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mirror of https://github.com/pcvolkmer/mv64e-etl-processor synced 2025-09-13 17:02:52 +00:00

10 Commits

Author SHA1 Message Date
328bf019af chore: bump version 2025-09-03 22:17:48 +02:00
6dfec5c341 fix: add status badge for 'NO_CONSENT' (#149) 2025-09-03 21:18:28 +02:00
4602032bcf chore: bump version 2025-09-01 13:33:29 +02:00
9cc9f130df chore: add custom banner file (#146) 2025-09-01 13:31:08 +02:00
b92fbae2c5 chore: update dependencies (#145) 2025-09-01 13:25:51 +02:00
5704282a1c docs: some additions to README.md (#143) 2025-08-28 19:37:57 +02:00
ba21d029d1 fix: add missing requestId to KafkaMtbFileSender (#142) 2025-08-27 15:07:43 +02:00
b7aa187293 fix: do not set unexpected config values (#141) 2025-08-26 09:16:07 +02:00
8402462c3b chore: use apache image including SSL config (#140)
The main purpose is to abandon bitnami kafka image.

The examples now include localhost certs and keys for development
purposes only.
More advanced support for SSL connections to kafka will be
available in later versions.
2025-08-25 12:43:32 +02:00
d3e6aa5821 fix: mime type representation in kafka header (#139) 2025-08-25 12:13:44 +02:00
12 changed files with 265 additions and 38 deletions

View File

@@ -268,7 +268,7 @@ zur Nutzung des MTB-File-Endpunkts eine HTTP-Basic-Authentifizierung voraussetze
![Tokenverwaltung](docs/tokens.png) ![Tokenverwaltung](docs/tokens.png)
In diesem Fall kann der Endpunkt für das Onkostar-Plugin * In diesem Fall kann der Endpunkt für das Onkostar-Plugin *
*[onkostar-plugin-dnpmexport](https://github.com/CCC-MF/onkostar-plugin-dnpmexport)** wie folgt *[mv64e-onkostar-plugin-export](https://github.com/pcvolkmer/mv64e-onkostar-plugin-export)** wie folgt
konfiguriert werden: konfiguriert werden:
``` ```
@@ -427,9 +427,9 @@ Die PEM-Datei mit dem/den Root CA Zertifikat(en) muss dabei im vorbereiteten Ver
#### Integration zur Laufzeit #### Integration zur Laufzeit
Hier muss die Umgebungsvariable `SERVICE_BINDING_ROOT` z.B. auf den Wert `/bindings` gesetzt sein. Hier muss die Umgebungsvariable `SERVICE_BINDING_ROOT` z.B. auf den Wert `/bindings` gesetzt sein.
Zudem muss ein Verzeichnis `bindings/ca-certificates` - analog zum Verzeichnis [ Zudem muss ein Verzeichnis `bindings/ca-certificates` - analog zum Verzeichnis
`bindings/ca-certificates`](bindings/ca-certificates) mit einer PEM-Datei als Docker-Volume [`bindings/ca-certificates`](bindings/ca-certificates) mit einer PEM-Datei und der
eingebunden werden. Datei [`bindings/ca-certificates/type`](bindings/ca-certificates/type) als Docker-Volume eingebunden werden.
