fhirsmith 0.9.0 → 0.9.1

package/translations/Messages.properties

@@ -1298,7 +1298,7 @@ VIEWDEFINITION_SHOULD_HAVE_NAME = No name provided. A name is required in many c
 VIEWDEFINITION_TYPE_MISMATCH = The path expression ''{0}'' does not return a value of the type ''{1}'' - found ''{2}''{3}
 VIEWDEFINITION_UNABLE_TO_TYPE = Unable to determine a type (found ''{0}''){1}
 VIEWDEFINITION_UNKNOWN_RESOURCE = The name ''{0}'' is not a valid resource{1}
-VS_EXP_FILTER_UNK = ValueSet ''{0}'' Filter by property ''{1}'' and op ''{2}'' is not supported yet
+VS_EXP_FILTER_UNK = ValueSet ''{0}'' Filter by property ''{1}'' and op ''{2}'' is not supported (yet?)
 VS_EXP_IMPORT_CS = Cannot include value set ''{0}'' because it''s actually a code system
 VS_EXP_IMPORT_CS_PINNED =  Cannot include value set ''{0}'' version ''{1}'' because it''s actually a code system
 VS_EXP_IMPORT_CS_PINNED_X =  Cannot exclude value set ''{0}'' version ''{1}'' because it''s actually a code system
@@ -1400,7 +1400,7 @@ TEXT_LINK_NO_DATA = No data element was found in the textLink extension
 TEXT_LINK_SELECTOR_INVALID = The textLink selector ''{0}'' is invalid: {1}
 SD_CONTEXT_SHOULD_ELEMENT_NOT_FOUND = The element {0} is not valid
 SD_CONTEXT_SHOULD_ELEMENT_NOT_FOUND_VER = The element {0} is not valid in version {1}
-FILTER_NOT_UNDERSTOOD = The filter "{0} {1} {2}" from the value set {3} was not understood in the context of {4}
+FILTER_NOT_UNDERSTOOD = The filter "{0} {1} {2}" is not understood or supported
 XHTML_CONTROL_NO_SOURCE = The xhtml node at ''{0}'' does not have a class attribute to indicate its source (boilerplate, generated, or original) and this is required by the profile {1}
 XHTML_XHTML_MIXED_LANG = The xhtml has some language sections ({0}), and also has content that is not in a language section
 XHTML_CONTROL_NO_LANGS = The xhtml has some language sections ({0}), but language sections are prohibited in this context by the profile {1}

package/tx/cs/cs-cs.js

@@ -1224,7 +1224,7 @@ class FhirCodeSystemProvider extends BaseCSServices {
 
     // Handle concept/code hierarchy filters
     if ((prop === 'concept' || prop === 'code')) {
-      results = await this._handleConceptFilter(filterContext, op, value);
+      results = await this._handleConceptFilter(filterContext, prop, op, value);
     }
 
     // Handle child existence filter
@@ -1248,7 +1248,8 @@ class FhirCodeSystemProvider extends BaseCSServices {
     }
 
     if (!results) {
-      throw new Error(`The filter ${prop} ${op} ${value} was not understood`)
+      throw new Issue('error', 'exception', null, 'FILTER_NOT_UNDERSTOOD',
+            this.opContext.i18n.translate('FILTER_NOT_UNDERSTOOD', this.opContext.langs, [prop, op, value]), 'vs-invalid', 422);
     }
     // Add to filter context
     if (!filterContext.filters) {
@@ -1267,15 +1268,17 @@ class FhirCodeSystemProvider extends BaseCSServices {
    * @returns {Promise<FhirCodeSystemProviderFilterContext>} Filter results
    * @private
    */
-  async _handleConceptFilter(filterContext, op, value) {
+  async _handleConceptFilter(filterContext, prop, op, value) {
     const results = new FhirCodeSystemProviderFilterContext();
 
     if (op === 'is-a' || op === 'descendent-of') {
       // Find all descendants of the specified code
       const includeRoot = (op === 'is-a');
       await this._addDescendants(results, value, includeRoot);
-    }
-    else if (op === 'is-not-a') {
+    } else if (op === 'child-of') {
+      // Find all descendants of the specified code
+      await this._addChildren(results, value);
+    } else if (op === 'is-not-a') {
       // Find all concepts that are NOT descendants of the specified code
       const excludeDescendants = this.codeSystem.getDescendants(value);
       const excludeSet = new Set([value, ...excludeDescendants]);
@@ -1323,6 +1326,9 @@ class FhirCodeSystemProvider extends BaseCSServices {
       } catch (error) {
         throw new Issue('error', 'exception', null, 'INVALID_REGEX', this.opContext.i18n.translate('INVALID_REGEX', this.opContext.langs, [value, error.message]), 'vs-invalid', 422);
       }
+    } else {
+      throw new Issue('error', 'exception', null, 'FILTER_NOT_UNDERSTOOD',
+          this.opContext.i18n.translate('FILTER_NOT_UNDERSTOOD', this.opContext.langs, [prop, op, value]), 'vs-invalid', 422);
     }
 
     return results;
@@ -1353,6 +1359,27 @@ class FhirCodeSystemProvider extends BaseCSServices {
     }
   }
 
