Issue/448 upgrade dependencies

dsf-bpe/dsf-bpe-process-api-v1-base/pom.xml

@@ -92,4 +92,16 @@
 			</plugin>
 		</plugins>
 	</build>
+
+	<reporting>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-javadoc-plugin</artifactId>
+				<configuration>
+					<skip>true</skip>
+				</configuration>
+			</plugin>
+		</plugins>
+	</reporting>
 </project>

dsf-bpe/dsf-bpe-process-api-v1-impl/src/main/java/dev/dsf/bpe/v1/plugin/ProcessPluginFactoryImpl.java

@@ -56,10 +56,10 @@ protected ProcessPlugin createProcessPlugin(Object processPluginDefinition, bool
 	}
 
 	@Override
-	@SuppressWarnings("rawtypes")
-	public Stream<TypedValueSerializer> getSerializer()
+	public Stream<TypedValueSerializer<?>> getSerializer()
 	{
-		return apiApplicationContext.getBeansOfType(TypedValueSerializer.class).values().stream();
+		return apiApplicationContext.getBeansOfType(TypedValueSerializer.class).values().stream()
+				.map(s -> (TypedValueSerializer<?>) s);
 	}
 
 	@Override

dsf-bpe/dsf-bpe-process-api-v1-impl/src/main/java/dev/dsf/fhir/client/AbstractFhirWebserviceClientJerseyWithRetry.java

@@ -64,20 +64,24 @@ else if (nTimes != RetryClient.RETRY_FOREVER)
 				{
 					if (tryNumber < nTimes || nTimes == RetryClient.RETRY_FOREVER)
 					{
-						logger.warn("Caught {} - {}; trying again in {}s{}", e.getClass(), e.getMessage(), delay,
-								nTimes == RetryClient.RETRY_FOREVER ? " (retry " + (tryNumber + 1) + ")" : "");
+						logger.warn("Caught {} - {}; trying again in {}s{}", e.getClass().getName(), e.getMessage(),
+								delay, nTimes == RetryClient.RETRY_FOREVER ? " (retry " + (tryNumber + 1) + ")" : "");
 
 						try
 						{
 							Thread.sleep(delay);
 						}
 						catch (InterruptedException e1)
 						{
+							logger.warn("Thread interrupted; not trying again");
+							Thread.currentThread().interrupt();
+							e.addSuppressed(e1);
+							throw e;
 						}
 					}
 					else
 					{
-						logger.warn("Caught {} - {}; not trying again", e.getClass(), e.getMessage());
+						logger.warn("Caught {} - {}; not trying again", e.getClass().getName(), e.getMessage());
 					}
 
 					if (caughtException != null)

dsf-bpe/dsf-bpe-process-api-v2-impl/src/main/java/dev/dsf/bpe/v2/client/dsf/AbstractDsfClientJerseyWithRetry.java

@@ -68,7 +68,7 @@ else if (nTimes != RetryClient.RETRY_FOREVER)
 						if (tryNumber > 0)
 							delay = delayStrategy.getNextDelay(delay);
 
-						logger.warn("Caught {} - {}; trying again in {}{}", e.getClass(), e.getMessage(),
+						logger.warn("Caught {} - {}; trying again in {}{}", e.getClass().getName(), e.getMessage(),
 								delay.toString(),
 								nTimes == RetryClient.RETRY_FOREVER ? " (retry " + (tryNumber + 1) + ")" : "");
 
@@ -78,11 +78,15 @@ else if (nTimes != RetryClient.RETRY_FOREVER)
 						}
 						catch (InterruptedException e1)
 						{
+							logger.warn("Thread interrupted; not trying again");
+							Thread.currentThread().interrupt();
+							e.addSuppressed(e1);
+							throw e;
 						}
 					}
 					else
 					{
-						logger.warn("Caught {} - {}; not trying again", e.getClass(), e.getMessage());
+						logger.warn("Caught {} - {}; not trying again", e.getClass().getName(), e.getMessage());
 					}
 
 					if (caughtException != null)

dsf-bpe/dsf-bpe-process-api-v2-impl/src/main/java/dev/dsf/bpe/v2/plugin/ProcessPluginFactoryImpl.java

