Merge pull request #234 from srdc/draft-mapping

✨ feat: Implement draft mapping feature.

tofhir-engine/src/main/scala/io/tofhir/engine/mapping/job/FhirMappingJobManager.scala

@@ -348,21 +348,29 @@ class FhirMappingJobManager(
   /**
    * Read and join the source data
    *
-   * @param task           FHIR Mapping task
-   * @param sourceSettings The source settings of the mapping job
-   * @param timeRange      Time range for the source data to load
-   * @param jobId          The identifier of mapping job which executes the mapping
+   * @param task            FHIR Mapping task
+   * @param sourceSettings  The source settings of the mapping job
+   * @param timeRange       Time range for the source data to load
+   * @param jobId           The identifier of mapping job which executes the mapping
+   * @param isTestExecution Indicates whether the execution is a test
    */
   def readJoinSourceData(task: FhirMappingTask,
                          sourceSettings: Map[String, MappingJobSourceSettings],
                          timeRange: Option[(LocalDateTime, LocalDateTime)] = None,
-                         jobId: Option[String] = None): (FhirMapping, MappingJobSourceSettings, DataFrame) = {
+                         jobId: Option[String] = None,
+                         isTestExecution: Boolean = false): (FhirMapping, MappingJobSourceSettings, DataFrame) = {
     // if the FhirMapping task includes the mapping to be executed (the case where the mapping is being tested), use it,
     // otherwise retrieve it from the repository
     val mapping = task.mapping match {
       case Some(mapping) => mapping
       case None => fhirMappingRepository.getFhirMappingByUrl(task.mappingRef)
     }
+
+    // ensure that the mapping is not marked as draft unless this is a test execution.
+    if(mapping.isDraft && !isTestExecution){
+      throw FhirMappingException(s"Cannot execute mapping '${mapping.name}' because it is currently marked as draft.");
+    }
+
     // remove slice names from the mapping, otherwise FHIR resources will be created with slice names in fields starting with @
     val fhirMapping = mapping.removeSliceNames()
     // verify that the provided source bindings in the mapping job match the source aliases defined in the mapping

tofhir-engine/src/main/scala/io/tofhir/engine/model/FhirMapping.scala

@@ -12,6 +12,7 @@ import java.util.UUID
  * @param url         Canonical url for the mapping
  * @param name        Computer friendly name
  * @param title       Human friendly title
+ * @param isDraft     Indicates whether the mapping is in a draft state and not yet ready for execution
  * @param description Description of the mapping
  * @param source      Metadata about source for the mapping
  * @param context     Further context to use for mapping evaluation e.g. ConceptMap for terminology mapping, definition of unit conversion functions
@@ -22,6 +23,7 @@ case class FhirMapping(id: String,
                        url: String,
                        name: String,
                        title: Option[String] = None,
+                       isDraft: Boolean = false,
                        description: Option[String] = None,
                        source: Seq[FhirMappingSource],
                        context: Map[String, FhirMappingContextDefinition] = Map.empty,

tofhir-engine/src/test/resources/test-mappings/patient-mapping-with-draft.json

@@ -0,0 +1,74 @@
+{
+  "id": "patient-mapping-with-draft",
+  "url": "https://aiccelerate.eu/fhir/mappings/patient-mapping-with-draft",
+  "name": "patient-mapping-with-draft",
+  "isDraft": true,
+  "title": "Mapping of some patient data with draft",
+  "source": [{
+    "alias": "source",
+    "url": "https://aiccelerate.eu/fhir/StructureDefinition/Ext-patient-extra"
+  }],
+  "mapping": [
+    {
+      "expression": {
+        "name": "result",
+        "language": "application/fhir-template+json",
+        "value": {
+          "resourceType": "Parameters",
+          "parameter": [
+            {
+              "name": "operation",
+              "part": [
+                {
+                  "name": "type",
+                  "valueCode": "add"
+                },
+                {
+                  "name": "path",
+                  "valueString": "Patient"
+                },
+                {
+                  "name": "name",
+                  "valueString": "maritalStatus"
+                },
+                {
+                  "name": "value",
+                  "valueCodeableConcept": {
+                    "coding": [
+                      {
+                        "system":"http://terminology.hl7.org/CodeSystem/v3-MaritalStatus",
+                        "code": "{{maritalStatusCode}}",
+                        "display": "{{maritalStatusDisplay}}"
+                      }
+                    ]
+                  }
+                }
+              ]
+            },
+            {
+              "name": "operation",
+              "part": [
+                {
+                  "name": "type",
+                  "valueCode": "replace"
+                },
+                {
+                  "name": "path",
+                  "valueString": "Patient.gender"
+                },
+                {
+                  "name": "value",
+                  "valueCode": "{{gender}}"
+                }
+              ]
+            }
+          ]
+        }
+      },
+      "fhirInteraction": {
+        "type": "patch",
+        "rid": "Patient/{{mpp:getHashedId('Patient',pid)}}"
+      }
+    }
+  ]
+}

