Code cleanup

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

@@ -20,10 +20,13 @@
 package dev.dnpm.etl.processor
 
 import dev.dnpm.etl.processor.output.MtbFileSender
+import org.assertj.core.api.Assertions.assertThat
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.extension.ExtendWith
+import org.springframework.beans.factory.annotation.Autowired
 import org.springframework.boot.test.context.SpringBootTest
 import org.springframework.boot.test.mock.mockito.MockBean
+import org.springframework.context.ApplicationContext
 import org.springframework.test.context.junit.jupiter.SpringExtension
 import org.testcontainers.junit.jupiter.Testcontainers
 
@@ -34,7 +37,9 @@ import org.testcontainers.junit.jupiter.Testcontainers
 class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
 
     @Test
-    fun contextLoadsIfMtbFileSenderConfigured() {
+    fun contextLoadsIfMtbFileSenderConfigured(@Autowired context: ApplicationContext) {
+        // Simply check bean configuration
+        assertThat(context).isNotNull
     }
 
 }

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

@@ -69,13 +69,11 @@ import java.util.HashMap;
 
 public class GpasPseudonymGenerator implements Generator {
 
+    private final static FhirContext r4Context = FhirContext.forR4();
     private final String gPasUrl;
     private final String psnTargetDomain;
-    private static FhirContext r4Context = FhirContext.forR4();
     private final HttpHeaders httpHeader;
-
     private final RetryTemplate retryTemplate = defaultTemplate();
-
     private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
 
     private SSLContext customSslContext;

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

@@ -23,7 +23,7 @@ import org.springframework.boot.context.properties.ConfigurationProperties
 
 @ConfigurationProperties(AppConfigProperties.NAME)
 data class AppConfigProperties(
-    var bwhc_uri: String?,
+    var bwhcUri: String?,
     var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN
 ) {
     companion object {

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

@@ -38,7 +38,7 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     this.histologyReports.forEach { it.patient = patientPseudonym }
     this.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
     this.molecularPathologyFindings.forEach { it.patient = patientPseudonym }
-    this.molecularTherapies.forEach { it.history.forEach { it.patient = patientPseudonym } }
+    this.molecularTherapies.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
     this.ngsReports.forEach { it.patient = patientPseudonym }
     this.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
     this.rebiopsyRequests.forEach { it.patient = patientPseudonym }

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

@@ -30,7 +30,6 @@ import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
 import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
-import org.slf4j.LoggerFactory
 import org.springframework.context.ApplicationEventPublisher
 import org.springframework.stereotype.Service
 import java.time.Instant
@@ -45,8 +44,6 @@ class RequestProcessor(
     private val applicationEventPublisher: ApplicationEventPublisher
 ) {
 
-    private val logger = LoggerFactory.getLogger(RequestProcessor::class.java)
-
     fun processMtbFile(mtbFile: MtbFile) {
         val requestId = UUID.randomUUID().toString()
         val pid = mtbFile.patient.id

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

@@ -19,7 +19,6 @@
 
 package dev.dnpm.etl.processor.services
 
-import com.fasterxml.jackson.databind.ObjectMapper
 import dev.dnpm.etl.processor.monitoring.Report
 import dev.dnpm.etl.processor.monitoring.RequestRepository
 import dev.dnpm.etl.processor.monitoring.RequestStatus
@@ -33,8 +32,7 @@ import java.util.*
 @Service
 class ResponseProcessor(
     private val requestRepository: RequestRepository,
-    private val statisticsUpdateProducer: Sinks.Many<Any>,
+    private val statisticsUpdateProducer: Sinks.Many<Any>
-    private val objectMapper: ObjectMapper
 ) {
 
     private val logger = LoggerFactory.getLogger(ResponseProcessor::class.java)

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

@@ -83,9 +83,9 @@ class StatisticsRestController(
             .groupBy { formatter.format(it.processedAt) }
             .map {
                 val requestList = it.value
-                    .groupBy { it.status }
+                    .groupBy { request -> request.status }
-                    .map {
+                    .map { request ->
-                        Pair(it.key, it.value.size)
+                        Pair(request.key, request.value.size)
                     }
                     .toMap()
                 Pair(

src/test/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSenderTest.kt

@@ -105,7 +105,7 @@ class RestMtbFileSenderTest {
                 }
             """.trimIndent()
 
-        val mtbFile = MtbFile.builder()
+        val mtbFile: MtbFile = MtbFile.builder()
             .withPatient(
                 Patient.builder()
                     .withId("PID")
@@ -129,7 +129,7 @@ class RestMtbFileSenderTest {
             )
             .build()
 
