Merge remote-tracking branch 'origin/issues/100_upgrade_to_dsf_0.9.0'

hhund · hhund · commit 82e2e7fa8fd1 · 2022-10-17T22:24:53.000+02:00
into develop
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/crypto/CrrKeyProviderImpl.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/crypto/CrrKeyProviderImpl.java
@@ -26,7 +26,7 @@ public class CrrKeyProviderImpl implements CrrKeyProvider
 
 	/**
 	 * One or both parameters should be <code>null</code>
-	 * 
+	 *
 	 * @param crrPrivateKeyFile
 	 * @param crrPublicKeyFile
 	 * @return
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DecryptData.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DecryptData.java
@@ -108,7 +108,7 @@ private Optional<String> getPseudonym(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PSEUDONYM, Identifier.class).findFirst()
-						.map(Identifier::getValue);
+				.map(Identifier::getValue);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DownloadDataFromGth.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/DownloadDataFromGth.java
@@ -93,7 +93,7 @@ private Optional<String> getDataReference(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()
-						.map(Reference::getReference);
+				.map(Reference::getReference);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/DownloadValidationErrorFromGth.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/DownloadValidationErrorFromGth.java
@@ -92,7 +92,7 @@ private Optional<String> getDataReference(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()
-						.map(Reference::getReference);
+				.map(Reference::getReference);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ExtractPatientReference.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ExtractPatientReference.java
@@ -63,7 +63,7 @@ private Reference getPatientReference(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PATIENT, Reference.class).findFirst()
-						.orElseThrow(() -> new RuntimeException("No patient reference input parameter found"));
+				.orElseThrow(() -> new RuntimeException("No patient reference input parameter found"));
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/DownloadDataFromDic.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/DownloadDataFromDic.java
@@ -104,7 +104,7 @@ private Optional<String> getDataReference(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()
-						.map(Reference::getReference);
+				.map(Reference::getReference);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/DownloadValidationErrorFromCrr.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/DownloadValidationErrorFromCrr.java
@@ -61,7 +61,7 @@ private Optional<String> getDataReference(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()
-						.map(Reference::getReference);
+				.map(Reference::getReference);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/ReplacePseudonym.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/ReplacePseudonym.java
@@ -61,7 +61,7 @@ private Optional<String> getPseudonym(Task task)
 	{
 		return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,
 				CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PSEUDONYM, Identifier.class).findFirst()
-						.map(Identifier::getValue);
+				.map(Identifier::getValue);
 	}
 
 	private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/AbstractFhirResourceFileSystemCache.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/AbstractFhirResourceFileSystemCache.java
@@ -22,7 +22,7 @@ public abstract class AbstractFhirResourceFileSystemCache<T, R extends Resource>
 
 	/**
 	 * For JSON content with gzip compression using the <code>.json.gz</code> file name suffix.
-	 * 
+	 *
 	 * @param cacheFolder
 	 *            not <code>null</code>
 	 * @param resourceType
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/AbstractFileSystemCache.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/AbstractFileSystemCache.java
@@ -49,7 +49,7 @@ public interface BiConsumerWithIoException<T, U>
 
 	/**
 	 * For JSON content with gzip compression using the <code>.json.gz</code> file name suffix.
-	 * 
+	 *
 	 * @param cacheFolder
 	 *            not <code>null</code>
 	 * @see #FILENAME_SUFFIX
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/BundleValidator.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/BundleValidator.java
@@ -9,7 +9,7 @@ public interface BundleValidator extends ResourceValidator
 	/**
 	 * Validated all bundle entries with a <code>entry.resource</code>. The validation result will be added as a
 	 * {@link OperationOutcome} resource to the corresponding <code>entry.response.outcome</code> property.
-	 * 
+	 *
 	 * @param bundle
 	 *            not <code>null</code>
 	 * @return given bundle with added <code>entry.response.outcome</code> properties
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/PluginSnapshotGeneratorWithFileSystemCache.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/PluginSnapshotGeneratorWithFileSystemCache.java
@@ -27,7 +27,7 @@ public class PluginSnapshotGeneratorWithFileSystemCache
 
 	/**
 	 * For JSON content with gzip compression using the <code>.json.xz</code> file name suffix.
-	 * 
+	 *
 	 * @param cacheFolder
 	 *            not <code>null</code>
 	 * @param fhirContext
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageClientWithFileSystemCache.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageClientWithFileSystemCache.java
@@ -20,7 +20,7 @@ public class ValidationPackageClientWithFileSystemCache extends AbstractFileSyst
 
