Merge remote-tracking branch 'origin/release/0.5.0' into main

highmed · Aug 24, 2021 · d9daa3c · d9daa3c
2 parents fe19d75 + 65b2963
commit d9daa3c
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diff --git a/.github/workflows/maven-build.yml b/.github/workflows/maven-build.yml
@@ -17,4 +17,4 @@ jobs:
       with:
         java-version: 11
     - name: Build with Maven
-      run: mvn -B verify --file pom.xml
+      run: mvn -B verify -fae --file pom.xml
diff --git a/.gitignore b/.gitignore
@@ -29,36 +29,44 @@ dsf-fhir/dsf-fhir-validation/src/main/resources/fhir/bundle.xml
 ###
 # dsf-docker-test-setup ignores
 ###
-dsf-docker-test-setup/bpe/app/conf/*.p12
-dsf-docker-test-setup/bpe/app/last_event/time.file
-dsf-docker-test-setup/bpe/app/log/*.log
-dsf-docker-test-setup/bpe/app/log/*.log.gz
-dsf-docker-test-setup/bpe/app/plugin/*.jar
-dsf-docker-test-setup/bpe/app/process/*.jar
-dsf-docker-test-setup/bpe/db/postgres-data/
-dsf-docker-test-setup/bpe/proxy/ssl/*.pem
+dsf-docker-test-setup/bpe/last_event/time.file
+dsf-docker-test-setup/bpe/log/*.log
+dsf-docker-test-setup/bpe/log/*.log.gz
+dsf-docker-test-setup/bpe/plugin/*.jar
+dsf-docker-test-setup/bpe/process/*.jar
+dsf-docker-test-setup/bpe/psn/*.jceks
+dsf-docker-test-setup/bpe/secrets/*.pem
 
-dsf-docker-test-setup/fhir/app/conf/*.p12
-dsf-docker-test-setup/fhir/app/conf/bundle.xml
-dsf-docker-test-setup/fhir/app/conf/config.properties
-dsf-docker-test-setup/fhir/app/log/*.log
-dsf-docker-test-setup/fhir/app/log/*.log.gz
-dsf-docker-test-setup/fhir/db/postgres-data/
-dsf-docker-test-setup/fhir/proxy/ssl/*.pem
+dsf-docker-test-setup/fhir/log/*.log
+dsf-docker-test-setup/fhir/log/*.log.gz
+dsf-docker-test-setup/fhir/secrets/*.pem
+dsf-docker-test-setup/fhir/.env
 
 ###
 # dsf-docker-test-setup-3medic-ttp ignores
 ###
-dsf-docker-test-setup-3medic-ttp/**/bpe/app/conf/*.p12
-dsf-docker-test-setup-3medic-ttp/**/bpe/app/conf/config.properties
-dsf-docker-test-setup-3medic-ttp/**/bpe/app/plugin/*.jar
-dsf-docker-test-setup-3medic-ttp/**/bpe/app/process/*.jar
-dsf-docker-test-setup-3medic-ttp/**/bpe/proxy/ssl/*.pem
+dsf-docker-test-setup-3medic-ttp/**/bpe/plugin/*.jar
+dsf-docker-test-setup-3medic-ttp/**/bpe/process/*.jar
+dsf-docker-test-setup-3medic-ttp/**/bpe/secrets/*.pem
 
-dsf-docker-test-setup-3medic-ttp/**/fhir/app/conf/*.p12
-dsf-docker-test-setup-3medic-ttp/**/fhir/app/conf/bundle.xml
-dsf-docker-test-setup-3medic-ttp/**/fhir/app/conf/config.properties
-dsf-docker-test-setup-3medic-ttp/**/fhir/proxy/ssl/*.pem
+dsf-docker-test-setup-3medic-ttp/**/fhir/secrets/*.pem
+dsf-docker-test-setup-3medic-ttp/**/fhir/.env
+
+###
+# dsf-docker-test-setup-3medic-ttp-docker ignores
+###
+dsf-docker-test-setup-3medic-ttp-docker/**/bpe/last_event/time.file
+dsf-docker-test-setup-3medic-ttp-docker/**/bpe/log/*.log
+dsf-docker-test-setup-3medic-ttp-docker/**/bpe/log/*.log.gz
+dsf-docker-test-setup-3medic-ttp-docker/**/bpe/plugin/*.jar
+dsf-docker-test-setup-3medic-ttp-docker/**/bpe/process/*.jar
+dsf-docker-test-setup-3medic-ttp-docker/**/bpe/psn/*.jceks
+
+dsf-docker-test-setup-3medic-ttp-docker/**/fhir/log/*.log
+dsf-docker-test-setup-3medic-ttp-docker/**/fhir/log/*.log.gz
+
+dsf-docker-test-setup-3medic-ttp-docker/secrets/*.pem
+dsf-docker-test-setup-3medic-ttp-docker/.env
 
