fhirsmith 0.7.2 → 0.7.4

package/CHANGELOG.md

@@ -5,6 +5,40 @@ All notable changes to the Health Intersections Node Server will be documented i
 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).
 
+## [v0.7.4] - 2026-03-19
+
+### Changed
+
+- XIG: show using resource package explicitly
+- TX: Check conformance statement production at start up
+
+### Fixed
+- TX: Load URI provider on tx.fhir.org
+- TX: fix error getting SCT version for html format
+
+### Tx Conformance Statement
+
+FHIRsmith passed all 1452 HL7 terminology service tests (modes tx.fhir.org+omop+general+snomed, tests v1.9.1-SNAPSHOT, runner v6.9.0)
+
+## [v0.7.3] - 2026-03-19
+
+### Changed
+
+- Show total memory on home page
+- OCL improvements
+- Publisher: Allow editing websites
+- Publisher: separate out target folder and git folder
+- Publisher: use trusted git repo for ig_registry
+- Extend XIG for phinvads analysis
+
+### Fixed
+- Don't exempt tx/data from npm project
+- SNOMED CT fix: align getLanguageCode with mapLanguageCode byte mapping
+
+### Tx Conformance Statement
+
+FHIRsmith passed all 1452 HL7 terminology service tests (modes tx.fhir.org+omop+general+snomed, tests v1.9.1-SNAPSHOT, runner v6.9.0)
+
 ## [v0.7.2] - 2026-03-16
 
 ### Added

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirsmith",
-  "version": "0.7.2",
+  "version": "0.7.4",
   "description": "A Node.js server that provides a collection of tools to serve the FHIR ecosystem",
   "main": "server.js",
   "engines": {

package/publisher/publisher.js

@@ -198,6 +198,24 @@ class PublisherModule {
         });
       });
     }
+    const websiteColumns = await new Promise((resolve, reject) => {
+      this.db.all("PRAGMA table_info(websites)", (err, rows) => {
+        if (err) reject(err);
+        else resolve(rows || []);
+      });
+    });
+    const websiteColumnNames = websiteColumns.map(c => c.name);
+    if (!websiteColumnNames.includes('git_root')) {
+      await new Promise((resolve, reject) => {
+        this.db.run('ALTER TABLE websites ADD COLUMN git_root TEXT', (err) => {
+          if (err) reject(err);
+          else {
+            this.logger.info('Migration: added git_root column to websites table');
+            resolve();
+          }
+        });
+      });
+    }
   }
 
   async createDefaultAdmin() {
@@ -268,6 +286,8 @@ class PublisherModule {
     // Admin routes
     this.router.get('/admin/websites', this.requireAdmin.bind(this), this.renderWebsites.bind(this));
     this.router.post('/admin/websites', this.requireAdmin.bind(this), this.createWebsite.bind(this));
+    this.router.get('/admin/websites/:id/edit', this.requireAdmin.bind(this), this.renderEditWebsite.bind(this));
+    this.router.post('/admin/websites/:id/edit', this.requireAdmin.bind(this), this.updateWebsite.bind(this));
     this.router.get('/admin/users', this.requireAdmin.bind(this), this.renderUsers.bind(this));
     this.router.post('/admin/users', this.requireAdmin.bind(this), this.createUser.bind(this));
     this.router.post('/admin/permissions', this.requireAdmin.bind(this), this.updatePermissions.bind(this));
@@ -682,7 +702,7 @@ class PublisherModule {
     const historyDir = path.join(taskDir, 'fhir-ig-history-template');
     const templatesDir = path.join(taskDir, 'fhir-web-templates');
 
-    await this.runCommand('git', ['clone', 'https://github.com/FHIR/ig-registry.git', registryDir],
+    await this.runCommand('git', ['clone', 'git@github.com:FHIR/ig-registry.git', registryDir],
       {}, task.id, 'Cloning ig-registry');
 
     await this.runCommand('git', ['clone', 'https://github.com/HL7/fhir-ig-history-template.git', historyDir],
@@ -698,7 +718,7 @@ class PublisherModule {
     }
 
     // Step 3: Pull latest web folder before publishing into it
-    await this.runCommand('git', ['pull'], { cwd: website.local_folder }, task.id, 'Pulling latest web folder');
+    await this.runCommand('git', ['pull'], { cwd: website.git_root }, task.id, 'Pulling latest web folder');
 
     // Step 4: Run the IG publisher in go-publish mode
     await this.runPublisherGoPublish(task.id, publisherJar, draftDir, website.local_folder,
@@ -716,9 +736,9 @@ class PublisherModule {
     await this.logTaskMessage(task.id, 'info', 'Committing changes to web folder...');
     const gitUrl = 'https://github.com/' + task.github_org + '/' + task.github_repo + '.git';
     const commitMsg = 'publish ' + task.npm_package_id + '#' + task.version + ' from ' + gitUrl + ' ' + task.git_branch;
-    await this.runCommand('git', ['add', '.'], { cwd: website.local_folder }, task.id, 'Staging web folder changes');
-    await this.runCommand('git', ['commit', '-m', commitMsg], { cwd: website.local_folder }, task.id, 'Committing web folder changes');
-    await this.runCommand('git', ['push'], { cwd: website.local_folder }, task.id, 'Pushing web folder changes');
+    await this.runCommand('git', ['add', '.'], { cwd: website.git_root }, task.id, 'Staging web folder changes');
+    await this.runCommand('git', ['commit', '-m', commitMsg], { cwd: website.git_root }, task.id, 'Committing web folder changes');
+    await this.runCommand('git', ['push'], { cwd: website.git_root }, task.id, 'Pushing web folder changes');
 
     // Step 7: Commit and push the ig-registry
     await this.logTaskMessage(task.id, 'info', 'Committing changes to ig-registry...');
@@ -1583,6 +1603,71 @@ class PublisherModule {
     }
   }
 
