fhirsmith 0.7.5 → 0.8.0

package/server.js

@@ -269,7 +269,6 @@ async function loadTemplates() {
 
 async function buildRootPageContent() {
   stats.requestCount++;
-  let mc = 0;
   let content = '<div class="row mb-4">';
   content += '<div class="col-12">';
 
@@ -278,35 +277,30 @@ async function buildRootPageContent() {
 
   // Check which modules are enabled and add them to the list
   if (config.modules.packages.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/packages" class="text-decoration-none">Package Server</a>: Browse and download FHIR Implementation Guide packages';
     content += '</li>';
   }
 
   if (config.modules.xig.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/xig" class="text-decoration-none">FHIR IG Statistics</a>: Statistics and analysis of FHIR Implementation Guides';
     content += '</li>';
   }
 
   if (config.modules.shl.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/shl" class="text-decoration-none">SHL Server</a>: SMART Health Links management and validation';
     content += '</li>';
   }
 
   if (config.modules.vcl.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/VCL" class="text-decoration-none">VCL Server</a>: ValueSet Compose Language expression parsing';
     content += '</li>';
   }
 
   if (config.modules.registry && config.modules.registry.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/tx-reg" class="text-decoration-none">Terminology Server Registry</a>: ';
     content += 'Discover and query FHIR terminology servers for code system and value set support';
@@ -314,7 +308,6 @@ async function buildRootPageContent() {
   }
 
   if (config.modules.publisher && config.modules.publisher.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/publisher" class="text-decoration-none">FHIR Publisher</a>: ';
     content += 'Manage FHIR Implementation Guide publication tasks and approvals';
@@ -322,7 +315,6 @@ async function buildRootPageContent() {
   }
 
   if (config.modules.token && config.modules.token.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/token" class="text-decoration-none">Token Server</a>: ';
     content += 'OAuth authentication and API key management for FHIR services';
@@ -330,7 +322,6 @@ async function buildRootPageContent() {
   }
 
   if (config.modules.npmprojector && config.modules.npmprojector.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/npmprojector" class="text-decoration-none">NpmProjector</a>: ';
     content += 'Hot-reloading FHIR server with FHIRPath-based search indexes';
@@ -338,7 +329,6 @@ async function buildRootPageContent() {
   }
 
   if (config.modules?.['ext-tracker']?.enabled) {
-    mc++;
     content += '<li class="list-group-item">';
     content += '<a href="/ext-tracker" class="text-decoration-none">Extension Tracker</a>: ';
     content += 'View of Extension Usage';
@@ -353,7 +343,6 @@ async function buildRootPageContent() {
     content += '<ul class="mt-2 mb-0">';
     for (const fc of folders) {
       if (fc.enabled === false) continue;
-      mc++;
       content += '<li>';
       content += `<a href="${fc.url}" class="text-decoration-none">${fc.name}</a>: `;
       content += 'File folder with write control';
@@ -370,7 +359,6 @@ async function buildRootPageContent() {
     if (config.modules.tx.endpoints && config.modules.tx.endpoints.length > 0) {
       content += '<ul class="mt-2 mb-0">';
       for (const endpoint of config.modules.tx.endpoints) {
-        mc++;
         content += `<li><a href="${endpoint.path}" class="text-decoration-none">${endpoint.path}</a> (FHIR v${endpoint.fhirVersion}${endpoint.context ? ', context: ' + endpoint.context : ''})</li>`;
       }
       content += '</ul>';
@@ -382,7 +370,6 @@ async function buildRootPageContent() {
 
   content += '<hr/>';
 
-
   // Calculate uptime
   const uptimeMs = Date.now() - stats.startTime;
   const uptimeSeconds = Math.floor(uptimeMs / 1000);
@@ -399,7 +386,7 @@ async function buildRootPageContent() {
   // Memory usage
   const memUsage = process.memoryUsage();
   const heapUsedMB = (memUsage.heapUsed / 1024 / 1024).toFixed(2);
-  const heapTotalMB = (memUsage.heapTotal / 1024 / 1024).toFixed(2);
+  const heapAvailableMB = ((memUsage.heapTotal - memUsage.heapUsed) / 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);
@@ -407,20 +394,18 @@ async function buildRootPageContent() {
   content += '<table class="grid">';
   content += '<tr>';
   content += `<td><strong>Uptime:</strong> ${escape(uptimeStr)}</td>`;
-  content += `<td><strong>Request Count:</strong> ${stats.requestCount}</td>`;
+  content += `<td><strong>Request Count:</strong> ${stats.requestCount} (static: ${stats.staticRequestCount})</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>`;
-  content += `<td><strong>Heap Total:</strong> ${heapTotalMB} MB</td>`;
+  content += `<td><strong>Heap Available:</strong> ${heapAvailableMB} MB</td>`;
   content += `<td><strong>Process Memory:</strong> ${rssMB} MB</td>`;
   content += '</tr>';
   content += getLogStats();
   content += '</table>';
 
