#414: further lib updates

oehf · Jan 29, 2024 · af18eda · af18eda
1 parent 8216cd8
commit af18eda
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Showing 17 changed files with 120 additions and 68 deletions.
diff --git a/commons/audit/src/main/java/org/openehealth/ipf/commons/audit/server/TlsSyslogServer.java b/commons/audit/src/main/java/org/openehealth/ipf/commons/audit/server/TlsSyslogServer.java
@@ -23,8 +23,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import reactor.netty.DisposableChannel;
+import reactor.netty.internal.util.Metrics;
 import reactor.netty.tcp.TcpServer;
-import reactor.util.Metrics;
 
 import java.time.Duration;
 import java.util.Map;
@@ -63,7 +63,7 @@ public TlsSyslogServer doStart(String host, int port) {
                 .option(ChannelOption.CONNECT_TIMEOUT_MILLIS, 10000)
                 .option(ChannelOption.RCVBUF_ALLOCATOR, new FixedRecvByteBufAllocator(65535))
                 .wiretap(getClass().getName(), LogLevel.TRACE)
-                .metrics(Metrics.isInstrumentationAvailable())
+                .metrics(Metrics.isMicrometerAvailable())
                 .secure(spec -> spec.sslContext(sslContext))
                 .doOnBind(serverBootstrap -> LOG.info("TLS Syslog Server is about to be started"))
                 .doOnBound(disposableServer -> LOG.info("TLS Syslog Server bound on {}", disposableServer.address()))

diff --git a/commons/ihe/fhir/core/pom.xml b/commons/ihe/fhir/core/pom.xml
@@ -36,6 +36,10 @@
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-validation</artifactId>
         </dependency>
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-caching-caffeine</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.fasterxml.woodstox</groupId>
             <artifactId>woodstox-core</artifactId>

diff --git a/...e/src/main/java/org/openehealth/ipf/commons/ihe/fhir/audit/GenericPatientIdExtractor.java b/...e/src/main/java/org/openehealth/ipf/commons/ihe/fhir/audit/GenericPatientIdExtractor.java
@@ -56,7 +56,8 @@ public Optional<? extends IBaseReference> patientReferenceFromResource(IBaseReso
                 try {
                     return SearchParameterUtil.getOnlyPatientSearchParamForResourceType(fhirContext, resourceDefinition.getName())
                             .map(RuntimeSearchParam::getPath)
-                            .flatMap(path -> fhirContext.newFhirPath().evaluateFirst(resource, simplifyPath(path), IBaseReference.class));
+                            .map(this::simplifyPath)
+                            .flatMap(path -> fhirContext.newFhirPath().evaluateFirst(resource, path, IBaseReference.class));
                 } catch (Exception e) {
                     return Optional.empty();
                 }

diff --git a/.../src/main/java/org/openehealth/ipf/commons/ihe/hl7v2/definitions/pam/v25/segment/ZBE.java b/.../src/main/java/org/openehealth/ipf/commons/ihe/hl7v2/definitions/pam/v25/segment/ZBE.java
@@ -15,6 +15,7 @@
  */
 package org.openehealth.ipf.commons.ihe.hl7v2.definitions.pam.v25.segment;
 
