fhirsmith 0.8.5 → 0.8.6

package/server.js

@@ -28,7 +28,7 @@ try {
 }
 
 const Logger = require('./library/logger');
-const serverLog = Logger.getInstance().child({ module: 'server' });
+const serverLog = Logger.getInstance(config.logging || {}).child({ module: 'server' });
 const packageJson = require('./package.json');
 
 // Startup banner
@@ -64,6 +64,7 @@ const FolderModule = require("./folder/folder");
 const ExtensionTrackerModule = require("./extension-tracker/extension-tracker");
 
 htmlServer.useLog(serverLog);
+htmlServer.setSponsorMessage(config.sponsorMessage ? config.sponsorMessage : '');
 
 const app = express();
 
@@ -386,22 +387,44 @@ async function buildRootPageContent() {
 
   // Memory usage
   const memUsage = process.memoryUsage();
-  const heapUsedMB = (memUsage.heapUsed / 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 heapStats = v8.getHeapStatistics();
+
+  // V8 heap: used vs limit
+  const v8UsedMB = (memUsage.heapUsed / 1024 / 1024).toFixed(0);
+  const v8LimitMB = (heapStats.heap_size_limit / 1024 / 1024).toFixed(0);
+  const v8PCT = (memUsage.heapUsed * 100) / heapStats.heap_size_limit;
+
+  // Process RSS vs cgroup limit (or system total)
+  const rssMB = (memUsage.rss / 1024 / 1024).toFixed(0);
+  let memLimit;
+  try {
+    const raw = fs.readFileSync('/sys/fs/cgroup/memory.max', 'utf8').trim();
+    memLimit = raw === 'max' ? os.totalmem() : parseInt(raw);
+  } catch {
+    memLimit = os.totalmem();
+  }
+  const memLimitMB = (memLimit / 1024 / 1024).toFixed(0);
+  const processPCT = (memUsage.rss * 100) / memLimit;
+
+  // System memory
   const totalMemMB = (os.totalmem() / 1024 / 1024).toFixed(0);
+  const usedMemMB = ((os.totalmem() - os.freemem()) / 1024 / 1024).toFixed(0);
+  const sysMemPCT = ((os.totalmem() - os.freemem()) * 100) / os.totalmem();
+
+  // Average requests per minute
+  const uptimeMinutesTotal = uptimeMs / 60000;
+  const avgReqPerMin = uptimeMinutesTotal > 0 ? (stats.requestCount / uptimeMinutesTotal).toFixed(1) : '0.0';
 
   content += '<table class="grid">';
   content += '<tr>';
   content += `<td><strong>Uptime:</strong> ${escape(uptimeStr)}</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 += `<td><strong>Avg Requests/min:</strong> ${avgReqPerMin}</td>`;
   content += '</tr>';
   content += '<tr>';
-  content += `<td><strong>Heap Used:</strong> ${heapUsedMB} MB</td>`;
-  content += `<td><strong>Heap Available:</strong> ${heapAvailableMB} MB</td>`;
-  content += `<td><strong>Process Memory:</strong> ${rssMB} MB</td>`;
+  content += `<td style="background-color:${pctColor(v8PCT)}"><strong>V8 Memory:</strong> ${v8UsedMB} MB of ${v8LimitMB} MB (${v8PCT.toFixed(0)}%)</td>`;
+  content += `<td style="background-color:${pctColor(processPCT)}"><strong>Process Memory:</strong> ${rssMB} MB of ${memLimitMB} MB (${processPCT.toFixed(0)}%)</td>`;
+  content += `<td style="background-color:${pctColor(sysMemPCT)}"><strong>System Memory:</strong> ${usedMemMB} MB of ${totalMemMB} MB (${sysMemPCT.toFixed(0)}%)</td>`;
   content += '</tr>';
   content += getLogStats();
   content += '</table>';
@@ -543,10 +566,24 @@ app.get('/dashboard', async (req, res) => {
     // Memory usage
     const memUsage = process.memoryUsage();
     const heapStats = v8.getHeapStatistics();
-    const nodeMemPCT = (memUsage.heapUsed * 100) / heapStats.heap_size_limit;  // % of Node.js memory limit used
+    const v8PCT = (memUsage.heapUsed * 100) / heapStats.heap_size_limit;  // % of V8 heap limit used
+
+    // Process RSS as % of cgroup memory limit (or system total as fallback)
+    let memLimit;
+    try {
+      const raw = fs.readFileSync('/sys/fs/cgroup/memory.max', 'utf8').trim();
+      memLimit = raw === 'max' ? os.totalmem() : parseInt(raw);
+    } catch {
+      memLimit = os.totalmem();
+    }
+    const processPCT = (memUsage.rss * 100) / memLimit;
+
     const totalMemBytes = os.totalmem();
     const freeMemBytes = os.freemem();
     const sysMemPCT = ((totalMemBytes - freeMemBytes) * 100) / totalMemBytes;  // % of system memory used
+
+    const memMaxPCT = Math.max(v8PCT, processPCT, sysMemPCT);
+
     const fstats = fs.statfsSync(folders.logsDir());
     const diskPCT = 100 - ((fstats.bavail * 100) / fstats.blocks);  // % of disk used
 
