Add FHIR Type to fromFHIR function signature

lib/generateClass.js

@@ -153,13 +153,14 @@ function generateClassBody(def, specs, fhir, fhirProfile, fhirExtension, cw) {
     cw.ln(`Deserializes FHIR JSON data to an instance of the ${clazzName} class.`)
       .ln(`The FHIR must be valid against the ${clazzName} FHIR profile, although this is not validated by the function.`)
       .ln(`@param {object} fhir - the FHIR JSON data to deserialize`)
+      .ln(`@param {string} fhirType - the type of the FHIR object that was passed in, in case not otherwise identifiable from the object itself`)
       .ln(`@param {string} shrId - a unique, persistent, permanent identifier for the overall health record belonging to the Patient; will be auto-generated if not provided`)
       .ln(`@param {Array} allEntries - the list of all entries that references in 'fhir' refer to`)
       .ln(`@param {object} mappedResources - any resources that have already been mapped to SHR objects. Format is { fhir_key: {shr_obj} }`)
       .ln(`@param {Array} referencesOut - list of all SHR ref() targets that were instantiated during this function call`)
       .ln(`@param {boolean} asExtension - Whether the provided instance is an extension`)
       .ln(`@returns {${clazzName}} An instance of ${clazzName} populated with the FHIR data`);
-  }).bl('static fromFHIR(fhir, shrId=uuid(), allEntries=[], mappedResources={}, referencesOut=[], asExtension=false)', () => writeFromFhir(def, specs, fhir, fhirProfile, fhirExtension, cw))
+  }).bl('static fromFHIR(fhir, fhirType, shrId=uuid(), allEntries=[], mappedResources={}, referencesOut=[], asExtension=false)', () => writeFromFhir(def, specs, fhir, fhirProfile, fhirExtension, cw))
     .ln();
 }
 
@@ -474,13 +475,13 @@ function writeFromFhir(def, specs, fhir, fhirProfile, fhirExtension, cw) {
   cw.ln(`const inst = new ${className(def.identifier.name)}();`);
 
   if (def.isEntry) {
-    cw.ln(`inst.entryInfo = FHIRHelper.createInstanceFromFHIR('shr.base.Entry', {});`); // do it this way so we don't have to import Entry
-    cw.ln(`inst.entryInfo.shrId = FHIRHelper.createInstanceFromFHIR('shr.base.ShrId', shrId);`);
-    cw.ln(`inst.entryInfo.entryId = FHIRHelper.createInstanceFromFHIR('shr.base.EntryId', fhir['id'] || uuid());`); // re-use the FHIR id if it exists, otherwise generate a new uuid
+    cw.ln(`inst.entryInfo = FHIRHelper.createInstanceFromFHIR('shr.base.Entry', {}, null);`); // do it this way so we don't have to import Entry
+    cw.ln(`inst.entryInfo.shrId = FHIRHelper.createInstanceFromFHIR('shr.base.ShrId', shrId, 'string');`);
+    cw.ln(`inst.entryInfo.entryId = FHIRHelper.createInstanceFromFHIR('shr.base.EntryId', fhir['id'] || uuid(), 'string');`); // re-use the FHIR id if it exists, otherwise generate a new uuid
 
     // copied from writeToJson above --- should this URL be configurable?
     const url = `http://standardhealthrecord.org/spec/${def.identifier.namespace.replace('.', '/')}/${className(def.identifier.name)}`;
-    cw.ln(`inst.entryInfo.entryType = FHIRHelper.createInstanceFromFHIR('shr.base.EntryType', '${url}');`);
+    cw.ln(`inst.entryInfo.entryType = FHIRHelper.createInstanceFromFHIR('shr.base.EntryType', '${url}', 'uri');`);
   }
 
   if(fhirProfile){
@@ -655,7 +656,7 @@ function writeFromFhirProfile(def, specs, fhir, fhirProfile, cw) {
       if(mapping.map === '<Value>'){
         // Mapping to the value of this es6 instance
         if (def.value instanceof IdentifiableValue && def.value.identifier.isPrimitive) {
-          generateFromFHIRAssignment(def.value, element, fhirElementPath, [], 'value', fhirProfile, null, cw);
+          generateFromFHIRAssignment(def.value, element, fhirElementPath, [], 'value', fhirProfile, null, cw, fhir);
         } else {
           logger.error('Value referenced in mapping but none exist on this element.');
         }
@@ -697,13 +698,13 @@ function writeFromFhirProfile(def, specs, fhir, fhirProfile, cw) {
           }
 
