fhirsmith 0.8.6 → 0.9.1

package/tx/library/extensions.js

@@ -56,7 +56,13 @@ const Extensions = {
     if (!resource) {
       return undefined;
     }
-    const extensions = Array.isArray(resource) ? resource : (resource.extension || []);
+    let extensions = Array.isArray(resource) ? resource : (resource.extension || []);
+    for (let ext of extensions || []) {
+      if (ext.url === url) {
+        return getValuePrimitive(ext);
+      }
+    }
+    extensions = Array.isArray(resource) ? resource : (resource.modifierExtension || []);
     for (let ext of extensions || []) {
       if (ext.url === url) {
         return getValuePrimitive(ext);

package/tx/library/renderer.js

@@ -466,14 +466,15 @@ class Renderer {
         li.tx(" "+ this.translate('VALUE_SET_WHERE')+" ");
         li.startCommaList("and");
         for (let f of inc.filter) {
-          if (f.op == 'exists') {
+          let op = this.readFilterOp(f);
+          if (op == 'exists') {
             if (f.value == "true") {
               li.commaItem(f.property+" "+ this.translate('VALUE_SET_EXISTS'));
             } else {
               li.commaItem(f.property+" "+ this.translate('VALUE_SET_DOESNT_EXIST'));
             }
           } else {
-            li.commaItem(f.property + " " + f.op + " ");
+            li.commaItem(f.property + " " + op + " ");
             const loc = this.linkResolver ? await this.linkResolver.resolveCode(this.opContext, inc.system, inc.version, f.value) : null;
             if (loc) {
               li.ah(loc.link).tx(loc.description);
@@ -2243,6 +2244,14 @@ class Renderer {
         return defn+' = ' + value;
     }
   }
+
+  readFilterOp(f) {
+    if (f._op) {
+      return Extensions.readString(f._op, 'http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op');
+    } else {
+      return f.op;
+    }
+  }
 }
 
 module.exports = { Renderer };

package/tx/library/ucum-parsers.js

@@ -10,6 +10,7 @@ const {
   BaseUnit, DefinedUnit, Prefix, Value, Term, Symbol, Factor, Canonical, CanonicalUnit,
   Registry
 } = require('./ucum-types.js');
+const regexUtilities = require("../../library/regex-utilities");
 
 // Lexer for tokenizing UCUM expressions (port of Lexer.java)
 class Lexer {
@@ -763,7 +764,7 @@ class Search {
 
     if (isRegex) {
       try {
-        const regex = new RegExp(text);
+        const regex = regexUtilities.compile(text);
         return regex.test(value);
       } catch (e) {
         this.log.error(e);

package/tx/ocl/cs-ocl.cjs

@@ -13,6 +13,7 @@ const { OCLBackgroundJobQueue } = require('./jobs/background-queue');
 const { OCLConceptFilterContext } = require('./model/concept-filter-context');
 const { toConceptContext } = require('./mappers/concept-mapper');
 const { patchSearchWorkerForOCLCodeFiltering } = require('./shared/patches');
+const regexUtilities = require("../../library/regex-utilities");
 
 patchSearchWorkerForOCLCodeFiltering();
 
@@ -735,6 +736,17 @@ class OCLSourceCodeSystemProvider extends CodeSystemProvider {
       return { context: this.conceptCache.get(code), message: null };
     }
 
+    // OCL concept IDs may differ in case from the FHIR code (e.g. "y" vs "Y").
+    // Try a case-insensitive cache lookup before hitting the network.
+    const codeLower = code.toLowerCase();
+    for (const [key, value] of this.conceptCache.entries()) {
+      if (key.toLowerCase() === codeLower) {
+        // Cache under the requested case as well so future lookups are O(1).
+        this.conceptCache.set(code, value);
+        return { context: value, message: null };
+      }
+    }
+
     if (this.scheduleBackgroundLoad) {
       this.scheduleBackgroundLoad('lookup-miss');
     }
@@ -1032,23 +1044,26 @@ class OCLSourceCodeSystemProvider extends CodeSystemProvider {
       this.scheduleBackgroundLoad('concept-miss');
     }
 