Beispiel für Docker-Compose: Beispiel für Docker-Compose:

View File

@@ -5,7 +5,7 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
plugins { plugins {
war war
id("org.springframework.boot") version "3.5.3" id("org.springframework.boot") version "3.5.5"
id("io.spring.dependency-management") version "1.1.7" id("io.spring.dependency-management") version "1.1.7"
kotlin("jvm") version "1.9.25" kotlin("jvm") version "1.9.25"
kotlin("plugin.spring") version "1.9.25" kotlin("plugin.spring") version "1.9.25"
@@ -13,7 +13,7 @@ plugins {
} }
group = "dev.dnpm" group = "dev.dnpm"
version = "0.11.0-SNAPSHOT" version = "0.11.1"
var versions = mapOf( var versions = mapOf(
"mtb-dto" to "0.1.0-SNAPSHOT", "mtb-dto" to "0.1.0-SNAPSHOT",
@@ -111,6 +111,8 @@ dependencies {
integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}") integrationTestImplementation("com.tngtech.archunit:archunit:${versions["archunit"]}")
integrationTestImplementation("org.htmlunit:htmlunit") integrationTestImplementation("org.htmlunit:htmlunit")
integrationTestImplementation("org.springframework:spring-webflux") integrationTestImplementation("org.springframework:spring-webflux")
// Fix for CVE-2024-25710
integrationTestImplementation("org.apache.commons:commons-compress:1.26.0")
} }
tasks.withType<KotlinCompile> { tasks.withType<KotlinCompile> {

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@@ -1,26 +1,121 @@
services: services:
kafka: kafka:
image: bitnami/kafka image: apache/kafka
hostname: kafka hostname: kafka
ports: ports:
- "9092:9092" - "9092:9092"
- "9094:9094" - "9094:9094"
environment: environment:
ALLOW_PLAINTEXT_LISTENER: "yes" ALLOW_PLAINTEXT_LISTENER: "yes"
KAFKA_CFG_NODE_ID: "0" KAFKA_NODE_ID: "0"
KAFKA_CFG_PROCESS_ROLES: "controller,broker" KAFKA_KRAFT_CLUSTER_ID: "mv64e-etl-processor-dev"
KAFKA_CFG_LISTENERS: PLAINTEXT://:9092,CONTROLLER://:9093,EXTERNAL://:9094 KAFKA_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093
KAFKA_CFG_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:9094 KAFKA_PROCESS_ROLES: "controller,broker"
KAFKA_CFG_LISTENER_SECURITY_PROTOCOL_MAP: CONTROLLER:PLAINTEXT,EXTERNAL:PLAINTEXT,PLAINTEXT:PLAINTEXT KAFKA_CONTROLLER_LISTENER_NAMES: CONTROLLER
KAFKA_CFG_INTER_BROKER_LISTENER_NAME: PLAINTEXT KAFKA_INTER_BROKER_LISTENER_NAME: PLAINTEXT
KAFKA_CFG_AUTO_CREATE_TOPICS_ENABLE: true KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: "1"
KAFKA_CFG_CONTROLLER_QUORUM_VOTERS: 0@kafka:9093 KAFKA_TRANSACTION_STATE_LOG_REPLICATION_FACTOR: "1"
KAFKA_CFG_CONTROLLER_LISTENER_NAMES: CONTROLLER KAFKA_TRANSACTION_STATE_LOG_MIN_ISR: "1"
healthcheck: KAFKA_GROUP_INITIAL_REBALANCE_DELAY_MS: "0"
test: kafka-topics --bootstrap-server kafka:9092 --list KAFKA_AUTO_CREATE_TOPICS_ENABLE: "true"
interval: 30s # Without SSL
timeout: 10s KAFKA_LISTENERS: PLAINTEXT://:9092,CONTROLLER://:9093,EXTERNAL://:9094
retries: 3 KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:9094
KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: CONTROLLER:PLAINTEXT,EXTERNAL:PLAINTEXT,PLAINTEXT:PLAINTEXT
