build: bump version

This mitigates CVE-2023-6378, CVE-2023-2976 and CVE-2020-8908

README.md

@@ -49,6 +49,20 @@ Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfiguri
 * `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort
 * `APP_PSEUDONYMIZE_GPAS_SSLCALOCATION`: Root Zertifikat für gPas, falls es dediziert hinzugefügt werden muss.
 
+## Transformation von Werten
+
+In Onkostar kann es vorkommen, dass ein Wert eines Merkmalskatalogs an einem Standort angepasst wurde und dadurch nicht dem Wert entspricht,
+der vom bwHC-Backend akzeptiert wird.
+
+Diese Anwendung bietet daher die Möglichkeit, eine Transformation vorzunehmen. Hierzu muss der "Pfad" innerhalb des JSON-MTB-Files angegeben werden und
+welcher Wert wie ersetzt werden soll.
+
+Hier ein Beispiel für die erste (Index 0 - weitere dann mit 1,2,...) Transformationsregel:
+
+* `APP_TRANSFORMATIONS_0_PATH`: Pfad zum Wert in der JSON-MTB-Datei. Beispiel: `diagnoses[*].icd10.version` für **alle** Diagnosen
+* `APP_TRANSFORMATIONS_0_FROM`: Angabe des Werts, der ersetzt werden soll. Andere Werte bleiben dabei unverändert.
+* `APP_TRANSFORMATIONS_0_TO`: Angabe des neuen Werts.
+
 ## Mögliche Endpunkte
 
 Für REST-Requests als auch zur Nutzung von Kafka-Topics können Endpunkte konfiguriert werden.

build.gradle.kts

@@ -4,26 +4,22 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
 
 plugins {
     war
-    id("org.springframework.boot") version "3.1.3"
+    id("org.springframework.boot") version "3.2.1"
-    id("io.spring.dependency-management") version "1.1.3"
+    id("io.spring.dependency-management") version "1.1.4"
-    kotlin("jvm") version "1.9.10"
+    kotlin("jvm") version "1.9.21"
-    kotlin("plugin.spring") version "1.9.10"
+    kotlin("plugin.spring") version "1.9.21"
 }
 
 group = "de.ukw.ccc"
-version = "0.1.2"
+version = "0.3.1"
 
 var versions = mapOf(
     "bwhc-dto-java" to "0.2.0",
-    "hapi-fhir" to "6.6.2",
+    "hapi-fhir" to "6.10.2",
     "httpclient5" to "5.2.1",
     "mockito-kotlin" to "5.1.0"
 )
 
-// Override Apache Kafka to be used
-// Fixes: CVE-2023-34455, CVE-2023-34454, CVE-2023-34453
-extra["kafka.version"] = "3.5.1"
-
 java {
     sourceCompatibility = JavaVersion.VERSION_17
 }
@@ -60,8 +56,6 @@ dependencies {
     implementation("org.springframework.boot:spring-boot-starter-data-jdbc")
     implementation("com.fasterxml.jackson.module:jackson-module-kotlin")
     implementation("org.springframework.kafka:spring-kafka")
-    // fix CVE-2022-1471
-    implementation("org.yaml:snakeyaml:2.1")
     implementation("org.flywaydb:flyway-mysql")
     implementation("commons-codec:commons-codec")
     implementation("io.projectreactor.kotlin:reactor-kotlin-extensions")
@@ -69,6 +63,7 @@ dependencies {
     implementation("ca.uhn.hapi.fhir:hapi-fhir-base:${versions["hapi-fhir"]}")
     implementation("ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${versions["hapi-fhir"]}")
     implementation("org.apache.httpcomponents.client5:httpclient5:${versions["httpclient5"]}")
+    implementation("com.jayway.jsonpath:json-path")
     runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
     runtimeOnly("org.postgresql:postgresql")
     developmentOnly("org.springframework.boot:spring-boot-devtools")

dev-compose.yml

@@ -1,6 +1,4 @@
 services:
-  # Note: Make sure, hostname "kafka" points to 127.0.0.1
-  # otherwise connection will not be available
   kafka:
     image: bitnami/kafka
     hostname: kafka

