fhirsmith 0.4.2 → 0.5.0

package/tx/params.js

@@ -34,6 +34,8 @@ class TxParameters {
   limit = -1;
   offset = -1;
   validating = false;
+  abstractOk = true; // note true!
+  inferSystem = false;
 
   constructor(languages, i18n, validating) {
     validateParameter(languages, 'languages', LanguageDefinitions);
@@ -45,6 +47,7 @@ class TxParameters {
     this.FVersionRules = [];
     this.FProperties = [];
     this.FDesignations = [];
+    this.supplements = new Set;
     this.FGenerateNarrative = true;
 
     this.FHTTPLanguages = null;
@@ -54,13 +57,11 @@ class TxParameters {
 
     this.FActiveOnly = false;
     this.FExcludeNested = false;
-    this.FLimitedExpansion = false;
     this.FExcludeNotForUI = false;
     this.FExcludePostCoordinated = false;
     this.FIncludeDesignations = false;
     this.FIncludeDefinition = false;
     this.FDefaultToLatestVersion = false;
-    this.FIncompleteOK = false;
     this.FDisplayWarning = false;
     this.FMembershipOnly = false;
     this.FDiagnostics = false;
@@ -68,13 +69,11 @@ class TxParameters {
     this.hasActiveOnly = false;
     this.hasExcludeNested = false;
     this.hasGenerateNarrative = false;
-    this.hasLimitedExpansion = false;
     this.hasExcludeNotForUI = false;
     this.hasExcludePostCoordinated = false;
     this.hasIncludeDesignations = false;
     this.hasIncludeDefinition = false;
     this.hasDefaultToLatestVersion = false;
-    this.hasIncompleteOK = false;
     this.hasDisplayWarning = false;
     this.hasMembershipOnly = false;
   }
@@ -85,6 +84,12 @@ class TxParameters {
     if (!params.parameter) {
       return;
     }
+    if (!this.hasHTTPLanguages && this.hasParam(params, "__Content-Language")) {
+      this.HTTPLanguages = Languages.fromAcceptLanguage(this.paramstr(params, "__Content-Language"), this.languageDefinitions, !this.validating);
+    }
+    if (!this.hasHTTPLanguages && this.hasParam(params, "__Accept-Language")) {
+      this.HTTPLanguages = Languages.fromAcceptLanguage(this.paramstr(params, "__Accept-Language"), this.languageDefinitions, !this.validating);
+    }
 
     for (let p of params.parameter) {
       switch (p.name) {
@@ -118,7 +123,7 @@ class TxParameters {
           try {
             this.DisplayLanguages = Languages.fromAcceptLanguage(getValuePrimitive(p), this.languageDefinitions, !this.validating);
           } catch (error) {
-            throw new Issue("error", "processing", null, 'INVALID_DISPLAY_NAME', this.i18n.translate('INVALID_DISPLAY_NAME', this.HTTPLanguages, getValuePrimitive(p))).handleAsOO(400);
+            throw new Issue("error", "processing", null, 'INVALID_DISPLAY_NAME', this.i18n.translate('INVALID_DISPLAY_NAME', this.HTTPLanguages, [getValuePrimitive(p)]), "invalid-display").handleAsOO(400);
           }
           break;
         }
@@ -198,6 +203,7 @@ class TxParameters {
           if (value && (value.resourceType === 'Parameters' || value.resourceType === 'ExpansionProfile')) {
             this.readParams(value);
           }
+          break;
         }
         // eslint-disable-next-line no-fallthrough
         case 'term': // jQuery support
@@ -218,15 +224,30 @@ class TxParameters {
           this.limit = Utilities.parseIntOrDefault(getValuePrimitive(p), -1);
           break;
         }
+
+        case 'useSupplement' : {
+          this.supplements.add(getValuePrimitive(p));
+          break;
+        }
+
+        case 'abstract': {
+          if (getValuePrimitive(p) == true) {
+            this.abstractOk = true;
+          } else if (getValuePrimitive(p) == false) {
+            this.abstractOk = false;
+          }
+          break;
+        }
+        case 'inferSystem': {
+          if (getValuePrimitive(p) == true) this.inferSystem = true;
+          break;
+        }
+        case "exclude-system": {
+          throw new Issue('error', 'not-supported', null, null, "The parameter 'exclude-system' is not supported by this system", null, 400);
+        }
       }
     }
 