+  async renderEditWebsite(req, res) {
+    const start = Date.now();
+    try {
+      const htmlServer = require('../library/html-server');
+      const website = await this.getWebsite(req.params.id);
+      if (!website) return res.status(404).send('Website not found');
+
+      let content = '<h3>Edit Website</h3>';
+      content += '<form method="post" action="/publisher/admin/websites/' + website.id + '/edit" class="row g-3">';
+      content += '<div class="col-md-4"><label class="form-label">Website Name</label>';
+      content += '<input type="text" class="form-control" name="name" value="' + escape(website.name) + '" required></div>';
+      content += '<div class="col-md-4"><label class="form-label">Local Folder</label>';
+      content += '<input type="text" class="form-control" name="local_folder" value="' + escape(website.local_folder) + '" required></div>';
+      content += '<div class="col-md-4"><label class="form-label">Git Root (repo root for git operations)</label>';
+      content += '<input type="text" class="form-control" name="git_root" value="' + escape(website.git_root || '') + '"></div>';
+      content += '<div class="col-md-4"><label class="form-label">History Templates</label>';
+      content += '<input type="text" class="form-control" name="history_templates" value="' + escape(website.history_templates) + '" required></div>';
+      content += '<div class="col-md-4"><label class="form-label">Web Templates</label>';
+      content += '<input type="text" class="form-control" name="web_templates" value="' + escape(website.web_templates) + '" required></div>';
+      content += '<div class="col-md-4"><label class="form-label">Update Script</label>';
+      content += '<input type="text" class="form-control" name="server_update_script" value="' + escape(website.server_update_script) + '" required></div>';
+      content += '<div class="col-md-4"><label class="form-label">Active</label>';
+      content += '<select class="form-control" name="is_active"><option value="1"' + (website.is_active ? ' selected' : '') + '>Yes</option><option value="0"' + (!website.is_active ? ' selected' : '') + '>No</option></select></div>';
+      content += '<div class="col-12"><button type="submit" class="btn btn-primary">Save Changes</button> ';
+      content += '<a href="/publisher/admin/websites" class="btn btn-secondary">Cancel</a></div>';
+      content += '</form>';
+
+      const html = htmlServer.renderPage('publisher', 'Edit Website - FHIR Publisher', content, {
+        templateVars: { loginTitle: 'Logout', loginPath: 'logout', loginAction: 'POST' }
+      });
+      res.setHeader('Content-Type', 'text/html');
+      res.send(html);
+    } catch (error) {
+      this.logger.error('Error rendering edit website:', error);
+      res.status(500).send('Internal server error');
+    } finally {
+      this.stats.countRequest('websites-edit', Date.now() - start);
+    }
+  }
+
+  async updateWebsite(req, res) {
+    const start = Date.now();
+    try {
+      const { name, local_folder,  git_root, history_templates, web_templates, server_update_script, is_active } = req.body;
+      const websiteId = req.params.id;
+
+      await new Promise((resolve, reject) => {
+        this.db.run(
+          'UPDATE websites SET name=?, local_folder=?,  git_root = ?, history_templates=?, web_templates=?, server_update_script=?, is_active=? WHERE id=?',
+          [name, local_folder,  git_root, history_templates, web_templates, server_update_script, is_active === '1' ? 1 : 0, websiteId],
+          (err) => err ? reject(err) : resolve()
+        );
+      });
+
+      this.logUserAction(req.session.userId, 'update_website', websiteId, req.ip);
+      this.logger.info('Website updated: ' + websiteId + ' by user ' + req.session.userId);
+      res.redirect('/publisher/admin/websites');
+    } catch (error) {
+      this.logger.error('Error updating website:', error);
+      res.status(500).send('Failed to update website');
+    } finally {
+      this.stats.countRequest('websites-update', Date.now() - start);
+    }
+  }
+
   async renderWebsites(req, res) {
     const start = Date.now();
     try {
@@ -1607,6 +1692,10 @@ class PublisherModule {
         content += '<input type="text" class="form-control" id="local_folder" name="local_folder" required>';
         content += '</div>';
         content += '<div class="col-md-4">';
+        content += '<label class="form-label">Git Root (repo root for git operations)</label>';
+        content += '<input type="text" class="form-control" name="git_root" required>';
+        content += '</div>';
+        content += '<div class="col-md-4">';
         content += '<label for="history_templates" class="form-label">History Templates</label>';
         content += '<input type="text" class="form-control" id="history_templates" name="history_templates" required>';
         content += '</div>';
@@ -1634,18 +1723,20 @@ class PublisherModule {
         } else {
           content += '<div class="table-responsive">';
           content += '<table class="table table-striped">';
-          content += '<thead><tr><th>Name</th><th>Local Folder</th><th>Update Script</th><th>Active</th><th>Created</th></tr></thead>';
+          content += '<thead><tr><th>Name</th><th>Local Folder</th><th>Git Root</th><th>Update Script</th><th>Active</th><th>Created</th><th>Actions</th></tr></thead>';
           content += '<tbody>';
 
           websites.forEach(website => {
             content += '<tr>';
             content += '<td>' + website.name + '</td>';
-            content += '<td><code>' + website.local_folder + '</code></td>';
-            content += '<td><code>' + website.history_templates + '</code></td>';
-            content += '<td><code>' + website.web_templates + '</code></td>';
-            content += '<td><code>' + website.server_update_script + '</code></td>';
+            content += '<td><code>' + escape(website.local_folder) + '</code></td>';
+            content += '<td><code>' + escape(website.git_root || '') + '</code></td>';
+            content += '<td><code>' + escape(website.history_templates) + '</code></td>';
+            content += '<td><code>' + escape(website.web_templates) + '</code></td>';
+            content += '<td><code>' + escape(website.server_update_script) + '</code></td>';
             content += '<td>' + (website.is_active ? '✓' : '✗') + '</td>';
             content += '<td>' + new Date(website.created_at).toLocaleString() + '</td>';
+            content += '<td><a href="/publisher/admin/websites/' + website.id + '/edit" class="btn btn-sm btn-outline-primary">Edit</a></td>';
             content += '</tr>';
           });
 
