fhirsmith 0.8.6 → 0.9.0

package/translations/Messages.properties

@@ -1511,3 +1511,4 @@ CONFORMANCE_STATEMENT_WORD = The html source contains the word ''{0}'' but it is
 VALUESET_CODE_CONCEPT_HINT = {3}. Note that the display in the ValueSet does not have to match; this check exists to help check that it''s not accidentally the wrong code
 VALUESET_CODE_CONCEPT_HINT_VER ={3}. Note that the display in the ValueSet does not have to match; this check exists to help check that it''s not accidentally the wrong code
 TERMINOLOGY_TX_SYSTEM_UNSUPPORTED = The code cannot be checked because codeSystem ''{0}'' version ''{1}'' is not supported ({2})
+INVALID_REGEX = The regex ''{0}'' is not valid: {1}

package/tx/cs/cs-country.js

@@ -2,6 +2,7 @@ const { CodeSystemProvider, FilterExecutionContext } = require('../../tx/cs/cs-a
 const assert = require('assert');
 const { CodeSystem } = require("../library/codesystem");
 const {CodeSystemFactoryProvider} = require("./cs-api");
+const regexUtilities = require("../../library/regex-utilities");
 
 class CountryCodeConcept {
   constructor(userDefined, code, display, french) {
@@ -199,7 +200,7 @@ class CountryCodeServices extends CodeSystemProvider {
 
       try {
         // Create regex with anchors to match the Pascal implementation (^value$)
-        const regex = new RegExp('^' + value + '$');
+        const regex = regexUtilities.compile('^' + value + '$');
 
         for (const concept of this.codes) {
           if (regex.test(concept.code)) {

package/tx/cs/cs-cs.js

@@ -6,6 +6,7 @@ const { validateOptionalParameter, getValuePrimitive, validateArrayParameter} =
 const {Issue} = require("../library/operation-outcome");
 const {Extensions} = require("../library/extensions");
 const {BaseCSServices} = require("./cs-base");
+const regexUtilities = require("../../library/regex-utilities");
 
 /**
  * Context class for FHIR CodeSystem provider concepts
@@ -1309,7 +1310,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
     else if (op === 'regex') {
       // Regular expression match
       try {
-        const regex = new RegExp('^' + value + '$');
+        const regex = regexUtilities.compile('^' + value + '$');
         const allCodes = this.codeSystem.getAllCodes();
         for (const code of allCodes) {
           if (regex.test(code)) {
@@ -1320,7 +1321,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
           }
         }
       } catch (error) {
-        throw new Error(`Invalid regex pattern: ${value}`);
+        throw new Issue('error', 'exception', null, 'INVALID_REGEX', this.opContext.i18n.translate('INVALID_REGEX', this.opContext.langs, [value, error.message]), 'vs-invalid', 422);
       }
     }
 
@@ -1428,7 +1429,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
     }
     else if (op === 'regex') {
       try {
-        const regex = new RegExp('^' + value + '$');
+        const regex = regexUtilities.compile('^' + value + '$');
         return properties.some(p => regex.test(this._getPropertyValue(p)));
       } catch (error) {
         return false;

package/tx/cs/cs-loinc.js

@@ -6,6 +6,7 @@ const { CodeSystemFactoryProvider} = require('./cs-api');
 const { validateOptionalParameter, validateArrayParameter} = require("../../library/utilities");
 const {BaseCSServices} = require("./cs-base");
 const {sqlEscapeString} = require("../../xig/xig");
+const regexUtilities = require('../../library/regex-utilities');
 
 // Context kinds matching Pascal enum
 const LoincProviderContextKind = {
@@ -938,7 +939,7 @@ class LoincServices extends BaseCSServices {
 // Helper method for regex matching
   async #findRegexMatches(sql, pattern, valueColumn, keyColumn = 'Key') {
     return new Promise((resolve, reject) => {
-      const regex = new RegExp(pattern);
+      const regex = regexUtilities.compile(pattern);
       const matchingKeys = [];
 
       this.db.all(sql, (err, rows) => {

package/tx/cs/cs-snomed.js

@@ -1622,7 +1622,7 @@ class SnomedServicesFactory extends CodeSystemFactoryProvider {
         internalSource : this,
         relationship: relationship,
         id : id,
-        url: `${this.system}?fhir_cm=${id}`,
+        url: `${this.system()}?fhir_cm=${id}`,
         version: this.version(),
         name: `SNOMED CT ${name} Concept Map`,
         description: `The concept map implicitly defined by the ${name} Association Reference Set`,