+import ca.uhn.hl7v2.HL7Exception;
 import ca.uhn.hl7v2.model.AbstractSegment;
 import ca.uhn.hl7v2.model.Group;
 import ca.uhn.hl7v2.model.v25.datatype.*;
@@ -42,15 +43,19 @@ public class ZBE extends AbstractSegment {
     public ZBE(Group parent, ModelClassFactory factory) {
         super(parent, factory);
         var message = getMessage();
-        add(EI.class, true, 0, 427, new Object[] { message }, "Movement ID");
-        add(TS.class, true, 1, 26, new Object[] { message }, "Start Movement Date/Time");
-        add(TS.class, false, 1, 26, new Object[] { message }, "End Movement Date/Time");
-        add(ST.class, true, 1, 6, new Object[] { message }, "Movement Action");
-        add(ID.class, true, 1, 1, new Object[] { message }, "Historical Movement Indicator");
-        add(ID.class, false, 1, 3, new Object[] { message }, "Original trigger event code");
-        add(XON.class, false, 1, 567, new Object[] { message }, "Responsible Ward");
-        add(XON.class, false, 1, 567, new Object[] { message }, "Responsible Nursing Ward");
-        add(CWE.class, false, 1, 3, new Object[] { message }, "Movement Scope");
+        try {
+            add(EI.class, true, 0, 427, new Object[] { message }, "Movement ID");
+            add(TS.class, true, 1, 26, new Object[] { message }, "Start Movement Date/Time");
+            add(TS.class, false, 1, 26, new Object[] { message }, "End Movement Date/Time");
+            add(ST.class, true, 1, 6, new Object[] { message }, "Movement Action");
+            add(ID.class, true, 1, 1, new Object[] { message }, "Historical Movement Indicator");
+            add(ID.class, false, 1, 3, new Object[] { message }, "Original trigger event code");
+            add(XON.class, false, 1, 567, new Object[] { message }, "Responsible Ward");
+            add(XON.class, false, 1, 567, new Object[] { message }, "Responsible Nursing Ward");
+            add(CWE.class, false, 1, 3, new Object[] { message }, "Movement Scope");
+        } catch(HL7Exception e) {
+            log.error("Unexpected error creating ZBE - this is probably a bug in the source code generator.", e);
+        }
     }
 
     /**

diff --git a/.../src/main/java/org/openehealth/ipf/commons/ihe/hl7v2/definitions/pdq/v25/segment/QPD.java b/.../src/main/java/org/openehealth/ipf/commons/ihe/hl7v2/definitions/pdq/v25/segment/QPD.java
@@ -21,6 +21,7 @@
 import ca.uhn.hl7v2.model.Type;
 import ca.uhn.hl7v2.model.v25.datatype.*;
 import ca.uhn.hl7v2.parser.ModelClassFactory;
+import org.openehealth.ipf.modules.hl7.HL7v2Exception;
 
 
 /**
@@ -46,14 +47,18 @@ public class QPD extends AbstractSegment {
     public QPD(Group parentGroup, ModelClassFactory modelFactory) {
         super(parentGroup, modelFactory);
         var msg = getMessage();
-        add(CE.class, true, 1, 250, new Object[]{msg}, "Message Query Name");
-        add(ST.class, true, 1, 32, new Object[]{msg}, "Query Tag");
-        add(QIP.class, true, 0, 256, new Object[]{msg}, "Demographics Fields");
-        add(NM.class, false, 1, 16, new Object[]{msg}, "Search Confidence Threshold");
-        add(ST.class, false, 1, 199, new Object[]{msg}, "Algorithm Name");
-        add(ST.class, false, 1, 199, new Object[]{msg}, "Algorithm Version");
-        add(ST.class, false, 1, 199, new Object[]{msg}, "Algorithm Description");
-        add(CX.class, false, 0, 256, new Object[]{msg}, "What domains returned");
+        try {
+            add(CE.class, true, 1, 250, new Object[]{msg}, "Message Query Name");
+            add(ST.class, true, 1, 32, new Object[]{msg}, "Query Tag");
+            add(QIP.class, true, 0, 256, new Object[]{msg}, "Demographics Fields");
+            add(NM.class, false, 1, 16, new Object[]{msg}, "Search Confidence Threshold");
+            add(ST.class, false, 1, 199, new Object[]{msg}, "Algorithm Name");
+            add(ST.class, false, 1, 199, new Object[]{msg}, "Algorithm Version");
+            add(ST.class, false, 1, 199, new Object[]{msg}, "Algorithm Description");
+            add(CX.class, false, 0, 256, new Object[]{msg}, "What domains returned");
+        } catch (HL7Exception e) {
+            throw new HL7v2Exception(e);
+        }
     }
 