 	/**
 	 * For JSON content with gzip compression using the <code>.json.xz</code> file name suffix.
-	 * 
+	 *
 	 * @param cacheFolder
 	 *            not <code>null</code>
 	 * @param mapper
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageEntry.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageEntry.java
@@ -16,7 +16,7 @@ public class ValidationPackageEntry
 {
 	/**
 	 * Does not close the input stream.
-	 * 
+	 *
 	 * @param entry
 	 *            not <code>null</code>
 	 * @param in
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManager.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManager.java
@@ -10,7 +10,7 @@ public interface ValidationPackageManager
 {
 	/**
 	 * Downloads the given FHIR package and all its dependencies.
-	 * 
+	 *
 	 * @param name
 	 *            not <code>null</code>
 	 * @param version
@@ -24,7 +24,7 @@ default ValidationPackageWithDepedencies downloadPackageWithDependencies(String
 
 	/**
 	 * Downloads the given FHIR package and all its dependencies.
-	 * 
+	 *
 	 * @param name
 	 *            not <code>null</code>
 	 * @param version
@@ -38,7 +38,7 @@ default ValidationPackageWithDepedencies downloadPackageWithDependencies(String
 	 * will try to expand all {@link ValueSet}s with binding strength {@link BindingStrength#EXTENSIBLE},
 	 * {@link BindingStrength#PREFERRED} or {@link BindingStrength#REQUIRED} used by the {@link StructureDefinition} of
 	 * the root package or their dependencies, before returning a {@link IValidationSupport}.
-	 * 
+	 *
 	 * @param packageWithDependencies
 	 *            not <code>null</code>
 	 * @return validation support for the validator
@@ -63,7 +63,7 @@ BundleValidator createBundleValidator(IValidationSupport validationSupport,
 	 * {@link ValueSet}s with binding strength {@link BindingStrength#EXTENSIBLE}, {@link BindingStrength#PREFERRED} or
 	 * {@link BindingStrength#REQUIRED} used by the {@link StructureDefinition} of the specified (root) package or their
 	 * dependencies, before returning a {@link IValidationSupport}.
-	 * 
+	 *
 	 * @param name
 	 *            not <code>null</code>
 	 * @param version
@@ -81,7 +81,7 @@ default BundleValidator createBundleValidator(String name, String version)
 	 * {@link ValueSet}s with binding strength {@link BindingStrength#EXTENSIBLE}, {@link BindingStrength#PREFERRED} or
 	 * {@link BindingStrength#REQUIRED} used by the {@link StructureDefinition} of the specified (root) package or their
 	 * dependencies, before returning a {@link IValidationSupport}.
-	 * 
+	 *
 	 * @param identifier
 	 *            not <code>null</code>
 	 * @return {@link BundleValidator} for the specified FHIR package
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpanderWithFileSystemCache.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpanderWithFileSystemCache.java
@@ -26,7 +26,7 @@ public class ValueSetExpanderWithFileSystemCache
 
 	/**
 	 * For JSON content with gzip compression using the <code>.json.xz</code> file name suffix.
-	 * 
+	 *
 	 * @param cacheFolder
 	 *            not <code>null</code>
 	 * @param resourceType
diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithFileSystemCache.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithFileSystemCache.java
@@ -27,7 +27,7 @@ public class ValueSetExpansionClientWithFileSystemCache extends AbstractFhirReso
 
 	/**
 	 * For JSON content with gzip compression using the <code>.json.xz</code> file name suffix.
-	 * 
+	 *
 	 * @param cacheFolder
 	 *            not <code>null</code>
 	 * @param fhirContext
diff --git a/pom.xml b/pom.xml
@@ -19,7 +19,7 @@
 
 		<main.basedir>${project.basedir}</main.basedir>
 		<hapi.version>5.1.0</hapi.version>
-		<dsf.version>0.9.0-RC1</dsf.version>
+		<dsf.version>0.9.0</dsf.version>
 	</properties>
 
 	<description>Business processes for the NUM CODEX project (AP1) as plugins for the HiGHmed Data Sharing Framework.</description>
@@ -104,12 +104,12 @@
 			<dependency>
 				<groupId>de.hs-heilbronn.mi</groupId>
 				<artifactId>log4j2-utils</artifactId>
-				<version>0.13.0</version>
+				<version>0.14.0</version>
 			</dependency>
 			<dependency>
 				<groupId>de.hs-heilbronn.mi</groupId>
 				<artifactId>crypto-utils</artifactId>
-				<version>3.3.0</version>
+				<version>3.4.0</version>
 			</dependency>
 