-    const url = this.#buildConceptUrl(code);
     const pending = (async () => {
-      let response;
-      try {
-        response = await this.httpClient.get(url, { params: { verbose: true } });
-      } catch (error) {
-        // Missing concept should be treated as not-found, not as an internal server failure.
-        if (error && error.response && error.response.status === 404) {
-          return null;
-        }
-        throw error;
+      const concept = await this.#fetchConceptByCode(code);
+      if (concept) {
+        return concept;
       }
-      const concept = this.#toConceptContext(response.data);
-      if (concept && concept.code) {
-        this.conceptCache.set(concept.code, concept);
+      // OCL concept IDs may differ in case from the FHIR code (e.g. "y" vs "Y").
+      // Try common case alternatives before giving up.
+      const lower = code.toLowerCase();
+      const upper = code.toUpperCase();
+      for (const alt of [lower, upper]) {
+        if (alt !== code) {
+          const altConcept = await this.#fetchConceptByCode(alt);
+          if (altConcept) {
+            // Cache under the originally requested code so future lookups hit directly.
+            this.conceptCache.set(code, altConcept);
+            return altConcept;
+          }
+        }
       }
-      return concept;
+      return null;
     })();
 
     this.pendingConceptRequests.set(pendingKey, pending);
@@ -1059,6 +1074,24 @@ class OCLSourceCodeSystemProvider extends CodeSystemProvider {
     }
   }
 
+  async #fetchConceptByCode(code) {
+    const url = this.#buildConceptUrl(code);
+    let response;
+    try {
+      response = await this.httpClient.get(url, { params: { verbose: true } });
+    } catch (error) {
+      if (error && error.response && error.response.status === 404) {
+        return null;
+      }
+      throw error;
+    }
+    const concept = this.#toConceptContext(response.data);
+    if (concept && concept.code) {
+      this.conceptCache.set(concept.code, concept);
+    }
+    return concept;
+  }
+
   async #allConceptContexts() {
     const concepts = new Map();
 
@@ -1135,7 +1168,7 @@ class OCLSourceCodeSystemProvider extends CodeSystemProvider {
 
   #buildPropertyMatcher(prop, op, value) {
     if (op === 'regex') {
-      const regex = new RegExp(String(value), 'i');
+      const regex = regexUtilities.compile(String(value), 'i');
       return concept => {
         const candidate = this.#valueForFilter(concept, prop);
         if (candidate == null) {

package/tx/ocl/vs-ocl.cjs

@@ -389,20 +389,26 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
   }
 
   #indexValueSet(vs) {
-    const existing = this.valueSetMap.get(vs.url)
-      || (vs.version ? this.valueSetMap.get(`${vs.url}|${vs.version}`) : null)
-      || this._idMap.get(vs.id)
-      || null;
-
-    // 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);
+    const existing = this.valueSetMap.get(vs.url) || null;
+
+    // When fresh discovery metadata replaces a cold-cached entry, carry over
+    // the enumerated compose so the expand engine doesn't fall back to
+    // "include whole CodeSystem".  The background expansion will eventually
+    // refresh it with up-to-date collection contents.
+    if (existing && existing !== vs
+      && Array.isArray(existing.jsonObj?.compose?.include)
+      && existing.jsonObj.compose.include.some(inc => Array.isArray(inc.concept) && inc.concept.length > 0)
+      && (!vs.jsonObj.compose || !Array.isArray(vs.jsonObj.compose.include) || vs.jsonObj.compose.include.length === 0)
+    ) {
+      vs.jsonObj.compose = existing.jsonObj.compose;
+    }
+
+    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);
   }
 
   #toValueSet(collection) {
@@ -568,6 +574,17 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
         ? vs.jsonObj.compose.include
         : [];
 
+      // If the compose already has enumerated concepts (from background expansion),
+      // it is the authoritative representation of the collection contents — don't
+      // overwrite it with system-only entries that would cause the expand engine
+      // to include ALL concepts from the CodeSystem.
+      const hasEnumeratedConcepts = existingInclude.some(
+        inc => Array.isArray(inc.concept) && inc.concept.length > 0
+      );
+      if (hasEnumeratedConcepts) {
+        return;
+      }
+
       // Always normalize existing compose entries first because discovery metadata
       // can carry non-canonical preferred_source values.
       const include = this.#normalizeComposeIncludes(existingInclude);
@@ -972,9 +989,12 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
       return;
     }
 
-    const cached = this.backgroundExpansionCache.get(cacheKey);
+    let cached = this.backgroundExpansionCache.get(cacheKey);
+    let invalidated = false;
     if (cached && !this.#isCachedExpansionValid(vs, cached)) {
       this.backgroundExpansionCache.delete(cacheKey);
+      cached = null;
+      invalidated = true;
     }
 