src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt

@@ -19,15 +19,27 @@
 
 package dev.dnpm.etl.processor
 
+import com.fasterxml.jackson.databind.ObjectMapper
+import de.ukw.ccc.bwhc.dto.*
+import dev.dnpm.etl.processor.monitoring.RequestRepository
+import dev.dnpm.etl.processor.monitoring.RequestStatus
 import dev.dnpm.etl.processor.output.MtbFileSender
 import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Nested
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.extension.ExtendWith
+import org.mockito.kotlin.*
 import org.springframework.beans.factory.annotation.Autowired
+import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc
 import org.springframework.boot.test.context.SpringBootTest
 import org.springframework.boot.test.mock.mockito.MockBean
 import org.springframework.context.ApplicationContext
+import org.springframework.http.MediaType
+import org.springframework.test.context.TestPropertySource
 import org.springframework.test.context.junit.jupiter.SpringExtension
+import org.springframework.test.web.servlet.MockMvc
+import org.springframework.test.web.servlet.post
 import org.testcontainers.junit.jupiter.Testcontainers
 
 @Testcontainers
@@ -42,4 +54,85 @@ class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
         assertThat(context).isNotNull
     }
 
+    @Nested
+    @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK)
+    @AutoConfigureMockMvc
+    @TestPropertySource(
+        properties = [
+            "app.transformations[0].path=diagnoses[*].icd10.version",
+            "app.transformations[0].from=2013",
+            "app.transformations[0].to=2014",
+        ]
+    )
+    inner class TransformationTest {
+
+        @MockBean
+        private lateinit var mtbFileSender: MtbFileSender
+
+        @Autowired
+        private lateinit var mockMvc: MockMvc
+
+        @Autowired
+        private lateinit var objectMapper: ObjectMapper
+
+        @BeforeEach
+        fun setup(@Autowired requestRepository: RequestRepository) {
+            requestRepository.deleteAll()
+        }
+
+        @Test
+        fun mtbFileIsTransformed() {
+            doAnswer {
+                MtbFileSender.Response(RequestStatus.SUCCESS)
+            }.whenever(mtbFileSender).send(any<MtbFileSender.MtbFileRequest>())
+
+            val mtbFile = MtbFile.builder()
+                .withPatient(
+                    Patient.builder()
+                        .withId("TEST_12345678")
+                        .withBirthDate("2000-08-08")
+                        .withGender(Patient.Gender.MALE)
+                        .build()
+                )
+                .withConsent(
+                    Consent.builder()
+                        .withId("1")
+                        .withStatus(Consent.Status.ACTIVE)
+                        .withPatient("TEST_12345678")
+                        .build()
+                )
+                .withEpisode(
+                    Episode.builder()
+                        .withId("1")
+                        .withPatient("TEST_12345678")
+                        .withPeriod(PeriodStart("2023-08-08"))
+                        .build()
+                )
+                .withDiagnoses(
+                    listOf(
+                        Diagnosis.builder()
+                            .withId("1234")
+                            .withIcd10(Icd10.builder().withCode("F79.9").withVersion("2013").build())
+                            .build()
+                    )
+                )
+                .build()
+
+            mockMvc.post("/mtbfile") {
+                content = objectMapper.writeValueAsString(mtbFile)
+                contentType = MediaType.APPLICATION_JSON
+            }.andExpect {
+                status {
+                    isAccepted()
+                }
+            }
+
+            val captor = argumentCaptor<MtbFileSender.MtbFileRequest>()
+            verify(mtbFileSender).send(captor.capture())
+            assertThat(captor.firstValue.mtbFile.diagnoses).hasSize(1).allMatch { diagnosis ->
+                diagnosis.icd10.version == "2014"
+            }
+        }
+    }
+
 }

src/integrationTest/kotlin/dev/dnpm/etl/processor/config/AppConfigurationTest.kt

@@ -31,13 +31,13 @@ import org.springframework.beans.factory.NoSuchBeanDefinitionException
 import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
 import org.springframework.boot.test.context.SpringBootTest
 import org.springframework.boot.test.mock.mockito.MockBean
-import org.springframework.boot.test.mock.mockito.MockBeans
 import org.springframework.context.ApplicationContext
 import org.springframework.test.context.ContextConfiguration
 import org.springframework.test.context.TestPropertySource
 
 @SpringBootTest
-@ContextConfiguration(classes = [KafkaAutoConfiguration::class, AppKafkaConfiguration::class, AppRestConfiguration::class])
+@ContextConfiguration(classes = [AppConfiguration::class, KafkaAutoConfiguration::class, AppKafkaConfiguration::class, AppRestConfiguration::class])
+@MockBean(ObjectMapper::class)
 class AppConfigurationTest {
 
