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Code Issues Releases Activity

Code cleanup

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This commit is contained in:
Paul-Christian Volkmer 2023-08-12 22:19:29 +02:00
parent bc48a7217e
commit 72295202ec
10 changed files with 26 additions and 32 deletions
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7
src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt
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@ -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
}
}

4
src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java
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@ -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;

2
src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
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@ -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 {

2
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
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@ -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 }

3
src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
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@ -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

4
src/main/kotlin/dev/dnpm/etl/processor/services/ResponseProcessor.kt
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@ -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 objectMapper: ObjectMapper
private val statisticsUpdateProducer: Sinks.Many<Any>
) {
private val logger = LoggerFactory.getLogger(ResponseProcessor::class.java)

6
src/main/kotlin/dev/dnpm/etl/processor/web/StatisticsRestController.kt
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@ -83,9 +83,9 @@ class StatisticsRestController(
.groupBy { formatter.format(it.processedAt) }
.map {
val requestList = it.value
.groupBy { it.status }
.map {
Pair(it.key, it.value.size)
.groupBy { request -> request.status }
.map { request ->
Pair(request.key, request.value.size)
}
.toMap()
Pair(

16
src/test/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSenderTest.kt
View File

@ -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)
)
)
}

6
src/test/kotlin/dev/dnpm/etl/processor/services/ResponseProcessorTest.kt
View File

@ -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

8
src/test/kotlin/dev/dnpm/etl/processor/services/kafka/KafkaResponseProcessorTest.kt
View File

@ -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>())
}