@@ -48,10 +48,10 @@ protected ProcessPlugin createProcessPlugin(Object processPluginDefinition, bool
 	}
 
 	@Override
-	@SuppressWarnings("rawtypes")
-	public Stream<TypedValueSerializer> getSerializer()
+	public Stream<TypedValueSerializer<?>> getSerializer()
 	{
-		return apiApplicationContext.getBeansOfType(TypedValueSerializer.class).values().stream();
+		return apiApplicationContext.getBeansOfType(TypedValueSerializer.class).values().stream()
+				.map(s -> (TypedValueSerializer<?>) s);
 	}
 
 	@Override

dsf-bpe/dsf-bpe-process-api/src/main/java/dev/dsf/bpe/api/plugin/ProcessPluginFactory.java

@@ -26,8 +26,7 @@ public interface ProcessPluginFactory
 {
 	int getApiVersion();
 
-	@SuppressWarnings("rawtypes")
-	Stream<TypedValueSerializer> getSerializer();
+	Stream<TypedValueSerializer<?>> getSerializer();
 
 	ListenerFactory getListenerFactory();
 

dsf-bpe/dsf-bpe-server-jetty/docker/Dockerfile

@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM debian:trixie-slim@sha256:1d3c811171a08a5adaa4a163fbafd96b61b87aa871bbc7aa15431ac275d3d430 AS builder
+FROM debian:trixie-slim@sha256:4ffb3a1511099754cddc70eb1b12e50ffdb67619aa0ab6c13fcd800a78ef7c7a AS builder
 WORKDIR /opt/bpe
 COPY --chown=root:2202 ./ ./
 RUN chown root:2202 ./ && \
@@ -23,7 +23,7 @@ RUN chown root:2202 ./ && \
     chmod 1775 ./log
 
 
-FROM azul/zulu-openjdk:25-jre-headless@sha256:c8e35e74e2cfbdeffb4e4850123c41378d3ec0a6d80f17d2f9f3a9293f9236e6
+FROM azul/zulu-openjdk:25-jre-headless@sha256:205a88e67ff7acca2c4452c60fd078a95f6e5a7c9a3bc8bad83dbd3a140c58f4
 LABEL org.opencontainers.image.source=https://github.com/datasharingframework/dsf
 LABEL org.opencontainers.image.description="DSF BPE Server"
 LABEL org.opencontainers.image.licenses="Apache License, Version 2.0"

dsf-bpe/dsf-bpe-server/src/main/java/dev/dsf/bpe/client/dsf/AbstractWebserviceClientJerseyWithRetry.java

@@ -63,7 +63,7 @@ else if (nTimes != RetryClient.RETRY_FOREVER)
 				{
 					if (tryNumber < nTimes || nTimes == RetryClient.RETRY_FOREVER)
 					{
-						logger.warn("Caught {} - {}; trying again in {}s{}", e.getClass(), e.getMessage(),
+						logger.warn("Caught {} - {}; trying again in {}s{}", e.getClass().getName(), e.getMessage(),
 								delay.toSeconds(),
 								nTimes == RetryClient.RETRY_FOREVER ? " (retry " + (tryNumber + 1) + ")" : "");
 
@@ -73,11 +73,15 @@ else if (nTimes != RetryClient.RETRY_FOREVER)
 						}
 						catch (InterruptedException e1)
 						{
+							logger.warn("Thread interrupted; not trying again");
+							Thread.currentThread().interrupt();
+							e.addSuppressed(e1);
+							throw e;
 						}
 					}
 					else
 					{
-						logger.warn("Caught {} - {}; not trying again", e.getClass(), e.getMessage());
+						logger.warn("Caught {} - {}; not trying again", e.getClass().getName(), e.getMessage());
 					}
 
 					if (caughtException != null)

dsf-bpe/dsf-bpe-server/src/main/java/dev/dsf/bpe/plugin/ProcessPluginApiClassLoader.java