-
   // ===== Metrics Graphs =====
-
   const liquid = new Liquid({
     root: path.join(__dirname, 'tx', 'html'),
     extname: '.liquid'
@@ -468,6 +453,10 @@ app.get('/', async (req, res) => {
         const templatePath = path.join(__dirname, 'root-template.html');
         htmlServer.loadTemplate('root', templatePath);
       }
+      if (!htmlServer.hasTemplate('root-bare')) {
+        const templatePath = path.join(__dirname, 'root-bare-template.html');
+        htmlServer.loadTemplate('root-bare', templatePath);
+      }
 
       const content = await buildRootPageContent();
 
@@ -503,6 +492,15 @@ app.get('/', async (req, res) => {
 app.get('/fhirsmith', (req, res) => serveFhirsmithHome(req, res));
 
 // Serve static files
+// Count static file hits separately from API/page requests
+app.use((req, res, next) => {
+  res.on('finish', () => {
+    if (res.statusCode >= 200 && res.statusCode < 300) {
+      stats.staticRequestCount++;
+    }
+  });
+  next();
+});
 if (config.server?.webBase) {
   const overrideDir = path.resolve(config.server.webBase);
   app.use((req, res, next) => {
@@ -518,6 +516,85 @@ if (config.server?.webBase) {
 }
 app.use(express.static(path.join(__dirname, 'static')));
 
+// Dashboard endpoint - server name, stats, graphs, and background tasks (no modules list)
+app.get('/dashboard', async (req, res) => {
+  stats.requestCount++;
+  try {
+    if (!htmlServer.hasTemplate('root-bare')) {
+      const templatePath = path.join(__dirname, 'root-bare-template.html');
+      htmlServer.loadTemplate('root-bare', templatePath);
+    }
+
+    const startTime = Date.now();
+    // Calculate uptime
+    const uptimeMs = Date.now() - stats.startTime;
+    const uptimeSeconds = Math.floor(uptimeMs / 1000);
+    const uptimeDays = Math.floor(uptimeSeconds / 86400);
+    const uptimeHours = Math.floor((uptimeSeconds % 86400) / 3600);
+    const uptimeMinutes = Math.floor((uptimeSeconds % 3600) / 60);
+    const uptimeSecs = uptimeSeconds % 60;
+    let uptimeStr = '';
+    if (uptimeDays > 0) uptimeStr += `${uptimeDays}d `;
+    if (uptimeHours > 0 || uptimeDays > 0) uptimeStr += `${uptimeHours}h `;
+    if (uptimeMinutes > 0 || uptimeHours > 0 || uptimeDays > 0) uptimeStr += `${uptimeMinutes}m `;
+    uptimeStr += `${uptimeSecs}s`;
+
+    // Memory usage
+    const memUsage = process.memoryUsage();
+    const heapUsedPCT =  (memUsage.heapUsed * 100) / memUsage.heapTotal;
+    const freeMemMB = (os.freemem() / 1024 / 1024).toFixed(0);
+    const totalMemMB = (os.totalmem() / 1024 / 1024).toFixed(0);
+    const usedMemPCT = 100 - ((freeMemMB * 100) / totalMemMB);
+    const fstats = fs.statfsSync(folders.logsDir());
+    const diskPCT = (fstats.bavail * 100) / fstats.blocks;
+
+    let content = '';
+    content += '<table border="1">';
+    content += '<tr>';
+    content += `<td><strong>Uptime:</strong> ${escape(uptimeStr)}</td>`;
+    content += `<td><strong>Request Count:</strong> ${stats.requestCount} (static: ${stats.staticRequestCount})</td>`;
+    content += `<td style="background-color:${pctColor(usedMemPCT)}"><strong>Memory:</strong> ${usedMemPCT.toFixed(0)}%</td>`;
+    content += `<td style="background-color:${pctColor(heapUsedPCT)}"><strong>Heap:</strong> ${heapUsedPCT.toFixed(0)}%</td>`;
+    content += `<td style="background-color:${pctColor(diskPCT)}"><strong>Disk:</strong> ${diskPCT.toFixed(0)}%</td>`;
+    content += '</tr>';
+    content += '</table>';
+
+    // ===== Metrics Graphs =====
+    const liquid = new Liquid({
+      root: path.join(__dirname, 'tx', 'html'),
+      extname: '.liquid'
+    });
+    content += await liquid.renderFile('dash-metrics', {
+      historyJson: JSON.stringify(stats.history),
+      startTime: stats.startTime
+    });
+    content += stats.taskDetails();
+    content += `<p>Data: ${folders.dataDir()}</p>`;
+
+    content = '<div class="row mb-4"><div class="col-12">' + content + '</div></div>';
+
+    const pageStats = {
+      version: packageJson.version,
+      enabledModules: Object.keys(config.modules).filter(m => config.modules[m].enabled).length,
+      processingTime: Date.now() - startTime
+    };
+
+    const title = (config.hostName ? escape(config.hostName) : 'FHIRsmith Server')+' v'+packageJson.version;
+    const html = htmlServer.renderPage('root-bare', title, content, pageStats);
+    res.setHeader('Content-Type', 'text/html');
+    res.send(html);
+  } catch (error) {
+    serverLog.error('Error rendering dashboard:', error);
+    htmlServer.sendErrorResponse(res, 'root', error);
+  }
+});
+
+function pctColor(pct) {
+  const r = Math.round(pct * 2.55);
+  const g = Math.round((100 - pct) * 2.55);
+  return `rgb(${r}, ${g}, 100)`;  // the 100 keeps it pastel/light
+}
+
 // Health check endpoint
 app.get('/health', async (req, res) => {
   const healthStatus = {
@@ -564,10 +641,10 @@ function getLogStats() {
     let diskInfo = '';
     try {
       // statfs available in Node 18.15+
-      const stats = fs.statfsSync(logDir);
-      const blockSize = stats.bsize;
-      const freeSpace = stats.bavail * blockSize;
-      const totalSpace = stats.blocks * blockSize;
+      const fstats = fs.statfsSync(logDir);
+      const blockSize = fstats.bsize;
+      const freeSpace = fstats.bavail * blockSize;
+      const totalSpace = fstats.blocks * blockSize;
       const freeGB = (freeSpace / 1024 / 1024 / 1024).toFixed(2);
       const totalGB = (totalSpace / 1024 / 1024 / 1024).toFixed(2);
       diskInfo = `<td><strong>Disk Space:</strong> ${freeGB} GB of ${totalGB} GB</td>`;

