fhirsmith 0.9.6 → 0.9.7

package/CHANGELOG.md

@@ -6,6 +6,26 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [v0.9.7] - 2026-06-12
+
+### Added
+
+- Support for tx modele to load resources directly 
+- Missing overwork protection processing ECL
+
+### Fixed
+
+- Fix bug validating secondary displays across languages
+- Fix CORS issue (double headers)
+- Fix czech code in snomed import
+- Many minor validation fixes
+- ECL processing bugs
+- Publishing: better logging, and fix timeout & restart error
+
+### Tx Conformance Statement
+
+FHIRsmith passed all 2503 HL7 terminology service tests (modes tx.fhir.org+omop+general+snomed, tests v1.9.1, runner v6.9.10)
+
 ## [v0.9.6] - 2026-05-21
 
 ### Added

package/library/folder-content-loader.js

@@ -0,0 +1,91 @@
+const fs = require('fs').promises;
+const path = require('path');
+const { PackageContentLoader } = require('./package-manager');
+
+/**
+ * A content loader that scans a folder for JSON FHIR terminology resources
+ * (CodeSystem, ValueSet, ConceptMap). It synthesizes the package layout that
+ * PackageContentLoader expects so the existing PackageValueSetProvider /
+ * PackageConceptMapProvider machinery can be reused without modification.
+ *
+ * The user's source folder is treated as read-only. Any SQLite caches built
+ * by the Package*Provider classes are written to the cacheFolder passed in,
+ * not to the source folder.
+ */
+class FolderContentLoader extends PackageContentLoader {
+  /**
+   * @param {string} sourceFolder - Folder to scan for JSON resources
+   * @param {string} cacheFolder - Folder where Package*Provider DBs may live
+   */
+  constructor(sourceFolder, cacheFolder) {
+    super(cacheFolder);
+    this.sourceFolder = sourceFolder;
+    // Resources are read directly from the source folder rather than from
+    // <packageFolder>/package as PackageContentLoader assumes.
+    this.packageSubfolder = sourceFolder;
+  }
+
+  /**
+   * Replaces the standard initialize: there is no package.json or .index.json
+   * to read, so we synthesize an index from the JSON files in the folder.
+   */
+  async initialize() {
+    if (this.loaded) {
+      return;
+    }
+
+    try {
+      const stat = await fs.stat(this.sourceFolder);
+      if (!stat.isDirectory()) {
+        throw new Error(`Folder source path is not a directory: ${this.sourceFolder}`);
+      }
+    } catch (err) {
+      if (err.code === 'ENOENT') {
+        throw new Error(`Folder source path does not exist: ${this.sourceFolder}`);
+      }
+      throw err;
+    }
+
+    // Synthesize package metadata so id()/version()/pid() return something usable.
+    this.package = {
+      name: 'folder.' + path.basename(this.sourceFolder),
+      version: '0.0.0',
+      fhirVersions: ['5.0.0']
+    };
+
+    const files = [];
+    const entries = await fs.readdir(this.sourceFolder, { withFileTypes: true });
+    for (const entry of entries) {
+      if (!entry.isFile()) continue;
+      if (!entry.name.toLowerCase().endsWith('.json')) continue;
+
+      const fullPath = path.join(this.sourceFolder, entry.name);
+      let json;
+      try {
+        const content = await fs.readFile(fullPath, 'utf8');
+        json = JSON.parse(content);
+      } catch {
+        // Skip unreadable / non-JSON files rather than failing the whole load.
+        continue;
+      }
+
+      if (!json || typeof json !== 'object') continue;
+      const rt = json.resourceType;
+      if (rt !== 'CodeSystem' && rt !== 'ValueSet' && rt !== 'ConceptMap') continue;
+
+      files.push({
+        filename: entry.name,
+        resourceType: rt,
+        id: json.id,
+        url: json.url,
+        version: json.version
+      });
+    }
+
+    this.index = { files, 'index-version': 2 };
+    this.buildIndexes();
+    this.loaded = true;
+  }
+}
+
+module.exports = { FolderContentLoader };

package/npmprojector/npmprojector.js

@@ -127,12 +127,8 @@ class NpmProjectorModule {
    * Set up Express routes
    */
   setupRoutes() {
-    // CORS for browser access
-    this.router.use((req, res, next) => {
-      res.header('Access-Control-Allow-Origin', '*');
-      res.header('Access-Control-Allow-Headers', 'Origin, X-Requested-With, Content-Type, Accept');
-      next();
-    });
+    // CORS is handled once at the app level (server.js, from config.server.cors).
+    // Do not set Access-Control-* headers here.
 