-        private val errorResponseBody = "Sonstiger Fehler bei der Übertragung"
+        private const val ERROR_RESPONSE_BODY = "Sonstiger Fehler bei der Übertragung"
 
         /**
          * Synthetic http responses with related request status
@@ -147,23 +147,23 @@ class RestMtbFileSenderTest {
                 RequestWithResponse(
                     HttpStatus.BAD_REQUEST,
                     "??",
-                    MtbFileSender.Response(RequestStatus.ERROR, errorResponseBody)
+                    MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
                 ),
                 RequestWithResponse(
                     HttpStatus.UNPROCESSABLE_ENTITY,
                     errorBody,
-                    MtbFileSender.Response(RequestStatus.ERROR, errorResponseBody)
+                    MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
                 ),
                 // Some more errors not mentioned in documentation
                 RequestWithResponse(
                     HttpStatus.NOT_FOUND,
                     "what????",
-                    MtbFileSender.Response(RequestStatus.ERROR, errorResponseBody)
+                    MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
                 ),
                 RequestWithResponse(
                     HttpStatus.INTERNAL_SERVER_ERROR,
                     "what????",
-                    MtbFileSender.Response(RequestStatus.ERROR, errorResponseBody)
+                    MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
                 )
             )
         }
@@ -180,12 +180,12 @@ class RestMtbFileSenderTest {
                 RequestWithResponse(
                     HttpStatus.NOT_FOUND,
                     "what????",
-                    MtbFileSender.Response(RequestStatus.ERROR, errorResponseBody)
+                    MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
                 ),
                 RequestWithResponse(
                     HttpStatus.INTERNAL_SERVER_ERROR,
                     "what????",
-                    MtbFileSender.Response(RequestStatus.ERROR, errorResponseBody)
+                    MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
                 )
             )
         }

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

@@ -19,8 +19,6 @@
 
 package dev.dnpm.etl.processor.services
 
-import com.fasterxml.jackson.databind.ObjectMapper
-import com.fasterxml.jackson.module.kotlin.KotlinModule
 import dev.dnpm.etl.processor.monitoring.Request
 import dev.dnpm.etl.processor.monitoring.RequestRepository
 import dev.dnpm.etl.processor.monitoring.RequestStatus
@@ -62,12 +60,10 @@ class ResponseProcessorTest {
         @Mock requestRepository: RequestRepository,
         @Mock statisticsUpdateProducer: Sinks.Many<Any>
     ) {
-        val objectMapper = ObjectMapper().registerModule(KotlinModule.Builder().build())
-
         this.requestRepository = requestRepository
         this.statisticsUpdateProducer = statisticsUpdateProducer
 
-        this.responseProcessor = ResponseProcessor(requestRepository, statisticsUpdateProducer, objectMapper)
+        this.responseProcessor = ResponseProcessor(requestRepository, statisticsUpdateProducer)
     }
 
     @Test

src/test/kotlin/dev/dnpm/etl/processor/services/kafka/KafkaResponseProcessorTest.kt

@@ -45,7 +45,7 @@ class KafkaResponseProcessorTest {
 
     private lateinit var kafkaResponseProcessor: KafkaResponseProcessor
 
-    private fun createkafkaRecord(
+    private fun createKafkaRecord(
         requestId: String? = null,
         statusCode: Int = 200,
         statusBody: Map<String, Any>? = mapOf()
@@ -79,14 +79,14 @@ class KafkaResponseProcessorTest {
 
     @Test
     fun shouldNotProcessRecordsWithoutValidKey() {
-        this.kafkaResponseProcessor.onMessage(createkafkaRecord(null, 200))
+        this.kafkaResponseProcessor.onMessage(createKafkaRecord(null, 200))
 
         verify(eventPublisher, never()).publishEvent(any())
     }
 
     @Test
     fun shouldNotProcessRecordsWithoutValidBody() {
-        this.kafkaResponseProcessor.onMessage(createkafkaRecord(requestId = "TestID1234", statusBody = null))
+        this.kafkaResponseProcessor.onMessage(createKafkaRecord(requestId = "TestID1234", statusBody = null))
 
         verify(eventPublisher, never()).publishEvent(any())
     }
@@ -94,7 +94,7 @@ class KafkaResponseProcessorTest {
     @ParameterizedTest
     @MethodSource("statusCodeSource")
     fun shouldProcessValidRecordsWithStatusCode(statusCode: Int) {
-        this.kafkaResponseProcessor.onMessage(createkafkaRecord("TestID1234", statusCode))
+        this.kafkaResponseProcessor.onMessage(createKafkaRecord("TestID1234", statusCode))
         verify(eventPublisher, times(1)).publishEvent(any<ResponseEvent>())
     }