@@ -555,8 +592,7 @@ app.get('/dashboard', async (req, res) => {
     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(nodeMemPCT)}"><strong>Node Memory:</strong> ${nodeMemPCT.toFixed(0)}%</td>`;
-    content += `<td style="background-color:${pctColor(sysMemPCT)}"><strong>System Memory:</strong> ${sysMemPCT.toFixed(0)}%</td>`;
+    content += `<td style="background-color:${pctColor(memMaxPCT)}"><strong>Memory:</strong> ${v8PCT.toFixed(0)}% V8, ${processPCT.toFixed(0)}% Process, ${sysMemPCT.toFixed(0)}% System</td>`;
     content += `<td style="background-color:${pctColor(diskPCT)}"><strong>Disk:</strong> ${diskPCT.toFixed(0)}%</td>`;
     content += '</tr>';
     content += '</table>';

package/translations/Messages.properties

@@ -1274,7 +1274,7 @@ VALUESET_SHAREABLE_MISSING = Published value sets SHOULD conform to the Shareabl
 VALUESET_SHAREABLE_MISSING_HL7 = Value sets published by HL7 SHALL conform to the ShareableValueSet profile, which says that the element ValueSet.{0} is mandatory, but it is not present
 VALUESET_SUPPLEMENT_MISSING_one = Required supplement not found: {1}
 VALUESET_SUPPLEMENT_MISSING_other = Required supplements not found: {1}
-VALUESET_TOO_COSTLY = The value set ''{0}'' expansion has too many codes to display ({1})
+VALUESET_TOO_COSTLY = The value set ''{0}'' expansion has too many codes to produce ({1})
 VALUESET_TOO_COSTLY_COUNT = The value set ''{0}'' expansion has {2} codes, which is too many to display ({1})
 VALUESET_TOO_COSTLY_TIME = The value set ''{0}'' {2} took too long to process (>{1}sec)
 VALUESET_UNC_SYSTEM_WARNING = Unknown System ''{0}'' specified, so Concepts and Filters can''t be checked (Details: {1})

package/translations/rendering-phrases.properties

@@ -1214,4 +1214,6 @@ CONSENT_HT_RESOURCE_TYPE = Resource Type
 CONSENT_HT_DOC_TYPE = Document Type
 CONSENT_HT_CODE = Code
 WEB_SOURCE = Web Source
-GENERAL_COPY = Click to Copy
+GENERAL_COPY = Click to Copy
+CODESYSTEM_LVL = Level
+FEATURE = Feature

package/tx/cs/cs-api.js

@@ -719,7 +719,11 @@ class CodeSystemProvider {
     return false;
   }
 
+  hasMultiHierarchy() {
+    return false;
+  }
   /**
+   *
    * @returns {string} valueset for the code system
    */
   valueSet() {

package/tx/cs/cs-cs.js

@@ -1521,7 +1521,11 @@ class FhirCodeSystemProvider extends BaseCSServices {
   }
 
   versionNeeded() {
-    return this.codeSystem.jsonObj.versionNeeded;
+    return this.codeSystem.jsonObj.versionNeeded ? true : false;
+  }
+
+  hasMultiHierarchy() {
+    return this.codeSystem.hasMultiHierarchy;
   }
 
 }

package/tx/cs/cs-snomed.js

@@ -1348,6 +1348,10 @@ class SnomedProvider extends BaseCSServices {
     return result;
   }
 