# Using SSL
# KAFKA_LISTENERS: PLAINTEXT://:9092,CONTROLLER://:9093,EXTERNAL://:9094
# KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:9094
# KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: CONTROLLER:PLAINTEXT,EXTERNAL:SSL,PLAINTEXT:PLAINTEXT
# KAFKA_SSL_KEYSTORE_TYPE: "PEM"
# KAFKA_SSL_KEYSTORE_CERTIFICATE_CHAIN: -----BEGIN CERTIFICATE-----
# MIIDCzCCAfOgAwIBAgIUaXNh4PahaKeLUaab2rUPSVESx28wDQYJKoZIhvcNAQEL
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# 8tTDVXQn08BT9H3jZTnF
# -----END CERTIFICATE-----
# -----BEGIN CERTIFICATE-----
# MIIC+TCCAeGgAwIBAgIUUoCwz8GS6xQ3mmI7RUUYSNPIOi4wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODE0NDhaFw0zNTA4
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# -----END CERTIFICATE-----
# KAFKA_SSL_KEYSTORE_KEY: -----BEGIN PRIVATE KEY-----
# MIIEvQIBADANBgkqhkiG9w0BAQEFAASCBKcwggSjAgEAAoIBAQC/T1vfTIYQcHRJ
# kx8mYH54X068WT6zVOs9VHVfG/Ni5N6e+aPHgimvYjneww0JaO+YUAYYV9Pl3N5r
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# Vz5Ekt6wQflHrWoQlpv0CivKSNzCONZ2IJazrGHti0mXwSeXzptEyApRDaiNVnrV
# mKdnrjcQThw7iPXgSaWS9/vwMmhgayLy5ABkBi4GhsjINlKP7wctw1vZP+N6NCNd
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# fcfgTiQaXRJmlVx6jfbfZd4=
# -----END PRIVATE KEY-----
# #KAFKA_SSL_KEYSTORE_CREDENTIALS: example
# KAFKA_SSL_KEY_CREDENTIALS: example
# KAFKA_SSL_TRUSTSTORE_TYPE: "PEM"
# KAFKA_SSL_TRUSTSTORE_CERTIFICATES: -----BEGIN CERTIFICATE-----
# MIIDCzCCAfOgAwIBAgIUaXNh4PahaKeLUaab2rUPSVESx28wDQYJKoZIhvcNAQEL
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# -----END CERTIFICATE-----
# KAFKA_SSL_CLIENT_AUTH: none
###
## Use AKHQ as Kafka web frontend ## Use AKHQ as Kafka web frontend
akhq: akhq:

View File

@@ -282,6 +282,30 @@ class HomeControllerTest {
assertThat(page.querySelectorAll("tbody tr")).isEmpty() assertThat(page.querySelectorAll("tbody tr")).isEmpty()
assertThat(page.querySelectorAll("div.notification.info")).hasSize(1) assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
} }
@Test
@WithMockUser(username = "admin", roles = ["ADMIN"])
fun testShouldShowNoConsentStatusBadge() {
whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
PageImpl(
listOf(
Request(
1L,
randomRequestId(),
PatientPseudonym("PSEUDO1"),
PatientId("PATIENT1"),
Fingerprint("ashdkasdh"),
RequestType.MTB_FILE,
RequestStatus.NO_CONSENT
)
)
)
)
val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
assertThat(page.querySelectorAll("tbody tr")).hasSize(1)
assertThat(page.querySelectorAll("tbody tr > td > small").first().textContent).isEqualTo("NO_CONSENT")
}
} }
} }

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@@ -31,6 +31,7 @@ import org.apache.kafka.clients.consumer.ConsumerRecord
import org.slf4j.LoggerFactory import org.slf4j.LoggerFactory
import org.springframework.http.MediaType import org.springframework.http.MediaType
import org.springframework.kafka.listener.MessageListener import org.springframework.kafka.listener.MessageListener
import java.nio.charset.Charset
class KafkaInputListener( class KafkaInputListener(
private val requestProcessor: RequestProcessor, private val requestProcessor: RequestProcessor,
@@ -49,19 +50,16 @@ class KafkaInputListener(
} }
} }
private fun guessMimeType(record: ConsumerRecord<String, String>): String { private fun guessMimeType(record: ConsumerRecord<String, String>): String? {
if (record.headers().headers("contentType").toList().isEmpty()) { if (record.headers().headers("contentType").toList().isEmpty()) {
