fhirsmith 0.9.6 → 0.9.7

package/tx/xversion/xv-valueset.js

@@ -14,10 +14,10 @@ function valueSetToR5(jsonObj, sourceVersion) {
   if (VersionUtilities.isR5Ver(sourceVersion)) {
     return jsonObj; // No conversion needed
   }
-  for (const inc of jsonObj.compose.include || []) {
+  for (const inc of jsonObj.compose?.include || []) {
     valueSetIncludeToR5(inc);
   }
-  for (const inc of jsonObj.compose.exclude || []) {
+  for (const inc of jsonObj.compose?.exclude || []) {
     valueSetIncludeToR5(inc);
   }
   if (VersionUtilities.isR4Ver(sourceVersion)) {
@@ -90,7 +90,7 @@ function valueSetR5ToR4(r5Obj) {
       if (include.filter && Array.isArray(include.filter)) {
         include.filter = include.filter.map(filter => {
           if (filter.op && isR5OnlyFilterOperator(filter.op)) {
-            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            filter._op = { "extension": [{ url: "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}]};
             delete filter.op;
           }
           return filter;
@@ -105,7 +105,7 @@ function valueSetR5ToR4(r5Obj) {
       if (exclude.filter && Array.isArray(exclude.filter)) {
         exclude.filter = exclude.filter.map(filter => {
           if (filter.op && isR5OnlyFilterOperator(filter.op)) {
-            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            filter._op = { "extension": [{ url: "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}]};
             delete filter.op;
           }
           return filter;
@@ -155,7 +155,7 @@ function valueSetR5ToR3(r5Obj) {
       if (include.filter && Array.isArray(include.filter)) {
         include.filter = include.filter.map(filter => {
           if (filter.op && !isR3CompatibleFilterOperator(filter.op)) {
-            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            filter._op = { "extension": [{ url: "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}]};
             delete filter.op;
           }
           return filter;
@@ -170,7 +170,7 @@ function valueSetR5ToR3(r5Obj) {
       if (exclude.filter && Array.isArray(exclude.filter)) {
         exclude.filter = exclude.filter.map(filter => {
           if (filter.op && !isR3CompatibleFilterOperator(filter.op)) {
-            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            filter._op = { "extension": [{ url: "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}]};
             delete filter.op;
           }
           return filter;
@@ -223,7 +223,7 @@ function convertContainsPropertyR5ToR4(containsList) {
  */
 function isR5OnlyFilterOperator(operator) {
   const r5OnlyOperators = [
-    'child-of', ' descendent-leaf' // Added in R5
+    'child-of', 'descendent-leaf' // Added in R5
   ];
   return r5OnlyOperators.includes(operator);
 }

package/publisher/task-draft.js

@@ -1,463 +0,0 @@
-const fs = require('fs');
-const path = require('path');
-const { spawn } = require('child_process');
-const axios = require('axios');
-
-class DraftTaskProcessor {
-  constructor(config, logger, logTaskMessage, updateTaskStatus) {
-    this.config = config;
-    this.logger = logger;
-    this.logTaskMessage = logTaskMessage;
-    this.updateTaskStatus = updateTaskStatus;
-  }
-
-  async processDraftBuild(task) {
-    this.logger.info('Processing draft build for task #' + task.id + ' (' + task.npm_package_id + '#' + task.version + ')');
-
-    try {
-      // Update status to building
-      await this.updateTaskStatus(task.id, 'building');
-      await this.logTaskMessage(task.id, 'info', 'Started draft build');
-
-      // Run actual build process
-      await this.runDraftBuild(task);
-
-      // Update status to waiting for approval
-      await this.updateTaskStatus(task.id, 'waiting for approval');
-      await this.logTaskMessage(task.id, 'info', 'Draft build completed - waiting for approval');
-
-      this.logger.info('Draft build completed for task #' + task.id);
-
-    } catch (error) {
-      this.logger.error('Draft build failed for task #' + task.id + ':', error);
-      await this.updateTaskStatus(task.id, 'failed', {
-        failure_reason: error.message
-      });
-      await this.logTaskMessage(task.id, 'error', 'Draft build failed: ' + error.message);
-      throw error; // Re-throw so the main processor knows it failed
-    }
-  }
-
-  async runDraftBuild(task) {
-    const taskDir = path.join(this.config.workspaceRoot, 'task-' + task.id);
-    const draftDir = path.join(taskDir, 'draft');
-    const logFile = path.join(taskDir, 'draft-build.log');
-
-    await this.logTaskMessage(task.id, 'info', 'Creating task directory: ' + taskDir);
-
-    // Step 1: Create/scrub task directory
-    await this.createTaskDirectory(taskDir);
-
-    // Step 2: Download latest publisher
-    const publisherJar = await this.downloadPublisher(taskDir, task.id);
-
-    // Step 3: Clone GitHub repository
-    await this.cloneRepository(task, draftDir);
-
-    // Step 4: Install FSH Sushi globally
-    await this.installFshSushi(task.id);
-
-    // Step 5: Run IG publisher