           if (i == mapping.fieldChain.length - 1) { // if it's the last field in the chain
-            generateFromFHIRAssignment(field, element, fhirElementPath, mapping.fieldMapPath, shrElementPath, fhirProfile, slicing, cw);
+            generateFromFHIRAssignment(field, element, fhirElementPath, mapping.fieldMapPath, shrElementPath, fhirProfile, slicing, cw, fhir);
           } else {
             // if it's not the last element in the field chain, it's an intermediate one so we just want to initialize the value so it's not null
             const dec = field.card.isList ? 'const ' : ''; // if in a list, we need to declare the new variable, so do `const x = new()`
             const nullCheck = field.card.isList ? '' : `${shrElementPath} || `; // if not in a list, consider that the field was already init'ed, so do `x = x || new()`
 
-            let rhs = `FHIRHelper.createInstanceFromFHIR('${field.effectiveIdentifier.fqn}', {}, shrId)`;
+            let rhs = `FHIRHelper.createInstanceFromFHIR('${field.effectiveIdentifier.fqn}', {}, null, shrId)`;
             if (field instanceof RefValue) {
               rhs = `FHIRHelper.createReference( ${rhs}, referencesOut)`;
             }
@@ -805,7 +806,7 @@ function writeFromFhirExtension(def, specs, fhir, fhirExtension, cw) {
         const varName = `match_${i}`; // ensure a unique variable name here
         cw.ln(`const ${varName} = fhir['extension'].find(e => e.url == '${profileUrl}');`);
         cw.bl(`if (${varName} != null)`, () => {
-          cw.ln(`inst.${methodName} = FHIRHelper.createInstanceFromFHIR('${instance}', ${varName}, shrId, allEntries, mappedResources, referencesOut, true);`); // asExtension = true here, false(default value) everywhere else
+          cw.ln(`inst.${methodName} = FHIRHelper.createInstanceFromFHIR('${instance}', ${varName}, 'Extension', shrId, allEntries, mappedResources, referencesOut, true);`); // asExtension = true here, false(default value) everywhere else
         });
       }
     });
@@ -827,12 +828,12 @@ function writeFromFhirValue(def, specs, cw) {
         cw.ln(`inst.value = fhir;`);
       } else {
         const shrType = def.value.effectiveIdentifier.fqn;
-        cw.ln(`inst.value = FHIRHelper.createInstanceFromFHIR('${shrType}', fhir, shrId, allEntries, mappedResources, referencesOut);`);
+        cw.ln(`inst.value = FHIRHelper.createInstanceFromFHIR('${shrType}', fhir, fhirType, shrId, allEntries, mappedResources, referencesOut);`);
       }
     } else {
       // it could be any of the options, and we can't necessarily tell which one here
       // so just call createInstance to leverage the logic that looks up profiles
-      cw.ln(`inst.value = FHIRHelper.createInstanceFromFHIR(null, fhir, shrId, allEntries, mappedResources, referencesOut);`);
+      cw.ln(`inst.value = FHIRHelper.createInstanceFromFHIR(null, fhir, fhirType, shrId, allEntries, mappedResources, referencesOut);`);
     }
   });
 }
@@ -1683,8 +1684,9 @@ function generateToFHIRAssignment(cardIsList, baseCardIsList, constraintsLength,
  * @param {StructureDefinition} fhirProfile - the FHIR profile the element comes from
  * @param {Object} slicing - information on this element related to slicing, if any
  * @param {CodeWriter} cw - the CodeWriter that is writing the file for this element
+ * @param {object} fhir - All exported FHIR profiles and extensions.
  */
-function generateFromFHIRAssignment(field, fhirElement, fhirElementPath, shrElementMapping, shrElementPath, fhirProfile, slicing, cw) {
+function generateFromFHIRAssignment(field, fhirElement, fhirElementPath, shrElementMapping, shrElementPath, fhirProfile, slicing, cw, fhir) {
   const cardIsList = field.card.isList;
   const isRef = field instanceof RefValue;
   const fhirPathString = bracketNotation(fhirElementPath);
@@ -1702,9 +1704,14 @@ function generateFromFHIRAssignment(field, fhirElement, fhirElementPath, shrElem
       cw.bl('if (referencedEntry)', () => {
         const profileUrl = getTargetProfile(fhirElement, fhirProfile.fhirVersion);
         const parts = profileUrl.split('/');
-        shrType = parts[parts.length - 1].replace(/-/g, '.');
+        shrType = parts[parts.length - 1];
+
+        const allFHIRProfiles = [...fhir.profiles, ...fhir._noDiffProfiles];
+        const matchingProfile = allFHIRProfiles.find(p => p.id === shrType);
+        const fhirType = matchingProfile ? `'${matchingProfile.type}'` : null;
 