-    if (!this.hasHTTPLanguages && this.hasParam(params, "__Content-Language")) {
-      this.HTTPLanguages = Languages.fromAcceptLanguage(this.paramstr(params, "__Content-Language"), this.languageDefinitions, !this.validating);
-    }
-    if (!this.hasHTTPLanguages && this.hasParam(params, "__Accept-Language")) {
-      this.HTTPLanguages = Languages.fromAcceptLanguage(this.paramstr(params, "__Accept-Language"), this.languageDefinitions, !this.validating);
-    }
   }
 
   paramstr(params, name) {
@@ -298,15 +319,6 @@ class TxParameters {
     this.hasGenerateNarrative = true;
   }
 
-  get limitedExpansion() {
-    return this.FLimitedExpansion;
-  }
-
-  set limitedExpansion(value) {
-    this.FLimitedExpansion = value;
-    this.hasLimitedExpansion = true;
-  }
-
   get excludeNotForUI() {
     return this.FExcludeNotForUI;
   }
@@ -352,15 +364,6 @@ class TxParameters {
     this.hasDefaultToLatestVersion = true;
   }
 
-  get incompleteOK() {
-    return this.FIncompleteOK;
-  }
-
-  set incompleteOK(value) {
-    this.FIncompleteOK = value;
-    this.hasIncompleteOK = true;
-  }
-
   get displayWarning() {
     return this.FDisplayWarning;
   }
@@ -489,14 +492,12 @@ class TxParameters {
     b('active-only', this.FActiveOnly);
     b('exclude-nested', this.FExcludeNested);
     b('generate-narrative', this.FGenerateNarrative);
-    b('limited-expansion', this.FLimitedExpansion);
     b('for-ui', this.FExcludeNotForUI);
     b('exclude-post-coordinated', this.FExcludePostCoordinated);
     b('include-designations', this.FIncludeDesignations);
     b('include-definition', this.FIncludeDefinition);
     b('membership-only', this.FMembershipOnly);
     b('default-to-latest', this.FDefaultToLatestVersion);
-    b('incomplete-ok', this.FIncompleteOK);
     b('display-warning', this.FDisplayWarning);
 
     return result;
@@ -521,10 +522,10 @@ class TxParameters {
 
     let s = '|'+this.count+'|'+this.limit+'|'+this.offset+
       this.FUid + '|' + b(this.FMembershipOnly) + '|' + this.FProperties.join(',') + '|' +
-      b(this.FActiveOnly) + b(this.FIncompleteOK) + b(this.FDisplayWarning) + b(this.FExcludeNested) + b(this.FGenerateNarrative) + b(this.FLimitedExpansion) + b(this.FExcludeNotForUI) + b(this.FExcludePostCoordinated) +
+      b(this.FActiveOnly) + b(this.FDisplayWarning) + b(this.FExcludeNested) + b(this.FGenerateNarrative) + b(this.FExcludeNotForUI) + b(this.FExcludePostCoordinated) +
       b(this.FIncludeDesignations) + b(this.FIncludeDefinition) + b(this.hasActiveOnly) + b(this.hasExcludeNested) + b(this.hasGenerateNarrative) +
-      b(this.hasLimitedExpansion) + b(this.hasExcludeNotForUI) + b(this.hasExcludePostCoordinated) + b(this.hasIncludeDesignations) +
-      b(this.hasIncludeDefinition) + b(this.hasDefaultToLatestVersion) + b(this.hasIncompleteOK) + b(this.hasDisplayWarning) + b(this.hasExcludeNotForUI) + b(this.hasMembershipOnly) + b(this.FDefaultToLatestVersion);
+      b(this.hasExcludeNotForUI) + b(this.hasExcludePostCoordinated) + b(this.hasIncludeDesignations) +
+      b(this.hasIncludeDefinition) + b(this.hasDefaultToLatestVersion) + b(this.hasDisplayWarning) + b(this.hasExcludeNotForUI) + b(this.hasMembershipOnly) + b(this.FDefaultToLatestVersion);
 
