Issue #12: Transform MTBFile objects by using transformation rules

src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt

@@ -26,6 +26,7 @@ import dev.dnpm.etl.processor.pseudonym.Generator
 import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
 import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
 import dev.dnpm.etl.processor.services.Transformation
+import dev.dnpm.etl.processor.services.TransformationService
 import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
 import org.springframework.boot.context.properties.EnableConfigurationProperties
 import org.springframework.context.annotation.Bean
@@ -73,10 +74,13 @@ class AppConfiguration {
     }
 
     @Bean
-    fun transformations(configProperties: AppConfigProperties): List<Transformation> {
+    fun transformationService(
-        return configProperties.transformations.map {
+        objectMapper: ObjectMapper,
+        configProperties: AppConfigProperties
+    ): TransformationService {
+        return TransformationService(objectMapper, configProperties.transformations.map {
             Transformation.of(it.path) from it.from to it.to
-        }
+        })
     }
 
 }

src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt

@@ -38,6 +38,7 @@ import java.util.*
 @Service
 class RequestProcessor(
     private val pseudonymizeService: PseudonymizeService,
+    private val transformationService: TransformationService,
     private val sender: MtbFileSender,
     private val requestService: RequestService,
     private val objectMapper: ObjectMapper,
@@ -50,7 +51,7 @@ class RequestProcessor(
 
         mtbFile pseudonymizeWith pseudonymizeService
 
-        val request = MtbFileSender.MtbFileRequest(requestId, mtbFile)
+        val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
 
         requestService.save(
             Request(

src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt

@@ -24,8 +24,8 @@ import com.jayway.jsonpath.JsonPath
 import com.jayway.jsonpath.PathNotFoundException
 import de.ukw.ccc.bwhc.dto.MtbFile
 
-class TransformationService(private val objectMapper: ObjectMapper) {
+class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
-    fun transform(mtbFile: MtbFile, vararg transformations: Transformation): MtbFile {
+    fun transform(mtbFile: MtbFile): MtbFile {
         var json = objectMapper.writeValueAsString(mtbFile)
 
         transformations.forEach { transformation ->

src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt

@@ -37,6 +37,7 @@ import org.mockito.Mockito.*
 import org.mockito.junit.jupiter.MockitoExtension
 import org.mockito.kotlin.any
 import org.mockito.kotlin.argumentCaptor
+import org.mockito.kotlin.whenever
 import org.springframework.context.ApplicationEventPublisher
 import java.time.Instant
 import java.util.*
@@ -46,6 +47,7 @@ import java.util.*
 class RequestProcessorTest {
 
     private lateinit var pseudonymizeService: PseudonymizeService
+    private lateinit var transformationService: TransformationService
     private lateinit var sender: MtbFileSender
     private lateinit var requestService: RequestService
     private lateinit var applicationEventPublisher: ApplicationEventPublisher
@@ -55,11 +57,13 @@ class RequestProcessorTest {
     @BeforeEach
     fun setup(
         @Mock pseudonymizeService: PseudonymizeService,
+        @Mock transformationService: TransformationService,
         @Mock sender: RestMtbFileSender,
         @Mock requestService: RequestService,
         @Mock applicationEventPublisher: ApplicationEventPublisher
     ) {
         this.pseudonymizeService = pseudonymizeService
+        this.transformationService = transformationService
         this.sender = sender
         this.requestService = requestService
         this.applicationEventPublisher = applicationEventPublisher
@@ -68,6 +72,7 @@ class RequestProcessorTest {
 
         requestProcessor = RequestProcessor(
             pseudonymizeService,
+            transformationService,
             sender,
             requestService,
             objectMapper,
@@ -98,6 +103,10 @@ class RequestProcessorTest {
             it.arguments[0] as String
         }.`when`(pseudonymizeService).patientPseudonym(any())
 
+        doAnswer {
+            it.arguments[0]
+        }.whenever(transformationService).transform(any())
+
         val mtbFile = MtbFile.builder()
             .withPatient(
                 Patient.builder()
@@ -153,6 +162,10 @@ class RequestProcessorTest {
             it.arguments[0] as String
         }.`when`(pseudonymizeService).patientPseudonym(any())
 
+        doAnswer {
+            it.arguments[0]
+        }.whenever(transformationService).transform(any())
+
         val mtbFile = MtbFile.builder()
             .withPatient(
                 Patient.builder()
@@ -212,6 +225,10 @@ class RequestProcessorTest {
             it.arguments[0] as String
         }.`when`(pseudonymizeService).patientPseudonym(any())
 
+        doAnswer {
+            it.arguments[0]
+        }.whenever(transformationService).transform(any())
+
         val mtbFile = MtbFile.builder()
             .withPatient(
                 Patient.builder()
@@ -271,6 +288,10 @@ class RequestProcessorTest {
             it.arguments[0] as String
         }.`when`(pseudonymizeService).patientPseudonym(any())
 
+        doAnswer {
+            it.arguments[0]
+        }.whenever(transformationService).transform(any())
+
         val mtbFile = MtbFile.builder()
             .withPatient(
                 Patient.builder()

src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt

@@ -34,15 +34,16 @@ class TransformationServiceTest {
 
     @BeforeEach
     fun setup() {
-        this.service = TransformationService(ObjectMapper())
+        this.service = TransformationService(
+            ObjectMapper(), listOf(
+                Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED,
+                Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
+            )
+        )
     }
 
     @Test
     fun shouldTransformMtbFile() {
-        val transformations = arrayOf(
-            Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
-        )
-
         val mtbFile = MtbFile.builder().withDiagnoses(
             listOf(
                 Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
@@ -51,7 +52,7 @@ class TransformationServiceTest {
             )
         ).build()
 
-        val actual = this.service.transform(mtbFile, *transformations)
+        val actual = this.service.transform(mtbFile)
 
         assertThat(actual).isNotNull
         assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014")
@@ -59,10 +60,6 @@ class TransformationServiceTest {
 
     @Test
     fun shouldOnlyTransformGivenValues() {
-        val transformations = arrayOf(
-            Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
-        )
-
         val mtbFile = MtbFile.builder().withDiagnoses(
             listOf(
                 Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
@@ -74,7 +71,7 @@ class TransformationServiceTest {
             )
         ).build()
 
-        val actual = this.service.transform(mtbFile, *transformations)
+        val actual = this.service.transform(mtbFile)
 
         assertThat(actual).isNotNull
         assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9")
@@ -85,15 +82,11 @@ class TransformationServiceTest {
 
     @Test
     fun shouldTransformMtbFileWithConsentEnum() {
-        val transformations = arrayOf(
-            Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED,
-        )
-
         val mtbFile = MtbFile.builder().withConsent(
             Consent("123", "456", Consent.Status.ACTIVE)
         ).build()
 
-        val actual = this.service.transform(mtbFile, *transformations)
+        val actual = this.service.transform(mtbFile)
 
         assertThat(actual.consent).isNotNull
         assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED)