fhirsmith 0.8.3 → 0.8.4

package/CHANGELOG.md

@@ -5,6 +5,29 @@ All notable changes to the Health Intersections Node Server will be documented i
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
+
+## [v0.8.4] - 2026-04-01
+
+### Added
+
+- add .npmrc to defend against supply chain attacks
+
+### Changed
+
+- Rework extension handling to make sure uzbek loinc works - load supplements from store
+
+### Fixed
+
+- tx/expand: fix for bug where filter array is present but empty
+- tx/SCT: support filters generalizes and child-of
+- tx/SCT: fix bug evaluating property filters
+- Fix version conversion issues
+
+### Tx Conformance Statement
+
+FHIRsmith passed all 1497 HL7 terminology service tests (modes tx.fhir.org+omop+general+snomed, tests v1.9.1, runner v6.9.4)
+
 ## [v0.8.3] - 2026-03-31
 
 ### Changed
@@ -15,15 +38,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Publisher: Allow non-admin users to delete non-approved tasks
 
 ### Fixed
- 
+
 - Publisher: fix task logging
-- SHL: path fixes 
+- SHL: path fixes
 
 ### Tx Conformance Statement
 
 FHIRsmith passed all 1497 HL7 terminology service tests (modes tx.fhir.org+omop+general+snomed, tests v1.9.1, runner v6.9.4)
 
-
 ## [v0.8.2] - 2026-03-29
 
 ### Added

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirsmith",
-  "version": "0.8.3",
+  "version": "0.8.4",
   "description": "A Node.js server that provides a collection of tools to serve the FHIR ecosystem",
   "main": "server.js",
   "engines": {

package/tx/cs/cs-api.js

@@ -221,10 +221,11 @@ class CodeSystemProvider {
   }
 
   /**
+   * @param {boolean} langPacks - whether to include language packs
    * @returns {string[]} all supplements in scope
    */
-  listSupplements() {
-    return this.supplements ? this.supplements.map(s => s.vurl) : [];
+  listSupplements(langPacks) {
+    return this.supplements ? this.supplements.filter(s => langPacks || !s.isLangPack()).map(s => s.vurl) : [];
   }
 
   /**
@@ -385,12 +386,15 @@ class CodeSystemProvider {
         const concept= supplement.getConceptByCode(code);
         if (concept) {
           if (concept.display) {
-            displays.addDesignation(true, 'active', supplement.jsonObj.language, CodeSystem.makeUseForDisplay(), concept.display);
+            // sometimes the display is just repeated from the base code system
+            if (!displays.hasAnyDisplay(concept.display)) {
+              displays.addDesignation(true, 'active', supplement.jsonObj.language, CodeSystem.makeUseForDisplay(), concept.display).supplement = supplement;
+            }
           }
           if (concept.designation) {
             for (const d of concept.designation) {
               let status = Extensions.readString(d, "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status");
-              displays.addDesignation(false, status || 'active', d.language, d.use, d.value, d.extension?.length > 0 ? d.extension : []);
+              displays.addDesignation(false, status || 'active', d.language, d.use, d.value, d.extension?.length > 0 ? d.extension : []).supplement = supplement;
             }
           }
         }
@@ -854,6 +858,17 @@ class CodeSystemFactoryProvider {
     return [];
   }
 
+  /**
+   *
+   * @param supplements - the list of supplements to populate - fill with any supplements matching url(+version)
+   * @param url - url of code system
+   * @param version - version of codesystem
+   * @param {Map} statedSupplements - return language packs and supplements that are listed in stated supplements, by versioned URL
+   * @returns {Promise<void>}
+   */
+  async listSupplements(supplements, url, version, statedSupplements) {
+    // do nothing
+  }
   /**
    * see comments for registerSupplements()
    *

package/tx/cs/cs-base.js

@@ -41,6 +41,19 @@ class BaseCSServices extends CodeSystemProvider {
     return property;
   }
 