-    await this.runIGPublisher(publisherJar, draftDir, logFile, task.id);
-
-    // Update task with build output path
-    await this.updateTaskStatus(task.id, 'building', {
-      build_output_path: logFile,
-      local_folder: taskDir
-    });
-
-    this.logger.info('Draft build completed for ' + task.npm_package_id + '#' + task.version);
-  }
-
-  async createTaskDirectory(taskDir) {
-    await this.logTaskMessage(null, 'info', 'Creating/cleaning task directory: ' + taskDir);
-
-    // Remove existing directory if it exists
-    if (fs.existsSync(taskDir)) {
-      // Use Node.js built-in fs.rm (Node 14.14+) or fs.rmSync (Node 14.14+)
-      if (fs.promises && fs.promises.rm) {
-        // Use promise-based API
-        await fs.promises.rm(taskDir, { recursive: true, force: true });
-      } else if (fs.rmSync) {
-        // Use synchronous API
-        fs.rmSync(taskDir, { recursive: true, force: true });
-      } else {
-        // Fallback for older Node versions
-        const rimraf = require('rimraf');
-        await new Promise((resolve, reject) => {
-          if (typeof rimraf === 'function') {
-            rimraf(taskDir, (err) => {
-              if (err) reject(err);
-              else resolve();
-            });
-          } else if (rimraf.rimraf) {
-            rimraf.rimraf(taskDir).then(resolve).catch(reject);
-          } else {
-            reject(new Error('Unable to remove directory - unsupported rimraf version'));
-          }
-        });
-      }
-    }
-
-    // Create fresh directory
-    fs.mkdirSync(taskDir, { recursive: true });
-  }
-
-  async downloadPublisher(taskDir, taskId) {
-    const publisherJar = path.join(taskDir, 'publisher.jar');
-
-    await this.logTaskMessage(taskId, 'info', 'Downloading latest FHIR IG Publisher...');
-
-    // Ensure the target directory exists
-    if (!fs.existsSync(taskDir)) {
-      fs.mkdirSync(taskDir, { recursive: true });
-    }
-
-    try {
-      // Get latest release info from GitHub API
-      const releaseResponse = await axios.get('https://api.github.com/repos/HL7/fhir-ig-publisher/releases/latest', {
-        timeout: 30000 // 30 second timeout
-      });
-
-      const downloadUrl = releaseResponse.data.assets.find(asset =>
-        asset.name === 'publisher.jar'
-      )?.browser_download_url;
-
-      if (!downloadUrl) {
-        throw new Error('Could not find publisher.jar in latest release');
-      }
-
-      await this.logTaskMessage(taskId, 'info', 'Downloading from: ' + downloadUrl);
-
-      // Download the file with progress tracking
-      const response = await axios({
-        method: 'GET',
-        url: downloadUrl,
-        responseType: 'stream',
-        timeout: 300000 // 5 minute timeout for download
-      });
-
-      const writer = fs.createWriteStream(publisherJar);
-
-      // Track download progress
-      let downloadedBytes = 0;
-      const totalBytes = parseInt(response.headers['content-length'] || '0');
-      let lastProgressPercent = -1;
-
-      response.data.on('data', (chunk) => {
-        downloadedBytes += chunk.length;
-        if (totalBytes > 0) {
-          const progress = Math.round((downloadedBytes / totalBytes) * 100);
-          // Log every 10% but avoid duplicate logs
-          if (progress % 10 === 0 && progress !== lastProgressPercent) {
-            this.logTaskMessage(taskId, 'info', 'Download progress: ' + progress + '%');
-            lastProgressPercent = progress;
-          }
-        }
-      });
-
-      response.data.pipe(writer);
-
-      await new Promise((resolve, reject) => {
-        writer.on('finish', resolve);
-        writer.on('error', reject);
-      });
-
-      await this.logTaskMessage(taskId, 'info', 'Publisher downloaded successfully (' + Math.round(downloadedBytes / 1024 / 1024) + 'MB)');
-      return publisherJar;
-
-    } catch (error) {
-      if (error.code === 'ECONNABORTED') {
-        throw new Error('Publisher download timed out - please try again');
-      }
-      throw new Error('Failed to download publisher: ' + error.message);
-    }
-  }
-
-  async cloneRepository(task, draftDir) {
-    const gitUrl = 'https://github.com/' + task.github_org + '/' + task.github_repo + '.git';
-
-    await this.logTaskMessage(task.id, 'info', 'Cloning repository: ' + gitUrl + ' (branch: ' + task.git_branch + ')');
-
-    return new Promise((resolve, reject) => {
-      const git = spawn('git', [
-        'clone',
-        '--branch', task.git_branch,
-        '--single-branch',
-        '--depth', '1', // Shallow clone for faster download
-        gitUrl,
-        draftDir
-      ], {
-        stdio: ['pipe', 'pipe', 'pipe']
-      });
-
-      // eslint-disable-next-line no-unused-vars
-      let stdout = '';
-      let stderr = '';
-
-      git.stdout.on('data', (data) => {
-        stdout += data.toString();
-      });
-
-      git.stderr.on('data', (data) => {
-        stderr += data.toString();
-      });
-
-      git.on('close', async (code) => {
-        if (code === 0) {