     /**

diff --git a/.../src/main/java/org/openehealth/ipf/commons/ihe/hl7v2/definitions/pix/v25/segment/QPD.java b/.../src/main/java/org/openehealth/ipf/commons/ihe/hl7v2/definitions/pix/v25/segment/QPD.java
@@ -15,14 +15,15 @@
  */
 package org.openehealth.ipf.commons.ihe.hl7v2.definitions.pix.v25.segment;
 
+import ca.uhn.hl7v2.HL7Exception;
 import ca.uhn.hl7v2.model.AbstractSegment;
 import ca.uhn.hl7v2.model.Group;
 import ca.uhn.hl7v2.model.Type;
 import ca.uhn.hl7v2.model.v25.datatype.CE;
 import ca.uhn.hl7v2.model.v25.datatype.CX;
 import ca.uhn.hl7v2.model.v25.datatype.ST;
 import ca.uhn.hl7v2.parser.ModelClassFactory;
-
+import org.openehealth.ipf.modules.hl7.HL7v2Exception;
 
 
 /**
@@ -43,10 +44,14 @@ public class QPD extends AbstractSegment {
     public QPD(Group parentGroup, ModelClassFactory modelFactory) {
         super(parentGroup, modelFactory);
         var msg = getMessage();
-        add(CE.class, true, 1, 250, new Object[]{msg}, "Message Query Name");
-        add(ST.class, true, 1, 32, new Object[]{msg}, "Query Tag");
-        add(CX.class, true, 1, 256, new Object[]{msg}, "Person Identifier");
-        add(CX.class, false, 0, 256, new Object[]{msg}, "What domains returned");
+        try {
+            add(CE.class, true, 1, 250, new Object[]{msg}, "Message Query Name");
+            add(ST.class, true, 1, 32, new Object[]{msg}, "Query Tag");
+            add(CX.class, true, 1, 256, new Object[]{msg}, "Person Identifier");
+            add(CX.class, false, 0, 256, new Object[]{msg}, "What domains returned");
+        } catch (HL7Exception e) {
+            throw new HL7v2Exception(e);
+        }
     }
 
     /**

diff --git a/dependencies/pom.xml b/dependencies/pom.xml
@@ -11,38 +11,38 @@
         <gpg-plugin-version>1.6</gpg-plugin-version>
         <bouncycastle-version>1.76</bouncycastle-version>
         <brave-version>5.16.0</brave-version>
-        <camel-version>4.0.3</camel-version>
+        <camel-version>4.3.0</camel-version>
         <!-- resolve dependency convergence between guava and hapi caffeine -->
         <checker-qual-version>3.19.0</checker-qual-version>
         <cxf-version>4.0.3</cxf-version>
         <commons-io-version>2.15.0</commons-io-version>
         <equinox-app.version>1.3.200-v20130910-1609</equinox-app.version>
         <equinox-common.version>3.6.200-v20130402-1505</equinox-common.version>
-        <groovy-version>4.0.15</groovy-version>
+        <groovy-version>4.0.18</groovy-version>
         <hapi-version>2.5.1</hapi-version>
-        <hapi-fhir-version>6.11.7-SNAPSHOT</hapi-fhir-version>
+        <hapi-fhir-version>7.0.0-SNAPSHOT</hapi-fhir-version>
         <herasaf-version>3.0.2</herasaf-version>
         <ipf-gazelle-version>3.0-SNAPSHOT</ipf-gazelle-version>
         <ipf-oht-mdht-version>1.2.0.201212201425</ipf-oht-mdht-version>
         <!-- hapi-fhir already require jackson 2.15 while spring-boot is on 2.13 -->
-        <jackson-version>2.15.3</jackson-version>
-        <jaxb-version>4.0.4 </jaxb-version>
+        <jackson-version>2.16.0</jackson-version>
+        <jaxb-version>4.0.4</jaxb-version>
         <jakarta-jwsapi-version>3.0.0</jakarta-jwsapi-version>
         <jdom-version>2.0.6.1</jdom-version>
         <kotlin.dokka.version>1.8.10</kotlin.dokka.version>
         <kotlin.version>1.9.10</kotlin.version>
         <kotlin.logging.version>3.0.5</kotlin.logging.version>
         <methanol-version>1.7.0</methanol-version>
-        <ph-schematron-version>5.6.5</ph-schematron-version>
-        <ph-commons-version>9.5.5</ph-commons-version>
+        <ph-schematron-version>7.1.2</ph-schematron-version>
+        <ph-commons-version>11.1.0</ph-commons-version>
         <saxon-he-version>12.3</saxon-he-version>
         <simple-syslog-version>0.0.16</simple-syslog-version>
-        <spring-boot-version>3.2.0</spring-boot-version>
+        <spring-boot-version>3.2.2</spring-boot-version>
         <velocity-version>2.3</velocity-version>
         <vertx-version>4.3.8</vertx-version>
         <vibur-version>25.0</vibur-version>
         <woodstox-version>6.5.1</woodstox-version>
-        <xmlsec-version>3.0.2</xmlsec-version>
+        <xmlsec-version>4.0.1</xmlsec-version>
 