     // Root - module info
     this.router.get('/', (req, res) => {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirsmith",
-  "version": "0.9.6",
+  "version": "0.9.7",
   "txVersion": "1.9.1",
   "description": "A Node.js server that provides a collection of tools to serve the FHIR ecosystem",
   "main": "server.js",

package/publisher/publisher.js

@@ -17,6 +17,7 @@ class PublisherModule {
     this.logger = null;
     this.taskProcessor = null;
     this.isProcessing = false;
+    this.activeTaskIds = new Set();
     this.shutdownRequested = false;
     this.stats = stats;
   }
@@ -308,13 +309,19 @@ class PublisherModule {
       if (this.shutdownRequested) return;
 
       if (this.isProcessing) {
+        // A publication can legitimately run for longer than an hour (go-publish on a
+        // large IG), so never reset isProcessing while a task is in flight — doing so
+        // lets the poller start a second, concurrent run of the same task, which then
+        // fails on 'ig-registry already exists' and stomps the real run's status.
+        // Recovery from a genuinely hung IG Publisher is handled by the
+        // igPublisherTimeoutMinutes kill in runIgPublisher/runPublisherGoPublish.
         const stuckMs = this.isProcessingStarted ? Date.now() - this.isProcessingStarted : 0;
-        if (stuckMs > 60 * 60 * 1000) {
-          this.logger.warn('Task processor appears stuck (' + Math.round(stuckMs / 60000) + ' min) — resetting');
-          this.isProcessing = false;
-        } else {
-          return;
+        const warnAfterMs = ((this.config.igPublisherTimeoutMinutes || 60) + 30) * 60 * 1000;
+        if (stuckMs > warnAfterMs) {
+          this.logger.warn('Task processor still busy after ' + Math.round(stuckMs / 60000) + ' min (tasks: ' +
+            Array.from(this.activeTaskIds).join(', ') + ') — possible hang, not starting new work');
         }
+        return;
       }
 
       await this.processNextTask();
@@ -325,10 +332,14 @@ class PublisherModule {
     this.isProcessing = true;
     this.isProcessingStarted = Date.now();
 
+    let claimedTaskId = null;
     try {
       // Look for queued tasks first (draft builds)
       let task = await this.getNextQueuedTask();
       if (task) {
+        if (this.activeTaskIds.has(task.id)) return; // already being processed
+        claimedTaskId = task.id;
+        this.activeTaskIds.add(task.id);
         this.stats.task('Publisher', 'Building ' + task.npm_package_id + '#' + task.version);
         await this.processDraftBuild(task);
         this.stats.taskDone('Publisher', 'Built ' + task.npm_package_id + '#' + task.version);
@@ -338,6 +349,9 @@ class PublisherModule {
       // Then look for approved tasks (publishing)
       task = await this.getNextApprovedTask();
       if (task) {
+        if (this.activeTaskIds.has(task.id)) return; // already being processed
+        claimedTaskId = task.id;
+        this.activeTaskIds.add(task.id);
         this.stats.task('Publisher', 'Publishing ' + task.npm_package_id + '#' + task.version);
         await this.processPublication(task);
         this.stats.taskDone('Publisher', 'Published ' + task.npm_package_id + '#' + task.version);
@@ -349,6 +363,9 @@ class PublisherModule {
       this.logger.error('Error in task processor:', error);
       this.stats.taskError('Publisher', 'Error: ' + error.message);
     } finally {
+      if (claimedTaskId !== null) {
+        this.activeTaskIds.delete(claimedTaskId);
+      }
       this.isProcessing = false;
     }
   }
@@ -390,6 +407,9 @@ class PublisherModule {
       fields.push('waiting_approval_at = CURRENT_TIMESTAMP');
     } else if (status === 'complete') {
       fields.push('completed_at = CURRENT_TIMESTAMP');
+      // A successful completion invalidates any earlier failure (e.g. from a
+      // superseded duplicate run) — don't let a stale message outlive success.
+      fields.push('failure_reason = NULL');
     } else if (status === 'failed') {
       fields.push('failed_at = CURRENT_TIMESTAMP');
     }
@@ -414,6 +434,28 @@ class PublisherModule {
     });
   }
 