+  hasMultiHierarchy() {
+    return true;
+  }
+
 }
 
 /**

package/tx/html/tx-template.html

@@ -117,9 +117,10 @@
 		<div class="container">
 			<div class="inner-wrapper">
 				<p>
-                    <a href="http://www.hl7.org/fhir" style="color: gold" title="Fast Healthcare Interoperability Resources - Home Page"><img border="0" src="/icon-fhir-16.png" style="vertical-align: text-bottom"/> <b>FHIR</b></a> &copy; HL7.org 2011+.  &nbsp;|&nbsp;
+                    <a href="http://www.hl7.org/fhir" style="color: gold" title="Fast Healthcare Interoperability Resources - Home Page"><img border="0" src="/icon-fhir-16.png" style="vertical-align: text-bottom"/> <b>FHIR</b></a> v[%fhir-version%] &copy; HL7.org 2011+.  &nbsp;|&nbsp;
                     <a href="https://github.com/HealthIntersections/FHIRsmith/blob/main/README.md" style="color: gold"><img border="0" src="/FHIRsmith16.png" style="vertical-align: text-bottom"/> FHIRsmith</a>  [%ver%]  &copy; HealthIntersections.com.au 2023+ &nbsp;|&nbsp;
-         FHIR Version [%fhir-version%] &nbsp;|&nbsp; ([%ms%] ms)
+                    &nbsp; ([%ms%] ms)
+                    [%sponsorMessage%]
         </p>
 			</div>
 		</div>

package/tx/library/codesystem.js

@@ -74,6 +74,8 @@ class CodeSystem extends CanonicalResource {
    */
   childToParentsMap = new Map();
 
+  hasMultiHierarchy = false;
+
   /**
    * Static factory method for convenience
    * @param {string} jsonString - JSON string representation of CodeSystem
@@ -326,6 +328,8 @@ class CodeSystem extends CanonicalResource {
 
     // Third pass: handle nested concept structures
     this._buildNestedHierarchy(this.jsonObj.concept);
+
+    this.hasMultiHierarchy = Array.from(this.childToParentsMap.values()).some(parents => parents.length > 1);
   }
 
   /**

package/tx/library/renderer.js

@@ -133,7 +133,7 @@ class Renderer {
     return result;
   }
 
-  async renderMetadataTable(res, tbl) {
+  async renderMetadataTable(res, tbl, sourcePackage) {
     this.renderMetadataVersion(res, tbl);
     await this.renderMetadataProfiles(res, tbl);
     this.renderMetadataTags(res, tbl);
@@ -154,6 +154,11 @@ class Renderer {
     this.renderProperty(tbl, 'EXT_FMM_LEVEL', Extensions.readString(res, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm'));
     this.renderProperty(tbl, 'PAT_PERIOD', res.effectivePeriod);
     this.renderPropertyLink(tbl, 'WEB_SOURCE', Extensions.readString(res, 'http://hl7.org/fhir/StructureDefinition/web-source'));
+    this.renderProperty(tbl, 'GENERAL_SOURCE', sourcePackage);
+    for (let ext of Extensions.list(res, 'http://hl7.org/fhir/uv/application-feature/StructureDefinition/feature')) {
+      this.renderProperty(tbl, 'FEATURE', this.featureSummary(ext));
+    }
+
 
     // capability statement things
     this.renderProperty(tbl, 'Kind', res.kind);
@@ -165,7 +170,6 @@ class Renderer {
       }
     }
     this.renderProperty(tbl, 'GENERAL_URL', res.implementation?.url);
-    this.renderProperty(tbl, 'Kind', res.kind);
     this.renderProperty(tbl, 'EX_SCEN_FVER', res.fhirVersion);
 
     if (res.content === 'supplement' && res.supplements) {
@@ -364,7 +368,7 @@ class Renderer {
     return div_.toString();
   }
 
-  async renderCodeSystem(cs) {
+  async renderCodeSystem(cs, sourcePackage) {
     if (cs.json) {
       cs = cs.json;
     }
@@ -373,7 +377,7 @@ class Renderer {
 
     // Metadata table
     div_.h3().tx("Properties");
-    await this.renderMetadataTable(cs, div_.table("grid"));
+    await this.renderMetadataTable(cs, div_.table("grid"), sourcePackage);
 
     // Code system properties
     const hasProps = this.generateProperties(div_, cs);
@@ -2227,6 +2231,18 @@ class Renderer {
     }
   }
 