// Fallback if no contentType set (old behavior) // Fallback if no contentType set (old behavior)
return MediaType.APPLICATION_JSON_VALUE return MediaType.APPLICATION_JSON_VALUE
} }
return record.headers().headers("contentType")?.firstOrNull()?.value().contentToString() return record.headers().headers("contentType")?.firstOrNull()?.value()?.toString(Charset.forName("UTF-8"))
} }
private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) { private fun handleDnpmV2Message(record: ConsumerRecord<String, String>) {
// Do not handle DNPM-V2 for now
logger.warn("Ignoring MTB File in DNPM V2 format: Not implemented yet")
val mtbFile = objectMapper.readValue(record.value(), Mtb::class.java) val mtbFile = objectMapper.readValue(record.value(), Mtb::class.java)
val patientId = PatientId(mtbFile.patient.id) val patientId = PatientId(mtbFile.patient.id)
val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull() val firstRequestIdHeader = record.headers().headers("requestId")?.firstOrNull()

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@@ -27,7 +27,6 @@ import dev.pcvolkmer.mv64e.mtb.Mtb
import dev.pcvolkmer.mv64e.mtb.MvhMetadata import dev.pcvolkmer.mv64e.mtb.MvhMetadata
import org.apache.kafka.clients.producer.ProducerRecord import org.apache.kafka.clients.producer.ProducerRecord
import org.slf4j.LoggerFactory import org.slf4j.LoggerFactory
import org.springframework.http.MediaType
import org.springframework.kafka.core.KafkaTemplate import org.springframework.kafka.core.KafkaTemplate
import org.springframework.retry.support.RetryTemplate import org.springframework.retry.support.RetryTemplate
@@ -47,8 +46,9 @@ class KafkaMtbFileSender(
ProducerRecord( ProducerRecord(
kafkaProperties.outputTopic, kafkaProperties.outputTopic,
key(request), key(request),
objectMapper.writeValueAsString(request) objectMapper.writeValueAsString(request),
) )
record.headers().add("requestId", request.requestId.value.toByteArray())
when (request) { when (request) {
is DnpmV2MtbFileRequest -> record.headers() is DnpmV2MtbFileRequest -> record.headers()
.add( .add(
@@ -82,7 +82,6 @@ class KafkaMtbFileSender(
ProducerRecord( ProducerRecord(
kafkaProperties.outputTopic, kafkaProperties.outputTopic,
key(request), key(request),
// Always use old BwhcV1FileRequest with Consent REJECT
objectMapper.writeValueAsString( objectMapper.writeValueAsString(
DnpmV2MtbFileRequest( DnpmV2MtbFileRequest(
request.requestId, request.requestId,
@@ -90,7 +89,7 @@ class KafkaMtbFileSender(
) )
) )
) )
record.headers().add("requestId", request.requestId.value.toByteArray())
val result = kafkaTemplate.send(record) val result = kafkaTemplate.send(record)
if (result.get() != null) { if (result.get() != null) {
logger.debug("Sent deletion request via KafkaMtbFileSender") logger.debug("Sent deletion request via KafkaMtbFileSender")

View File

@@ -18,13 +18,107 @@ spring:
issuer-uri: https://dnpm.dev/auth/realms/intern issuer-uri: https://dnpm.dev/auth/realms/intern
user-name-attribute: name user-name-attribute: name
# kafka:
# security:
# protocol: "SSL"
# ssl:
# key-store-type: "PEM"
# key-store-certificate-chain: -----BEGIN CERTIFICATE-----
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# qBAEHctqavfMI27UQmIzw4pGMkGzEQxRMc6a9pdabBhbMMTJsjtmOv2YMYHj1HHK