+  // Update arbitrary task fields WITHOUT touching status. Use this from long-running
+  // work (e.g. saving the announcement mid-publication) — writing back the in-memory
+  // task.status can resurrect a stale status and cause the poller to re-run the task.
+  async updateTaskFields(taskId, fields) {
+    const keys = Object.keys(fields);
+    if (keys.length === 0) return;
+    const assignments = keys.map(key => key + ' = ?');
+    const values = keys.map(key => fields[key]);
+    values.push(taskId);
+
+    return new Promise((resolve, reject) => {
+      this.db.run(
+          'UPDATE tasks SET ' + assignments.join(', ') + ' WHERE id = ?',
+          values,
+          (err) => {
+            if (err) reject(err);
+            else resolve();
+          }
+      );
+    });
+  }
+
   async logTaskMessage(taskId, level, message) {
     return new Promise((resolve) => {
       this.db.run(
@@ -622,14 +664,38 @@ class PublisherModule {
       // Create log file stream
       const logStream = fs.createWriteStream(logFile);
 
+      const buildStart = Date.now();
+      let lastDataAt = Date.now();
+
       java.stdout.on('data', (data) => {
+        lastDataAt = Date.now();
         logStream.write(data);
       });
 
       java.stderr.on('data', (data) => {
+        lastDataAt = Date.now();
         logStream.write(data);
       });
 
+      // Heartbeat: emit a status line every 60s regardless of stdout activity,
+      // so silent phases of the Publisher (e.g. "Validating Resources") still
+      // surface a signal-of-life in the task log.
+      const heartbeat = setInterval(async () => {
+        const elapsedMs = Date.now() - buildStart;
+        const sinceDataMs = Date.now() - lastDataAt;
+        let logKb = 0;
+        try { logKb = Math.round(fs.statSync(logFile).size / 1024); } catch (_) {}
+        const elapsedMin = Math.floor(elapsedMs / 60000);
+        const elapsedSec = Math.floor(elapsedMs / 1000) % 60;
+        const idleSec = Math.floor(sinceDataMs / 1000);
+        await this.logTaskMessage(
+          taskId,
+          'info',
+          'IG Publisher heartbeat: elapsed ' + elapsedMin + 'm' + elapsedSec + 's, ' +
+          'log ' + logKb + ' KB, last output ' + idleSec + 's ago'
+        );
+      }, 60 * 1000);
+
       java.on('close', async (code) => {
         logStream.end();
 
@@ -660,6 +726,7 @@ class PublisherModule {
 
       java.on('close', () => {
         clearTimeout(timeout);
+        clearInterval(heartbeat);
       });
     });
   }
@@ -789,7 +856,7 @@ class PublisherModule {
     if (fs.existsSync(announcementPath)) {
       try {
         const announcement = fs.readFileSync(announcementPath, 'utf8');
-        await this.updateTaskStatus(task.id, task.status, { announcement: announcement });
+        await this.updateTaskFields(task.id, { announcement: announcement });
         await this.logTaskMessage(task.id, 'info', 'Announcement text saved (' + announcement.length + ' chars)');
       } catch (err) {
         await this.logTaskMessage(task.id, 'warn', 'Failed to read announcement file: ' + err.message);
@@ -830,14 +897,37 @@ class PublisherModule {
 
       const logStream = fs.createWriteStream(logFile);
 
+      const buildStart = Date.now();
+      let lastDataAt = Date.now();
+
       java.stdout.on('data', (data) => {
+        lastDataAt = Date.now();
         logStream.write(data);
       });
 
       java.stderr.on('data', (data) => {
+        lastDataAt = Date.now();
         logStream.write(data);
       });
 
+      // Heartbeat: emit a status line every 60s regardless of stdout activity,
+      // so silent phases of the Publisher still surface a signal-of-life.
+      const heartbeat = setInterval(async () => {
+        const elapsedMs = Date.now() - buildStart;
+        const sinceDataMs = Date.now() - lastDataAt;
+        let logKb = 0;
+        try { logKb = Math.round(fs.statSync(logFile).size / 1024); } catch (_) {}
+        const elapsedMin = Math.floor(elapsedMs / 60000);
+        const elapsedSec = Math.floor(elapsedMs / 1000) % 60;
+        const idleSec = Math.floor(sinceDataMs / 1000);
+        await this.logTaskMessage(
+          taskId,
+          'info',
+          'IG Publisher go-publish heartbeat: elapsed ' + elapsedMin + 'm' + elapsedSec + 's, ' +
+          'log ' + logKb + ' KB, last output ' + idleSec + 's ago'
+        );
+      }, 60 * 1000);
+
       java.on('close', async (code) => {
         logStream.end();
         if (code === 0) {
@@ -856,16 +946,18 @@ class PublisherModule {
         reject(error);
       });
 