-          await this.logTaskMessage(task.id, 'info', 'Repository cloned successfully');
-
-          // Log some info about what was cloned
-          try {
-            const stats = fs.statSync(draftDir);
-            if (stats.isDirectory()) {
-              const files = fs.readdirSync(draftDir);
-              await this.logTaskMessage(task.id, 'info', 'Cloned ' + files.length + ' files/directories');
-            }
-          } catch (e) {
-            // Don't fail if we can't get stats
-          }
-
-          resolve();
-        } else {
-          const error = 'Git clone failed with code ' + code + ': ' + stderr;
-          await this.logTaskMessage(task.id, 'error', error);
-          reject(new Error(error));
-        }
-      });
-
-      git.on('error', async (error) => {
-        await this.logTaskMessage(task.id, 'error', 'Git clone error: ' + error.message);
-        reject(error);
-      });
-
-      // Timeout for git clone (10 minutes)
-      const timeout = setTimeout(async () => {
-        git.kill();
-        await this.logTaskMessage(task.id, 'error', 'Git clone timed out after 10 minutes');
-        reject(new Error('Git clone timed out'));
-      }, 10 * 60 * 1000);
-
-      git.on('close', () => {
-        clearTimeout(timeout);
-      });
-    });
-  }
-
-  async installFshSushi(taskId) {
-    await this.logTaskMessage(taskId, 'info', 'Installing FSH Sushi globally...');
-
-    return new Promise((resolve, reject) => {
-      const npm = spawn('npm', [
-        'install',
-        '-g',
-        'fsh-sushi'
-      ], {
-        stdio: ['pipe', 'pipe', 'pipe']
-      });
-
-      // eslint-disable-next-line no-unused-vars
-      let stdout = '';
-      let stderr = '';
-
-      npm.stdout.on('data', (data) => {
-        stdout += data.toString();
-      });
-
-      npm.stderr.on('data', (data) => {
-        stderr += data.toString();
-      });
-
-      npm.on('close', async (code) => {
-        if (code === 0) {
-          await this.logTaskMessage(taskId, 'info', 'FSH Sushi installed successfully');
-
-          // Verify installation by checking version
-          try {
-            await this.checkSushiVersion(taskId);
-          } catch (versionError) {
-            this.logTaskMessage(taskId, 'warn', 'FSH Sushi installed but version check failed: ' + versionError.message);
-          }
-
-          resolve();
-        } else {
-          const error = 'NPM install failed with code ' + code + ': ' + stderr;
-          await this.logTaskMessage(taskId, 'error', error);
-          reject(new Error(error));
-        }
-      });
-
-      npm.on('error', async (error) => {
-        await this.logTaskMessage(taskId, 'error', 'NPM install error: ' + error.message);
-        reject(error);
-      });
-
-      // Timeout after 5 minutes
-      const timeout = setTimeout(async () => {
-        npm.kill('SIGTERM');
-
-        // Force kill after 10 seconds if still running
-        setTimeout(() => {
-          npm.kill('SIGKILL');
-        }, 10000);
-
-        await this.logTaskMessage(taskId, 'error', 'FSH Sushi installation timed out after 5 minutes');
-        reject(new Error('FSH Sushi installation timed out'));
-      }, 5 * 60 * 1000);
-
-      npm.on('close', () => {
-        clearTimeout(timeout);
-      });
-    });
-  }
-
-  async checkSushiVersion(taskId) {
-    return new Promise((resolve, reject) => {
-      const sushi = spawn('sushi', ['--version'], {
-        stdio: ['pipe', 'pipe', 'pipe']
-      });
-
-      let stdout = '';
-      // eslint-disable-next-line no-unused-vars
-      let stderr = '';
-
-      sushi.stdout.on('data', (data) => {
-        stdout += data.toString();
-      });
-
-      sushi.stderr.on('data', (data) => {
-        stderr += data.toString();
-      });
-
-      sushi.on('close', async (code) => {
-        if (code === 0) {
-          const version = stdout.trim();
-          await this.logTaskMessage(taskId, 'info', 'FSH Sushi version: ' + version);
-          resolve(version);
-        } else {
-          reject(new Error('Sushi version check failed with code ' + code));
-        }
-      });
-
-      sushi.on('error', (error) => {
-        reject(error);
-      });
-
-      // Quick timeout for version check
-      setTimeout(() => {
-        sushi.kill();
-        reject(new Error('Sushi version check timed out'));
-      }, 30000);
-    });
-  }
-
-  async runIGPublisher(publisherJar, draftDir, logFile, taskId) {
-    await this.logTaskMessage(taskId, 'info', 'Running FHIR IG Publisher...');
-
-    // Check if sushi.config.yaml exists and log it
-    const sushiConfigPath = path.join(draftDir, 'sushi-config.yaml');
-    if (fs.existsSync(sushiConfigPath)) {
-      await this.logTaskMessage(taskId, 'info', 'Found sushi-config.yaml');
-    } else {
-      await this.logTaskMessage(taskId, 'info', 'No sushi-config.yaml found');
-    }
-
-    return new Promise((resolve, reject) => {
-      const java = spawn('java', [
-        '-jar',
-        '-Xmx20000m',
-        publisherJar,
-        '-ig',
-        '.'
