Merge remote-tracking branch 'origin/issue/239_Port_1_6_0_to_2_0_0' into

develop_2

CITATION.cff

@@ -25,7 +25,7 @@ preferred-citation:
   type: proceedings
 title: "Data Sharing Framework (DSF)"
 version: 2.0.0
-date-released: 2024-07-15
+date-released: 2024-10-15
 url: https://dsf.dev
 repository-code: https://github.com/datasharingframework/dsf
 repository-artifact: https://github.com/datasharingframework/dsf/releases
@@ -241,3 +241,23 @@ references:
     year: 2024
     pages: 28-32
     doi: 10.3233/SHTI230921
+  - type: proceedings
+    authors:
+      - family-names: Schweizer
+        given-names: Simon Tobias
+      - family-names: Hund
+        given-names: Hauke
+      - family-names: Kurscheidt
+        given-names: Maximilian
+      - family-names: Zilske
+        given-names: Christoph
+      - family-names: Böhringer
+        given-names: Jan P.
+      - family-names: Fegeler
+        given-names: Christian
+    title: "Handling Complexity in Decentralized Research Networks: The Data Sharing Framework Allowlist Management Application"
+    journal: Stud Health Technol Inform
+    volume: 317
+    year: 2024
+    pages: 85-93
+    doi: 10.3233/SHTI240841

dsf-bpe/dsf-bpe-server-jetty/conf/log4j2.xml

@@ -1,4 +1,4 @@
-<Configuration status="INFO" monitorInterval="30"
+<Configuration status="WARN" monitorInterval="30"
 			   verbose="false">
 
 	<Appenders>

dsf-bpe/dsf-bpe-server-jetty/docker/conf/log4j2.xml

@@ -1,4 +1,4 @@
-<Configuration status="INFO" monitorInterval="30" verbose="false">
+<Configuration status="WARN" monitorInterval="30" verbose="false">
 	<Appenders>
 		<Console name="CONSOLE" target="SYSTEM_OUT">
 			<PatternLayout pattern="%highlight{%p %t - %C{1}.%M(%L) | %m}{FATAL=red, ERROR=red, WARN=yellow, INFO=white, DEBUG=white, TRACE=white}%n" />
@@ -17,6 +17,7 @@
 		<Logger name="dev.dsf" level="DEBUG" />
 		<Logger name="de.netzwerk_universitaetsmedizin" level="DEBUG" />
 		<Logger name="de.medizininformatik_initiative" level="DEBUG" />
+		<Logger name="de.dkfz.nct" level="DEBUG" />
 		<Logger name="org.eclipse.jetty" level="INFO" />
 		<Logger name="ca.uhn.fhir.parser.LenientErrorHandler" level="ERROR" />
 

dsf-bpe/dsf-bpe-server/src/main/java/dev/dsf/bpe/camunda/MultiVersionSpringProcessEngineConfiguration.java

@@ -11,17 +11,10 @@ public MultiVersionSpringProcessEngineConfiguration(DelegateProvider delegatePro
 	}
 
 	@Override
-	protected void initTelemetry()
+	protected void initDiagnostics()
 	{
 		// override to turn telemetry collection of
-		// see also CamundaConfig
-	}
 
-	@Override
-	public TelemetryDataImpl getTelemetryData()
-	{
-		// NPE fix after turning off telemetry collection
-		// see also CamundaConfig
-		return new TelemetryDataImpl(null, null);
+		setTelemetryData(new TelemetryDataImpl(null, null));
 	}
-}
+}

dsf-bpe/dsf-bpe-server/src/main/java/dev/dsf/bpe/spring/config/CamundaConfig.java

@@ -99,10 +99,6 @@ public SpringProcessEngineConfiguration processEngineConfiguration()
 				processPluginFactories.stream().flatMap(ProcessPluginFactory::getSerializer).toList());
 		c.setFallbackSerializerFactory(fallbackSerializerFactory());
 
-		// see also MultiVersionSpringProcessEngineConfiguration
-		c.setInitializeTelemetry(false);
-		c.setTelemetryReporterActivate(false);
-
 		DefaultJobExecutor jobExecutor = new DefaultJobExecutor();
 		jobExecutor.setCorePoolSize(propertiesConfig.getProcessEngineJobExecutorCorePoolSize());
 		jobExecutor.setQueueSize(propertiesConfig.getProcessEngineJobExecutorQueueSize());

dsf-bpe/dsf-bpe-server/src/main/java/dev/dsf/bpe/subscription/LocalFhirConnectorImpl.java

@@ -228,7 +228,7 @@ private void connectWebsocket(Subscription subscription)
 	{
 		try
 		{
-			WebsocketClient client = clientProvider.getLocalWebsocketClient(() -> connect(),
+			WebsocketClient client = clientProvider.getLocalWebsocketClient(this::connect,
 					subscription.getIdElement().getIdPart());
 