-      // Timeout after 60 minutes for publication (longer than draft build)
+      // Timeout configurable via publisher.igPublisherTimeoutMinutes (default: 60 minutes)
+      const timeoutMinutes = this.config.igPublisherTimeoutMinutes || 60;
       const timeout = setTimeout(async () => {
         java.kill();
         logStream.end();
-        await this.logTaskMessage(taskId, 'error', 'IG Publisher go-publish timed out after 60 minutes');
+        await this.logTaskMessage(taskId, 'error', 'IG Publisher go-publish timed out after ' + timeoutMinutes + ' minutes');
         reject(new Error('IG Publisher go-publish timed out'));
-      }, 60 * 60 * 1000);
+      }, timeoutMinutes * 60 * 1000);
 
       java.on('close', () => {
         clearTimeout(timeout);
+        clearInterval(heartbeat);
       });
     });
   }

package/registry/registry.js

@@ -758,7 +758,7 @@ class RegistryModule {
       case '11000267109': edition = 'KR'; break;
       case '900000001000122104': edition = 'ES-ES'; break;
       case '2011000195101': edition = 'CH'; break;
-      case '11000279109': edition = 'CX'; break;
+      case '11000279109': edition = 'CZ'; break;
       case '999000021000000109': edition = 'UK+Clinical'; break;
       case '5631000179106': edition = 'UY'; break;
       case '21000325107': edition = 'CL'; break;
@@ -1233,7 +1233,7 @@ class RegistryModule {
     // FHIR Version field
     html += '<p>';
     html += '<label for="fhirVersion" class="form-label fw-bold">FHIR Version <span class="text-danger">*</span></label>';
-    html += `<input type="text" class="form-control" id="fhirVersion" name="fhirVersion" size="8" 
+    html += `<input type="text" class="form-control" id="fhirVersion" name="fhirVersion" size="8"
            value="${escape(fhirVersion)}" required>`;
     html += '</p>';
     html += '<p class="text-muted small">Examples: R4, 4.0.1, 5.0.0, etc.</p>';
@@ -1241,7 +1241,7 @@ class RegistryModule {
     html += '<div class="alert alert-info">Either Code System URL or Value Set URL must be provided:</div>';
     html += '<p>';
     html += '<label for="url" class="form-label fw-bold">Code System URL</label>';
-    html += `<input type="url" class="form-control" id="url" name="url" 
+    html += `<input type="url" class="form-control" id="url" name="url"
            value="${escape(url)}">`;
     html += '</p>';
     html += '<p class="text-muted small">Example: http://loinc.org</p>';
@@ -1249,7 +1249,7 @@ class RegistryModule {
     // ValueSet URL field - now vertical
     html += '<p>';
     html += '<label for="valueSet" class="form-label fw-bold">Value Set URL</label>';
-    html += `<input type="url" class="form-control" id="valueSet" name="valueSet" 
+    html += `<input type="url" class="form-control" id="valueSet" name="valueSet"
            value="${escape(valueSet)}">`;
     html += '</p>';
     html += '<p class="text-muted small">Example: http://hl7.org/fhir/ValueSet/observation-codes</p>';
@@ -1257,7 +1257,7 @@ class RegistryModule {
 
     // Authoritative Only checkbox
     html += '<p>';
-    html += `<input type="checkbox" class="form-check-input" id="authoritativeOnly" 
+    html += `<input type="checkbox" class="form-check-input" id="authoritativeOnly"
            name="authoritativeOnly" value="true" ${authoritativeOnly ? 'checked' : ''}>`;
     html += '<label class="form-check-label" for="authoritativeOnly">&nbsp;Show only authoritative servers</label>';
     html += '</p>';
@@ -1276,7 +1276,7 @@ class RegistryModule {
     document.querySelector('form').addEventListener('submit', function(e) {
       const url = document.getElementById('url').value.trim();
       const valueSet = document.getElementById('valueSet').value.trim();
-      
+
       if (!url && !valueSet) {
         e.preventDefault();
         alert('You must provide either a Code System URL or a Value Set URL');

package/server.js

@@ -7,7 +7,7 @@
 //
 
 const express = require('express');
-// const cors = require('cors');
+const cors = require('cors');
 const path = require('path');
 const fs = require('fs');
 const os = require('os');
@@ -82,7 +82,11 @@ app.use((req, res, next) => {
   next();
 });
 
-// app.use(cors(config.server.cors));
+// Single, app-level CORS policy for all modules, driven by config.server.cors.
+// This also handles OPTIONS preflight, so modules must NOT set their own
+// Access-Control-* headers (doing so stacks a second CORS layer and produces
+// duplicate, conflicting headers that browsers reject).
+app.use(cors(config.server.cors));
 