     // Already have a cached compose ready
@@ -982,23 +1002,22 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
       return;
     }
 
-    const cacheFilePath = getCacheFilePath(CACHE_VS_DIR, vs.url, vs.version || null, paramsKey);
-    const cacheAgeFromFileMs = getColdCacheAgeMs(cacheFilePath);
-    const persistedCache = this.backgroundExpansionCache.get(cacheKey);
-    const cacheAgeFromMetadataMs = Number.isFinite(persistedCache?.createdAt)
-      ? Math.max(0, Date.now() - persistedCache.createdAt)
-      : null;
-
-    // Treat cache as fresh when either file mtime or persisted timestamp is recent.
-    const freshnessCandidates = [cacheAgeFromFileMs, cacheAgeFromMetadataMs].filter(age => age != null);
-    const freshestCacheAgeMs = freshnessCandidates.length > 0 ? Math.min(...freshnessCandidates) : null;
-    if (freshestCacheAgeMs != null && freshestCacheAgeMs <= COLD_CACHE_FRESHNESS_MS) {
-      const freshnessSource = cacheAgeFromFileMs != null && cacheAgeFromMetadataMs != null
-        ? 'file+metadata'
-        : cacheAgeFromFileMs != null
-          ? 'file'
-          : 'metadata';
-      return;
+    // Skip freshness check when cache was just invalidated (VS metadata changed
+    // on the server) — the cold cache file is stale even if recently written.
+    if (!invalidated) {
+      const cacheFilePath = getCacheFilePath(CACHE_VS_DIR, vs.url, vs.version || null, paramsKey);
+      const cacheAgeFromFileMs = getColdCacheAgeMs(cacheFilePath);
+      const persistedCache = this.backgroundExpansionCache.get(cacheKey);
+      const cacheAgeFromMetadataMs = Number.isFinite(persistedCache?.createdAt)
+        ? Math.max(0, Date.now() - persistedCache.createdAt)
+        : null;
+
+      // Treat cache as fresh when either file mtime or persisted timestamp is recent.
+      const freshnessCandidates = [cacheAgeFromFileMs, cacheAgeFromMetadataMs].filter(age => age != null);
+      const freshestCacheAgeMs = freshnessCandidates.length > 0 ? Math.min(...freshnessCandidates) : null;
+      if (freshestCacheAgeMs != null && freshestCacheAgeMs <= COLD_CACHE_FRESHNESS_MS) {
+        return;
+      }
     }
 
     const jobKey = `vs:${cacheKey}`;
@@ -1121,7 +1140,11 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
         if (!systemConcepts.has(entry.system)) {
           systemConcepts.set(entry.system, []);
         }
-        systemConcepts.get(entry.system).push(entry.code);
+        const concept = { code: entry.code };
+        if (Array.isArray(entry.designation) && entry.designation.length > 0) {
+          concept.designation = entry.designation;
+        }
+        systemConcepts.get(entry.system).push(concept);
         totalCount++;
       }
       if (progressState) {
@@ -1138,9 +1161,9 @@ class OCLValueSetProvider extends AbstractValueSetProvider {
     }
 
     return {
-      include: Array.from(systemConcepts.entries()).map(([system, codes]) => ({
+      include: Array.from(systemConcepts.entries()).map(([system, concepts]) => ({
         system,
-        concept: codes.map(code => ({ code }))
+        concept: concepts
       }))
     };
   }

package/tx/tx.fhir.org.yml

@@ -18,11 +18,11 @@ sources:
   - unii:unii_20240622.db
   - snomed:sct_intl_20240201.cache
   - snomed!:sct_intl_20250201.cache
-  - snomed:sct_se_20231130.cache
-  - snomed:sct_au_20230731.cache
-  - snomed:sct_be_20231115.cache
+#  - snomed:sct_se_20231130.cache
+#  - snomed:sct_au_20230731.cache
+#  - snomed:sct_be_20231115.cache
   - snomed:sct_ch_20230607.cache
-  - snomed:sct_dk_20250930.cache
+#  - snomed:sct_dk_20250930.cache
   - snomed:sct_ips_20241216.cache
   - snomed:sct_nl_20240930.cache
   - snomed:sct_uk_20230412.cache