-        cw.ln(`mappedResources[entryId] = FHIRHelper.createInstanceFromFHIR('${shrType}', referencedEntry['resource'], shrId, allEntries, mappedResources, referencesOut);`);
+        shrType = shrType.replace(/-/g, '.');
+        cw.ln(`mappedResources[entryId] = FHIRHelper.createInstanceFromFHIR('${shrType}', referencedEntry['resource'], ${fhirType}, shrId, allEntries, mappedResources, referencesOut);`);
       });
     });
 
@@ -1740,7 +1747,8 @@ function generateFromFHIRAssignment(field, fhirElement, fhirElementPath, shrElem
       if (shrType.isPrimitive && !isExtension) {
         rhs = fhirPathString;
       } else {
-        rhs = `FHIRHelper.createInstanceFromFHIR('${shrType.fqn}', ${fhirPathString}, shrId, allEntries, mappedResources, referencesOut, ${isExtension})`;
+        const fhirType = fhirElement.type[0].code;
+        rhs = `FHIRHelper.createInstanceFromFHIR('${shrType.fqn}', ${fhirPathString}, '${fhirType}', shrId, allEntries, mappedResources, referencesOut, ${isExtension})`;
       }
       if (isRef) {
         rhs = `FHIRHelper.createReference( ${rhs}, referencesOut)`;

lib/generateFactory.js

@@ -41,15 +41,16 @@ function generateFactory(namespaces) {
       cw.blComment(() => {
         cw.ln('Create an instance of a class from its FHIR representation.')
           .ln('@param {Object} fhir - The element data in FHIR format (use `{}` and provide `type` for a blank instance)')
-          .ln(`@param {string} [type] - The (optional) type of the element (e.g., 'http://standardhealthrecord.org/spec/shr/demographics/PersonOfRecord').  This is only used if the type cannot be extracted from the JSON.`)
+          .ln(`@param {string} fhirType - the type of the FHIR object that was passed in, in case not otherwise identifiable from the object itself`)
+          .ln(`@param {string} shrType - The (optional) type of the element (e.g., 'http://standardhealthrecord.org/spec/shr/demographics/PersonOfRecord').  This is only used if the type cannot be extracted from the JSON.`)
           .ln('@returns {Object} An instance of the requested class populated with the provided data');
       })
-        .bl('static createInstanceFromFHIR(fhir, type, shrId=uuid(), allEntries=[], mappedResources={}, referencesOut=[], asExtension=false)', () => {
-          cw.ln('const { namespace } = getNamespaceAndNameFromFHIR(fhir, type);')
+        .bl('static createInstanceFromFHIR(fhir, fhirType, shrType, shrId=uuid(), allEntries=[], mappedResources={}, referencesOut=[], asExtension=false)', () => {
+          cw.ln('const { namespace } = getNamespaceAndNameFromFHIR(fhir, shrType);')
             .ln('switch (namespace) {');
           for (const ns of namespaces) {
             const factory = factoryName(ns.namespace);
-            cw.ln(`case '${ns.namespace}': return ${factory}.createInstanceFromFHIR(fhir, type, shrId, allEntries, mappedResources, referencesOut, asExtension);`);
+            cw.ln(`case '${ns.namespace}': return ${factory}.createInstanceFromFHIR(fhir, fhirType, shrType, shrId, allEntries, mappedResources, referencesOut, asExtension);`);
           }
           cw.ln(`case 'primitive': return fhir;`);
           cw.ln(`default: throw new Error(\`Unsupported namespace: \${namespace}\`);`)