@@ -82,7 +82,7 @@ protected Class<?> loadClass(String className, boolean resolve) throws ClassNotF
 			if (isBpeClassAllowed(bpeClass))
 				return bpeClass;
 
-			logger.debug("Class " + className + " not found or hidden");
+			logger.debug("Class {} not found or hidden", className);
 			throw new ClassNotFoundException(className);
 		}
 	}

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

@@ -167,7 +167,7 @@ private void testConnection(FhirClientConfig config)
 		}
 		catch (OidcClientException e)
 		{
-			logger.debug("Testing connection with OIDC provider at {} for '{}' [Failed] -> {}",
+			logger.debug("Testing connection with OIDC provider at {} for '{}' [Failed]",
 					config.oidcAuthentication().baseUrl(), config.fhirServerId(), e);
 			logger.warn("Testing connection with OIDC provider at {} for '{}' [Failed] -> {}",
 					config.oidcAuthentication().baseUrl(), config.fhirServerId(), e.getMessage());

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

@@ -153,6 +153,10 @@ private Subscription retry(Supplier<Subscription> supplier)
 					}
 					catch (InterruptedException e1)
 					{
+						logger.warn("Thread interrupted; not trying again");
+						Thread.currentThread().interrupt();
+						e.addSuppressed(e1);
+						throw e;
 					}
 				}
 
@@ -184,6 +188,10 @@ private Subscription retryForever(Supplier<Subscription> supplier)
 				}
 				catch (InterruptedException e1)
 				{
+					logger.warn("Thread interrupted; not trying again");
+					Thread.currentThread().interrupt();
+					e.addSuppressed(e1);
+					throw e;
 				}
 			}
 		}

dsf-bpe/dsf-bpe-test-plugin-v2/src/main/java/dev/dsf/bpe/test/service/QuestionnaireTestAnswer.java

@@ -162,9 +162,9 @@ else if ("identifiers".equals(type))
 				expectNotNull(idExts);
 				expectSame(3, idExts.size());
 
-				idExts.stream().filter(Extension::hasValue).filter(e -> e.getValue() instanceof Identifier)
+				expectTrue(idExts.stream().filter(Extension::hasValue).filter(e -> e.getValue() instanceof Identifier)
 						.map(e -> (Identifier) e.getValue()).map(Identifier::getSystem)
-						.allMatch(NamingSystems.PractitionerIdentifier.SID::equals);
+						.allMatch(NamingSystems.PractitionerIdentifier.SID::equals));
 
 				List<String> values = idExts.stream().filter(Extension::hasValue)
 						.filter(e -> e.getValue() instanceof Identifier).map(e -> (Identifier) e.getValue())

dsf-common/dsf-common-db/src/main/java/dev/dsf/common/db/migration/DbMigrator.java

@@ -18,6 +18,7 @@
 import java.io.ByteArrayOutputStream;
 import java.net.ConnectException;
 import java.net.UnknownHostException;
+import java.nio.charset.StandardCharsets;
 import java.sql.Connection;
 import java.sql.SQLException;
 import java.util.Arrays;
@@ -134,8 +135,8 @@ public void migrate()
 							logger.warn("Unlocking DB for migration ...");
 							unlockCommand.execute();
 
-							Arrays.stream(output.toString().split("[\r\n]+")).filter(row -> !row.isBlank())
-									.forEach(row -> logger.debug("{}", row));
+							Arrays.stream(output.toString(StandardCharsets.UTF_8).split("[\r\n]+"))
+									.filter(row -> !row.isBlank()).forEach(row -> logger.debug("{}", row));
 							logger.warn("Unlocking DB for migration [Done]");
 						}
 
@@ -156,8 +157,8 @@ public void migrate()
 						logger.info("Executing DB migration ...");
 						updateCommand.execute();
 
