Support User Provided Examples of Logical Models (#941)

* Ignore error that is thrown when converting an uknown FHIR type from XML to JSON * Do not add an entry to IG resource list for examples of Logical Models that already have a corresponding Binary entry in the config * Add tests for loading non FHIR resourceType JSON and XML and properly adding to IG resource * Use .some instead of .find Co-authored-by: Mint Thompson <[email protected]> Co-authored-by: Mint Thompson <[email protected]>
FHIR · Oct 22, 2021 · 740edc0 · 740edc0
1 parent a318d12
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diff --git a/src/fhirdefs/load.ts b/src/fhirdefs/load.ts
@@ -234,6 +234,11 @@ export function loadCustomResources(resourceDir: string, defs: FHIRDefinitions):
             continue;
           }
         } catch (e) {
+          if (e.message.startsWith('Unknown resource type:')) {
+            // Skip unknown FHIR resource types. When we have instances of Logical Models,
+            // the resourceType will not be recognized as a known FHIR resourceType, but that's okay.
+            continue;
+          }
           logger.error(`Loading ${file} failed with the following error:\n${e.message}`);
           continue;
         }

diff --git a/src/fhirtypes/ImplementationGuide.ts b/src/fhirtypes/ImplementationGuide.ts
@@ -1,5 +1,11 @@
 import { ContactDetail, UsageContext } from './metaDataTypes';
-import { CodeableConcept, Reference, BackboneElement, DomainResource } from './dataTypes';
+import {
+  BackboneElement,
+  CodeableConcept,
+  DomainResource,
+  Extension,
+  Reference
+} from './dataTypes';
 
 export type ImplementationGuide = DomainResource & {
   resourceType: 'ImplementationGuide';
@@ -60,6 +66,7 @@ export type ImplementationGuideDefinitionResource = {
   exampleBoolean?: boolean;
   exampleCanonical?: string;
   groupingId?: string;
+  extension?: Extension[];
 };
 
 export type ImplementationGuideDefinitionPage = {

diff --git a/src/ig/IGExporter.ts b/src/ig/IGExporter.ts
@@ -846,7 +846,24 @@ export class IGExporter {
               resource => resource.reference?.reference == referenceKey
             );
 
-            if (configResource?.omit !== true) {
+            // For predefined examples of Logical Models, the user must provide an entry in config
+            // that specifies the reference as Binary/[id], the extension that specifies the resource format,
+            // and the exampleCanonical that references the LogicalModel the resource is an example of.
+            // In that case, we do not want to add our own entry for the predefined resource - we just
+            // want to use the resource entry from the sushi-config.yaml
+            const hasBinaryExampleReference = (this.config.resources ?? []).some(
+              resource =>
+                resource.reference?.reference === `Binary/${resourceJSON.id}` &&
+                resource.exampleCanonical ===
+                  `${this.config.canonical}/StructureDefinition/${resourceJSON.resourceType}` &&
+                resource.extension?.some(
+                  e =>
+                    e.url ===
+                    'http://hl7.org/fhir/StructureDefinition/implementationguide-resource-format'
+                )
+            );
+
+            if (configResource?.omit !== true && !hasBinaryExampleReference) {
               const existingIndex = this.ig.definition.resource.findIndex(
                 r => r.reference.reference === referenceKey
               );

diff --git a/...defs/fixtures/customized-ig-with-resources/input/examples/Binary-LogicalModelExample.json b/...defs/fixtures/customized-ig-with-resources/input/examples/Binary-LogicalModelExample.json
@@ -0,0 +1,4 @@
+{
+  "resourceType": "CustomLogicalModel",
+  "id": "example-logical-model"
+}
diff --git a/...rdefs/fixtures/customized-ig-with-resources/input/examples/Binary-LogicalModelExample.xml b/...rdefs/fixtures/customized-ig-with-resources/input/examples/Binary-LogicalModelExample.xml
@@ -0,0 +1,3 @@
+<CustomLogicalModel>
+  <id value="custom-logical-model" />
+</CustomLogicalModel>
diff --git a/test/fhirdefs/load.test.ts b/test/fhirdefs/load.test.ts
@@ -442,6 +442,11 @@ describe('#loadCustomResources', () => {
     expect(
       defs.getPredefinedResource(path.join(pathToInput, 'examples', 'Patient-MyPatient.json')).id
     ).toBe('MyPatient');
+    expect(
+      defs.getPredefinedResource(
+        path.join(pathToInput, 'examples', 'Binary-LogicalModelExample.json')
+      ).id
+    ).toBe('example-logical-model');
     expect(
       defs.getPredefinedResource(
         path.join(pathToInput, 'extensions', 'StructureDefinition-patient-birthPlace.json')
@@ -507,6 +512,12 @@ describe('#loadCustomResources', () => {
     });
   });
 
+  it('should not log an error for invalid FHIR types parsed from XML', () => {
+    loggerSpy.getAllMessages('error').forEach(m => {
+      expect(m).not.toMatch(/Unknown resource type:/);
+    });
+  });
+
   it('should log an info message when it finds spreadsheets', () => {
     expect(loggerSpy.getFirstMessage('info')).toMatch(/Found spreadsheets in directory/);
   });

diff --git a/test/ig/IGExporter.IG.test.ts b/test/ig/IGExporter.IG.test.ts
@@ -1586,6 +1586,112 @@ describe('IGExporter', () => {
     });
   });
 