tofhir-engine/src/test/scala/io/tofhir/test/FhirMappingJobManagerTest.scala

@@ -82,6 +82,12 @@ class FhirMappingJobManagerTest extends AsyncFlatSpec with BeforeAndAfterAll wit
     sourceBinding = Map("source" -> FileSystemSource(path = "patients.zip", contentType = SourceContentTypes.CSV))
   )
 
+  val patientMappingTaskWithDraftMapping: FhirMappingTask = FhirMappingTask(
+    name = "patient-mapping-with-draft",
+    mappingRef = "https://aiccelerate.eu/fhir/mappings/patient-mapping-with-draft",
+    sourceBinding = Map("source" -> FileSystemSource(path = "patients.csv", contentType = SourceContentTypes.CSV))
+  )
+
   val testMappingJobFilePath: String = getClass.getResource("/test-mappingjob.json").toURI.getPath
   val testMappingJobWithIdentityServiceFilePath: String = getClass.getResource("/test-mappingjob-using-services.json").toURI.getPath
 
@@ -176,6 +182,20 @@ class FhirMappingJobManagerTest extends AsyncFlatSpec with BeforeAndAfterAll wit
     }
   }
 
+  it should "not execute the draft patient mapping task and return error" in {
+    val fhirMappingJobManager = new FhirMappingJobManager(mappingRepository, contextLoader, schemaRepository, Map.empty, sparkSession)
+    val fhirMappingJobWithDraftMapping = fhirMappingJob.copy(mappings = Seq(patientMappingTaskWithDraftMapping));
+    fhirMappingJobManager.executeMappingTaskAndReturn(mappingJobExecution = FhirMappingJobExecution(
+      job = fhirMappingJobWithDraftMapping,
+      mappingTasks = Seq(patientMappingTaskWithDraftMapping)) , mappingJobSourceSettings = mappingJobSourceSettings) flatMap { _ =>
+      fail("The draft mapping should not be executed!")
+    } recover {
+      case fhirMappingException: FhirMappingException =>
+        fhirMappingException.getMessage shouldBe "Cannot execute mapping 'patient-mapping-with-draft' because it is currently marked as draft."
+      case _ => fail("Unexpected error is thrown!")
+    }
+  }
+
   it should "execute a mapping job with two data sources" in {
     val mappingJob = FhirMappingJobFormatter.readMappingJobFromFile(getClass.getResource("/patient-mapping-job-with-two-sources.json").toURI.getPath)
 

tofhir-server/src/main/scala/io/tofhir/server/service/ExecutionService.scala

@@ -224,7 +224,7 @@ class ExecutionService(jobRepository: IJobRepository, mappingRepository: IMappin
       toFhirEngine.functionLibraries,
       toFhirEngine.sparkSession
     )
-    val (fhirMapping, mappingJobSourceSettings, dataFrame) = fhirMappingJobManager.readJoinSourceData(mappingTask, mappingJob.sourceSettings, jobId = Some(jobId))
+    val (fhirMapping, mappingJobSourceSettings, dataFrame) = fhirMappingJobManager.readJoinSourceData(mappingTask, mappingJob.sourceSettings, jobId = Some(jobId), isTestExecution = true)
     val selected = DataFrameUtil.applyResourceFilter(dataFrame, testResourceCreationRequest.resourceFilter)
     fhirMappingJobManager.executeTask(mappingJob.id, mappingTask.name, fhirMapping, selected, mappingJobSourceSettings, mappingJob.terminologyServiceSettings, mappingJob.getIdentityServiceSettings(), projectId = Some(projectId))
       .map { dataFrame =>