     @Nested
@@ -65,10 +65,7 @@ class AppConfigurationTest {
             "app.kafka.group-id=test"
         ]
     )
-    @MockBeans(value = [
+    @MockBean(RequestRepository::class)
-        MockBean(ObjectMapper::class),
-        MockBean(RequestRepository::class)
-    ])
     inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
 
         @Test
@@ -99,4 +96,24 @@ class AppConfigurationTest {
 
     }
 
+    @Nested
+    @TestPropertySource(
+        properties = [
+            "app.transformations[0].path=consent.status",
+            "app.transformations[0].from=rejected",
+            "app.transformations[0].to=accept",
+        ]
+    )
+    inner class AppConfigurationTransformationTest(private val context: ApplicationContext) {
+
+        @Test
+        fun shouldRecognizeTransformations() {
+            val appConfigProperties = context.getBean(AppConfigProperties::class.java)
+
+            assertThat(appConfigProperties).isNotNull
+            assertThat(appConfigProperties.transformations).hasSize(1)
+        }
+
+    }
+
 }

src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java

@@ -127,7 +127,21 @@ public class GpasPseudonymGenerator implements Generator {
             .orElseGet(ParametersParameterComponent::new).getValue();
 
         // pseudonym
-        return identifier.getSystem() + "|" + identifier.getValue();
+        return sanitizeValue(identifier.getValue());
+    }
+
+    /**
+     * Allow only filename friendly values
+     *
+     * @param psnValue GAPS pseudonym value
+     * @return cleaned up value
+     */
+    public static String sanitizeValue(String psnValue) {
+        // pattern to match forbidden characters
+        String forbiddenCharsRegex = "[\\\\/:*?\"<>|;]";
+
+        // Replace all forbidden characters with underscores
+        return psnValue.replaceAll(forbiddenCharsRegex, "_");
     }
 
 

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

@@ -24,7 +24,8 @@ import org.springframework.boot.context.properties.ConfigurationProperties
 @ConfigurationProperties(AppConfigProperties.NAME)
 data class AppConfigProperties(
     var bwhcUri: String?,
-    var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN
+    var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
+    var transformations: List<TransformationProperties> = listOf()
 ) {
     companion object {
         const val NAME = "app"
@@ -78,4 +79,10 @@ data class KafkaTargetProperties(
 enum class PseudonymGenerator {
     BUILDIN,
     GPAS
-}
+}
+
+data class TransformationProperties(
+    val path: String,
+    val from: String,
+    val to: String
+)

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

@@ -25,6 +25,9 @@ import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
 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.slf4j.LoggerFactory
 import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
 import org.springframework.boot.context.properties.EnableConfigurationProperties
 import org.springframework.context.annotation.Bean
@@ -41,6 +44,8 @@ import reactor.core.publisher.Sinks
 )
 class AppConfiguration {
 
+    private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
+
     @ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
     @Bean
     fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator {
@@ -71,5 +76,16 @@ class AppConfiguration {
         return Sinks.many().multicast().directBestEffort()
     }
 
+    @Bean
+    fun transformationService(
+        objectMapper: ObjectMapper,
+        configProperties: AppConfigProperties
+    ): TransformationService {
+        logger.info("Apply ${configProperties.transformations.size} transformation rules")
+        return TransformationService(objectMapper, configProperties.transformations.map {
+            Transformation.of(it.path) from it.from to it.to
+        })
+    }
+
 }
 

src/main/kotlin/dev/dnpm/etl/processor/monitoring/ReportService.kt

@@ -34,7 +34,10 @@ class ReportService(
             return listOf()
         }
         return try {
-            objectMapper.readValue(dataQualityReport, DataQualityReport::class.java).issues
+            objectMapper
+                .readValue(dataQualityReport, DataQualityReport::class.java)
+                .issues
+                .sortedBy { it.severity }
         } catch (e: Exception) {
             val otherIssue =
                 Issue(Severity.ERROR, "Not parsable data quality report '$dataQualityReport'")
@@ -56,5 +59,6 @@ class ReportService(
     enum class Severity(@JsonValue val value: String) {
         ERROR("error"),
         WARNING("warning"),
+        INFO("info")
     }
 }