+  describe('#customized-ig-with-logical-model-example', () => {
+    let pkg: Package;
+    let exporter: IGExporter;
+    let tempOut: string;
+    let fixtures: string;
+    let config: Configuration;
+    let defs: FHIRDefinitions;
+
+    beforeAll(() => {
+      defs = new FHIRDefinitions();
+      loadFromPath(
+        path.join(__dirname, '..', 'testhelpers', 'testdefs', 'package'),
+        'testPackage',
+        defs
+      );
+      fixtures = path.join(__dirname, 'fixtures', 'customized-ig-with-logical-model-example');
+      loadCustomResources(path.join(fixtures, 'input'), defs);
+    });
+
+    beforeEach(() => {
+      loggerSpy.reset();
+      tempOut = temp.mkdirSync('sushi-test');
+      config = cloneDeep(minimalConfig);
+      config.resources = [
+        {
+          reference: {
+            reference: 'Binary/example-logical-model-json'
+          },
+          extension: [
+            {
+              url: 'http://hl7.org/fhir/StructureDefinition/implementationguide-resource-format',
+              valueCode: 'application/json'
+            }
+          ],
+          name: 'Example of LM JSON',
+          exampleCanonical: `${config.canonical}/StructureDefinition/MyLM`
+        },
+        {
+          reference: {
+            reference: 'Binary/example-logical-model-xml'
+          },
+          extension: [
+            {
+              url: 'http://hl7.org/fhir/StructureDefinition/implementationguide-resource-format',
+              valueCode: 'application/xml'
+            }
+          ],
+          name: 'Example of LM XML',
+          exampleCanonical: `${config.canonical}/StructureDefinition/MyLM`
+        }
+      ];
+      pkg = new Package(config);
+      exporter = new IGExporter(pkg, defs, fixtures);
+    });
+
+    afterAll(() => {
+      temp.cleanupSync();
+    });
+
+    it('should add logical model and example resource references to the ImplementationGuide resource', () => {
+      exporter.export(tempOut);
+      const igPath = path.join(
+        tempOut,
+        'fsh-generated',
+        'resources',
+        'ImplementationGuide-fhir.us.minimal.json'
+      );
+      expect(fs.existsSync(igPath)).toBeTruthy();
+      const igContent: ImplementationGuide = fs.readJSONSync(igPath);
+      expect(igContent.definition.resource).toHaveLength(3);
+      expect(igContent.definition.resource).toContainEqual({
+        reference: {
+          reference: 'StructureDefinition/MyLM'
+        },
+        name: 'MyLM',
+        exampleBoolean: false
+      });
+      expect(igContent.definition.resource).toContainEqual({
+        reference: {
+          reference: 'Binary/example-logical-model-json'
+        },
+        extension: [
+          {
+            url: 'http://hl7.org/fhir/StructureDefinition/implementationguide-resource-format',
+            valueCode: 'application/json'
+          }
+        ],
+        name: 'Example of LM JSON',
+        exampleCanonical: `${config.canonical}/StructureDefinition/MyLM`
+      });
+      expect(igContent.definition.resource).toContainEqual({
+        reference: {
+          reference: 'Binary/example-logical-model-xml'
+        },
+        extension: [
+          {
+            url: 'http://hl7.org/fhir/StructureDefinition/implementationguide-resource-format',
+            valueCode: 'application/xml'
+          }
+        ],
+        name: 'Example of LM XML',
+        exampleCanonical: `${config.canonical}/StructureDefinition/MyLM`
+      });
+    });
+  });
+
   describe('#pages-folder-ig', () => {
     let pkg: Package;
     let exporter: IGExporter;

diff --git a/...mized-ig-with-logical-model-example/input/examples/Binary-example-logical-model-json.json b/...mized-ig-with-logical-model-example/input/examples/Binary-example-logical-model-json.json
@@ -0,0 +1,4 @@
+{
+  "resourceType": "MyLM",
+  "id": "example-logical-model-json"
+}
diff --git a/...tomized-ig-with-logical-model-example/input/examples/Binary-example-logical-model-xml.xml b/...tomized-ig-with-logical-model-example/input/examples/Binary-example-logical-model-xml.xml
@@ -0,0 +1,3 @@
+<MyLM>
+  <id value="example-logical-model-xml" />
+</MyLM>
diff --git a/...tures/customized-ig-with-logical-model-example/input/models/StructureDefinition-MyLM.json b/...tures/customized-ig-with-logical-model-example/input/models/StructureDefinition-MyLM.json
@@ -0,0 +1,25 @@
+{
+  "resourceType": "StructureDefinition",
+  "id": "MyLM",
+  "url": "http://hl7.org/fhir/us/mcode/StructureDefinition/MyLM",
+  "name": "MyLM",
+  "status": "active",
+  "fhirVersion": "4.0.1",
+  "type": "MyLM",
+  "baseDefinition" : "http://hl7.org/fhir/StructureDefinition/Element",
+  "kind": "logical",
+  "derivation": "specialization",
+  "snapshot": {
+    "element": [
+      {
+        "id": "modeling-woo",
+        "path": "modeling-woo",
+        "type": [
+          {
+            "code": "boolean"
+          }
+        ]
+      }
+    ]
+  }
+}