 
     </properties>
@@ -98,6 +98,17 @@
                     </exclusion>
                 </exclusions>
             </dependency>
+            <dependency>
+                <groupId>ca.uhn.hapi.fhir</groupId>
+                <artifactId>hapi-fhir-caching-caffeine</artifactId>
+                <version>${hapi-fhir-version}</version>
+                <exclusions>
+                    <exclusion>
+                        <groupId>com.google.errorprone</groupId>
+                        <artifactId>error_prone_annotations</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
             <dependency>
                 <groupId>org.apache.cxf</groupId>
                 <artifactId>cxf-bom</artifactId>
@@ -400,8 +411,8 @@
                 <version>${jakarta-jwsapi-version}</version>
             </dependency>
             <dependency>
-                <groupId>com.helger</groupId>
-                <artifactId>ph-schematron</artifactId>
+                <groupId>com.helger.schematron</groupId>
+                <artifactId>ph-schematron-xslt</artifactId>
                 <version>${ph-schematron-version}</version>
                 <exclusions>
                     <exclusion>
@@ -411,7 +422,7 @@
                 </exclusions>
             </dependency>
             <dependency>
-                <groupId>com.helger</groupId>
+                <groupId>com.helger.commons</groupId>
                 <artifactId>ph-commons</artifactId>
                 <version>${ph-commons-version}</version>
             </dependency>

diff --git a/.../src/test/java/org/openehealth/ipf/modules/hl7/parser/test/hl7v2/def/v25/segment/ZBE.java b/.../src/test/java/org/openehealth/ipf/modules/hl7/parser/test/hl7v2/def/v25/segment/ZBE.java
@@ -15,6 +15,7 @@
  */
 package org.openehealth.ipf.modules.hl7.parser.test.hl7v2.def.v25.segment;
 
+import ca.uhn.hl7v2.HL7Exception;
 import ca.uhn.hl7v2.model.AbstractSegment;
 import ca.uhn.hl7v2.model.Group;
 import ca.uhn.hl7v2.model.v25.datatype.EI;
@@ -44,10 +45,14 @@ public class ZBE extends AbstractSegment {
     public ZBE(Group parent, ModelClassFactory factory) {
         super(parent, factory);
         var message = getMessage();
-        add(EI.class, true, 0, 999, new Object[] { message }, null);
-        add(TS.class, true, 1, 26, new Object[] { message }, null);
-        add(TS.class, false, 1, 26, new Object[] { message }, null);
-        add(ST.class, true, 1, 10, new Object[] { message }, null);
+        try {
+            add(EI.class, true, 0, 999, new Object[] { message }, null);
+            add(TS.class, true, 1, 26, new Object[] { message }, null);
+            add(TS.class, false, 1, 26, new Object[] { message }, null);
+            add(ST.class, true, 1, 10, new Object[] { message }, null);
+        } catch(HL7Exception e) {
+            log.error("Unexpected error creating ZBE - this is probably a bug in the source code generator.", e);
+        }
     }
 