 			EventType eventType = toEventType(subscription.getChannel().getPayload());
@@ -260,7 +260,7 @@ private Void onError(Throwable t)
 	{
 		// no debug log, exception previously logged by retrieveWebsocketSubscription, loadNewResources and
 		// connectWebsocket methods
-		logger.error("Error while loading existing {} resources and connecting websocket: {} - {}", resourceName,
+		logger.error("Error loading existing {} resources and connecting websocket: {} - {}", resourceName,
 				t.getClass().getName(), t.getMessage());
 
 		return null;

dsf-bpe/dsf-bpe-server/src/main/resources/db/camunda/postgres_engine_7.21_to_7.22.sql

@@ -0,0 +1,29 @@
+--
+-- Copyright Camunda Services GmbH and/or licensed to Camunda Services GmbH
+-- under one or more contributor license agreements. See the NOTICE file
+-- distributed with this work for additional information regarding copyright
+-- ownership. Camunda licenses this file to you under the Apache License,
+-- Version 2.0; you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--     http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+--
+
+insert into ACT_GE_SCHEMA_LOG
+values ('1100', CURRENT_TIMESTAMP, '7.22.0');
+
+alter table ACT_RU_TASK add column TASK_STATE_ varchar(64);
+
+alter table ACT_HI_TASKINST add column TASK_STATE_ varchar(64);
+
+alter table ACT_RU_JOB add column BATCH_ID_ varchar(64);
+alter table ACT_HI_JOB_LOG add column BATCH_ID_ varchar(64);
+
+alter table ACT_HI_PROCINST add RESTARTED_PROC_INST_ID_ varchar(64);
+create index ACT_IDX_HI_PRO_RST_PRO_INST_ID on ACT_HI_PROCINST(RESTARTED_PROC_INST_ID_);

dsf-bpe/dsf-bpe-server/src/main/resources/db/db.camunda_engine.changelog-1.6.0.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<databaseChangeLog
+	xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog
+                      http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.6.xsd">
+
+	<changeSet author="camunda.org" id="db.camunda_engine.changelog-1.6.0">
+		<sqlFile dbms="postgresql" encoding="utf8" path="db/camunda/postgres_engine_7.21_to_7.22.sql" />
+	</changeSet>
+
+</databaseChangeLog>

dsf-bpe/dsf-bpe-server/src/main/resources/db/db.changelog.xml

@@ -17,4 +17,6 @@
 	<include file="db/db.camunda_engine.changelog-1.3.0.xml" />
 
 	<include file="db/db.camunda_engine.changelog-1.5.1.xml" />
+
+	<include file="db/db.camunda_engine.changelog-1.6.0.xml" />
 </databaseChangeLog>

dsf-bpe/dsf-bpe-server/src/test/resources/log4j2.xml

@@ -1,4 +1,4 @@
-<Configuration status="INFO" monitorInterval="30"
+<Configuration status="WARN" monitorInterval="30"
 			   verbose="false">
 
 	<Appenders>

dsf-common/dsf-common-auth/src/test/resources/log4j2.xml

@@ -1,4 +1,4 @@
-<Configuration status="INFO" monitorInterval="30" verbose="false">
+<Configuration status="WARN" monitorInterval="30" verbose="false">
 
 	<Appenders>
 		<Console name="CONSOLE" target="SYSTEM_OUT">

dsf-common/dsf-common-config/src/test/resources/log4j2.xml

@@ -1,4 +1,4 @@
-<Configuration status="INFO" monitorInterval="30" verbose="false">
+<Configuration status="WARN" monitorInterval="30" verbose="false">
 
 	<Appenders>
 		<Console name="CONSOLE" target="SYSTEM_OUT">

dsf-common/dsf-common-jetty/src/main/java/dev/dsf/common/config/AbstractJettyConfig.java

@@ -431,7 +431,7 @@ private Duration oidcClientConnectTimeout()
 	private Proxy oidcClientProxy()
 	{
 		ProxyConfig config = new ProxyConfigImpl(proxyUrl, proxyUsername, proxyPassword, proxyNoProxy);
-		if (config.getUrl() != null && config.isNoProxyUrl(oidcProviderRealmBaseUrl))
+		if (config.getUrl() != null && !config.isNoProxyUrl(oidcProviderRealmBaseUrl))
 		{
 			try
 			{

dsf-common/dsf-common-jetty/src/test/resources/log4j2.xml

@@ -1,4 +1,4 @@
-<Configuration status="INFO" monitorInterval="30" verbose="false">
+<Configuration status="WARN" monitorInterval="30" verbose="false">
 
