map((param) => ({
-        code: param.code,
-        type: param.type,
-        expression: param.expression || null,
-        url: param.url,
-    }));
-    console.log(JSON.stringify(output, null, 2));
-}
-
-function outputCsv(searchParams: SearchParameter[]): void {
-    // CSV header
-    console.log("Code,Type,Expression,URL");
-
-    // CSV rows - no truncation for CSV output
-    for (const param of searchParams) {
-        const code = escapeCsv(param.code || "");
-        const type = escapeCsv(param.type || "");
-        const expression = escapeCsv(param.expression || "");
-        const url = escapeCsv(param.url || "");
-        console.log(`${code},${type},${expression},${url}`);
-    }
-}
-
-function escapeCsv(value: string): string {
-    // Escape CSV values that contain commas, quotes, or newlines
-    if (value.includes(",") || value.includes('"') || value.includes("\n")) {
-        return `"${value.replace(/"/g, '""')}"`;
-    }
-    return value;
-}