@@ -1677,12 +1768,12 @@ class PublisherModule {
     const start = Date.now();
     try {
       try {
-        const {name, local_folder, history_templates, web_templates, server_update_script} = req.body;
+        const {name, local_folder,  git_root, history_templates, web_templates, server_update_script} = req.body;
 
         await new Promise((resolve, reject) => {
           this.db.run(
-            'INSERT INTO websites (name, local_folder, history_templates, web_templates, server_update_script) VALUES (?, ?, ?, ?, ?)',
-            [name, local_folder, history_templates, web_templates, server_update_script],
+            'INSERT INTO websites (name, local_folder,  git_root, history_templates, web_templates, server_update_script) VALUES (?, ?, ?, ?, ?, ?)',
+            [name, local_folder, git_root, history_templates, web_templates, server_update_script],
             function (err) {
               if (err) reject(err);
               else resolve();

package/server.js

@@ -401,12 +401,14 @@ async function buildRootPageContent() {
   const heapUsedMB = (memUsage.heapUsed / 1024 / 1024).toFixed(2);
   const heapTotalMB = (memUsage.heapTotal / 1024 / 1024).toFixed(2);
   const rssMB = (memUsage.rss / 1024 / 1024).toFixed(2);
+  const freeMemMB = (os.freemem() / 1024 / 1024).toFixed(0);
+  const totalMemMB = (os.totalmem() / 1024 / 1024).toFixed(0);
 
   content += '<table class="grid">';
   content += '<tr>';
-  content += `<td><strong>Module Count:</strong> ${mc}</td>`;
   content += `<td><strong>Uptime:</strong> ${escape(uptimeStr)}</td>`;
   content += `<td><strong>Request Count:</strong> ${stats.requestCount}</td>`;
+  content += `<td><strong>Free Memory:</strong> ${freeMemMB} MB of ${totalMemMB} MB</td>`;
   content += '</tr>';
   content += '<tr>';
   content += `<td><strong>Heap Used:</strong> ${heapUsedMB} MB</td>`;

package/tx/cs/cs-snomed.js

@@ -615,10 +615,14 @@ class SnomedProvider extends BaseCSServices {
   getLanguageCode(langIndex) {
     const languageMap = {
       1: 'en',
-      2: 'en-GB',
-      3: 'es',
-      4: 'fr',
-      5: 'de'
+      2: 'fr',
+      3: 'nl',
+      4: 'es',
+      5: 'sv',
+      6: 'da',
+      7: 'de',
+      8: 'it',
+      9: 'cs'
     };
     return languageMap[langIndex] || 'en';
   }
@@ -1271,7 +1275,7 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
 
   id() {
     const match = this.version().match(/^http:\/\/snomed\.info\/sct\/(\d+)(?:\/version\/(\d{8}))?$/);
-    return "SCT-"+match[1]+"-"+match[2];
+    return match && match[1] && match[2] ? "SCT-"+match[1]+"-"+match[2] : null;
   }
 
   describeVersion(version) {

package/tx/cs/cs-uri.js

@@ -21,7 +21,7 @@ class UriServices extends CodeSystemProvider {
   }
 
   version() {
-    return 'n/a';
+    return null;
   }
 
   description() {
@@ -182,7 +182,7 @@ class UriServicesFactory extends CodeSystemFactoryProvider {
   }
 
   defaultVersion() {
-    return 'n/a';
+    return null;
   }
 
   system() {
@@ -190,7 +190,7 @@ class UriServicesFactory extends CodeSystemFactoryProvider {
   }
 
   version() {
-    return 'n/a';
+    return null;
   }
 
   // eslint-disable-next-line no-unused-vars

package/tx/library.js

@@ -34,6 +34,7 @@ const {VSACValueSetProvider} = require("./vs/vs-vsac");
 const { OCLCodeSystemProvider, OCLSourceCodeSystemFactory } = require('./ocl/cs-ocl');
 const { OCLValueSetProvider } = require('./ocl/vs-ocl');
 const { OCLConceptMapProvider } = require('./ocl/cm-ocl');
+const {UriServicesFactory} = require("./cs/cs-uri");
 
 /**
  * This class holds all the loaded content ready for processing
@@ -454,6 +455,12 @@ class Library {
         this.registerProvider('internal', hgvs);
         break;
       }
+      case "urls" : {
+        const urls = new UriServicesFactory(this.i18n);
+        await urls.load();
+        this.registerProvider('internal', urls);
+        break;
+      }
       case "vsac" : {
         if (!this.vsacCfg || !this.vsacCfg.apiKey) {
           throw new Error("Unable to load VSAC provider unless vsacCfg is provided in the configuration");

package/tx/ocl/jobs/background-queue.cjs

@@ -22,15 +22,17 @@ class OCLBackgroundJobQueue {
     const resolveAndEnqueue = async () => {
       const resolvedSize = await this.#resolveJobSize(options);
       const normalizedSize = this.#normalizeJobSize(resolvedSize);
-      this.#insertPendingJobOrdered({
+      const job = {
         jobKey,
         jobType: jobType || 'background-job',
         jobId: options?.jobId || jobKey,
         jobSize: normalizedSize,
         getProgress: typeof options?.getProgress === 'function' ? options.getProgress : null,
         runJob,
-        enqueueOrder: this.enqueueSequence++
-      });
+        enqueueOrder: this.enqueueSequence++,
+        userRequested: !!options.userRequested
+      };
+      this.#insertPendingJobOrdered(job);
       this.ensureHeartbeatRunning();
       console.log(`[OCL] ${jobType || 'Background job'} enqueued: ${jobKey} (size=${normalizedSize}, queue=${this.pendingJobs.length}, active=${this.activeCount})`);
       this.processNext();
@@ -72,17 +74,21 @@ class OCLBackgroundJobQueue {
   }
 