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# 8tTDVXQn08BT9H3jZTnF
# -----END CERTIFICATE-----
# -----BEGIN CERTIFICATE-----
# MIIC+TCCAeGgAwIBAgIUUoCwz8GS6xQ3mmI7RUUYSNPIOi4wDQYJKoZIhvcNAQEL
# BQAwFTETMBEGA1UEAwwKRXhhbXBsZSBDQTAeFw0yNTA4MjExODE0NDhaFw0zNTA4
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# -----END CERTIFICATE-----
# ### For dev/testing purposes only!
# key-store-key: -----BEGIN PRIVATE KEY-----
# MIIEvQIBADANBgkqhkiG9w0BAQEFAASCBKcwggSjAgEAAoIBAQC/T1vfTIYQcHRJ
# kx8mYH54X068WT6zVOs9VHVfG/Ni5N6e+aPHgimvYjneww0JaO+YUAYYV9Pl3N5r
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# fcfgTiQaXRJmlVx6jfbfZd4=
# -----END PRIVATE KEY-----
# trust-store-type: "PEM"
# trust-store-certificates: -----BEGIN CERTIFICATE-----
# MIIDCzCCAfOgAwIBAgIUaXNh4PahaKeLUaab2rUPSVESx28wDQYJKoZIhvcNAQEL
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# 8tTDVXQn08BT9H3jZTnF
# -----END CERTIFICATE-----
app: app:
rest: rest:
uri: http://localhost/api uri: http://localhost/api
#kafka: #kafka:
# topic: test
# response-topic: test_response
# servers: localhost:9094 # servers: localhost:9094
# group-id: "test1234"
# input-topic: test_input
# output-topic: test_output
# output-response-topic: test_response
security: security:
admin-user: admin admin-user: admin
admin-password: "{noop}very-secret" admin-password: "{noop}very-secret"

View File

@@ -16,7 +16,5 @@ spring:
content: content:
enabled: true enabled: true
paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg paths: /**/*.js,/**/*.css,/**/*.svg,/**/*.jpeg
app:
isGenomDeTestSubmission: true
server: server:
forward-headers-strategy: framework forward-headers-strategy: framework

View File

@@ -0,0 +1,7 @@
__ _ _ _ _
_ __ _____ __/ /_ | || | ___ ___| |_| | _ __ _ __ ___ ___ ___ ___ ___ ___ _ __
| '_ ` _ \ \ / / '_ \| || |_ / _ \_____ / _ \ __| |_____| '_ \| '__/ _ \ / __/ _ \/ __/ __|/ _ \| '__|
| | | | | \ V /| (_) |__ _| __/_____| __/ |_| |_____| |_) | | | (_) | (_| __/\__ \__ \ (_) | |
|_| |_| |_|\_/ \___/ |_| \___| \___|\__|_| | .__/|_| \___/ \___\___||___/___/\___/|_|
|_|
:: mv64e-etl-processor :: ${application.formatted-version}

View File

@@ -54,6 +54,7 @@
<td th:if="${request.status.value.contains('error')}" class="bg-red"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value.contains('error')}" class="bg-red"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'unknown'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value == 'unknown'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td> <td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'no-consent'}" class="bg-blue"><small>[[ ${request.status} ]]</small></td>
<td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td> <td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>
<td th:if="not ${request.report}">[[ ${request.uuid} ]]</td> <td th:if="not ${request.report}">[[ ${request.uuid} ]]</td>
<td th:if="${request.report}"> <td th:if="${request.report}">

View File

@@ -244,7 +244,14 @@ class KafkaInputListenerTest {
} }
@Test @Test
fun shouldNotProcessDnpmV2Request() { fun shouldProcessDnpmV2Request() {
whenever(consentEvaluator.check(any())).thenReturn(
ConsentEvaluation(
TtpConsentStatus.BROAD_CONSENT_GIVEN,
false
)
)
val mtbFile = Mtb.builder() val mtbFile = Mtb.builder()
.patient(Patient.builder().id("DUMMY_12345678").build()) .patient(Patient.builder().id("DUMMY_12345678").build())
.metadata( .metadata(
@@ -285,7 +292,7 @@ class KafkaInputListenerTest {
Optional.empty() Optional.empty()
) )
) )
verify(requestProcessor, times(0)).processDeletion( verify(requestProcessor, times(1)).processDeletion(
anyValueClass(), anyValueClass(), eq( anyValueClass(), anyValueClass(), eq(
TtpConsentStatus.UNKNOWN_CHECK_FILE TtpConsentStatus.UNKNOWN_CHECK_FILE
) )

View File

@@ -163,6 +163,8 @@ class KafkaMtbFileSenderTest {
assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}") assertThat(captor.firstValue.key()).isEqualTo("{\"pid\": \"PID\"}")
assertThat(captor.firstValue.headers().headers("contentType")).isNotNull assertThat(captor.firstValue.headers().headers("contentType")).isNotNull
assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray()) assertThat(captor.firstValue.headers().headers("contentType")?.firstOrNull()?.value()).isEqualTo(CustomMediaType.APPLICATION_VND_DNPM_V2_MTB_JSON_VALUE.toByteArray())
assertThat(captor.firstValue.headers().headers("requestId")).isNotNull
assertThat(captor.firstValue.headers().headers("requestId")?.firstOrNull()?.value()).isEqualTo(TEST_REQUEST_ID.value.toByteArray())
assertThat(captor.firstValue.value()).isNotNull assertThat(captor.firstValue.value()).isNotNull
assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(dnmpV2kafkaRecordData(TEST_REQUEST_ID))) assertThat(captor.firstValue.value()).isEqualTo(objectMapper.writeValueAsString(dnmpV2kafkaRecordData(TEST_REQUEST_ID)))
} }