 // Module instances
 const modules = {};

package/translations/Messages.properties

@@ -544,7 +544,7 @@ NO_VALID_DISPLAY_FOUND_LANG_NONE_other = ''{5}'' is the default display; the cod
 NO_VALID_DISPLAY_FOUND_LANG_SOME_one = ''{5}'' is the default display; no valid Display Names found for {1}#{2} in the language {4}
 NO_VALID_DISPLAY_FOUND_LANG_SOME_other = ''{5}'' is the default display; no valid Display Names found for {1}#{2} in the language {4}
 NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG_ERR = Wrong Display Name ''{0}'' for {1}#{2}. There are no valid display names found for language(s) ''{3}''. Default display is ''{4}''
-NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG_OK = There are no valid display names found for the code {1}#{2} for language(s) ''{3}''. The display is ''{4}'' which is the default language display
+NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG_OK = There are no valid display names found for the code {1}#{2} for language(s) ''{3}''. The display is ''{0}'' which is a valid display for the default language
 NO_VALID_DISPLAY_FOUND_one = No valid Display Names found for {1}#{2} in the language {4}
 NO_VALID_DISPLAY_FOUND_other = No valid Display Names found for {1}#{2} in the languages {4}
 No_validator_configured = No validator configured

package/tx/cs/cs-cs.js

@@ -1140,6 +1140,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
     const allConcepts = this.codeSystem.getAllConcepts();
 
     for (const concept of allConcepts) {
+      this.opContext.deadCheck('cs:searchFilter');
       const rating = this._calculateSearchRating(concept, searchTerm);
       if (rating > 0) {
         results.add(concept, rating);
@@ -1285,6 +1286,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
 
       const allCodes = this.codeSystem.getAllCodes();
       for (const code of allCodes) {
+        this.opContext.deadCheck('cs:conceptFilter:is-not-a');
         if (!excludeSet.has(code)) {
           const concept = this.codeSystem.getConceptByCode(code);
           if (concept) {
@@ -1316,6 +1318,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
         const regex = regexUtilities.compile('^' + value + '$');
         const allCodes = this.codeSystem.getAllCodes();
         for (const code of allCodes) {
+          this.opContext.deadCheck('cs:conceptFilter:regex');
           if (regex.test(code)) {
             const concept = this.codeSystem.getConceptByCode(code);
             if (concept) {
@@ -1349,6 +1352,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
       }
       const descendants = this.codeSystem.getDescendants(ancestorCode);
       for (const code of descendants) {
+        this.opContext.deadCheck('cs:addDescendants');
         if (code !== ancestorCode) {
           const concept = this.codeSystem.getConceptByCode(code);
           if (concept) {
@@ -1370,6 +1374,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
     if (concept) {
       const descendants = this.codeSystem.getChildren(parentCode);
       for (const code of descendants) {
+        this.opContext.deadCheck('cs:addChildren');
         if (code !== parentCode) { // should not be
           const concept = this.codeSystem.getConceptByCode(code);
           if (concept) {
@@ -1393,6 +1398,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
 
     const allCodes = this.codeSystem.getAllCodes();
     for (const code of allCodes) {
+      this.opContext.deadCheck('cs:childExistsFilter');
       const hasChildren = this.codeSystem.getChildren(code).length > 0;
       if (hasChildren === wantChildren) {
         const concept = this.codeSystem.getConceptByCode(code);
@@ -1419,6 +1425,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
     const allConcepts = this.codeSystem.getAllConcepts();
 
     for (const concept of allConcepts) {
+      this.opContext.deadCheck('cs:propertyFilter');
       if (this._conceptMatchesPropertyFilter(concept, propertyDef, op, value)) {
         results.add(concept, 0);
       }
@@ -1498,6 +1505,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
     const allConcepts = this.codeSystem.getAllConcepts();
 
     for (const concept of allConcepts) {
+      this.opContext.deadCheck('cs:knownPropertyFilter');
       let matches = false;
 
       if (prop === 'notSelectable') {

package/tx/cs/cs-loinc.js

@@ -947,6 +947,7 @@ class LoincServices extends BaseCSServices {
           reject(err);
         } else {
           for (const row of rows) {
+            if (this.opContext) this.opContext.deadCheck('loinc:findRegexMatches');
             if (regex.test(row[valueColumn])) {
               matchingKeys.push(row[keyColumn]);
             }

package/tx/cs/cs-provider-list.js

@@ -5,7 +5,8 @@ const { AbstractCodeSystemProvider } = require('./cs-provider-api');
  */
 class ListCodeSystemProvider extends AbstractCodeSystemProvider {
   /**
-   * {Map<String, CodeSystem>} A list of code system factories that contains all the preloaded native code systems
+   * {CodeSystem[]} The preloaded FHIR code systems in this list. This is an
+   * array — append with .push(), not Map-style .set().
    */
   codeSystems = [];