     /**

diff --git a/...ain/java/org/openehealth/ipf/platform/camel/core/config/CustomRouteBuilderConfigurer.java b/...ain/java/org/openehealth/ipf/platform/camel/core/config/CustomRouteBuilderConfigurer.java
@@ -15,12 +15,14 @@
  */
 package org.openehealth.ipf.platform.camel.core.config;
 
+import java.lang.reflect.Field;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
 
 import org.apache.camel.CamelContext;
+import org.apache.camel.builder.RouteBuilder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.openehealth.ipf.commons.core.config.OrderedConfigurer;
@@ -59,11 +61,16 @@ public void configure(CustomRouteBuilder customRouteBuilder) throws Exception{
         if (customRouteBuilder.getIntercepted() != null) {
             var intercepted = customRouteBuilder.getIntercepted();
             customRouteBuilder.setCamelContext(camelContext);
-            customRouteBuilder.setRouteCollection(intercepted.getRouteCollection());
+            customRouteBuilder.setTemplatedRouteCollection(intercepted.getTemplatedRouteCollection());
+            customRouteBuilder.setRouteTemplateCollection(intercepted.getRouteTemplateCollection());
             customRouteBuilder.setRestCollection(intercepted.getRestCollection());
-            customRouteBuilder.errorHandler(intercepted.getErrorHandlerFactory());
+            customRouteBuilder.setErrorHandlerFactory(intercepted.getErrorHandlerFactory());
 
-            // must invoke configure on the original builder so it adds its configuration to me
+            Field f1 = RouteBuilder.class.getDeclaredField("routeCollection");
+            f1.setAccessible(true);
+            f1.set(customRouteBuilder, intercepted.getRouteCollection());
+
+            // must invoke configure on the original builder, so it adds its configuration to me
             customRouteBuilder.configure();
 
         } else {

diff --git a/...main/java/org/openehealth/ipf/platform/camel/ihe/fhir/core/custom/CustomFhirEndpoint.java b/...main/java/org/openehealth/ipf/platform/camel/ihe/fhir/core/custom/CustomFhirEndpoint.java
@@ -16,6 +16,7 @@
 
 package org.openehealth.ipf.platform.camel.ihe.fhir.core.custom;
 
+import org.apache.camel.Category;
 import org.apache.camel.spi.UriEndpoint;
 import org.openehealth.ipf.commons.ihe.fhir.audit.FhirAuditDataset;
 import org.openehealth.ipf.platform.camel.ihe.fhir.core.FhirConsumer;
@@ -26,7 +27,7 @@
  * @author Christian Ohr
  * @since 3.1
  */
-@UriEndpoint(scheme = "fhir", title = "Generic FHIR", syntax = "fhir:host:port", consumerClass = FhirConsumer.class, label = "http")
+@UriEndpoint(scheme = "fhir", title = "Generic FHIR", syntax = "fhir:host:port", category = Category.HTTP)
 public class CustomFhirEndpoint<AuditDatasetType extends FhirAuditDataset>
         extends FhirEndpoint<AuditDatasetType, CustomFhirComponent<AuditDatasetType>> {
 

