✅ test: Add a test for JSON Patch mapping

srdc · Oct 9, 2024 · 7ea7cf3 · 7ea7cf3
1 parent eeb15b5
commit 7ea7cf3
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diff --git a/tofhir-engine/src/main/scala/io/tofhir/engine/mapping/MappingTaskExecutor.scala b/tofhir-engine/src/main/scala/io/tofhir/engine/mapping/MappingTaskExecutor.scala
@@ -195,7 +195,19 @@ object MappingTaskExecutor {
           ))
         } else {
           mappedResources.flatMap {
-            //If this is a JSON Patch, the resources are patches so return it as single result
+            // JSON Patch is a document that represents a series of operations to be applied to a target resource,
+            // formatted as an array of objects. Each object describes a single operation, such as testing, adding,
+            // removing, or replacing values at specific paths in the resource. Example format:
+            //
+            // [
+            //   { "op": "test", "path": "/component/0/code/coding/0/code", "value": "80-6" },
+            //   { "op": "remove", "path": "/component/0/code/coding/2" },
+            //   { "op": "add", "path": "/component/0/code/coding/1", "value": { "system": "test", "code": "test" } },
+            //   { "op": "replace", "path": "/component/0/code/coding/2/code", "value": "test3" }
+            // ]
+            //
+            // If the input is recognized as a JSON Patch, return the patch document as a single result so it can be
+            // passed directly to the body of a FHIR Patch interaction request.
             case (mappingExpr, resources, fhirInteraction) if fhirInteraction.exists(_.`type` == "patch") && resources.length > 1 =>
               Seq(FhirMappingResult(
                 jobId = fhirMappingService.jobId,

diff --git a/tofhir-engine/src/test/resources/test-mappings/patient-mapping-with-json-patch.json b/tofhir-engine/src/test/resources/test-mappings/patient-mapping-with-json-patch.json
@@ -0,0 +1,36 @@
+{
+  "id": "patient-mapping-with-json-patch",
+  "url": "https://aiccelerate.eu/fhir/mappings/patient-mapping-with-json-patch",
+  "name": "patient-mapping-with-json-patch",
+  "title": "Mapping of some patient data to a JSON patch for FHIR Patient resource",
+  "source": [
+	{
+	  "alias": "source",
+	  "url": "https://aiccelerate.eu/fhir/StructureDefinition/Ext-patient-extra"
+	}
+  ],
+  "mapping": [
+	{
+	  "expression": {
+		"name": "result",
+		"language": "application/fhir-template+json",
+		"value": [
+		  {
+			"op": "replace",
+			"path": "gender",
+			"value": "female"
+		  },
+		  {
+			"op": "replace",
+			"path": "birthDate",
+			"value": "2021-03-05"
+		  }
+		]
+	  },
+	  "fhirInteraction": {
+		"type": "patch",
+		"rid": "Patient/{{mpp:getHashedId('Patient',pid)}}"
+	  }
+	}
+  ]
+}
diff --git a/tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingJobManagerTest.scala b/tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingJobManagerTest.scala
@@ -208,6 +208,25 @@ class FhirMappingJobManagerTest extends AsyncFlatSpec with BeforeAndAfterAll wit
     )
   }
 
+  it should "execute the mapping with JSON patch" in {
+    val jsonPatchMapping: FhirMappingTask = FhirMappingTask(
+      name = "patient-mapping-with-json-patch",
+      mappingRef = "https://aiccelerate.eu/fhir/mappings/patient-mapping-with-json-patch",
+      sourceBinding = Map("source" -> FileSystemSource(path = "patients-extra.csv", contentType = SourceContentTypes.CSV))
+    )
+    val fhirMappingJobManager = new FhirMappingJobManager(mappingRepository, contextLoader, schemaRepository, Map.empty, sparkSession)
+
+    fhirMappingJobManager.executeMappingJob(mappingJobExecution = FhirMappingJobExecution(mappingTasks = Seq(patientMappingTask), job = fhirMappingJob), sourceSettings = fhirMappingJob.sourceSettings, sinkSettings = fhirMappingJob.sinkSettings).flatMap(_ =>
+      fhirMappingJobManager.executeMappingJob(mappingJobExecution = FhirMappingJobExecution(mappingTasks = Seq(jsonPatchMapping), job = fhirMappingJob), sourceSettings = fhirMappingJob.sourceSettings, sinkSettings = fhirMappingJob.sinkSettings) flatMap { response =>
+        response shouldBe()
+        onFhirClient.read("Patient", FhirMappingUtility.getHashedId("Patient", "p1")).executeAndReturnResource() flatMap { p1Resource =>
+          (p1Resource \ "gender").extract[String] shouldBe "female"
+          (p1Resource \ "birthDate").extract[String] shouldBe "2021-03-05"
+        }
+      }
+    )
+  }
+
   it should "execute the patient mapping task with given tsv file and return the results" in {
     val patientTsvFileMappingTask: FhirMappingTask = FhirMappingTask(
       name = "patient-mapping",