+  featureSummary(ext) {
+    let defn = Extensions.readString(ext, 'definition');
+    let value = Extensions.readString(ext, 'value');
+    switch (defn) {
+      case 'http://hl7.org/fhir/uv/tx-tests/FeatureDefinition/test-version':
+        return 'Tx Test version = ' + value;
+      case 'http://hl7.org/fhir/uv/tx-ecosystem/FeatureDefinition/CodeSystemAsParameter':
+        return 'CodeSystems as parameters = ' + value;
+      default:
+        return defn+' = ' + value;
+    }
+  }
 }
 
 module.exports = { Renderer };

package/tx/operation-context.js

@@ -15,7 +15,7 @@ function isDebugging() {
   }
   // Also check for debug flags in case inspector not yet attached
   return process.execArgv.some(arg =>
-    arg.includes('--inspect') || arg.includes('--debug')
+      arg.includes('--inspect') || arg.includes('--debug')
   );
 }
 
@@ -233,16 +233,16 @@ class ExpansionCache {
     // Resources are now CodeSystem/ValueSet wrappers, not raw JSON
     if (additionalResources && additionalResources.length > 0) {
       const resourceHashes = additionalResources
-        .map(r => {
-          // Get the JSON object from wrapper or use directly
-          const json = r.jsonObj || r;
-          // Create a content hash for this resource
-          return crypto.createHash('sha256')
-            .update(JSON.stringify(json))
-            .digest('hex')
-            .substring(0, 16); // Use first 16 chars for brevity
-        })
-        .sort();
+          .map(r => {
+            // Get the JSON object from wrapper or use directly
+            const json = r.jsonObj || r;
+            // Create a content hash for this resource
+            return crypto.createHash('sha256')
+                .update(JSON.stringify(json))
+                .digest('hex')
+                .substring(0, 16); // Use first 16 chars for brevity
+          })
+          .sort();
       keyParts.push(`additional:${resourceHashes.join(',')}`);
     }
 
@@ -314,7 +314,7 @@ class ExpansionCache {
 
     // Get entries sorted by lastUsed (oldest first)
     const entries = Array.from(this.cache.entries())
-      .sort((a, b) => a[1].lastUsed - b[1].lastUsed);
+        .sort((a, b) => a[1].lastUsed - b[1].lastUsed);
 
     const toEvict = Math.min(count, entries.length);
     for (let i = 0; i < toEvict; i++) {
@@ -413,7 +413,29 @@ class ExpansionCache {
 }
 
 
+/**
+ * Read the cgroup memory limit once at startup.
+ * Returns the byte limit, or 0 if unavailable (disables the check).
+ */
+function readMemoryLimit() {
+  try {
+    const raw = require('fs').readFileSync('/sys/fs/cgroup/memory.max', 'utf8').trim();
+    if (raw === 'max') return 0; // no cgroup limit
+    return parseInt(raw);
+  } catch {
+    return 0; // not on Linux / no cgroup
+  }
+}
+
+const MEMORY_LIMIT = readMemoryLimit();
+const MEMORY_FRACTION = 0.98;
+const MEMORY_THRESHOLD = MEMORY_LIMIT > 0 ? MEMORY_LIMIT * MEMORY_FRACTION : 0; // 90% of cgroup limit
+const CHECK_FREQUENCY = 100;
+
 class OperationContext {
+  // Shared counter across all instances — only check RSS every CHECK_FREQUENCY calls
+  static _checkCounter = 0;
+
   constructor(langs, i18n = null, id = null, timeLimit = 30, resourceCache = null, expansionCache = null) {
     this.i18n = i18n;
     this.langs = this._ensureLanguages(langs);
@@ -445,8 +467,8 @@ class OperationContext {
    */
   copy() {
     const newContext = new OperationContext(
-      this.langs, this.i18n, this.id, this.timeLimit / 1000,
-      this.resourceCache, this.expansionCache
+        this.langs, this.i18n, this.id, this.timeLimit / 1000,
+        this.resourceCache, this.expansionCache
     );
     newContext.contexts = [...this.contexts];
     newContext.startTime = this.startTime;
@@ -458,31 +480,64 @@ class OperationContext {
   }
 
   /**
-   * Check if operation has exceeded time limit
+   * Check if operation has exceeded time limit, or is pushing is over the memory limit
    * Skipped when running under debugger
+   *
+   * note: if the server pushes over the memory limit for the process, the process is terminated.
+   * the memory check here is intended to prevent process termination on the grounds that some
+   * big operation is pushing the limit. It might not be the big operation that is terminated first,
+   * but eventually it'll get terminated.
+   *
+   * this is called a *lot* so it's important to be efficient. Only check every CHECK_FREQUENCY
+   * times means that there could be a small overrun, but it's called often enough that the
+   * overrun won't be that signiifcant
+   *
    * @param {string} place - Location identifier for debugging
    * @returns {boolean} true if operation should be terminated
    */
   deadCheck(place = 'unknown') {
-    // Skip time limit checks when debugging
     if (this.debugging) {
       return false;
     }
 