package/tx/data/OperationDefinition-ValueSet-related.json

@@ -0,0 +1,133 @@
+{
+  "resourceType": "OperationDefinition",
+  "id": "ValueSet-related",
+  "url": "http://hl7.org/fhir/OperationDefinition/ValueSet-related",
+  "version": "5.0.0",
+  "name": "ValueSetRelated",
+  "title": "Value Set Related Determination",
+  "status": "active",
+  "kind": "operation",
+  "experimental": false,
+  "date": "2023-03-26T15:21:02+11:00",
+  "publisher": "FHIRsmith",
+  "description": "Determine the relationship between two value sets. Different versions of code systems are considered compatible unless versionNeeded = true for the code system",
+  "jurisdiction": [
+    {
+      "coding": [
+        {
+          "system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
+          "code": "001",
+          "display": "World"
+        }
+      ]
+    }
+  ],
+  "affectsState": false,
+  "code": "related",
+  "comment": "An $expand will be performed internally if needed.",
+  "resource": [
+    "ValueSet"
+  ],
+  "system": false,
+  "type": true,
+  "instance": false,
+  "parameter": [
+    {
+      "name": "thisUrl",
+      "use": "in",
+      "scope": [
+        "type"
+      ],
+      "min": 0,
+      "max": "1",
+      "documentation": "Value set Canonical URL for the first value set of the pair (the base). The server must know the value set (e.g. it is provided as an attached resource, it is defined explicitly in the server's value sets, or it is defined implicitly by some code system known to the server",
+      "type": "uri"
+    },
+    {
+      "name": "otherUrl",
+      "use": "in",
+      "scope": [
+        "type"
+      ],
+      "min": 0,
+      "max": "1",
+      "documentation": "Value set Canonical URL for the second value set of the pair (the one being compared to base). The server must know the value set (e.g. it is provided as an attached resource, it is defined explicitly in the server's value sets, or it is defined implicitly by some code system known to the server",
+      "type": "uri"
+    },
+    {
+      "name": "thisValueSet",
+      "use": "in",
+      "scope": [
+        "type"
+      ],
+      "min": 0,
+      "max": "1",
+      "documentation": "The first value set is provided directly as part of the request. Servers may choose not to accept value sets in this fashion. This parameter is used when the client wants the server to expand a value set that is not stored on the server",
+      "type": "ValueSet"
+    },
+    {
+      "name": "otherValueSet",
+      "use": "in",
+      "scope": [
+        "type"
+      ],
+      "min": 0,
+      "max": "1",
+      "documentation": "The other value set is provided directly as part of the request. Servers may choose not to accept value sets in this fashion. This parameter is used when the client wants the server to expand a value set that is not stored on the server",
+      "type": "ValueSet"
+    },
+    {
+      "name": "thisVersion",
+      "use": "in",
+      "scope": [
+        "type"
+      ],
+      "min": 0,
+      "max": "1",
+      "documentation": "The identifier that is used to identify a specific version of the value set to be used when validating the code. This is an arbitrary value managed by the value set author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available.",
+      "type": "string"
+    },
+    {
+      "name": "otherVersion",
+      "use": "in",
+      "scope": [
+        "type"
+      ],
+      "min": 0,
+      "max": "1",
+      "documentation": "The identifier that is used to identify a specific version of the value set to be used when validating the code. This is an arbitrary value managed by the value set author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available.",
+      "type": "string"
+    },
+    {
+      "name": "useSupplement",
+      "use": "in",
+      "min": 0,
+      "max": "*",
+      "documentation": "The supplement must be used when validating the code. Use of this parameter should result in $validate-code behaving the same way as if the supplements were included in the value set definition using the [http://hl7.org/fhir/StructureDefinition/valueset-supplement](http://hl7.org/fhir/extensions/StructureDefinition-valueset-supplement.html)",
+      "type": "canonical"
+    },
+    {
+      "name": "diagnostics",
+      "use": "in",
+      "min": 0,
+      "max": "1",
+      "documentation": "Whether to return information about the reasoning process"
+    },
+    {
+      "name": "result",
+      "use": "out",
+      "min": 1,
+      "max": "1",
+      "documentation": "The relationship between the ValueSets. One of: same, superset, subset, overlapping, dsjoint, empty, and indeterminate",
+      "type": "boolean"
+    },
+    {
+      "name": "message",
+      "use": "out",
+      "min": 0,
+      "max": "1",
+      "documentation": "Explanation of the code, with reason if appropriate",
+      "type": "string"
+    }
+  ]
+}

package/tx/importers/atc-to-fhir.js

@@ -6,7 +6,7 @@ const ATC_FILE = process.argv[2] || '2025_ATC.xml';
 const DDD_FILE = process.argv[3] || '2025_ATC_ddd.xml';
 const OUTPUT_FILE = process.argv[4] || 'atc-codesystem.json';
 
-const PROPERTY_GROUP_EXT_URL = 'http://hl7.org/fhir/property.group';
+const PROPERTY_GROUP_EXT_URL = 'http://hl7.org/fhir/StructureDefinition/Codesystem-property-group';
 
 // Parse XML files
 function parseXML(filePath) {
@@ -277,32 +277,7 @@ try {
     console.log(`Writing to ${OUTPUT_FILE}...`);
     fs.writeFileSync(OUTPUT_FILE, JSON.stringify(codeSystem, null, 2));
     console.log('Done!');
-    
-    // Print some stats
-    function countConcepts(concepts) {
-        let count = 0;
-        for (const c of concepts) {
-            count++;
-            if (c.concept) {
-                count += countConcepts(c.concept);
-            }
-        }
-        return count;
-    }
-    
-    function countWithDDD(concepts) {
-        let count = 0;
-        for (const c of concepts) {
-            if (c.property?.some(p => p.code === 'dddValue')) {
-                count++;
-            }
-            if (c.concept) {
-                count += countWithDDD(c.concept);
-            }
-        }
-        return count;
-    }
-    
+
     const totalConcepts = countConcepts(codeSystem.concept);
     const withDDD = countWithDDD(codeSystem.concept);
     console.log(`\nStatistics:`);
@@ -314,3 +289,28 @@ try {
     console.error('Error:', error.message);
     process.exit(1);
 }
+
+// Print some stats
+function countConcepts(concepts) {
+    let count = 0;
+    for (const c of concepts) {
+        count++;
+        if (c.concept) {
+            count += countConcepts(c.concept);
+        }
+    }
+    return count;
+}
+
+function countWithDDD(concepts) {
+    let count = 0;
+    for (const c of concepts) {
+        if (c.property?.some(p => p.code === 'dddValue')) {
+            count++;
+        }
+        if (c.concept) {
+            count += countWithDDD(c.concept);
+        }
+    }
+    return count;
+}

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