-      ], {
-        cwd: draftDir,
-        stdio: ['pipe', 'pipe', 'pipe']
-      });
-
-      // Create log file stream
-      const logStream = fs.createWriteStream(logFile);
-
-      // Write header to log file
-      const startTime = new Date().toISOString();
-      logStream.write('=== FHIR IG Publisher Build Log ===\n');
-      logStream.write('Started: ' + startTime + '\n');
-      logStream.write('Command: java -jar -Xmx20000m publisher.jar -ig .\n');
-      logStream.write('Working Directory: ' + draftDir + '\n');
-      logStream.write('=====================================\n\n');
-
-      // eslint-disable-next-line no-unused-vars
-      let hasOutput = false;
-      let lastProgressUpdate = Date.now();
-
-      java.stdout.on('data', (data) => {
-        hasOutput = true;
-        logStream.write(data);
-
-        // Log progress periodically
-        const now = Date.now();
-        if (now - lastProgressUpdate > 30000) { // Every 30 seconds
-          this.logTaskMessage(taskId, 'info', 'IG Publisher is still running...');
-          lastProgressUpdate = now;
-        }
-      });
-
-      java.stderr.on('data', (data) => {
-        hasOutput = true;
-        logStream.write(data);
-      });
-
-      java.on('close', async (code) => {
-        const endTime = new Date().toISOString();
-        logStream.write('\n=====================================\n');
-        logStream.write('Finished: ' + endTime + '\n');
-        logStream.write('Exit Code: ' + code + '\n');
-        logStream.end();
-
-        if (code === 0) {
-          await this.logTaskMessage(taskId, 'info', 'IG Publisher completed successfully');
-
-          // Check for QA report
-          const qaReportPath = path.join(draftDir, 'output', 'qa.html');
-          if (fs.existsSync(qaReportPath)) {
-            await this.logTaskMessage(taskId, 'info', 'QA report generated: output/qa.html');
-          }
-
-          resolve();
-        } else {
-          const error = 'IG Publisher failed with exit code: ' + code;
-          await this.logTaskMessage(taskId, 'error', error);
-          reject(new Error(error));
-        }
-      });
-
-      java.on('error', async (error) => {
-        logStream.write('\nERROR: ' + error.message + '\n');
-        logStream.end();
-        await this.logTaskMessage(taskId, 'error', 'IG Publisher error: ' + error.message);
-        reject(error);
-      });
-
-      // Timeout configurable via publisher.igPublisherTimeoutMinutes (default: 60 minutes)
-      const timeoutMinutes = this.config.igPublisherTimeoutMinutes || 60;
-      const timeout = setTimeout(async () => {
-        java.kill('SIGTERM'); // Try graceful shutdown first
-
-        // Force kill after 10 seconds if still running
-        setTimeout(() => {
-          java.kill('SIGKILL');
-        }, 10000);
-
-        logStream.write('\nTIMEOUT: Process killed after ' + timeoutMinutes + ' minutes\n');
-        logStream.end();
-        await this.logTaskMessage(taskId, 'error', 'IG Publisher timed out after ' + timeoutMinutes + ' minutes');
-        reject(new Error('IG Publisher timed out'));
-      }, timeoutMinutes * 60 * 1000);
-
-      java.on('close', () => {
-        clearTimeout(timeout);
-      });
-    });
-  }
-}
-
-module.exports = DraftTaskProcessor;