 ###
 # dsf-tools ignores

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,65 @@
+cff-version: 1.1.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Hund
+    given-names: Hauke
+  - family-names: Wettstein
+    given-names: Reto
+title: "HiGHmed Data Sharing Framework (HiGHmed DSF)"
+version: 0.5.0
+date-released: 2021-08-24
+url: https://github.com/highmed/highmed-dsf/wiki
+repository-code: https://github.com/highmed/highmed-dsf
+repository-artifact: https://github.com/highmed/highmed-dsf/releases
+license: Apache-2.0
+references:
+  - type: proceedings
+    authors:
+      - family-names: Hund
+        given-names: Hauke
+      - family-names: Wettstein
+        given-names: Reto
+      - family-names: Heidt
+        given-names: Christian M.
+      - family-names: Kobylinski
+        given-names: Insa
+      - family-names: Fegeler
+        given-names: Christian
+    title: "Executing Distributed Healthcare and Research Processes – The HiGHmed Data Sharing Framework"
+    journal: Stud Health Technol Inform
+    volume: 278
+    year: 2021
+    pages: 126-133
+    doi: 10.3233/SHTI210060
+  - type: proceedings
+    authors:
+      - family-names: Wettstein
+        given-names: Reto
+      - family-names: Hund
+        given-names: Hauke
+      - family-names: Kobylinski
+        given-names: Insa
+      - family-names: Fegeler
+        given-names: Christian
+      - family-names: Heinze
+        given-names: Oliver
+    title: "Feasibility Queries in Distributed Architectures – Concept and Implementation in HiGHmed"
+    journal: Stud Health Technol Inform
+    volume: 278
+    year: 2021
+    pages: 134-141
+    doi: 10.3233/SHTI210061
+  - type: proceedings
+    authors:
+      - family-names: Heidt
+        given-names: Christian M.
+      - family-names: Hund
+        given-names: Hauke
+      - family-names: Fegeler
+        given-names: Christian
+    title: "A Federated Record Linkage Algorithm for Secure Medical Data Sharing"
+    journal: Stud Health Technol Inform
+    volume: 278
+    year: 2021
+    pages: 142-149
+    doi: 10.3233/SHTI210062
diff --git a/dsf-bpe/dsf-bpe-process-base/pom.xml b/dsf-bpe/dsf-bpe-process-base/pom.xml
@@ -7,14 +7,18 @@
 	<parent>
 		<groupId>org.highmed.dsf</groupId>
 		<artifactId>dsf-bpe-pom</artifactId>
-		<version>0.4.0</version>
+		<version>0.5.0</version>
 	</parent>
 
 	<dependencies>
 		<dependency>
 			<groupId>org.highmed.dsf</groupId>
 			<artifactId>dsf-fhir-webservice-client</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.highmed.dsf</groupId>
+			<artifactId>dsf-fhir-auth</artifactId>
+		</dependency>
 
 		<dependency>
 			<groupId>org.highmed.dsf</groupId>
@@ -75,4 +79,42 @@
 			</plugin>
 		</plugins>
 	</build>
+
+	<profiles>
+		<profile>
+			<id>generate-source-and-javadoc-jars</id>
+
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-source-plugin</artifactId>
+						<executions>
+							<execution>
+								<id>attach-sources</id>
+								<goals>
+									<goal>test-jar</goal>
+								</goals>
+							</execution>
+						</executions>
+					</plugin>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-javadoc-plugin</artifactId>
+						<executions>
+							<execution>
+								<id>attach-javadocs</id>
+								<goals>
+									<goal>test-jar</goal>
+								</goals>
+								<configuration>
+									<detectOfflineLinks>false</detectOfflineLinks>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
 </project>
diff --git a/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ConstantsBase.java b/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ConstantsBase.java
@@ -4,23 +4,20 @@
 
 public interface ConstantsBase
 {
+	String BPMN_EXECUTION_VARIABLE_INSTANTIATES_URI = "instantiatesUri";
 	String BPMN_EXECUTION_VARIABLE_MESSAGE_NAME = "messageName";
-	String BPMN_EXECUTION_VARIABLE_PROCESS_DEFINITION_KEY = "processDefinitionKey";
-	String BPMN_EXECUTION_VARIABLE_VERSION_TAG = "versionTag";
 	String BPMN_EXECUTION_VARIABLE_PROFILE = "profile";
-	// String BPMN_EXECUTION_VARIABLE_TARGET_ORGANIZATION_ID = "targetOrganizationId";
-	// String BPMN_EXECUTION_VARIABLE_CORRELATION_KEY = "correlationKey";
 	String BPMN_EXECUTION_VARIABLE_TARGET = "target";
 	String BPMN_EXECUTION_VARIABLE_TARGETS = "targets";
 	String BPMN_EXECUTION_VARIABLE_TASK = "task";
 	String BPMN_EXECUTION_VARIABLE_LEADING_TASK = "leadingTask";
 	String BPMN_EXECUTION_VARIABLE_BUNDLE_ID = "bundleId";
 	String BPMN_EXECUTION_VARIABLE_QUERY_PARAMETERS = "queryParameters";
-	String BPMN_EXECUTION_VARIABLE_TTP_IDENTIFIER = "ttp";
+	String BPMN_EXECUTION_VARIABLE_TTP_IDENTIFIER = "ttpIdentifier";
+	String BPMN_EXECUTION_VARIABLE_LEADING_MEDIC_IDENTIFIER = "leadingMedicIdentifier";
 
