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Merge remote-tracking branch 'origin/release/1.6.0' into main
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hhund committed Oct 15, 2024
2 parents 731b8c5 + e3c59c5 commit f761d2d
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24 changes: 22 additions & 2 deletions CITATION.cff
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Expand Up @@ -24,8 +24,8 @@ preferred-citation:
doi: 10.3233/SHTI210060
type: proceedings
title: "Data Sharing Framework (DSF)"
version: 1.5.2
date-released: 2024-07-09
version: 1.6.0
date-released: 2024-10-15
url: https://dsf.dev
repository-code: https://github.com/datasharingframework/dsf
repository-artifact: https://github.com/datasharingframework/dsf/releases
Expand Down Expand Up @@ -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
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-process-api-v1/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-bpe-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
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2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/conf/log4j2.xml
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@@ -1,4 +1,4 @@
<Configuration status="INFO" monitorInterval="30"
<Configuration status="WARN" monitorInterval="30"
verbose="false">

<Appenders>
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3 changes: 2 additions & 1 deletion dsf-bpe/dsf-bpe-server-jetty/docker/conf/log4j2.xml
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@@ -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" />
Expand All @@ -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" />

<Root level="WARN">
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2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-bpe-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
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2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-bpe-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
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Expand Up @@ -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));
}
}
}
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Expand Up @@ -124,10 +124,6 @@ public SpringProcessEngineConfiguration processEngineConfiguration()
serializerConfig.fhirResourceSerializer(), serializerConfig.fhirResourcesListSerializer()));
c.setFallbackSerializerFactory(fallbackSerializerFactory());

// see also MultiVersionSpringProcessEngineConfiguration
c.setInitializeTelemetry(false);
c.setTelemetryReporterActivate(false);

DefaultJobExecutor jobExecutor = new DefaultJobExecutor();
jobExecutor.setCorePoolSize(propertiesConfig.getProcessEngineJobExecutorCorePoolSize());
jobExecutor.setQueueSize(propertiesConfig.getProcessEngineJobExecutorQueueSize());
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Expand Up @@ -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());
Expand Down Expand Up @@ -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;
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Expand Up @@ -100,6 +100,6 @@ public Type transformQuestionTypeToAnswerType(Questionnaire.QuestionnaireItemCom
public String getLocalVersionlessAbsoluteUrl(QuestionnaireResponse questionnaireResponse)
{
return questionnaireResponse.getIdElement().toVersionless()
.withServerBase(serverBaseUrl, ResourceType.Task.name()).getValue();
.withServerBase(serverBaseUrl, ResourceType.QuestionnaireResponse.name()).getValue();
}
}
Original file line number Diff line number Diff line change
@@ -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_);
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@@ -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>
2 changes: 2 additions & 0 deletions dsf-bpe/dsf-bpe-server/src/main/resources/db/db.changelog.xml
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Expand Up @@ -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>
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server/src/test/resources/log4j2.xml
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@@ -1,4 +1,4 @@
<Configuration status="INFO" monitorInterval="30"
<Configuration status="WARN" monitorInterval="30"
verbose="false">

<Appenders>
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2 changes: 1 addition & 1 deletion dsf-bpe/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<modules>
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2 changes: 1 addition & 1 deletion dsf-common/dsf-common-auth/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-common-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
Expand Down
2 changes: 1 addition & 1 deletion dsf-common/dsf-common-auth/src/test/resources/log4j2.xml
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@@ -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">
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2 changes: 1 addition & 1 deletion dsf-common/dsf-common-config/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-common-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
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2 changes: 1 addition & 1 deletion dsf-common/dsf-common-config/src/test/resources/log4j2.xml
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@@ -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">
Expand Down
2 changes: 1 addition & 1 deletion dsf-common/dsf-common-db/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-common-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
Expand Down
2 changes: 1 addition & 1 deletion dsf-common/dsf-common-documentation/pom.xml
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Expand Up @@ -6,6 +6,6 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-common-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>
</project>
2 changes: 1 addition & 1 deletion dsf-common/dsf-common-jetty/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-common-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
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Expand Up @@ -429,7 +429,7 @@ 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
{
Expand Down
2 changes: 1 addition & 1 deletion dsf-common/dsf-common-jetty/src/test/resources/log4j2.xml
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@@ -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">
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2 changes: 1 addition & 1 deletion dsf-common/dsf-common-status/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-common-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
Expand Down
2 changes: 1 addition & 1 deletion dsf-common/dsf-common-ui/pom.xml
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Expand Up @@ -6,7 +6,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-common-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<dependencies>
Expand Down
2 changes: 1 addition & 1 deletion dsf-common/pom.xml
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Expand Up @@ -7,7 +7,7 @@
<parent>
<groupId>dev.dsf</groupId>
<artifactId>dsf-pom</artifactId>
<version>1.5.2</version>
<version>1.6.0</version>
</parent>

<modules>
Expand Down
22 changes: 19 additions & 3 deletions dsf-docker-test-setup-3dic-ttp/docker-compose.yml
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@@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -944,6 +959,7 @@ networks:
- subnet: 172.20.0.56/29
ttp-bpe-backend:
internet:
forward-proxy:

volumes:
db-data:
Expand Down
4 changes: 4 additions & 0 deletions dsf-docker-test-setup-3dic-ttp/forward-proxy/Dockerfile
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@@ -0,0 +1,4 @@
FROM alpine:3.20
RUN apk add --no-cache tinyproxy
COPY tinyproxy.conf /etc/tinyproxy/tinyproxy.conf
CMD ["tinyproxy", "-d"]
6 changes: 6 additions & 0 deletions dsf-docker-test-setup-3dic-ttp/forward-proxy/tinyproxy.conf
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@@ -0,0 +1,6 @@
User tinyproxy
Group tinyproxy
Port 8080
Timeout 100
LogLevel Connect
BasicAuth proxy_user proxy_password
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