package/stats.js

@@ -5,6 +5,7 @@ const escape = require('escape-html');
 class ServerStats {
   started = false;
   requestCount = 0;
+  staticRequestCount = 0;
   requestTime = 0;
   // Collect metrics every 10 minutes
   intervalMs = 10 * 60 * 1000;
@@ -27,7 +28,8 @@ class ServerStats {
       const now = Date.now();
 
       const currentMem = process.memoryUsage().heapUsed;
-      const requestsDelta = this.requestCount - this.requestCountSnapshot;
+      const combinedCount = this.requestCount + this.staticRequestCount;
+      const requestsDelta = combinedCount - this.requestCountSnapshot;
       const requestsTat = requestsDelta > 0 ? this.requestTime / requestsDelta : 0;
       const minutesSinceStart = this.history.length > 1
         ? this.intervalMs / 60000
@@ -38,7 +40,7 @@ class ServerStats {
       const idleDelta = currentCpu.idle - this.lastUsage.idle;
       const totalDelta = currentCpu.total - this.lastUsage.total;
       const percent = totalDelta > 0 ? 100 * (1 - idleDelta / totalDelta) : 0;
-      
+
       const loopDelay = this.eventLoopMonitor.mean / 1e6;
       let cacheCount = 0;
       for (let m of this.cachingModules) {
@@ -48,11 +50,11 @@ class ServerStats {
       this.history.push({time: now, mem: currentMem - this.startMem, rpm: requestsPerMin, tat: requestsTat, cpu: percent, block: loopDelay, cache : cacheCount});
 
       this.eventLoopMonitor.reset();
-      this.requestCountSnapshot = this.requestCount;
+      this.requestCountSnapshot = combinedCount;
       this.requestTime = 0;
       this.lastTime = now;
       this.lastUsage = currentCpu;
-      
+
       // Prune old data (keep 24 hours)
       const cutoff = now - (24 * 60 * 60 * 1000); // 24 hours ago
       this.history = this.history.filter(m => m.time > cutoff);
@@ -82,6 +84,7 @@ class ServerStats {
     this.taskMap.set(name, info);
     info.frequency = frequency;
     info.state = "Started";
+    info.status = "started"
   }
 
   task(name, state) {
@@ -89,6 +92,25 @@ class ServerStats {
     if (info) {
       info.date = Date.now();
       info.state = state;
+      info.status = 'working';
+    }
+  }
+
+  taskDone(name, state) {
+    let info = this.taskMap.get(name);
+    if (info) {
+      info.date = Date.now();
+      info.state = state;
+      info.status = 'resting';
+    }
+  }
+
+  taskError(name, state) {
+    let info = this.taskMap.get(name);
+    if (info) {
+      info.date = Date.now();
+      info.state = state;
+      info.status = 'error';
     }
   }
 