   static #insertPendingJobOrdered(job) {
+    // Prioridade máxima para userRequested
+    if (job.userRequested) {
+      this.pendingJobs.unshift(job);
+      console.log(`[OCL] User-requested job prioritized: ${job.jobKey}`);
+      return;
+    }
     let index = this.pendingJobs.findIndex(existing => {
       if (existing.jobSize === job.jobSize) {
         return existing.enqueueOrder > job.enqueueOrder;
       }
       return existing.jobSize > job.jobSize;
     });
-
     if (index < 0) {
       index = this.pendingJobs.length;
     }
-
     this.pendingJobs.splice(index, 0, job);
   }
 

package/tx/ocl/shared/patches.cjs

@@ -178,6 +178,43 @@ function patchValueSetExpandWholeSystemForOcl() {
 
   const originalIncludeCodes = proto.includeCodes;
   proto.includeCodes = async function patchedIncludeCodes(cset, path, vsSrc, compose, filter, expansion, excludeInactive, notClosed) {
+    // ...existing code...
+    // PATCH: Para OCL ValueSet, só expandir códigos explicitamente listados em compose.include.code
+    if (Array.isArray(compose?.include)) {
+      const explicitCodes = [];
+      for (const include of compose.include) {
+        // Normaliza o system para URL canônico
+        const canonicalSystem = typeof include.system === 'string' ? include.system.trim() : include.system;
+        if (Array.isArray(include.code)) {
+          for (const code of include.code) {
+            explicitCodes.push({ system: canonicalSystem, code });
+          }
+        }
+        // Também verifica se há conceitos explícitos em include.concept
+        if (Array.isArray(include.concept)) {
+          for (const concept of include.concept) {
+            if (concept && concept.code) {
+              explicitCodes.push({ system: canonicalSystem, code: concept.code });
+            }
+          }
+        }
+      }
+      if (explicitCodes.length > 0) {
+        // Filtra expansão para só retornar os códigos explicitamente referenciados
+        const filtered = [];
+        for (const { system, code } of explicitCodes) {
+          // Busca conceito no CodeSystem
+          const resources = await originalIncludeCodes.call(this, { system, code }, path, vsSrc, compose, filter, expansion, excludeInactive, notClosed);
+          if (Array.isArray(resources)) {
+            filtered.push(...resources);
+          } else if (resources) {
+            filtered.push(resources);
+          }
+        }
+        return filtered;
+      }
+    }
+    // Fallback para comportamento original
     try {
       return await originalIncludeCodes.call(this, cset, path, vsSrc, compose, filter, expansion, excludeInactive, notClosed);
     } catch (error) {

package/tx/ocl/vs-ocl.cjs

@@ -15,7 +15,7 @@ const { computeValueSetExpansionFingerprint } = require('./fingerprint/fingerpri
 const { ensureTxParametersHashIncludesFilter, patchValueSetExpandWholeSystemForOcl } = require('./shared/patches');
 
 ensureTxParametersHashIncludesFilter(TxParameters);
-patchValueSetExpandWholeSystemForOcl();
+//patchValueSetExpandWholeSystemForOcl();
 
 function normalizeCanonicalSystem(system) {
   if (typeof system !== 'string') {
@@ -93,10 +93,42 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
             dependencyChecksums: cached.dependencyChecksums || {},
             createdAt: Number.isFinite(createdAt) ? createdAt : null
           });
-
+          // Instancia ValueSet para garantir jsonObj
+          // Reconstrói compose.include se não existir
+          let compose = cached.expansion?.compose;
+          if (!compose || !Array.isArray(compose.include)) {
+            // Reconstrói a partir dos sistemas/códigos em expansion.contains
+            const systemConcepts = new Map();
+            if (Array.isArray(cached.expansion?.contains)) {
+              for (const entry of cached.expansion.contains) {
+                if (!entry.system || !entry.code) continue;
+                if (!systemConcepts.has(entry.system)) {
+                  systemConcepts.set(entry.system, []);
+                }
+                systemConcepts.get(entry.system).push({ code: entry.code });
+              }
+            }
+            compose = { include: Array.from(systemConcepts.entries()).map(([system, concepts]) => ({ system, concept: concepts })) };
+          }
+          const valueSetObj = new ValueSet({
+            resourceType: 'ValueSet',
+            url: cached.canonicalUrl,
+            version: cached.version || null,
+            expansion: cached.expansion,
+            compose,
+            id: cached.canonicalUrl // ou outro identificador se necessário
+          }, 'R5');
+          this.#applyCachedExpansion(valueSetObj, paramsKey);
+          // Indexa o ValueSet restaurado para torná-lo disponível via fetchValueSet
+          this.valueSetMap.set(valueSetObj.url, valueSetObj);
+          if (valueSetObj.version) {
+            this.valueSetMap.set(`${valueSetObj.url}|${valueSetObj.version}`, valueSetObj);
+          }
+          this.valueSetMap.set(valueSetObj.id, valueSetObj);
+          this._idMap.set(valueSetObj.id, valueSetObj);
           this.valueSetFingerprints.set(cacheKey, cached.fingerprint || null);
           loadedCount++;
-          console.log(`[OCL-ValueSet] Loaded ValueSet from cold cache: ${cached.canonicalUrl}`);
+          console.log(`[OCL-ValueSet] Loaded ValueSet from cold cache into memory: ${cached.canonicalUrl}`);
         } catch (error) {
           console.error(`[OCL-ValueSet] Failed to load cold cache file ${file}:`, error.message);
         }
@@ -220,9 +252,10 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
     let key = `${url}|${version}`;
     if (this.valueSetMap.has(key)) {
       const vs = this.valueSetMap.get(key);
-      await this.#ensureComposeIncludes(vs);
+      // await this.#ensureComposeIncludes(vs);
       this.#clearInlineExpansion(vs);
-      this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset' });
+      console.log(`[OCL-ValueSet] fetchValueSet cache hit for ${url} (version: ${version || 'none'})`);
+      this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset', userRequested: true });
       return vs;
     }
 
@@ -232,7 +265,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
         key = `${url}|${majorMinor}`;
         if (this.valueSetMap.has(key)) {
           const vs = this.valueSetMap.get(key);
-          await this.#ensureComposeIncludes(vs);
+          // await this.#ensureComposeIncludes(vs);
           this.#clearInlineExpansion(vs);
           this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset-mm' });
           return vs;
@@ -242,7 +275,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
 
     if (this.valueSetMap.has(url)) {
       const vs = this.valueSetMap.get(url);
-      await this.#ensureComposeIncludes(vs);
+      // await this.#ensureComposeIncludes(vs);
       this.#clearInlineExpansion(vs);
       this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset-url' });
       return vs;
@@ -250,7 +283,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
 
     const resolved = await this.#resolveValueSetByCanonical(url, version);
     if (resolved) {
-      await this.#ensureComposeIncludes(resolved);
+      // await this.#ensureComposeIncludes(resolved);
       this.#clearInlineExpansion(resolved);
       this.#scheduleBackgroundExpansion(resolved, { reason: 'fetch-valueset-resolved' });
       return resolved;
@@ -261,7 +294,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
     key = `${url}|${version}`;
     if (this.valueSetMap.has(key)) {
       const vs = this.valueSetMap.get(key);
-      await this.#ensureComposeIncludes(vs);
+      // await this.#ensureComposeIncludes(vs);
       this.#clearInlineExpansion(vs);
       this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset-init' });
       return vs;
@@ -273,7 +306,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
         key = `${url}|${majorMinor}`;
         if (this.valueSetMap.has(key)) {
           const vs = this.valueSetMap.get(key);
-          await this.#ensureComposeIncludes(vs);
+          // await this.#ensureComposeIncludes(vs);
           this.#clearInlineExpansion(vs);
           this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset-init-mm' });
           return vs;
@@ -283,7 +316,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
 
     if (this.valueSetMap.has(url)) {
       const vs = this.valueSetMap.get(url);
-      await this.#ensureComposeIncludes(vs);
+      // await this.#ensureComposeIncludes(vs);
       this.#clearInlineExpansion(vs);
       this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset-init-url' });
       return vs;
@@ -295,7 +328,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
   async fetchValueSetById(id) {
     const local = this.#getLocalValueSetById(id);
     if (local) {
-      await this.#ensureComposeIncludes(local);
+      // await this.#ensureComposeIncludes(local);
       this.#clearInlineExpansion(local);
       this.#scheduleBackgroundExpansion(local, { reason: 'fetch-valueset-by-id' });
       return local;
@@ -304,7 +337,7 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
     await this.initialize();
 
     const vs = this.#getLocalValueSetById(id);
-    await this.#ensureComposeIncludes(vs);
+    // await this.#ensureComposeIncludes(vs);
     this.#clearInlineExpansion(vs);
     this.#scheduleBackgroundExpansion(vs, { reason: 'fetch-valueset-by-id-init' });
     return vs;
@@ -369,17 +402,15 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
       || this._idMap.get(vs.id)
       || null;
 
-    // Preserve hydrated cold-cache expansions on first index; invalidate only on replacement.
-    if (existing && existing !== vs) {
-      this.#invalidateExpansionCache(vs);
-    }
-
-    this.valueSetMap.set(vs.url, vs);
-    if (vs.version) {
-      this.valueSetMap.set(`${vs.url}|${vs.version}`, vs);
+    // Só indexa se não existe ou se for o mesmo objeto
+    if (!existing || existing === vs) {
+      this.valueSetMap.set(vs.url, vs);
+      if (vs.version) {
+        this.valueSetMap.set(`${vs.url}|${vs.version}`, vs);
+      }
+      this.valueSetMap.set(vs.id, vs);
+      this._idMap.set(vs.id, vs);
     }
-    this.valueSetMap.set(vs.id, vs);
-    this._idMap.set(vs.id, vs);
   }
 
   #toValueSet(collection) {
@@ -414,11 +445,11 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
       json.meta = { lastUpdated };
     }
 
-    if (preferredSource) {
-      json.compose = {
-        include: [{ system: preferredSource }]
-      };
-    }
+    // if (preferredSource) {
+    //   json.compose = {
+    //     include: [{ system: preferredSource }]
+    //   };
+    // }
 
     const conceptsUrl = this.#normalizePath(
       collection.concepts_url || collection.conceptsUrl || this.#buildCollectionConceptsPath(collection)
@@ -995,7 +1026,8 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
           const meta = this.#getCollectionMeta(vs);
           queuedJobSize = await this.#fetchConceptCountFromHeaders(meta?.conceptsUrl || null);
           return queuedJobSize;
-        }
+        },
+        userRequested: !!options.userRequested
       }
     );
   }
@@ -1080,10 +1112,10 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
     }
 