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt

@@ -35,7 +35,10 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     this.familyMemberDiagnoses.forEach { it.patient = patientPseudonym }
     this.geneticCounsellingRequests.forEach { it.patient = patientPseudonym }
     this.histologyReevaluationRequests.forEach { it.patient = patientPseudonym }
-    this.histologyReports.forEach { it.patient = patientPseudonym }
+    this.histologyReports.forEach {
+        it.patient = patientPseudonym
+        it.tumorMorphology.patient = patientPseudonym
+    }
     this.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
     this.molecularPathologyFindings.forEach { it.patient = patientPseudonym }
     this.molecularTherapies.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
@@ -45,6 +48,6 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     this.recommendations.forEach { it.patient = patientPseudonym }
     this.recommendations.forEach { it.patient = patientPseudonym }
     this.responses.forEach { it.patient = patientPseudonym }
-    this.specimens.forEach { it.patient = patientPseudonym }
+    this.studyInclusionRequests.forEach { it.patient = patientPseudonym }
     this.specimens.forEach { it.patient = patientPseudonym }
 }

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

@@ -0,0 +1,85 @@
+/*
+ * 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 com.jayway.jsonpath.JsonPath
+import com.jayway.jsonpath.PathNotFoundException
+import de.ukw.ccc.bwhc.dto.MtbFile
+
+class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
+    fun transform(mtbFile: MtbFile): MtbFile {
+        var json = objectMapper.writeValueAsString(mtbFile)
+
+        transformations.forEach { transformation ->
+            val jsonPath = JsonPath.parse(json)
+
+            try {
+                val before = transformation.path.substringBeforeLast(".")
+                val last = transformation.path.substringAfterLast(".")
+
+                val existingValue = if (transformation.existingValue is Number) transformation.existingValue else transformation.existingValue.toString()
+                val newValue = if (transformation.newValue is Number) transformation.newValue else transformation.newValue.toString()
+
+                jsonPath.set("$.$before.[?]$last", newValue, {
+                    it.item(HashMap::class.java)[last] == existingValue
+                })
+            } catch (e: PathNotFoundException) {
+                // Ignore
+            }
+
+            json = jsonPath.jsonString()
+        }
+
+        return objectMapper.readValue(json, MtbFile::class.java)
+    }
+
+    fun getTransformations(): List<Transformation> {
+        return this.transformations
+    }
+
+}
+
+class Transformation private constructor(val path: String) {
+
+    lateinit var existingValue: Any
+        private set
+    lateinit var newValue: Any
+        private set
+
+    infix fun from(value: Any): Transformation {
+        this.existingValue = value
+        return this
+    }
+
+    infix fun to(value: Any): Transformation {
+        this.newValue = value
+        return this
+    }
+
+    companion object {
+
+        fun of(path: String): Transformation {
+            return Transformation(path)
+        }
+
+    }
+
+}

src/main/kotlin/dev/dnpm/etl/processor/web/TransformationController.kt

@@ -0,0 +1,41 @@
+/*
+ * 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.web
+
+import dev.dnpm.etl.processor.services.TransformationService
+import org.springframework.stereotype.Controller
+import org.springframework.ui.Model
+import org.springframework.web.bind.annotation.GetMapping
+import org.springframework.web.bind.annotation.RequestMapping
+
+@Controller
+@RequestMapping(path = ["transformations"])
+class TransformationController(
+    private val transformationService: TransformationService
+) {
+
+    @GetMapping
+    fun index(model: Model): String {
+        model.addAttribute("transformations", transformationService.getTransformations())
+
+        return "transformations"
+    }
+
+}

src/main/resources/static/style.css

@@ -1,3 +1,24 @@
+:root {
+    --table-border: rgba(96, 96, 96, 1);
+
+    --bg-blue: rgb(0, 74, 157);
+    --bg-blue-op: rgba(0, 74, 157, .35);
+
+    --bg-green: rgb(0, 128, 0);
+    --bg-green-op: rgba(0, 128, 0, .35);
+
+
+    --bg-yellow: rgb(255, 140, 0);
+    --bg-yellow-op: rgba(255, 140, 0, .35);
+
+
+    --bg-red: rgb(255, 0, 0);
+    --bg-red-op: rgba(255, 0, 0, .35);
+
+    --bg-gray: rgb(112, 128, 144);
+    --bg-gray-op: rgba(112, 128, 144, .35);
+}
+
 body {
     margin: 0;
     font-family: sans-serif;
@@ -57,7 +78,7 @@ nav > ul > li:first-of-type {
     display: inline;
 }
 
-.breadcrumps ul li+li:before {
+.breadcrumps ul li + li:before {
     padding: .4rem;
     color: gray;
     content: "/\00a0";
@@ -68,6 +89,10 @@ nav > ul > li:first-of-type {
     text-decoration: none;
 }
 
