Merge pull request #13 from CCC-MF/issue_12

Transformation of MTBFile data based on rules

2 files changed, 116 insertions, 0 deletions

diff --git a/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt
index 7856833..9aaa091 100644
--- a/src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt
+++ b/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()
diff --git a/src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt b/src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt
new file mode 100644
index 0000000..487b502
--- /dev/null
+++ b/src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt
@@ -0,0 +1,95 @@
+/*
+ * This file is part of ETL-Processor
+ *
+ * Copyright (c) 2023  Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package dev.dnpm.etl.processor.services
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import de.ukw.ccc.bwhc.dto.Consent
+import de.ukw.ccc.bwhc.dto.Diagnosis
+import de.ukw.ccc.bwhc.dto.Icd10
+import de.ukw.ccc.bwhc.dto.MtbFile
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Test
+
+class TransformationServiceTest {
+
+    private lateinit var service: TransformationService
+
+    @BeforeEach
+    fun setup() {
+        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 mtbFile = MtbFile.builder().withDiagnoses(
+            listOf(
+                Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
+                    it.version = "2013"
+                }).build()
+            )
+        ).build()
+
+        val actual = this.service.transform(mtbFile)
+
+        assertThat(actual).isNotNull
+        assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014")
+    }
+
+    @Test
+    fun shouldOnlyTransformGivenValues() {
+        val mtbFile = MtbFile.builder().withDiagnoses(
+            listOf(
+                Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
+                    it.version = "2013"
+                }).build(),
+                Diagnosis.builder().withId("5678").withIcd10(Icd10("F79.8").also {
+                    it.version = "2019"
+                }).build()
+            )
+        ).build()
+
+        val actual = this.service.transform(mtbFile)
+
+        assertThat(actual).isNotNull
+        assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9")
+        assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014")
+        assertThat(actual.diagnoses[1].icd10.code).isEqualTo("F79.8")
+        assertThat(actual.diagnoses[1].icd10.version).isEqualTo("2019")
+    }
+
+    @Test
+    fun shouldTransformMtbFileWithConsentEnum() {
+        val mtbFile = MtbFile.builder().withConsent(
+            Consent("123", "456", Consent.Status.ACTIVE)
+        ).build()
+
+        val actual = this.service.transform(mtbFile)
+
+        assertThat(actual.consent).isNotNull
+        assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED)
+    }
+
+}
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