     const contains = [];
-    let offset = 0;
-
-    // Pull all concepts in fixed-size pages until exhausted.
-    // eslint-disable-next-line no-constant-condition
+    let offset = 0; // Moved this line up
+    // Agrupa conceitos por system
+    const systemConcepts = new Map();
+    // Removed duplicate offset declaration
     while (true) {
       const batch = await this.#fetchCollectionConcepts(meta, {
         count: CONCEPT_PAGE_SIZE,
@@ -1092,17 +1124,14 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
         filter: null,
         languageCodes: []
       });
-
       const entries = Array.isArray(batch?.contains) ? batch.contains : [];
       if (entries.length === 0) {
         break;
       }
-
       for (const entry of entries) {
         if (!entry?.system || !entry?.code) {
           continue;
         }
-
         const out = {
           system: entry.system,
           code: entry.code
@@ -1125,18 +1154,28 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
             }));
         }
         contains.push(out);
+        // Agrupa por system
+        if (!systemConcepts.has(entry.system)) {
+          systemConcepts.set(entry.system, []);
+        }
+        systemConcepts.get(entry.system).push(entry.code);
       }
-
       if (progressState) {
         progressState.processed = contains.length;
       }
-
       if (entries.length < CONCEPT_PAGE_SIZE) {
         break;
       }
       offset += entries.length;
     }
-
+    // Popular compose.include para cada system
+    if (!vs.jsonObj.compose) {
+      vs.jsonObj.compose = { include: [] };
+    }
+    vs.jsonObj.compose.include = Array.from(systemConcepts.entries()).map(([system, codes]) => ({
+      system,
+      concept: codes.map(code => ({ code }))
+    }));
     return {
       timestamp: new Date().toISOString(),
       identifier: `urn:uuid:${crypto.randomUUID()}`,

package/tx/tx.fhir.org.yml

@@ -8,6 +8,7 @@ sources:
   - internal:areacode
   - internal:mimetypes
   - internal:usstates
+  - internal:urls
   - internal:hgvs
   - ucum:tx/data/ucum-essence.xml
   - loinc:loinc-2.77-a.db

package/tx/tx.js

@@ -196,6 +196,9 @@ class TXModule {
     }
 
     this.log.info(`TX module initialized with ${config.endpoints.length} endpoint(s)`);
+
+    // Self-test: verify metadata generation works for each endpoint before accepting traffic
+    await this.selfTest();
   }
 
   /**
@@ -388,8 +391,8 @@ class TXModule {
       }
 
       if (contentType.includes('application/json') ||
-          contentType.includes('application/fhir+json') ||
-          contentType.includes('application/json+fhir')) {
+        contentType.includes('application/fhir+json') ||
+        contentType.includes('application/json+fhir')) {
 
         // If body is a Buffer, parse it
         if (Buffer.isBuffer(req.body)) {
@@ -731,11 +734,11 @@ class TXModule {
     router.get('/CodeSystem/:id/\\$validate-code', async (req, res) => {
       const start = Date.now();
       try {
-      let worker = new ValidateWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
+        let worker = new ValidateWorker(req.txOpContext, this.log, req.txProvider, this.languages, this.i18n);
         await worker.handleCodeSystemInstance(req, res, this.log);
-    } finally {
-      this.countRequest('$validate', Date.now() - start);
-    }
+      } finally {
+        this.countRequest('$validate', Date.now() - start);
+      }
     });
     router.post('/CodeSystem/:id/\\$validate-code', async (req, res) => {
       const start = Date.now();
@@ -745,7 +748,7 @@ class TXModule {
       } finally {
         this.countRequest('$validate', Date.now() - start);
       }
-      
+
     });
 
     // ValueSet/[id]/$validate-code
@@ -964,6 +967,79 @@ class TXModule {
     });
   }
 
+  /**
+   * Self-test: exercise CapabilityStatement and TerminologyCapabilities generation
+   * for each endpoint immediately after startup, throwing on any failure.
+   */
+  async selfTest() {
+    this.log.info('Running startup self-test for metadata endpoints...');
+
+    for (const endpointInfo of this.endpoints) {
+      const label = `${endpointInfo.path} (FHIR v${endpointInfo.fhirVersion})`;
+
+      // Build a minimal mock req/res that captures what metadataHandler.handle() produces
+      const makeMockReqRes = (mode) => {
+        const captured = { data: null, status: 200 };
+
+        const req = {
+          method: 'GET',
+          query: { mode },
+          headers: {},
+          // eslint-disable-next-line no-unused-vars
+          get: (name) => null,
+          txEndpoint: endpointInfo,
+          txProvider: endpointInfo.provider,
+        };
+
+        const res = {
+          statusCode: 200,
+          status(code) { captured.status = code; return this; },
+          setHeader() { return this; },
+          json(data) { captured.data = data; return this; },
+          send(data) { captured.data = data; return this; },
+        };
+
+        return { req, res, captured };
+      };
+
+      // Test 1: CapabilityStatement  (/metadata with no mode, or mode=full)
+      try {
+        const { req, res, captured } = makeMockReqRes(undefined);
+        await this.metadataHandler.handle(req, res);
+        if (!captured.data) {
+          throw new Error('No response data returned');
+        }
+        const rt = captured.data.resourceType;
+        if (rt !== 'CapabilityStatement') {
+          throw new Error(`Expected CapabilityStatement, got ${rt}`);
+        }
+        this.log.info(`  [OK] CapabilityStatement for ${label}`);
+      } catch (err) {
+        this.log.error(`  [FAIL] CapabilityStatement for ${label}: ${err.message}`);
+        throw new Error(`Startup self-test failed (CapabilityStatement, ${label}): ${err.message}`);
+      }
+
+      // Test 2: TerminologyCapabilities  (/metadata?mode=terminology)
+      try {
+        const { req, res, captured } = makeMockReqRes('terminology');
+        await this.metadataHandler.handle(req, res);
+        if (!captured.data) {
+          throw new Error('No response data returned');
+        }
+        const rt = captured.data.resourceType;
+        if (rt !== 'TerminologyCapabilities') {
+          throw new Error(`Expected TerminologyCapabilities, got ${rt}`);
+        }
+        this.log.info(`  [OK] TerminologyCapabilities for ${label}`);
+      } catch (err) {
+        this.log.error(`  [FAIL] TerminologyCapabilities for ${label}: ${err.message}`);
+        throw new Error(`Startup self-test failed (TerminologyCapabilities, ${label}): ${err.message}`);
+      }
+    }
+
+    this.log.info('Startup self-test passed.');
+  }
+
   /**
    * Build an OperationOutcome for errors
    */
@@ -1077,21 +1153,21 @@ class TXModule {
   ec = 0;
 