+  /**
+   * Add immediate children of a code to the results
+   * @param {FhirCodeSystemProviderFilterContext} results - Results to add to
+   * @param {string} ancestorCode - The parent code
+   * @private
+   */
+  async _addChildren(results, parentCode) {
+    const concept = this.codeSystem.getConceptByCode(parentCode);
+    if (concept) {
+      const descendants = this.codeSystem.getChildren(parentCode);
+      for (const code of descendants) {
+        if (code !== parentCode) { // should not be
+          const concept = this.codeSystem.getConceptByCode(code);
+          if (concept) {
+            results.add(concept, 0);
+          }
+        }
+      }
+    }
+  }
+
   /**
    * Handle child exists filter
    * @param {FilterExecutionContext} filterContext - Filter context

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/vs/vs-vsac.js

@@ -17,6 +17,7 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
    * @param {string} config.cacheFolder - Local folder for cached database
    * @param {number} [config.refreshIntervalHours=24] - Hours between refresh scans
    * @param {string} [config.baseUrl='http://cts.nlm.nih.gov/fhir'] - Base URL for VSAC FHIR server
+   * @param {number} [config.timeoutMs=120000] - HTTP request timeout in milliseconds
    */
   constructor(config, stats) {
     super();
@@ -43,7 +44,7 @@ class VSACValueSetProvider extends AbstractValueSetProvider {
     const authString = Buffer.from(`apikey:${this.apiKey}`).toString('base64');
     this.httpClient = axios.create({
       baseURL: this.baseUrl,
-      timeout: 30000,
+      timeout: config.timeoutMs || 120000,
       headers: {
         'Accept': 'application/fhir+json',
         'User-Agent': 'FHIR-ValueSet-Provider/1.0',

package/tx/workers/validate.js

@@ -839,7 +839,7 @@ class ValueSetChecker {
               } else {
                 bAdd = !unknownSystems.has(system + '|' + version);
                 if (bAdd) {
-                  let vl = await this.listVersions(system);
+                  let vl = await this.worker.listVersions(system);
                   if (vl.length == 0) {
                     mid = 'UNKNOWN_CODESYSTEM_VERSION_NONE';
                     vn = system;

package/tx/xversion/xv-valueset.js

@@ -1,5 +1,6 @@
 const {VersionUtilities} = require("../../library/version-utilities");
 const {getValueName} = require("../../library/utilities");
+const {Extensions} = require("../library/extensions");
 
 /**
  * Converts input ValueSet to R5 format (modifies input object for performance)
@@ -13,6 +14,12 @@ function valueSetToR5(jsonObj, sourceVersion) {
   if (VersionUtilities.isR5Ver(sourceVersion)) {
     return jsonObj; // No conversion needed
   }
+  for (const inc of jsonObj.compose.include || []) {
+    valueSetIncludeToR5(inc);
+  }
+  for (const inc of jsonObj.compose.exclude || []) {
+    valueSetIncludeToR5(inc);
+  }
   if (VersionUtilities.isR4Ver(sourceVersion)) {
     return jsonObj; // No conversion needed
   }
@@ -26,6 +33,19 @@ function valueSetToR5(jsonObj, sourceVersion) {
   throw new Error(`Unsupported FHIR version: ${sourceVersion}`);
 }
 
+function valueSetIncludeToR5(inc) {
+  for (const filter of inc.filter || []) {
+    if (filter._op) {
+      let code = Extensions.readString(filter._op, 'http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op');
+      if (code) {
+        filter.op = code;
+        delete filter._op;
+      }
+    }
+  }
+}
+
+
 /**
  * Converts R5 ValueSet to target version format (clones object first)
  * @param {Object} r5Obj - The R5 format ValueSet object
@@ -70,8 +90,8 @@ function valueSetR5ToR4(r5Obj) {
       if (include.filter && Array.isArray(include.filter)) {
         include.filter = include.filter.map(filter => {
           if (filter.op && isR5OnlyFilterOperator(filter.op)) {
-            // Remove R5-only operators
-            return null;
+            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            delete filter.op;
           }
           return filter;
         }).filter(filter => filter !== null);
@@ -85,8 +105,8 @@ function valueSetR5ToR4(r5Obj) {
       if (exclude.filter && Array.isArray(exclude.filter)) {
         exclude.filter = exclude.filter.map(filter => {
           if (filter.op && isR5OnlyFilterOperator(filter.op)) {
-            // Remove R5-only operators
-            return null;
+            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            delete filter.op;
           }
           return filter;
         }).filter(filter => filter !== null);
@@ -135,8 +155,8 @@ function valueSetR5ToR3(r5Obj) {
       if (include.filter && Array.isArray(include.filter)) {
         include.filter = include.filter.map(filter => {
           if (filter.op && !isR3CompatibleFilterOperator(filter.op)) {
-            // Remove non-R3-compatible operators
-            return null;
+            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            delete filter.op;
           }
           return filter;
         }).filter(filter => filter !== null);
@@ -150,8 +170,8 @@ function valueSetR5ToR3(r5Obj) {
       if (exclude.filter && Array.isArray(exclude.filter)) {
         exclude.filter = exclude.filter.map(filter => {
           if (filter.op && !isR3CompatibleFilterOperator(filter.op)) {
-            // Remove non-R3-compatible operators
-            return null;
+            filter._op = { "extension": "http://hl7.org/fhir/5.0/StructureDefinition/extension-ValueSet.compose.include.filter.op", "valueCode": filter.op}
+            delete filter.op;
           }
           return filter;
         }).filter(filter => filter !== null);