-    const elapsed = performance.now() - this.startTime;
+    OperationContext._checkCounter++;
+    if (OperationContext._checkCounter < CHECK_FREQUENCY) {
+      return false;
+    }
+    OperationContext._checkCounter = 0;
 
+    // Time check
+    const elapsed = performance.now() - this.startTime;
     if (elapsed > this.timeLimit) {
       const timeInSeconds = Math.round(this.timeLimit / 1000);
       this.log(`Operation took too long @ ${place} (${this.constructor.name})`);
-
-      const error = new Issue("error", "too-costly", null, `Operation exceeded time limit of ${timeInSeconds} seconds at ${place}`);
+      const error = new Issue("error", "too-costly", null,
+          `Operation exceeded time limit of ${timeInSeconds} seconds at ${place}`);
       error.diagnostics = this.diagnostics();
       throw error;
     }
 
+    // Memory check (piggyback on same sample)
+    if (MEMORY_THRESHOLD > 0) {
+      const rss = process.memoryUsage.rss();
+      if (rss > MEMORY_THRESHOLD) {
+        const usedGB = (rss / 1024 / 1024 / 1024).toFixed(1);
+        const limitGB = (MEMORY_LIMIT / 1024 / 1024 / 1024).toFixed(1);
+        this.log(`Memory Limit: ${usedGB} GB of ${limitGB} GB limit @ ${place}`);
+        const error = new Issue("error", "too-costly", null,
+            `Operation aborted: server memory usage (${usedGB} GB) exceeds safe threshold (${MEMORY_FRACTION * 100}% of ${limitGB} GB limit) at ${place}`);
+        error.diagnostics = this.diagnostics();
+        throw error;
+      }
+    }
+
     return false;
   }
 
+  unSeeAll() {
+    this.contexts = [];
+  }
+
   /**
    * Track a context URL and detect circular references
    * @param {string} vurl - Value set URL to track

package/tx/tx-html.js

@@ -319,7 +319,7 @@ class TxHtmlRenderer {
           case 'Parameters':
             return await this.renderParameters(json);
           case 'CodeSystem':
-            return await this.renderCodeSystem(json, inBundle, _fmt, op);
+            return await this.renderCodeSystem(json, inBundle, _fmt, op, req.sourcePackage);
           case 'ValueSet': {
             let exp = undefined;
             if (!inBundle && !op && (!_fmt || _fmt == 'html')) {
@@ -330,10 +330,10 @@ class TxHtmlRenderer {
                 exp = error;
               }
             }
-            return await this.renderValueSet(json, inBundle, _fmt, op, exp);
+            return await this.renderValueSet(json, inBundle, _fmt, op, exp, req.sourcePackage);
           }
           case 'ConceptMap':
-            return await this.renderConceptMap(json, inBundle, _fmt, op);
+            return await this.renderConceptMap(json, inBundle, _fmt, op, req.sourcePackage);
           case 'CapabilityStatement':
             return await this.renderCapabilityStatement(json, inBundle);
           case 'TerminologyCapabilities':
@@ -632,7 +632,7 @@ class TxHtmlRenderer {
   /**
    * Render CodeSystem resource
    */
-  async renderCodeSystem(json, inBundle, _fmt) {
+  async renderCodeSystem(json, inBundle, _fmt, op, sourcePackage) {
     if (inBundle) {
       return await this.renderResourceWithNarrative(json, await this.renderer.renderCodeSystem(json));
     } else {
@@ -645,7 +645,7 @@ class TxHtmlRenderer {
       html += `</ul>`;
 
       if (!_fmt || _fmt == 'html') {
-        html += await this.renderResourceWithNarrative(json, await this.renderer.renderCodeSystem(json));
+        html += await this.renderResourceWithNarrative(json, await this.renderer.renderCodeSystem(json, sourcePackage));
       } else if (_fmt == "html/json") {
         html += await this.renderResourceJson(json);
       } else if (_fmt == "html/xml") {

package/tx/tx.js

@@ -173,6 +173,7 @@ class TXModule {
     this.metadataHandler = new MetadataHandler({
       baseUrl: config.baseUrl,
       serverVersion: packageJson.version,
+      txVersion: packageJson.txVersion,
       softwareName: config.softwareName || 'FHIRsmith',
       name: config.name || 'FHIRTerminologyServer',
       title: config.title || 'FHIR Terminology Server',