+.centered {
+    text-align: center;
+}
+
 main {
     margin: 0 auto;
     max-width: 1140px;
@@ -115,8 +140,8 @@ form.samplecode-input input:focus-visible {
 }
 
 table {
-    border-top: 1px solid lightgray;
+    border-top: 1px solid var(--table-border);
-    border-left: 1px solid lightgray;
+    border-left: 1px solid var(--table-border);
     border-spacing: 0;
     border-radius: 3px;
 
@@ -145,10 +170,10 @@ th {
 }
 
 td, th {
-    padding: .2rem;
+    padding: 0.4rem .2rem;
 
-    border-right: 1px solid lightgray;
+    border-right: 1px solid var(--table-border);
-    border-bottom: 1px solid lightgray;
+    border-bottom: 1px solid var(--table-border);
 
     text-align: left;
     white-space: nowrap;
@@ -159,26 +184,66 @@ td {
     font-family: monospace;
 }
 
-td.bg-green, th.bg-green {
+td.bg-blue, th.bg-blue {
-    background: green;
+    background: var(--bg-blue);
     color: white;
 }
 
+tr:has(td.bg-blue) {
+    background: var(--bg-blue-op);
+}
+
+td.bg-green, th.bg-green {
+    background: var(--bg-green);
+    color: white;
+}
+
+tr:has(td.bg-green) {
+    background: var(--bg-green-op);
+}
+
 td.bg-yellow, th.bg-yellow {
-    background: darkorange;
+    background: var(--bg-yellow);
     color: white;
 }
 
+tr:has(td.bg-yellow) {
+    background: var(--bg-yellow-op);
+}
+
 td.bg-red, th.bg-red {
-    background: red;
+    background: var(--bg-red);
     color: white;
 }
 
+tr:has(td.bg-red) {
+    background: var(--bg-red-op);
+}
+
 td.bg-gray, th.bg-gray {
-    background: slategray;
+    background: var(--bg-gray);
     color: white;
 }
 
+.bg-path {
+    background: var(--bg-gray-op);
+}
+
+.bg-from {
+    background: var(--bg-red-op);
+}
+
+.bg-to {
+    background: var(--bg-green-op);
+}
+
+.bg-path, .bg-from, .bg-to {
+    padding: 0.25rem 0.5rem;
+    border-radius: 3px;
+
+    font-family: monospace;
+}
+
 td.bg-shaded, th.bg-shaded {
     background: repeating-linear-gradient(140deg, white, #e5e5f5 4px, white 8px);
 }
@@ -279,7 +344,7 @@ input.inline:focus-visible {
     padding: 1rem;
     margin: .2rem;
 
-    border: 1px solid lightgray;
+    border: 1px solid var(--table-border);
     border-radius: 3px;
 
     width: calc(100% - 2.4rem - 4px);

src/main/resources/templates/fragments.html

@@ -10,6 +10,7 @@
             <ul>
                 <li><a th:href="@{/}">Übersicht</a></li>
                 <li><a th:href="@{/statistics}">Statistiken</a></li>
+                <li><a th:href="@{/transformations}">Transformationen</a></li>
             </ul>
         </nav>
     </div>

src/main/resources/templates/report.html

@@ -45,6 +45,7 @@
             </thead>
             <tbody>
             <tr th:each="issue : ${issues}">
+                <td th:if="${issue.severity.value == 'info'}" class="bg-blue"><small>[[ ${issue.severity} ]]</small></td>
                 <td th:if="${issue.severity.value == 'warning'}" class="bg-yellow"><small>[[ ${issue.severity} ]]</small></td>
                 <td th:if="${issue.severity.value == 'error'}" class="bg-red"><small>[[ ${issue.severity} ]]</small></td>
                 <td>[[ ${issue.message} ]]</td>