@@ -96,17 +118,19 @@ class ServerStats {
     if (this.taskMap.size == 0) {
       return "";
     }
-    let html = '<table class="grid"><tr style="background-color: #EEEEEE"><th colspan="4">Background Tasks</th></tr>';
-    html += "<tr><th>Task</th><th>Status</th><th>Frequency</th><th>Last Seen</th></tr>";
+    let html = '<table class="grid">';
+    html += "<tr><th>Background Task</th><th>Status</th><th>Frequency</th><th>Last Seen</th></tr>";
     for (let m of this.taskMap.keys()) {
-      html += "<tr><td>";
+      let mm = this.taskMap.get(m);
+      let color = this.getTaskColor(mm.status);
+      html += `<tr style="background-color: ${color}"><td>`;
       html += escape(m);
       html += "</td><td>";
-      html += escape(this.taskMap.get(m).state);
+      html += escape(mm.state);
       html += "</td><td>";
-      html += this.taskMap.get(m).frequency;
+      html += mm.frequency;
       html += "</td><td>";
-      html += Utilities.formatDuration(this.taskMap.get(m).date, Date.now());
+      html += Utilities.formatDuration(mm.date, Date.now());
       html += "</td></tr>";
     }
     html += "</table>";
@@ -128,5 +152,14 @@ class ServerStats {
     return { idle, total };
   }
 
+  getTaskColor(status) {
+    switch (status) {
+      case "started": return "LightGrey";
+      case "working": return "LightGreen";
+      case "resting": return "White";
+      case "error": return "LightRed";
+      default: return "DarkBlue"; // should not happen
+    }
+  }
 }
 module.exports = ServerStats;

package/tx/README.md

@@ -201,7 +201,7 @@ Loads LOINC from a SQLite database file.
 ```
 
 The filename is downloaded from the base URL if not cached. Database files must be in the server's proprietary format.
-The file is built by importing LOINC (to be documented)
+The file is built by importing LOINC (see [documentation](importers/readme.md))
 
 #### `rxnorm` - RxNorm
 
@@ -211,7 +211,7 @@ Loads RxNorm drug terminology from a SQLite database file.
 - rxnorm:rxnorm_02032025-a.db
 ```
 
-The file is built by importing RxNorm (to be documented)
+The file is built by importing RxNorm (see [documentation](importers/readme.md))
 
 #### `ndc` - NDC (National Drug Code)
 
@@ -228,7 +228,7 @@ Loads FDA UNII codes from a SQLite database file.
 ```yaml
 - unii:unii_20240622.db
 ```
-The file is built by importing UNII (to be documented)
+The file is built by importing UNII (see [documentation](importers/readme.md))
 
 #### `snomed` - SNOMED CT
 
@@ -254,7 +254,7 @@ Common edition identifiers:
 - `nl` - Netherlands
 - `ips` - IPS (International Patient Summary) Free Set
 
-The file is built by importing SNOMED CT (to be documented)
+The file is built by importing SNOMED CT (see [documentation](importers/readme.md))
 
 
 #### `cpt` - CPT (Current Procedural Terminology)
@@ -267,7 +267,7 @@ Loads CPT codes from a SQLite database file.
 
 **Note:** CPT is copyrighted by the American Medical Association. Ensure you have appropriate licensing.
 
-The file is built by importing CPT (to be documented)
+The file is built by importing CPT (see [documentation](importers/readme.md))
 
 #### `omop` - OMOP Vocabularies
 
@@ -276,7 +276,7 @@ Loads OMOP (Observational Medical Outcomes Partnership) vocabulary mappings from
 ```yaml
 - omop:omop_v20250227.db
 ```
-The file is built by importing OMOP (to be documented)
+The file is built by importing OMOP (see [documentation](importers/readme.md))
 
 #### `npm` - FHIR NPM Packages
 

package/tx/cs/cs-api.js

@@ -9,6 +9,9 @@ const {validateParameter, validateArrayParameter} = require("../../library/utili
 const {I18nSupport} = require("../../library/i18nsupport");
 const {VersionUtilities} = require("../../library/version-utilities");
 
+/**
+ * For documentation, see cs-api.md
+ */
 class FilterExecutionContext {
   filters = [];
   forIterate = false;