   checkProperJson() { // jsonStr) {
-  //   const errors = [];
-  //   if (jsonStr.includes("[]")) errors.push("Found [] in json");
-  //   if (jsonStr.includes('""')) errors.push('Found "" in json');
-  //
-  //   if (errors.length > 0) {
-  //     this.ec++;
-  //     const filename = `/Users/grahamegrieve/temp/tx-err-log/err${this.ec}.json`;
-  //     writeFileSync(filename, jsonStr);
-  //     throw new Error(errors.join('; '));
-  //   }
+                      //   const errors = [];
+                      //   if (jsonStr.includes("[]")) errors.push("Found [] in json");
+                      //   if (jsonStr.includes('""')) errors.push('Found "" in json');
+                      //
+                      //   if (errors.length > 0) {
+                      //     this.ec++;
+                      //     const filename = `/Users/grahamegrieve/temp/tx-err-log/err${this.ec}.json`;
+                      //     writeFileSync(filename, jsonStr);
+                      //     throw new Error(errors.join('; '));
+                      //   }
   }
 
   transformResourceForVersion(data, fhirVersion) {
     if (fhirVersion == "5.0" || !data.resourceType) {
-        return data;
+      return data;
     }
     switch (data.resourceType) {
       case "CodeSystem": return codeSystemFromR5(data, fhirVersion);

package/xig/xig.js

@@ -99,14 +99,15 @@ function validateExternalUrl(url) {
 
 // Secure SQL query building with parameterized queries
 function buildSecureResourceQuery(queryParams, offset = 0, limit = 50) {
-  const { realm, auth, ver, type, rt, text } = queryParams;
+  const { realm, auth, ver, type, rt, text, pkg, onlyUsed } = queryParams;
 
   let baseQuery = `
       SELECT
           ResourceKey, ResourceType, Type, Kind, Description, PackageKey,
           Realm, Authority, R2, R2B, R3, R4, R4B, R5, R6,
           Id, Url, Version, Status, Date, Name, Title, Content,
-          Supplements, Details, FMM, WG, StandardsStatus, Web
+          Supplements, Details, FMM, WG, StandardsStatus, Web,
+          (SELECT COUNT(*) FROM DependencyList WHERE TargetKey = Resources.ResourceKey) AS UsageCount
       FROM Resources
       WHERE 1=1
   `;
@@ -225,6 +226,17 @@ function buildSecureResourceQuery(queryParams, offset = 0, limit = 50) {
     }
   }
 
+  // Package filter - matches packageId#version containing the search string
+  if (pkg && pkg !== '') {
+    conditions.push('AND PackageKey IN (SELECT PackageKey FROM Packages WHERE (Id || \'#\' || Version) LIKE ?)');
+    params.push(`%${pkg}%`);
+  }
+
+  // Only used filter
+  if (onlyUsed === 'true') {
+    conditions.push('AND EXISTS (SELECT 1 FROM DependencyList WHERE TargetKey = Resources.ResourceKey)');
+  }
+
   // Build final query
   const fullQuery = baseQuery + ' ' + conditions.join(' ') + ' ORDER BY ResourceType, Type, Description LIMIT ? OFFSET ?';
   params.push(limit, offset);
@@ -233,7 +245,7 @@ function buildSecureResourceQuery(queryParams, offset = 0, limit = 50) {
 }
 
 function buildSecureResourceCountQuery(queryParams) {
-  const { realm, auth, ver, type, rt, text } = queryParams;
+  const { realm, auth, ver, type, rt, text, pkg, onlyUsed } = queryParams;
 
   let baseQuery = 'SELECT COUNT(*) as total FROM Resources WHERE 1=1';
   const conditions = [];
@@ -324,6 +336,17 @@ function buildSecureResourceCountQuery(queryParams) {
     }
   }
 
+  // Package filter - matches packageId#version containing the search string
+  if (pkg && pkg !== '') {
+    conditions.push('AND PackageKey IN (SELECT PackageKey FROM Packages WHERE (Id || \'#\' || Version) LIKE ?)');
+    params.push(`%${pkg}%`);
+  }
+
+  // Only used filter
+  if (onlyUsed === 'true') {
+    conditions.push('AND EXISTS (SELECT 1 FROM DependencyList WHERE TargetKey = Resources.ResourceKey)');
+  }
+
   const fullQuery = baseQuery + ' ' + conditions.join(' ');
   return { query: fullQuery, params };
 }
@@ -449,7 +472,7 @@ function sqlEscapeString(str) {
 }
 
 function buildSqlFilter(queryParams) {
-  const { realm, auth, ver, type, rt, text } = queryParams;
+  const { realm, auth, ver, type, rt, text, pkg, onlyUsed } = queryParams;
   let filter = '';
 
   // Realm filter
@@ -555,6 +578,17 @@ function buildSqlFilter(queryParams) {
     }
   }
 