src/main/resources/templates/transformations.html

@@ -0,0 +1,47 @@
+<!DOCTYPE html>
+<html lang="de" xmlns:th="http://www.thymeleaf.org">
+<head>
+    <meta charset="UTF-8">
+    <title>ETL-Prozessor</title>
+    <link rel="stylesheet" th:href="@{/style.css}" />
+</head>
+<body>
+    <div th:replace="~{fragments.html :: nav}"></div>
+    <main>
+        <h1>Transformationen</h1>
+
+        <h2>Syntax</h2>
+        Hier einige Beispiele zum Syntax des JSON-Path
+        <ul>
+            <li style="padding: 0.6rem 0;"><span class="bg-path">diagnoses[*].icdO3T.version</span>: Ersetze die ICD-O3T-Version in allen Diagnosen, z.B. zur Version der deutschen Übersetzung</li>
+            <li style="padding: 0.6rem 0;"><span class="bg-path">patient.gender</span>: Ersetze das Geschlecht des Patienten, z.B. in das von bwHC verlangte Format</li>
+        </ul>
+
+        <h2>Konfigurierte Transformationen</h2>
+        <p>
+            Hier sehen Sie eine Übersicht der konfigurierten Transformationen.
+        </p>
+
+        <table>
+            <thead>
+            <tr>
+                <th>JSON-Path</th>
+                <th>Transformation von &rArr; nach</th>
+            </tr>
+            </thead>
+            <tbody>
+            <tr th:each="transformation : ${transformations}">
+                <td>
+                    <span class="bg-path" title="Ersetze Wert(e) an dieser Stelle im MTB-File">[[ ${transformation.path} ]]</span>
+                </td>
+                <td>
+                    <span class="bg-from" title="Ersetze immer dann, wenn dieser Wert enthalten ist">[[ ${transformation.existingValue} ]]</span>
+                    <strong>&rArr;</strong>
+                    <span class="bg-to" title="Ersetze durch diesen Wert">[[ ${transformation.newValue} ]]</span>
+                </td>
+            </tr>
+            </tbody>
+        </table>
+    </main>
+</body>
+</html>

src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt

@@ -0,0 +1,64 @@
+/*
+ * 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.pseudonym
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import de.ukw.ccc.bwhc.dto.MtbFile
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.extension.ExtendWith
+import org.mockito.ArgumentMatchers
+import org.mockito.Mock
+import org.mockito.junit.jupiter.MockitoExtension
+import org.mockito.kotlin.doAnswer
+import org.mockito.kotlin.whenever
+import org.springframework.core.io.ClassPathResource
+
+const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
+const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
+
+@ExtendWith(MockitoExtension::class)
+class ExtensionsTest {
+
+    private fun fakeMtbFile(): MtbFile {
+        val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
+        return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
+    }
+
+    private fun MtbFile.serialized(): String {
+        return ObjectMapper().writeValueAsString(this)
+    }
+
+    @Test
+    fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
+        doAnswer {
+            it.arguments[0]
+            "PSEUDO-ID"
+        }.whenever(pseudonymizeService).patientPseudonym(ArgumentMatchers.anyString())
+
+        val mtbFile = fakeMtbFile()
+
+        mtbFile.pseudonymizeWith(pseudonymizeService)
+
+        assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
+        assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
+    }
+
+}

src/test/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeServiceTest.kt

@@ -70,6 +70,13 @@ class PseudonymizeServiceTest {
         assertThat(mtbFile.patient.id).isEqualTo("123")
     }
 
+    @Test
+    fun sanitizeFileName(@Mock generator: GpasPseudonymGenerator) {
+        val result= GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
+
+        assertThat(result).isEqualTo("l___a_bs_1_2_3_")
+    }
+
     @Test
     fun shouldUsePseudonymPrefixForBuiltin(@Mock generator: AnonymizingGenerator) {
         doAnswer {

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

@@ -41,6 +41,7 @@ class ReportServiceTest {
             {
                 "patient": "4711",
                 "issues": [
+                    { "severity": "info", "message": "Info Message" },
                     { "severity": "warning", "message": "Warning Message" },
                     { "severity": "error", "message": "Error Message" }
                 ]
@@ -49,11 +50,13 @@ class ReportServiceTest {
 
         val actual = this.reportService.deserialize(json)
 
-        assertThat(actual).hasSize(2)
+        assertThat(actual).hasSize(3)
-        assertThat(actual[0].severity).isEqualTo(ReportService.Severity.WARNING)
+        assertThat(actual[0].severity).isEqualTo(ReportService.Severity.ERROR)
-        assertThat(actual[0].message).isEqualTo("Warning Message")
+        assertThat(actual[0].message).isEqualTo("Error Message")
-        assertThat(actual[1].severity).isEqualTo(ReportService.Severity.ERROR)
+        assertThat(actual[1].severity).isEqualTo(ReportService.Severity.WARNING)
-        assertThat(actual[1].message).isEqualTo("Error Message")
+        assertThat(actual[1].message).isEqualTo("Warning Message")
+        assertThat(actual[2].severity).isEqualTo(ReportService.Severity.INFO)
+        assertThat(actual[2].message).isEqualTo("Info Message")
     }
 
     @Test

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

@@ -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)
+    }
+
+}