 	<Appenders>
 		<Console name="CONSOLE" target="SYSTEM_OUT">

dsf-docker-test-setup-3dic-ttp/docker-compose.yml

@@ -1,7 +1,7 @@
 version: '3.8'
 services:
   proxy:
-    image: nginx:1.23
+    image: nginx:1.27
     restart: "no"
     ports:
       - 127.0.0.1:443:443
@@ -78,7 +78,7 @@ services:
         read_only: true
 
   keycloak:
-    image: quay.io/keycloak/keycloak:21.0
+    image: quay.io/keycloak/keycloak:25.0
     restart: "no"
     ports:
       - 127.0.0.1:8443:8443
@@ -104,7 +104,16 @@ services:
       --https-certificate-key-file=/run/secrets/keycloak_certificate_private_key.pem
       --spi-truststore-file-file=/run/secrets/keycloak_trust_store.jks
       --spi-truststore-file-password=password
-      --spi-truststore-file-hostname-verification-policy=STRICT
+      --spi-truststore-file-hostname-verification-policy=DEFAULT
+
+  forward-proxy:
+    build: ./forward-proxy
+    restart: "no"
+    environment:
+      TZ: Europe/Berlin
+    networks:
+      forward-proxy:
+      internet:
 
   dic1-fhir:
     build: ../dsf-fhir/dsf-fhir-server-jetty/docker
@@ -518,15 +527,21 @@ services:
       DEV_DSF_SERVER_AUTH_OIDC_PROVIDER_CLIENT_TRUST_SERVER_CERTIFICATE_CAS: /run/secrets/app_server_trust_certificates.pem
       DEV_DSF_SERVER_AUTH_OIDC_CLIENT_ID: dic1-bpe
       DEV_DSF_SERVER_AUTH_OIDC_CLIENT_SECRET: ytqFCErw9GfhVUrrM8xc0Grbu4r7qGig
+      DEV_DSF_PROXY_URL: http://forward-proxy:8080
+      DEV_DSF_PROXY_USERNAME: proxy_user
+      DEV_DSF_PROXY_PASSWORD: proxy_password
+      DEV_DSF_PROXY_NOPROXY: keycloak
     networks:
       dic1-bpe-frontend:
         ipv4_address: 172.20.0.35
       dic1-bpe-backend:
       internet:
+      forward-proxy:
     depends_on:
       - db
       - dic1-fhir
       - keycloak
+      - forward-proxy
 
   dic2-bpe:
     build: ../dsf-bpe/dsf-bpe-server-jetty/docker
@@ -944,6 +959,7 @@ networks:
       - subnet: 172.20.0.56/29
   ttp-bpe-backend:
   internet:
+  forward-proxy:
 
 volumes:
   db-data:

dsf-docker-test-setup-3dic-ttp/forward-proxy/Dockerfile

@@ -0,0 +1,4 @@
+FROM alpine:3.20
+RUN apk add --no-cache tinyproxy
+COPY tinyproxy.conf /etc/tinyproxy/tinyproxy.conf
+CMD ["tinyproxy", "-d"]

dsf-docker-test-setup-3dic-ttp/forward-proxy/tinyproxy.conf

@@ -0,0 +1,6 @@
+User tinyproxy
+Group tinyproxy
+Port 8080
+Timeout 100
+LogLevel Connect
+BasicAuth proxy_user proxy_password

dsf-docker-test-setup-3dic-ttp/proxy/nginx.conf

@@ -1,16 +1,6 @@
-
-user  nginx;
-worker_processes  1;
-
-error_log  /var/log/nginx/error.log warn;
-pid        /var/run/nginx.pid;
-
-
 events {
-    worker_connections  1024;
 }
 
-
 http {
     include       /etc/nginx/mime.types;
     default_type  application/octet-stream;
@@ -19,15 +9,6 @@ http {
                       '$status $body_bytes_sent "$http_referer" '
                       '"$http_user_agent" "$http_x_forwarded_for"';
 
-    access_log  /var/log/nginx/access.log  main;
-
-    sendfile        on;
-    #tcp_nopush     on;
-
-    keepalive_timeout  65;
-
-    #gzip  on;
-
     ssl_certificate /run/secrets/proxy_certificate_and_int_cas.pem;
     ssl_certificate_key /run/secrets/proxy_certificate_private_key.pem;
     ssl_protocols TLSv1.2 TLSv1.3;
@@ -45,4 +26,4 @@ http {
     }
 
     include /etc/nginx/conf.d/*.conf;
-}
+}

dsf-fhir/dsf-fhir-auth/src/test/resources/log4j2.xml

@@ -1,4 +1,4 @@
-<Configuration status="INFO" monitorInterval="30" verbose="false">
+<Configuration status="WARN" monitorInterval="30" verbose="false">
 
 	<Appenders>
 		<Console name="CONSOLE" target="SYSTEM_OUT">