+  _addDateTimeProperty(params, type, name, value) {
+
+    const property = {
+      name: type,
+      part: [
+        {name: 'code', valueCode: name},
+        {name: 'value', valueDateTime: value}
+      ]
+    };
+    params.push(property);
+    return property;
+  }
+
   _addStringProperty(params, type, name, value, language = null) {
 
     const property = {

package/tx/cs/cs-snomed.js

@@ -355,6 +355,52 @@ class SnomedServices {
     return result;
   }
 
+  filterChildOf(id = true) {
+    const result = new SnomedFilterContext();
+    const conceptResult = this.concepts.findConcept(id);
+
+    if (!conceptResult.found) {
+      throw new Error(`The SNOMED CT Concept ${id} is not known`);
+    }
+
+    const descendants = this.getConceptChildren(conceptResult.index);
+
+    result.descendants = descendants;
+
+    return result;
+  }
+
+
+  filterGeneralizes(id = true) {
+    const result = new SnomedFilterContext();
+    const conceptResult = this.concepts.findConcept(id);
+
+    if (!conceptResult.found) {
+      throw new Error(`The SNOMED CT Concept ${id} is not known`);
+    }
+
+    let ancestors = new Set();
+    let parents = this.getConceptParents(conceptResult.index);
+    let isNew = true;
+    while (isNew) {
+      isNew = false;
+      let np = [];
+      for (let parent of parents) {
+        if (!ancestors.has(parent)) {
+          isNew = true;
+          ancestors.add(parent);
+          np.push(...this.getConceptParents(parent));
+        }
+      }
+      parents = np;
+    }
+
+    result.descendants = [...ancestors];
+
+    return result;
+  }
+
+
   filterIn(id) {
     const result = new SnomedFilterContext();
     const conceptResult = this.concepts.findConcept(id);
@@ -775,6 +821,13 @@ class SnomedProvider extends BaseCSServices {
     const ctxt = await this.#ensureContext(context);
     if (ctxt) {
       if (!(ctxt instanceof SnomedExpressionContext) || ctxt.expression?.concepts.length == 1) {
+        const time = this.sct.concepts.getConcept(ctxt.getReference()).effectiveTime;
+        const pascalEpoch = new Date(1899, 11, 30);
+        const date = new Date(pascalEpoch.getTime() + time * 86400000);
+        const dateStr = date.toISOString().slice(0, 10);
+        this._addDateTimeProperty(params, 'property', 'effectiveTime', dateStr);
+
+
         const parents = this.sct.getConceptParents(ctxt.getReference());
         for (let parentRef of parents) {
           const code = this.sct.getConceptId(parentRef);
@@ -792,7 +845,7 @@ class SnomedProvider extends BaseCSServices {
         const moduleId = this.sct.concepts.getModuleId(ctxt.getReference());
         if (moduleId) {
           const code = this.sct.getConceptId(moduleId);
-          this._addCodeProperty(params, 'property', 'module', code, null, null);
+          this._addCodeProperty(params, 'property', 'module', code, null, this.sct.getDisplayName(moduleId));
         }
 
         const relationships = this.sct.getConceptRelationships(ctxt.getReference());
@@ -838,7 +891,7 @@ class SnomedProvider extends BaseCSServices {
   async doesFilter(prop, op, value) {
     if (prop === 'concept') {
       const id = this.sct.stringToIdOrZero(value);
-      if (id !== 0n && ['=', 'is-a', 'descendent-of', 'in'].includes(op)) {
+      if (id !== 0n && ['=', 'is-a', 'descendent-of', 'in', 'generalizes', 'child-of'].includes(op)) {
         return this.sct.conceptExists(value);
       }
     }
@@ -891,6 +944,14 @@ class SnomedProvider extends BaseCSServices {
           filterContext.filters.push(this.sct.filterIsA(id, false));
           return null;
         }
+        case 'child-of': {
+          filterContext.filters.push(this.sct.filterChildOf(id));
+          return null;
+        }
+        case 'generalizes': {
+          filterContext.filters.push(this.sct.filterGeneralizes(id, false));
+          return null;
+        }
         case 'in': {
           filterContext.filters.push(this.sct.filterIn(id));
           return null;
@@ -1121,7 +1182,7 @@ class SnomedProvider extends BaseCSServices {
     if (set.propProp || set.propValue) {
       for (let i = 0; i < this.sct.concepts.count(); i++) {
         let concept = this.sct.concepts.getConceptByCount(i);
-        const relationships = this.sct.getConceptRelationships(concept.getReference());
+        const relationships = this.sct.getConceptRelationships(concept.index);
         for (let relationshipRef of relationships) {
           const relationship = this.sct.relationships.getRelationship(relationshipRef);
           if (set.propProp === relationship.relType && set.propValue === relationship.target) {