 			<!-- logging -->
@@ -134,7 +134,7 @@
 			<dependency>
 			    <groupId>org.mockito</groupId>
 			    <artifactId>mockito-core</artifactId>
-			    <version>4.5.1</version>
+			    <version>4.8.0</version>
 			</dependency>
 		</dependencies>
 	</dependencyManagement>
@@ -145,7 +145,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.8.1</version>
+					<version>3.10.1</version>
 					<configuration>
 						<source>${compileSource}</source>
 						<target>${compileTarget}</target>
@@ -154,12 +154,12 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-surefire-plugin</artifactId>
-					<version>3.0.0-M5</version>
+					<version>3.0.0-M7</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-jar-plugin</artifactId>
-					<version>3.2.0</version>
+					<version>3.3.0</version>
 					<configuration>
 						<archive>
 							<manifest>
@@ -178,22 +178,22 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-dependency-plugin</artifactId>
-					<version>3.2.0</version>
+					<version>3.3.0</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-clean-plugin</artifactId>
-					<version>3.1.0</version>
+					<version>3.2.0</version>
 				</plugin>
 				<plugin>
 					<groupId>net.revelc.code.formatter</groupId>
 					<artifactId>formatter-maven-plugin</artifactId>
-					<version>2.17.1</version>
+					<version>2.20.0</version>
 				</plugin>
 				<plugin>
 					<groupId>net.revelc.code</groupId>
 					<artifactId>impsort-maven-plugin</artifactId>
-					<version>1.6.2</version>
+					<version>1.7.0</version>
 				</plugin>
 				<plugin>
 					<groupId>org.codehaus.mojo</groupId>

Original file line number	Diff line number	Diff line change
`@@ -108,7 +108,7 @@ private Optional<String> getPseudonym(Task task)`
`108`	`108`	`{`
`109`	`109`	`return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,`
`110`	`110`	`CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PSEUDONYM, Identifier.class).findFirst()`
`111`		`- .map(Identifier::getValue);`
	`111`	`+ .map(Identifier::getValue);`
`112`	`112`	`}`
`113`	`113`
`114`	`114`	`private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)`
Original file line number	Diff line number	Diff line change
`@@ -93,7 +93,7 @@ private Optional<String> getDataReference(Task task)`
`93`	`93`	`{`
`94`	`94`	`return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,`
`95`	`95`	`CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()`
`96`		`- .map(Reference::getReference);`
	`96`	`+ .map(Reference::getReference);`
`97`	`97`	`}`
`98`	`98`
`99`	`99`	`private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)`
Original file line number	Diff line number	Diff line change
`@@ -92,7 +92,7 @@ private Optional<String> getDataReference(Task task)`
`92`	`92`	`{`
`93`	`93`	`return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,`
`94`	`94`	`CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()`
`95`		`- .map(Reference::getReference);`
	`95`	`+ .map(Reference::getReference);`
`96`	`96`	`}`
`97`	`97`
`98`	`98`	`private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)`
Original file line number	Diff line number	Diff line change
`@@ -63,7 +63,7 @@ private Reference getPatientReference(Task task)`
`63`	`63`	`{`
`64`	`64`	`return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,`
`65`	`65`	`CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_PATIENT, Reference.class).findFirst()`
`66`		`- .orElseThrow(() -> new RuntimeException("No patient reference input parameter found"));`
	`66`	`+ .orElseThrow(() -> new RuntimeException("No patient reference input parameter found"));`
`67`	`67`	`}`
`68`	`68`
`69`	`69`	`private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)`
Original file line number	Diff line number	Diff line change
`@@ -104,7 +104,7 @@ private Optional<String> getDataReference(Task task)`
`104`	`104`	`{`
`105`	`105`	`return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,`
`106`	`106`	`CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()`
`107`		`- .map(Reference::getReference);`
	`107`	`+ .map(Reference::getReference);`
`108`	`108`	`}`
`109`	`109`
`110`	`110`	`private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)`
Original file line number	Diff line number	Diff line change
`@@ -61,7 +61,7 @@ private Optional<String> getDataReference(Task task)`
`61`	`61`	`{`
`62`	`62`	`return getInputParameterValues(task, CODESYSTEM_NUM_CODEX_DATA_TRANSFER,`
`63`	`63`	`CODESYSTEM_NUM_CODEX_DATA_TRANSFER_VALUE_DATA_REFERENCE, Reference.class).findFirst()`
`64`		`- .map(Reference::getReference);`
	`64`	`+ .map(Reference::getReference);`
`65`	`65`	`}`
`66`	`66`
`67`	`67`	`private <T extends Type> Stream<T> getInputParameterValues(Task task, String system, String code, Class<T> type)`