 	/**
-	 * Used to distinguish if I am at the moment in a process called
-	 * by another process by a CallActivity or not
+	 * Used to distinguish if I am at the moment in a process called by another process by a CallActivity or not
 	 */
 	String BPMN_EXECUTION_VARIABLE_IN_CALLED_PROCESS = "inCalledProcess";
 
@@ -43,15 +40,23 @@ public interface ConstantsBase
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE = "http://highmed.org/fhir/CodeSystem/organization-type";
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_TTP = "TTP";
 	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_MEDIC = "MeDIC";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_DTS = "DTS";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_COS = "COS";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_CRR = "CRR";
+	String CODESYSTEM_HIGHMED_ORGANIZATION_TYPE_VALUE_HRP = "HRP";
 
 	String CODESYSTEM_HIGHMED_QUERY_TYPE = "http://highmed.org/fhir/CodeSystem/query-type";
 	String CODESYSTEM_HIGMED_QUERY_TYPE_VALUE_AQL = "application/x-aql-query";
 
-	String NAMINGSYSTEM_HIGHMED_ORGANIZATION_IDENTIFIER = "http://highmed.org/fhir/NamingSystem/organization-identifier";
-	String NAMINGSYSTEM_HIGHMED_ENDPOINT_IDENTIFIER = "http://highmed.org/fhir/NamingSystem/endpoint-identifier";
-	String NAMINGSYSTEM_HIGHMED_RESEARCH_STUDY_IDENTIFIER = "http://highmed.org/fhir/NamingSystem/research-study-identifier";
+	String NAMINGSYSTEM_HIGHMED_ORGANIZATION_IDENTIFIER = "http://highmed.org/sid/organization-identifier";
+	String NAMINGSYSTEM_HIGHMED_ENDPOINT_IDENTIFIER = "http://highmed.org/sid/endpoint-identifier";
+	String NAMINGSYSTEM_HIGHMED_RESEARCH_STUDY_IDENTIFIER = "http://highmed.org/sid/research-study-identifier";
 
 	CodeType CODE_TYPE_AQL_QUERY = new CodeType(CODESYSTEM_HIGMED_QUERY_TYPE_VALUE_AQL)
 			.setSystem(CODESYSTEM_HIGHMED_QUERY_TYPE);
 	String OPENEHR_MIMETYPE_JSON = "application/json";
+
+	String NAMINGSYSTEM_HIGHMED_ORGANIZATION_IDENTIFIER_HIGHMED_CONSORTIUM = "highmed.org";
+	String NAMINGSYSTEM_HIGHMED_ORGANIZATION_IDENTIFIER_NUM_CODEX_CONSORTIUM = "netzwerk-universitaetsmedizin.de";
+	String NAMINGSYSTEM_HIGHMED_ORGANIZATION_IDENTIFIER_MEDICAL_INFORMATICS_INITIATIVE_CONSORTIUM = "medizininformatik-initiative.de";
 }
diff --git a/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ProcessPluginDefinition.java b/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ProcessPluginDefinition.java
@@ -9,6 +9,7 @@
 import org.highmed.dsf.fhir.resources.ResourceProvider;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.core.env.PropertyResolver;
 
 import ca.uhn.fhir.context.FhirContext;
 
@@ -54,7 +55,7 @@ default String getNameAndVersion()
 	Stream<String> getBpmnFiles();
 
 	/**
-	 * @return @{@link Configuration} annotated classes defining @{@link Bean} annotated factory methods
+	 * @return {@link Configuration} annotated classes defining {@link Bean} annotated factory methods
 	 */
 	Stream<Class<?>> getSpringConfigClasses();
 
@@ -63,9 +64,13 @@ default String getNameAndVersion()
 	 *            the applications fhir context, never <code>null</code>
 	 * @param classLoader
 	 *            the classLoader that was used to initialize the process plugin, never <code>null</code>
+	 * @param resolver
+	 *            the property resolver used to access config properties and to replace place holders in fhir resources,
+	 *            never <code>null</code>
 	 * @return {@link ResourceProvider} with FHIR resources needed to enable the included processes
 	 */
-	default ResourceProvider getResourceProvider(FhirContext fhirContext, ClassLoader classLoader)
+	default ResourceProvider getResourceProvider(FhirContext fhirContext, ClassLoader classLoader,
+			PropertyResolver resolver)
 	{
 		return ResourceProvider.empty();
 	}