package/tx/library/codesystem.js

@@ -2,6 +2,7 @@ const { Language } = require("../../library/languages");
 const {CanonicalResource} = require("./canonical-resource");
 const {codeSystemFromR5, codeSystemToR5} = require("../xversion/xv-codesystem");
 const {getValuePrimitive} = require("../../library/utilities");
+const {VersionUtilities} = require("../../library/version-utilities");
 
 const CodeSystemContentMode = Object.freeze({
   Complete: 'complete',
@@ -614,12 +615,31 @@ class CodeSystem extends CanonicalResource {
   }
 
   isLangPack() {
+    // todo: this is a temporary work around until fhir.tx.support.r4#0.37.0 is released that properly marks this as a language pack
+    if (this.jsonObj.url === 'https://terminology.dhp.uz/fhir/CodeSystem/loinc-supplement-uz') {
+      return true;
+    }
     return (this.jsonObj.extension || []).find(x => x.url == 'http://hl7.org/fhir/StructureDefinition/codesystem-supplement-type' && getValuePrimitive(x) == 'lang-pack');
   }
 
   isPropUri(code, uri) {
     return (this.jsonObj.property || []).find(x => x.code == code && x.uri == uri);
   }
+
+  isSupplementFor(url, version) {
+    if (this.jsonObj.content !== 'supplement') {
+      return false;
+    }
+    let suppU = this.jsonObj.supplements;
+    if (suppU == url) {
+      return true;
+    }
+    if (suppU.startsWith(url + '|')) {
+      let suppV = suppU.substring(suppU.indexOf('|') + 1);
+      return VersionUtilities.versionMatchesByAlgorithm(suppV, version, VersionUtilities.guessVersionAlgorithmFromVersion(version));
+    }
+    return false;
+  }
 }
 
 module.exports = { CodeSystem, CodeSystemContentMode };

package/tx/library/designations.js

@@ -404,6 +404,15 @@ class Designations {
     // }
   }
 
+  hasAnyDisplay(value) {
+    for (let designation of this.designations) {
+      if (designation.value === value) {
+        return true;
+      }
+    }
+    return false;
+  }
+
   /**
    * Check if a display value exists with specified matching criteria
    */
@@ -551,7 +560,7 @@ class Designations {
   /**
    * Find the preferred designation for given language preferences
    */
-  preferredDesignation(langList = null) {
+  preferredDesignation(langList = null, supplements = null) {
     if (this.designations.length === 0) {
       return null;
     }
@@ -560,24 +569,39 @@ class Designations {
       // No language list, prefer base designations
       for (const cd of this.designations) {
         if (this._isPreferred(cd) && cd.isActive()) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
       for (const cd of this.designations) {
         if (this.isDisplay(cd) && cd.isActive()) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
       for (const cd of this.designations) {
         if (this.isDisplay(cd)) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
       for (const cd of this.designations) {
         if (this._isPreferred(cd)) {
+          if (supplements && cd.source) {
+            supplements.add(cd.source);
+          }
           return cd;
         }
       }
+      if (supplements && this.designations[0].source) {
+        supplements.add(this.designations[0].source);
+      }
       return this.designations[0];
     }
 