-						Arrays.stream(output.toString().split("[\r\n]+")).filter(row -> !row.isBlank())
-								.forEach(row -> logger.debug("{}", row));
+						Arrays.stream(output.toString(StandardCharsets.UTF_8).split("[\r\n]+"))
+								.filter(row -> !row.isBlank()).forEach(row -> logger.debug("{}", row));
 						logger.info("Executing DB migration [Done]");
 					}
 				}
@@ -214,6 +215,10 @@ public static void retryOnConnectException(int times, Runnable run)
 				}
 				catch (InterruptedException e1)
 				{
+					logger.warn("Thread interrupted; not trying again");
+					Thread.currentThread().interrupt();
+					e.addSuppressed(e1);
+					throw e;
 				}
 				retryOnConnectException(--times, run);
 			}
@@ -226,19 +231,28 @@ else if (cause instanceof UnknownHostException && times > 1)
 				}
 				catch (InterruptedException e1)
 				{
+					logger.warn("Thread interrupted; not trying again");
+					Thread.currentThread().interrupt();
+					e.addSuppressed(e1);
+					throw e;
 				}
 				retryOnConnectException(--times, run);
 			}
-			else if (cause instanceof PSQLException p
+			else if (cause instanceof PSQLException p && p.getServerErrorMessage() != null
 					&& POSTGRES_TRY_AGAIN_ERROR_MESSAGES.contains(p.getServerErrorMessage().getMessage()) && times > 1)
 			{
-				logger.warn("PSQLException ({}): trying again in 5s", p.getServerErrorMessage().getMessage());
+				logger.warn("PSQLException ({}): trying again in 5s",
+						p.getServerErrorMessage() != null ? p.getServerErrorMessage().getMessage() : "?");
 				try
 				{
 					Thread.sleep(5_000);
 				}
 				catch (InterruptedException e1)
 				{
+					logger.warn("Thread interrupted; not trying again");
+					Thread.currentThread().interrupt();
+					e.addSuppressed(e1);
+					throw e;
 				}
 				retryOnConnectException(--times, run);
 			}

dsf-common/dsf-common-jetty/src/main/java/dev/dsf/common/jetty/HttpClientWithGetRetry.java

@@ -75,6 +75,10 @@ public ContentResponse GETWithRetryOnConnectException(int times, URI uri)
 				}
 				catch (InterruptedException e1)
 				{
+					logger.warn("Thread interrupted; not trying again");
+					Thread.currentThread().interrupt();
+					e.addSuppressed(e1);
+					throw e;
 				}
 
 				return GETWithRetryOnConnectException(--times, uri);
@@ -90,6 +94,10 @@ else if (cause instanceof UnknownHostException && times > 1)
 				}
 				catch (InterruptedException e1)
 				{
+					logger.warn("Thread interrupted; not trying again");
+					Thread.currentThread().interrupt();
+					e.addSuppressed(e1);
+					throw e;
 				}
 
 				return GETWithRetryOnConnectException(--times, uri);

dsf-fhir/dsf-fhir-server-jetty/docker/Dockerfile

@@ -14,7 +14,7 @@
 # limitations under the License.
 #
 
-FROM debian:trixie-slim@sha256:1d3c811171a08a5adaa4a163fbafd96b61b87aa871bbc7aa15431ac275d3d430 AS builder
+FROM debian:trixie-slim@sha256:4ffb3a1511099754cddc70eb1b12e50ffdb67619aa0ab6c13fcd800a78ef7c7a AS builder
 WORKDIR /opt/fhir
 COPY --chown=root:2101 ./ ./
 RUN chown root:2101 ./ && \
@@ -23,7 +23,7 @@ RUN chown root:2101 ./ && \
     chmod 1775 ./log
 
 
-FROM azul/zulu-openjdk:25-jre-headless@sha256:c8e35e74e2cfbdeffb4e4850123c41378d3ec0a6d80f17d2f9f3a9293f9236e6
+FROM azul/zulu-openjdk:25-jre-headless@sha256:205a88e67ff7acca2c4452c60fd078a95f6e5a7c9a3bc8bad83dbd3a140c58f4
 LABEL org.opencontainers.image.source=https://github.com/datasharingframework/dsf
 LABEL org.opencontainers.image.description="DSF FHIR Server"
 LABEL org.opencontainers.image.licenses="Apache License, Version 2.0"

dsf-fhir/dsf-fhir-server/src/main/java/dev/dsf/fhir/adapter/ResourceBinary.java

@@ -70,7 +70,7 @@ private String toDataSize(Binary resource)
 			unitIndex++;
 		}
 