diff --git a/platform-camel/ihe/fhir/r4/chppqm/pom.xml b/platform-camel/ihe/fhir/r4/chppqm/pom.xml
@@ -96,12 +96,12 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.helger</groupId>
-            <artifactId>ph-schematron</artifactId>
+            <groupId>com.helger.schematron</groupId>
+            <artifactId>ph-schematron-xslt</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.helger</groupId>
+            <groupId>com.helger.commons</groupId>
             <artifactId>ph-commons</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/platform-camel/ihe/fhir/r4/mhd/pom.xml b/platform-camel/ihe/fhir/r4/mhd/pom.xml
@@ -79,12 +79,12 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.helger</groupId>
-            <artifactId>ph-schematron</artifactId>
+            <groupId>com.helger.schematron</groupId>
+            <artifactId>ph-schematron-xslt</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.helger</groupId>
+            <groupId>com.helger.commons</groupId>
             <artifactId>ph-commons</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/...pixpdq/src/main/java/org/openehealth/ipf/platform/camel/ihe/fhir/iti83/Iti83Endpoint.java b/...pixpdq/src/main/java/org/openehealth/ipf/platform/camel/ihe/fhir/iti83/Iti83Endpoint.java
@@ -16,6 +16,7 @@
 
 package org.openehealth.ipf.platform.camel.ihe.fhir.iti83;
 
+import org.apache.camel.Category;
 import org.apache.camel.spi.UriEndpoint;
 import org.openehealth.ipf.commons.ihe.fhir.audit.FhirQueryAuditDataset;
 import org.openehealth.ipf.platform.camel.ihe.fhir.core.FhirConsumer;
@@ -28,7 +29,7 @@
  * @author Christian Ohr
  * @since 3.1
  */
-@UriEndpoint(scheme = "pixm-iti83", title = "ITI-83 PIXm", syntax = "pixm-iti83:host:port", consumerClass = FhirConsumer.class, label = "http")
+@UriEndpoint(scheme = "pixm-iti83", title = "ITI-83 PIXm", syntax = "pixm-iti83:host:port", category = Category.HTTP)
 public class Iti83Endpoint extends FhirEndpoint<FhirQueryAuditDataset, Iti83Component> {
 
     public Iti83Endpoint(String uri, Iti83Component fhirComponent, FhirEndpointConfiguration<FhirQueryAuditDataset> config) {

diff --git a/platform-camel/ihe/fhir/stu3/mhd/pom.xml b/platform-camel/ihe/fhir/stu3/mhd/pom.xml
@@ -74,12 +74,12 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.helger</groupId>
-            <artifactId>ph-schematron</artifactId>
+            <groupId>com.helger.schematron</groupId>
+            <artifactId>ph-schematron-xslt</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.helger</groupId>
+            <groupId>com.helger.commons</groupId>
             <artifactId>ph-commons</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/...pixpdq/src/main/java/org/openehealth/ipf/platform/camel/ihe/fhir/iti83/Iti83Endpoint.java b/...pixpdq/src/main/java/org/openehealth/ipf/platform/camel/ihe/fhir/iti83/Iti83Endpoint.java
@@ -16,6 +16,7 @@
 
 package org.openehealth.ipf.platform.camel.ihe.fhir.iti83;
 
+import org.apache.camel.Category;
 import org.apache.camel.spi.UriEndpoint;
 import org.openehealth.ipf.commons.ihe.fhir.audit.FhirQueryAuditDataset;
 import org.openehealth.ipf.platform.camel.ihe.fhir.core.FhirConsumer;
@@ -28,7 +29,7 @@
  * @author Christian Ohr
  * @since 3.1
  */
-@UriEndpoint(scheme = "pixm-iti83", title = "ITI-83 PIXm", syntax = "pixm-iti83:host:port", consumerClass = FhirConsumer.class, label = "http")
+@UriEndpoint(scheme = "pixm-iti83", title = "ITI-83 PIXm", syntax = "pixm-iti83:host:port", category = Category.HTTP)
 public class Iti83Endpoint extends FhirEndpoint<FhirQueryAuditDataset, Iti83Component> {
 
     public Iti83Endpoint(String uri, Iti83Component fhirComponent, FhirEndpointConfiguration<FhirQueryAuditDataset> config) {