lib/generateNamespaceFactory.js

@@ -42,21 +42,22 @@ function generateNamespaceFactory(ns, defs) {
 
       cw.blComment(() => {
         cw.ln('Convert an instance of a class from its FHIR representation.')
-          .ln('@param {Object} fhir - The element data in JSON format (use `{}` and provide `type` for a blank instance)')
-          .ln(`@param {string} [type] - The (optional) type of the element (e.g., 'http://standardhealthrecord.org/spec/shr/demographics/PersonOfRecord').  This is only used if the type cannot be extracted from the JSON.`)
+          .ln('@param {Object} fhir - The element data in JSON format (use `{}` and provide `shrType` for a blank instance)')
+          .ln(`@param {string} fhirType - the type of the FHIR object that was passed in, in case not otherwise identifiable from the object itself`)
+          .ln(`@param {string} [shrType] - The (optional) type of the element (e.g., 'http://standardhealthrecord.org/spec/shr/demographics/PersonOfRecord').  This is only used if the type cannot be extracted from the JSON.`)
           .ln('@returns {Object} An instance of the requested class populated with the provided data');
       })
-        .bl('static createInstanceFromFHIR(fhir, type, shrId=uuid(), allEntries=[], mappedResources={}, referencesOut=[], asExtension=false)', () => {
-          cw.ln('const { namespace, elementName } = getNamespaceAndNameFromFHIR(fhir, type);')
+        .bl('static createInstanceFromFHIR(fhir, fhirType, shrType, shrId=uuid(), allEntries=[], mappedResources={}, referencesOut=[], asExtension=false)', () => {
+          cw.ln('const { namespace, elementName } = getNamespaceAndNameFromFHIR(fhir, shrType);')
             .bl(`if (namespace !== '${ns.namespace}')`, () => {
-              cw.ln(`throw new Error(\`Unsupported type in ${factory}: \${type}\`);`);
+              cw.ln(`throw new Error(\`Unsupported type in ${factory}: \${shrType}\`);`);
             })
             .ln('switch (elementName) {');
           for (const def of defs) {
             const elName = className(def.identifier.name);
-            cw.ln(`case '${elName}': return ${elName}.fromFHIR(fhir, shrId, allEntries, mappedResources, referencesOut, asExtension);`);
+            cw.ln(`case '${elName}': return ${elName}.fromFHIR(fhir, fhirType, shrId, allEntries, mappedResources, referencesOut, asExtension);`);
           }
-          cw.ln(`default: throw new Error(\`Unsupported type in ${factory}: \${type}\`);`)
+          cw.ln(`default: throw new Error(\`Unsupported type in ${factory}: \${shrType}\`);`)
             .ln('}');
         });
     });

lib/includes/json-helper.js

@@ -194,20 +194,20 @@ export const FHIRHelper = {
 
   /**
    * Creates an ES6 class instance based on a value extracted from the JSON.
-   * @param {string} key - the original key under which the value was stored.  This is used as a backup in case the value
-   *   does not declare its type.
-   * @param {object} value - the FHIR data to create an ES6 class instance for
+   * @param {string} shrType - the fqn of the class to be instantiated
+   * @param {object} fhir - the FHIR data to create an ES6 class instance for
+   * @param {string} fhirType - the type of the FHIR object passed in, just in case it's not otherwise available by inspecting the object
    * @returns {object} an instance of an ES6 class representing the data
    * @private
    */
-  createInstanceFromFHIR: function(key, value, shrId, allEntries=[], mappedResources={}, referencesOut=[], asExtension=false) {
-    if (Array.isArray(value)) {
-      return value.map(v => FHIRHelper.createInstanceFromFHIR(key, v, shrId, allEntries, mappedResources, referencesOut, asExtension));
+  createInstanceFromFHIR: function(shrType, fhir, fhirType, shrId, allEntries=[], mappedResources={}, referencesOut=[], asExtension=false) {
+    if (Array.isArray(fhir)) {
+      return fhir.map(v => FHIRHelper.createInstanceFromFHIR(shrType, v, fhirType, shrId, allEntries, mappedResources, referencesOut, asExtension));
     }
     if (OBJECT_FACTORY == null) {
       throw new Error(`SHR ES6 module is not initialized.  Import 'init' before using the ES6 factories and classes`);
     }
-    return OBJECT_FACTORY.createInstanceFromFHIR(value, key, shrId, allEntries, mappedResources, referencesOut, asExtension);
+    return OBJECT_FACTORY.createInstanceFromFHIR(fhir, fhirType, shrType, shrId, allEntries, mappedResources, referencesOut, asExtension);
   },
 