+  // Package filter - matches packageId#version containing the search string
+  if (pkg && pkg !== '') {
+    const escapedPkg = sqlEscapeString(pkg);
+    filter += ` and PackageKey in (select PackageKey from Packages where (Id || '#' || Version) like '%${escapedPkg}%')`;
+  }
+
+  // Only used filter
+  if (onlyUsed === 'true') {
+    filter += ` and exists (select 1 from DependencyList where TargetKey = Resources.ResourceKey)`;
+  }
+
   // Convert to proper WHERE clause
   if (filter !== '') {
     // Remove the first " and " and prepend "WHERE "
@@ -600,7 +634,8 @@ function buildResourceListQuery(queryParams, offset = 0, limit = 50) {
           FMM,
           WG,
           StandardsStatus,
-          Web
+          Web,
+          (SELECT COUNT(*) FROM DependencyList WHERE TargetKey = Resources.ResourceKey) AS UsageCount
       FROM Resources
           ${whereClause}
       ORDER BY ResourceType, Type, Description
@@ -784,6 +819,7 @@ async function buildResourceTable(queryParams, resourceCount, offset = 0) {
         break;
     }
 
+    parts.push('<th>Usage #</th>');
     parts.push('</tr>');
 
     const resourceRows = await new Promise((resolve, reject) => {
@@ -912,6 +948,10 @@ async function buildResourceTable(queryParams, resourceCount, offset = 0) {
         }
       }
 
+      // Usage count column
+      const usageCount = row.UsageCount || 0;
+      parts.push(`<td>${usageCount > 0 ? usageCount.toLocaleString() : ''}</td>`);
+
       parts.push('</tr>');
     }
 
@@ -1116,7 +1156,7 @@ function makeSelect(selectedValue, optionsList, name = 'rt') {
 }
 
 function buildAdditionalForm(queryParams) {
-  const { ver, realm, auth, type, rt, text } = queryParams;
+  const { ver, realm, auth, type, rt, text, pkg, onlyUsed } = queryParams;
 
   let html = '<form method="GET" action="" style="background-color: #eeeeee; border: 1px black solid; padding: 6px; font-size: 12px; font-family: verdana;">';
 
@@ -1142,6 +1182,7 @@ function buildAdditionalForm(queryParams) {
       const profileResources = getCachedSet('profileResources');
       if (profileResources.length > 0) {
         html += 'Type: ' + makeSelect(rt, profileResources) + ' ';
+        html += '<br/>';
       }
       break;
     }
@@ -1150,6 +1191,7 @@ function buildAdditionalForm(queryParams) {
       const profileTypes = getCachedSet('profileTypes');
       if (profileTypes.length > 0) {
         html += 'Type: ' + makeSelect(rt, profileTypes) + ' ';
+        html += '<br/>';
       }
       break;
     }
@@ -1162,6 +1204,7 @@ function buildAdditionalForm(queryParams) {
       const extensionContexts = getCachedSet('extensionContexts');
       if (extensionContexts.length > 0) {
         html += 'Context: ' + makeSelect(rt, extensionContexts) + ' ';
+        html += '<br/>';
       }
       break;
     }
@@ -1172,6 +1215,7 @@ function buildAdditionalForm(queryParams) {
         // Convert txSources map to "code=display" format
         const sourceOptions = Object.keys(txSources).map(code => `${code}=${txSources[code]}`);
         html += 'Source: ' + makeSelect(rt, sourceOptions) + ' ';
+        html += '<br/>';
       }
       break;
     }
@@ -1182,6 +1226,7 @@ function buildAdditionalForm(queryParams) {
         // Convert txSources map to "code=display" format
         const sourceOptionsCM = Object.keys(txSourcesCM).map(code => `${code}=${txSourcesCM[code]}`);
         html += 'Source: ' + makeSelect(rt, sourceOptionsCM) + ' ';
+        html += '<br/>';
       }
       break;
     }
@@ -1190,15 +1235,20 @@ function buildAdditionalForm(queryParams) {
       const resourceTypes = getCachedSet('resourceTypes');
       if (resourceTypes.length > 0) {
         html += 'Type: ' + makeSelect(rt, resourceTypes);
+        html += '<br/>';
       }
       break;
     }
   }
 
-  // Add text search field
+
+  // Add text search field and package filter field
   html += `Text: <input type="text" name="text" value="${escape(text || '')}" class="" style="width: 200px;"/> `;
+  html += `Package: <input type="text" name="pkg" value="${escape(pkg || '')}" placeholder="e.g. hl7.fhir.us" class="" style="width: 200px;"/> `;
 
-  // Add submit button
+  // Add submit button with 'only used' checkbox immediately before it
+  const onlyUsedChecked = onlyUsed === 'true' ? ' checked' : '';
+  html += `<input type="checkbox" name="onlyUsed" value="true"${onlyUsedChecked}/> Only Show Used `;
   html += '<input type="submit" value="Search" style="color:rgb(89, 137, 241)"/>';
 
   html += '</form>';
@@ -2252,6 +2302,8 @@ router.get('/', async (req, res) => {
         type: req.query.type || '',
         rt: req.query.rt || '',
         text: req.query.text || '',
+        pkg: req.query.pkg || '',
+        onlyUsed: req.query.onlyUsed || '',
         offset: req.query.offset || '0'
       };
 
@@ -2696,11 +2748,14 @@ function buildDependencyTable(dependencies) {
       }
       currentType = dep.ResourceType;
       html += '<table class="table table-bordered">';
-      html += `<tr style="background-color: #eeeeee"><td colspan="2"><strong>${escape(currentType)}</strong></td></tr>`;
+      html += `<tr style="background-color: #eeeeee"><td colspan="3"><strong>${escape(currentType)}</strong></td></tr>`;
     }
 
     html += '<tr>';
 
+    // Package column
+    html += `<td>${escape(dep.PID || '')}</td>`;
+
     // Build the link to the resource detail page
     const packagePid = dep.PID.replace(/#/g, '|'); // Convert # to | for URL
     const resourceUrl = `/xig/resource/${encodeURIComponent(packagePid)}/${encodeURIComponent(dep.ResourceType)}/${encodeURIComponent(dep.Id)}`;