@@ -589,16 +613,25 @@ class Designations {
       for (const matchType of matchTypes) {
         for (const cd of this.designations) {
           if (this._langMatches(lang, cd.language, matchType) && this.isDisplay(cd)) {
+            if (supplements && cd.source) {
+              supplements.add(cd.source);
+            }
             return cd;
           }
         }
         for (const cd of this.designations) {
           if (this._langMatches(lang, cd.language, matchType) && this._isPreferred(cd)) {
+            if (supplements && cd.source) {
+              supplements.add(cd.source);
+            }
             return cd;
           }
         }
         for (const cd of this.designations) {
           if (this._langMatches(lang, cd.language, matchType)) {
+            if (supplements && cd.source) {
+              supplements.add(cd.source);
+            }
             return cd;
           }
         }
@@ -606,6 +639,9 @@ class Designations {
     }
     for (const cd of this.designations) {
       if (!cd.language && this.isDisplay(cd)) {
+        if (supplements && cd.source) {
+          supplements.add(cd.source);
+        }
         return cd;
       }
     }

package/tx/provider.js

@@ -107,6 +107,36 @@ class Provider {
     return null;
   }
 
+  loadSupplements(url, version, statedSupplements) {
+    let supplements = new Map();
+    for (let csp of this.codeSystemFactories.values()) {
+      csp.listSupplements(supplements, url, version, statedSupplements);
+    }
+    for (let cs of this.codeSystems.values()) {
+      if (cs.isSupplementFor(url, version)) {
+        if (cs.isLangPack() || this.isStatedSupplement(cs, statedSupplements)) {
+          supplements.set(cs.vurl, cs);
+        }
+      }
+    }
+    return [...supplements.values()];
+  }
+
+  isStatedSupplement(cs, statedSupplements) {
+    if (statedSupplements == null) {
+      return false;
+    }
+    for (let suppU of statedSupplements) {
+      if (suppU === cs.url) {
+        return true;
+      }
+      if (suppU.startsWith(cs.url+"|")) {
+        let suppV = suppU.substring(suppU.indexOf('|') + 1);
+        return VersionUtilities.versionMatchesByAlgorithm(suppV, cs.version, VersionUtilities.guessVersionAlgorithmFromVersion(cs.version));
+      }
+    }
+    return false;
+  }
   /**
    * Create a code system provider from a CodeSystem resource
    * @param {OperationContext} opContext - The code system resource

package/tx/workers/expand.js

@@ -204,6 +204,7 @@ class ValueSetExpander {
   hasExclusions = false;
   requiredSupplements = new Set();
   usedSupplements = new Set();
+  reportedSupplements = new Set();
   internalLimit = INTERNAL_DEFAULT_LIMIT;
   externalLimit = EXTERNAL_DEFAULT_LIMIT;
 
@@ -339,9 +340,9 @@ class ValueSetExpander {
       const s = this.canonical(system, version);
       this.addParamUri(expansion, 'used-codesystem', s);
       if (cs != null) {
-        const ts = cs.listSupplements();
+        const ts = cs.listSupplements(false);
         for (const vs of ts) {
-          this.addParamUri(expansion, 'used-supplement', vs);
+          this.reportedSupplements.add(vs);
         }
       }
     }
@@ -415,7 +416,7 @@ class ValueSetExpander {
       }
 
       // display and designations
-      const pref = displays.preferredDesignation(this.params.workingLanguages());
+      const pref = displays.preferredDesignation(this.params.workingLanguages(), this.reportedSupplements);
       if (pref && pref.value) {
         n.display = pref.value;
       }
@@ -426,6 +427,9 @@ class ValueSetExpander {
             if (!n.designation) {
               n.designation = [];
             }
+            if (t.source) {
+              this.reportedSupplements.add(t.source);
+            }
             n.designation.push(t.asObject());
           }
         }
@@ -490,9 +494,9 @@ class ValueSetExpander {
       const s = this.canonical(system, version);
       this.addParamUri(expansion, 'used-codesystem', s);
       if (cs) {
-        const ts= cs.listSupplements();
+        const ts= cs.listSupplements(false);
         for (const vs of ts) {
-          this.addParamUri(expansion, 'used-supplement', vs);
+          this.reportedSupplements.add(vs);
         }
       }
     }
@@ -813,7 +817,7 @@ class ValueSetExpander {
           this.worker.opContext.log('iterate concepts done');
         }
 