   /**

package.json

@@ -17,6 +17,7 @@
     "lint:fix": "./node_modules/.bin/eslint . --fix"
   },
   "dependencies": {
+    "chai-spies": "^1.0.0",
     "reserved-words": "^0.1.2"
   },
   "devDependencies": {

test/es6FromFHIRJSONTest.js

@@ -1,4 +1,7 @@
-const { expect } = require('chai');
+const chai = require('chai');
+const expect = chai.expect;
+const spies = require('chai-spies');
+chai.use(spies);
 const setup = require('./setup');
 require('babel-register')({
   presets: [ 'es2015' ]
@@ -370,7 +373,7 @@ describe('#FromFHIR_STU3', () => {
       const allEntries = [json, memberA, memberB].map(j => {
         return { fullUrl: `http://example.org/fhir/Observation/${j.id}`, resource:  j };
       });
-      const entry = PanelSliceByProfile.fromFHIR(json, '12345', allEntries);
+      const entry = PanelSliceByProfile.fromFHIR(json, 'Observation', '12345', allEntries);
       expect(entry).instanceOf(PanelSliceByProfile);
 
       const expected = new PanelSliceByProfile()
@@ -409,18 +412,19 @@ describe('#FromFHIR_STU3', () => {
 
   describe('#Observation()', () => {
 
-    let Observation, Reference, ShrId, EntryId, EntryType;
+    let Observation, Reference, ShrId, EntryId, EntryType, DataValue;
     before(() => {
       Observation = context.importResult('shr/slicing/Observation');
       Reference = context.importResult('Reference');
       ShrId = context.importResult('shr/base/ShrId');
       EntryId = context.importResult('shr/base/EntryId');
       EntryType = context.importResult('shr/base/EntryType');
+      DataValue = context.importResult('shr/slicing/DataValue');
     });
 
     it('should deserialize a FHIR JSON instance', () => {
       const json = context.getFHIR('Observation');
-      const entry = Observation.fromFHIR(json, '1-1');
+      const entry = Observation.fromFHIR(json, 'Observation', '1-1');
       expect(entry).instanceOf(Observation);
 
       const expected = new Observation()
@@ -435,6 +439,30 @@ describe('#FromFHIR_STU3', () => {
 
       expect(entry).to.eql(expected);
     });
+
+    it('should correctly pass the FHIR type to nested object fromFHIR', () => {
+
+      const spy = chai.spy.on(DataValue, 'fromFHIR');
+      const json1 = context.getFHIR('Observation_valueString');
+      try {
+        // TODO: fix the bug that causes this to throw
+        // this will error out because DataValue.fromFHIR doesn't know what to do with the given fhir (yet)
+        // but at this point all we care about is that it's passed the right parameter
+        Observation.fromFHIR(json1, 'Observation', '1-1');
+      } catch (e) {} 
+
+      expect(spy).to.have.been.called.with('string');
+
+      const json2 = context.getFHIR('Observation_valueCodeableConcept');
+      try {
+        // TODO: fix the bug that causes this to throw
+        // this will error out because DataValue.fromFHIR doesn't know what to do with the given fhir (yet)
+        // but at this point all we care about is that it's passed the right parameter
+        Observation.fromFHIR(json2, 'Observation', '1-1');
+      } catch (e) {} 
+
+      expect(spy).to.have.been.called.with('CodeableConcept');
+    });
   });
 });
 
@@ -462,7 +490,7 @@ describe('#FromFHIR_DSTU2', () => {
 
     it('should deserialize a FHIR JSON instance', () => {
       const json = context.getFHIR('Observation');
-      const entry = Observation.fromFHIR(json, '1-1');
+      const entry = Observation.fromFHIR(json, 'Observation', '1-1');
       expect(entry).instanceOf(Observation);
 
       const expected = new Observation()

test/fixtures/fhir/Observation_valueCodeableConcept.json

@@ -0,0 +1,12 @@
+{
+  "resourceType": "Observation",
+  "id": "0000-0000",
+  "subject": { "reference": "abcd-1234" },
+  "valueCodeableConcept": {
+    "coding": [{
+      "system": "SNOMED-CT",
+      "code": "1234567890",
+      "display": "Dummy SNOMED Code"
+    }]
+  }
+}

test/fixtures/fhir/Observation_valueString.json

@@ -0,0 +1,6 @@
+{
+  "resourceType": "Observation",
+  "id": "0000-0000",
+  "subject": { "reference": "abcd-1234" },
+  "valueString": "something or other"
+}

test/fixtures/spec/shr_slicing.txt

@@ -36,6 +36,10 @@ Value:    CodeableConcept
 
 EntryElement: 		Observation
 0..1			ref(PatientEntry)
+0..1      DataValue
+
+Element:  DataValue
+Value:  CodeableConcept or Quantity or string or time or dateTime
 
 EntryElement: MemberA
 Based on: Observation