-		if (value == (long) value)
+		if (Math.abs(value - (long) value) < .0000001)
 			return String.format("%d %s", (long) value, UNITS[unitIndex]);
 		else
 			return String.format("%.2f %s", value, UNITS[unitIndex]);

dsf-fhir/dsf-fhir-server/src/main/java/dev/dsf/fhir/adapter/SearchSetBinary.java

@@ -66,7 +66,7 @@ private String toDataSize(Binary resource)
 			unitIndex++;
 		}
 
-		if (value == (long) value)
+		if (Math.abs(value - (long) value) < .0000001)
 			return String.format("%d %s", (long) value, UNITS[unitIndex]);
 		else
 			return String.format("%.2f %s", value, UNITS[unitIndex]);

dsf-fhir/dsf-fhir-server/src/main/java/dev/dsf/fhir/dao/jdbc/BinaryDaoJdbc.java

@@ -272,6 +272,7 @@ public void stopLargeObjectUnlinker()
 		catch (InterruptedException ex)
 		{
 			loUnlinker.shutdownNow();
+			Thread.currentThread().interrupt();
 		}
 	}
 }

dsf-fhir/dsf-fhir-validation/src/main/java/dev/dsf/fhir/validation/SnapshotGeneratorImpl.java

@@ -67,8 +67,8 @@ public SnapshotWithValidationMessages generateSnapshot(StructureDefinition diffe
 			String baseAbsoluteUrlPrefix)
 	{
 		if (differential == null)
-			return new SnapshotWithValidationMessages(differential, List.of(new ValidationMessage(null,
-					IssueType.PROCESSING, null, "StructureDefinition is null", IssueSeverity.ERROR)));
+			return new SnapshotWithValidationMessages(null, List.of(new ValidationMessage(null, IssueType.PROCESSING,
+					null, "StructureDefinition is null", IssueSeverity.ERROR)));
 		if (!differential.hasBaseDefinition())
 			return new SnapshotWithValidationMessages(differential, List.of(new ValidationMessage(null,
 					IssueType.PROCESSING, null, "StructureDefinition.baseDefinition missing", IssueSeverity.ERROR)));

dsf-fhir/dsf-fhir-validation/src/main/java/dev/dsf/fhir/validation/StructureDefinitionReader.java

@@ -112,9 +112,6 @@ private StructureDefinition doReadXml(Path xmlPath)
 	{
 		try (InputStream in = Files.newInputStream(xmlPath))
 		{
-			if (in == null)
-				logger.warn("File {} not found", xmlPath);
-
 			return context.newXmlParser().parseResource(StructureDefinition.class, in);
 		}
 		catch (DataFormatException | IOException e)
@@ -127,9 +124,6 @@ private StructureDefinition doReadXmlAndReplaceVersion(Path xmlPath, String vers
 	{
 		try (InputStream in = Files.newInputStream(xmlPath))
 		{
-			if (in == null)
-				logger.warn("File {} not found", xmlPath);
-
 			String read = IOUtils.toString(in, StandardCharsets.UTF_8);
 			read = replaceVersionAndDate(read, version, date);
 

dsf-fhir/dsf-fhir-validation/src/main/java/dev/dsf/fhir/validation/ValidationSupportRule.java

@@ -151,7 +151,7 @@ private void warnForDeprecatedResources(String resource, List<String> file)
 			}
 			catch (IOException e)
 			{
-				logger.warn("FHIR resource " + f + " is deprecated, unable to read replacement message: {}",
+				logger.warn("FHIR resource {} is deprecated, unable to read replacement message: {}", f,
 						e.getMessage());
 			}
 		});