fhirsmith 0.8.4 → 0.8.6

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);
@@ -141,8 +141,8 @@ class Renderer {
     this.renderMetadataLastUpdated(res, tbl);
     this.renderMetadataSource(res, tbl);
     this.renderProperty(tbl, 'TEST_PLAN_LANG', res.language);
-    this.renderProperty(tbl, 'GENERAL_DEFINING_URL', res.url);
-    this.renderProperty(tbl, 'GENERAL_VER', res.version);
+    this.renderPropertyCopy(tbl, 'GENERAL_DEFINING_URL', res.url);
+    this.renderPropertyCopy(tbl, 'GENERAL_VER', res.version);
     this.renderProperty(tbl, 'GENERAL_NAME', res.name);
     this.renderProperty(tbl, 'GENERAL_TITLE', res.title);
     this.renderProperty(tbl, 'GENERAL_STATUS', res.status);
@@ -150,9 +150,15 @@ class Renderer {
     this.renderPropertyMD(tbl, 'GENERAL_PURPOSE', res.purpose);
     this.renderProperty(tbl, 'CANON_REND_PUBLISHER', res.publisher);
     this.renderProperty(tbl, 'CANON_REND_COMMITTEE', Extensions.readString(res, 'http://hl7.org/fhir/StructureDefinition/structuredefinition-wg'));
-    this.renderProperty(tbl, 'GENERAL_COPYRIGHT', res.copyright);
+    this.renderPropertyCopy(tbl, 'GENERAL_COPYRIGHT', res.copyright);
     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);
@@ -164,7 +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) {
@@ -253,15 +258,32 @@ class Renderer {
     }
   }
 
-  async renderPropertyLink(tbl, msgId, value) {
+  renderPropertyCopy(tbl, msgId, value) {
     if (value) {
       let tr = tbl.tr();
       tr.td().b().tx(this.translate(msgId));
-      const linkinfo = await this.linkResolver.resolveURL(this.opContext, value);
-      if (linkinfo) {
-        tr.td().ah(linkinfo.link).tx(linkinfo.description);
+      if (value instanceof Object) {
+        tr.td().tx("todo");
       } else {
-        tr.td().tx(value);
+        let td = tr.td();
+        let span = td.span("copy-text");
+        span.tx(value);
+        let btn = span.button();
+        btn.attr("class", "btn-copy");
+        btn.attr("data-clipboard-text", value);
+        btn.attr("data-original-title", this.translate('GENERAL_COPY'));
+      }
+    }
+  }
+
+  renderPropertyLink(tbl, msgId, value) {
+    if (value) {
+      let tr = tbl.tr();
+      tr.td().b().tx(this.translate(msgId));
+      if (value instanceof Object) {
+        tr.td().tx("todo");
+      } else {
+        tr.td().ah(value).tx(value);
       }
     }
   }
@@ -346,7 +368,7 @@ class Renderer {
     return div_.toString();
   }
 
-  async renderCodeSystem(cs) {
+  async renderCodeSystem(cs, sourcePackage) {
     if (cs.json) {
       cs = cs.json;
     }
@@ -355,7 +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);
@@ -2209,6 +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.fhir.org.yml

@@ -12,7 +12,7 @@ sources:
   - internal:hgvs
   - ucum:tx/data/ucum-essence.xml
   - loinc:loinc-2.77-a.db
-  - loinc!:loinc-2.81-b.db
+  - loinc!:Loinc_2.82.db
   - rxnorm:rxnorm_03022026.db
   - ndc:ndc-20211101.db
   - unii:unii_20240622.db

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',