     if (this.hasHTTPLanguages) {
       s = s + this.FHTTPLanguages.asString(true) + '|';
@@ -565,7 +566,6 @@ class TxParameters {
     this.FActiveOnly = other.FActiveOnly;
     this.FExcludeNested = other.FExcludeNested;
     this.FGenerateNarrative = other.FGenerateNarrative;
-    this.FLimitedExpansion = other.FLimitedExpansion;
     this.FExcludeNotForUI = other.FExcludeNotForUI;
     this.FExcludePostCoordinated = other.FExcludePostCoordinated;
     this.FIncludeDesignations = other.FIncludeDesignations;
@@ -573,19 +573,16 @@ class TxParameters {
     this.FUid = other.FUid;
     this.FMembershipOnly = other.FMembershipOnly;
     this.FDefaultToLatestVersion = other.FDefaultToLatestVersion;
-    this.FIncompleteOK = other.FIncompleteOK;
     this.FDisplayWarning = other.FDisplayWarning;
     this.FDiagnostics = other.FDiagnostics;
     this.hasActiveOnly = other.hasActiveOnly;
     this.hasExcludeNested = other.hasExcludeNested;
     this.hasGenerateNarrative = other.hasGenerateNarrative;
-    this.hasLimitedExpansion = other.hasLimitedExpansion;
     this.hasExcludeNotForUI = other.hasExcludeNotForUI;
     this.hasExcludePostCoordinated = other.hasExcludePostCoordinated;
     this.hasIncludeDesignations = other.hasIncludeDesignations;
     this.hasIncludeDefinition = other.hasIncludeDefinition;
     this.hasDefaultToLatestVersion = other.hasDefaultToLatestVersion;
-    this.hasIncompleteOK = other.hasIncompleteOK;
     this.hasMembershipOnly = other.hasMembershipOnly;
     this.hasDisplayWarning = other.hasDisplayWarning;
 

package/tx/provider.js

@@ -135,6 +135,7 @@ class Provider {
     const resources = await contentLoader.getResourcesByType("CodeSystem");
     for (const resource of resources) {
       const cs = new CodeSystem(await contentLoader.loadFile(resource, contentLoader.fhirVersion()));
+      cs.sourcePackage = contentLoader.pid();
       this.codeSystems.set(cs.url, cs);
       this.codeSystems.set(cs.vurl, cs);
     }
@@ -224,7 +225,7 @@ class Provider {
   async listCodeSystemVersions(url) {
     let result = new Set();
     for (let cs of this.codeSystems.values()) {
-      if (cs.url == url) {
+      if (cs.url == url && cs.version) {
         result.add(cs.version);
       }
     }
@@ -363,16 +364,16 @@ class Provider {
       factory = this.codeSystemFactories.get(vurlMM);
     }
     if (factory != null) {
-      const csp = factory.build(opContext, []);
-      const c = csp.locate(code);
+      const csp = await factory.build(opContext, []);
+      const c = csp ? csp.locate(code) : null;
       if (c) {
-        if (factory.iterable()) {
+        if (factory.iteratable()) {
           return {
             link: this.path + "/CodeSystem/x-" + factory.id(),
             description: csp.display(c)
           }
         } else {
-           const link = csp.codeLink(c);
+           const link = factory.codeLink(c);
            if (link) {
              return {
                link: link,

package/tx/sct/expressions.js

@@ -770,7 +770,7 @@ class SnomedExpressionParser {
    */
   rule(test, message) {
     if (!test) {
-      throw new Error(message + ' at character ' + this.cursor);
+      throw new Error(message + ' at character ' + (this.cursor+1));
     }
   }
 
@@ -1469,7 +1469,7 @@ class SnomedExpressionServices {
   /**
    * Validate concept reference
    */
-  checkConcept(concept) {
+  checkConcept(concept, limit) {
     if (concept.code) {
       const conceptId = BigInt(concept.code);
       const result = this.concepts.findConcept(conceptId);
@@ -1480,6 +1480,15 @@ class SnomedExpressionServices {
         throw new Error(`Concept ${concept.code} not found`);
       }
     }
+    if (limit && concept.reference) {
+      // if a limit is specified, then the concept has to be a specialization of that.
+      let parentRef = this.concepts.findConcept(limit);
+      let descendentsRef = this.concepts.getAllDesc(parentRef.index);
+      const descendants = this.refs.getReferences(descendentsRef);
+      if (descendants && !descendants.includes(concept.reference)) {
+        throw new Error(`Concept ${concept.code} is not valid in this context (must be a ${limit})`);
+      }
+    }
 
     // Validate description if provided
     if (concept.reference !== NO_REFERENCE && concept.description) {
@@ -1606,7 +1615,7 @@ class SnomedExpressionServices {
    * Validate refinement
    */
   checkRefinement(refinement) {
-    this.checkConcept(refinement.name);
+    this.checkConcept(refinement.name, '410662002');
     this.checkExpression(refinement.value);
   }