-        if (cset.filter) {
+        if (cset.filter && cset.filter.length > 0) {
           this.worker.opContext.log('prepare filters');
           const fcl = cset.filter;
           const prep = await cs.getPrepContext(true);
@@ -1040,10 +1044,9 @@ class ValueSetExpander {
     if (expansion) {
       const vs = this.canonical(await cs.system(), await cs.version());
       this.addParamUri(expansion, 'used-codesystem', vs);
-      const ts = cs.listSupplements();
+      const ts = cs.listSupplements(false);
       for (const v of ts) {
-        this.worker.deadCheck('processCodeAndDescendants');
-        this.addParamUri(expansion, 'used-supplement', v);
+        this.reportedSupplements.add(v);
       }
     }
 
@@ -1081,10 +1084,9 @@ class ValueSetExpander {
     if (expansion) {
       const vs = this.canonical(await cs.system(), await cs.version());
       this.addParamUri(expansion, 'used-codesystem', vs);
-      const ts= cs.listSupplements();
+      const ts= cs.listSupplements(false);
       for (const v of ts) {
-        this.worker.deadCheck('processCodeAndDescendants');
-        this.addParamUri(expansion, 'used-supplement', v);
+        this.reportedSupplements.add(v);
       }
     }
 
@@ -1303,6 +1305,11 @@ class ValueSetExpander {
       }
     }
 
+    const ts = this.reportedSupplements;
+    for (const v of ts) {
+      this.addParamUri(exp, 'used-supplement', v);
+    }
+
     this.worker.opContext.log('finish up');
 
     let list;

package/tx/workers/lookup.js

@@ -149,14 +149,15 @@ class LookupWorker extends TerminologyWorker {
 
       // check supplements
       const used = new Set();
-      this.checkSupplements(csProvider, null, txp.supplements, used);
+      const reported = new Set();
+      this.checkSupplements(csProvider, null, txp.supplements, used, reported);
       const unused = new Set([...txp.supplements].filter(s => !used.has(s)));
       if (unused.size > 0) {
         throw new Issue('error', 'not-found', null, 'VALUESET_SUPPLEMENT_MISSING', this.i18n.translatePlural(unused.size, 'VALUESET_SUPPLEMENT_MISSING', txp.HTTPLanguages, [[...unused].join(',')]), 'not-found').handleAsOO(400);
       }
 
       // Perform the lookup
-      const result = await this.doLookup(csProvider, code, txp);
+      const result = await this.doLookup(csProvider, code, txp, reported);
       return res.status(200).json(result);
     } catch (error) {
       this.log.error(error);
@@ -242,9 +243,10 @@ class LookupWorker extends TerminologyWorker {
    * @param {CodeSystemProvider} csProvider - CodeSystem provider
    * @param {string} code - Code to look up
    * @param {Object} params - Parsed parameters
+   * @param {Set} reportedSupplements - Set of supplements that are to be reported
    * @returns {Object} Parameters resource with lookup result
    */
-  async doLookup(csProvider, code, params) {
+  async doLookup(csProvider, code, params, reportedSupplements) {
     this.deadCheck('doLookup');
 
     await this.checkSupplements(csProvider, null, params.supplements);
@@ -352,6 +354,12 @@ class LookupWorker extends TerminologyWorker {
           this.deadCheck('doLookup-designations');
           const designationParts = [];
 
+          if (designation.supplement) {
+            designationParts.push({
+              name: 'source',
+              valueCanonical: designation.supplement.vurl
+            });
+          }
           if (designation.language) {
             designationParts.push({
               name: 'language',
@@ -382,6 +390,14 @@ class LookupWorker extends TerminologyWorker {
     // Let the provider add additional properties
     await csProvider.extendLookup(ctxt, params.properties || [], responseParams);
 
+    if (reportedSupplements) {
+      for (const supplement of reportedSupplements) {
+        responseParams.push({
+          name: 'used-supplement',
+          valueCanonical: supplement
+        });
+      }
+    }
     return {
       resourceType: 'Parameters',
       parameter: responseParams

package/tx/workers/worker.js

@@ -252,6 +252,7 @@ class TerminologyWorker {
   loadSupplements(url, version = '', statedSupplements) {
     const supplements = [];
 
+    supplements.push(...this.provider.loadSupplements(url, version, statedSupplements));
     // todo: look in provider for supplements
 
     if (!this.additionalResources) {
@@ -306,7 +307,7 @@ class TerminologyWorker {
    * @param {CodeSystemProvider} cs - Code system provider
    * @param {Object} src - Source element (for extensions)
    */
-  checkSupplements(cs, src, requiredSupplements, usedSupplements = null) {
+  checkSupplements(cs, src, requiredSupplements, usedSupplements = null, reportedSupplements = null) {
     // Check for required supplements in extensions
     if (src && src.extension) {
       const supplementExtensions = src.extension.filter(x => x.url == 'http://hl7.org/fhir/StructureDefinition/valueset-supplement');
@@ -318,7 +319,12 @@ class TerminologyWorker {
       }
     }
 
-    // Note required supplements that are satisfied
+    if (reportedSupplements) {
+      for (let s of cs.listSupplements(true)) {
+        reportedSupplements.add(s);
+      }
+    }
+    // Note required supplements that are satisfied - and might be version independent
     if (usedSupplements) {
       for (const s of requiredSupplements) {
         if (cs.hasSupplement(s)) {

package/tx/xversion/xv-codesystem.js

@@ -9,11 +9,11 @@ const {VersionUtilities} = require("../../library/version-utilities");
  */
 
 function codeSystemToR5(jsonObj, version) {
-  if (version === 'R5') {
+  if (VersionUtilities.isR5Ver(version)) {
     return jsonObj; // Already R5, no conversion needed
   }
 
-  if (version === 'R3') {
+  if (VersionUtilities.isR3Ver(version)) {
     // R3 to R5: Convert identifier from single object to array
     if (jsonObj.identifier && !Array.isArray(jsonObj.identifier)) {
       jsonObj.identifier = [jsonObj.identifier];
@@ -21,7 +21,7 @@ function codeSystemToR5(jsonObj, version) {
     return jsonObj;
   }
 
-  if (version === 'R4') {
+  if (VersionUtilities.isR4Ver(version)) {
     // R4 to R5: identifier is already an array, no conversion needed
     return jsonObj;
   }

package/tx/xversion/xv-parameters.js

@@ -17,10 +17,10 @@ function parametersToR5(jsonObj, sourceVersion) {
     }
   }
 
-  const {convertResourceFromR5} = require("./xv-resource");
+  const {convertResourceToR5} = require("./xv-resource");
   for (let p of jsonObj.parameter) {
     if (p.resource) {
-      p.resource = convertResourceFromR5(p.resource, sourceVersion);
+      p.resource = convertResourceToR5(p.resource, sourceVersion);
     }
   }
   return jsonObj;

package/tx/xversion/xv-valueset.js

@@ -203,8 +203,7 @@ function convertContainsPropertyR5ToR4(containsList) {
  */
 function isR5OnlyFilterOperator(operator) {
   const r5OnlyOperators = [
-    'generalizes',  // Added in R5
-    // Add other R5-only operators as they're identified
+    'child-of', ' descendent-leaf' // Added in R5
   ];
   return r5OnlyOperators.includes(operator);
 }