Updated Libraries, fixed Docker Compose (#908)

madduci · web-flow · commit a3d6fdb52a83 · 2026-01-20T07:59:11.000+01:00
* Updated SpringBoot, HAPI FHIR, Docker

* Fixed docker compose

* Fixed Chart README

* Replaced Tomcat image

* Replaced Tomcat image

* Fixing Tomcat image

* Corrected Helm Chart value
diff --git a/.github/workflows/build-images.yaml b/.github/workflows/build-images.yaml
@@ -17,7 +17,7 @@ env:
 jobs:
   build:
     name: Build
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Container meta for default (distroless) image
         id: docker_meta
diff --git a/.github/workflows/chart-test.yaml b/.github/workflows/chart-test.yaml
@@ -9,7 +9,7 @@ on:
 
 jobs:
   lint:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     container: quay.io/helmpack/chart-testing:v3.11.0@sha256:f2fd21d30b64411105c7eafb1862783236a219d29f2292219a09fe94ca78ad2a
     steps:
       - name: Install helm-docs
@@ -38,10 +38,10 @@ jobs:
         run: ct lint --config .github/ct/config.yaml
 
   test:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
-        k8s-version: [1.30.8, 1.31.4, 1.32.0]
+        k8s-version: [1.32.0, 1.33.0, 1.34.0, 1.35.0]
     needs:
       - lint
     steps:
diff --git a/Dockerfile b/Dockerfile
@@ -1,7 +1,7 @@
-FROM docker.io/library/maven:3.9.9-eclipse-temurin-17 AS build-hapi
+FROM docker.io/library/maven:3.9.12-eclipse-temurin-17 AS build-hapi
 WORKDIR /tmp/hapi-fhir-jpaserver-starter
 
-ARG OPENTELEMETRY_JAVA_AGENT_VERSION=2.13.1
+ARG OPENTELEMETRY_JAVA_AGENT_VERSION=2.24.0
 RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar
 
 COPY pom.xml .
@@ -16,28 +16,26 @@ RUN mvn package -DskipTests spring-boot:repackage -Pboot
 RUN mkdir /app && cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
 
 
-########### bitnami tomcat version is suitable for debugging and comes with a shell
+########### Use the official Tomcat image as base image for the Tomcat variant
 ########### it can be built using eg. `docker build --target tomcat .`
-FROM docker.io/bitnamilegacy/tomcat:10.1.43-debian-12-r0 AS tomcat
+FROM docker.io/library/tomcat:10-jre21-temurin-noble AS tomcat
 
 USER root
-RUN rm -rf /opt/bitnami/tomcat/webapps/ROOT && \
-    mkdir -p /opt/bitnami/hapi/data/hapi/lucenefiles && \
-    chown -R 1001:1001 /opt/bitnami/hapi/data/hapi/lucenefiles && \
-    chmod 775 /opt/bitnami/hapi/data/hapi/lucenefiles
+RUN rm -rf /usr/local/tomcat/webapps/ROOT && \
+    mkdir -p /usr/local/tomcat/data/hapi/lucenefiles && \
+    chown -R 65532:65532 /usr/local/tomcat/data/hapi/lucenefiles && \
+    chmod 775 /usr/local/tomcat/data/hapi/lucenefiles
 
-RUN mkdir -p /target && chown -R 1001:1001 target
-USER 1001
+RUN mkdir -p /target && chown -R 65532:65532 /target
+USER 65532
 
-COPY --chown=1001:1001 catalina.properties /opt/bitnami/tomcat/conf/catalina.properties
-COPY --chown=1001:1001 server.xml /opt/bitnami/tomcat/conf/server.xml
-COPY --from=build-hapi --chown=1001:1001 /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /opt/bitnami/tomcat/webapps/ROOT.war
-COPY --from=build-hapi --chown=1001:1001 /tmp/hapi-fhir-jpaserver-starter/opentelemetry-javaagent.jar /app
-
-ENV ALLOW_EMPTY_PASSWORD=yes
+COPY --chown=65532:65532 catalina.properties /usr/local/tomcat/conf/catalina.properties
+COPY --chown=65532:65532 server.xml /usr/local/tomcat/conf/server.xml
+COPY --from=build-hapi --chown=65532:65532 /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /usr/local/tomcat/webapps/ROOT.war
+COPY --from=build-hapi --chown=65532:65532 /tmp/hapi-fhir-jpaserver-starter/opentelemetry-javaagent.jar /app
 
 ########### distroless brings focus on security and runs on plain spring boot - this is the default image
-FROM gcr.io/distroless/java17-debian12:nonroot AS default
+FROM gcr.io/distroless/java21-debian13:nonroot AS default
 # 65532 is the nonroot user's uid
 # used here instead of the name to allow Kubernetes to easily detect that the container
 # is running as a non-root (uid != 0) user.
diff --git a/charts/hapi-fhir-jpaserver/Chart.yaml b/charts/hapi-fhir-jpaserver/Chart.yaml
@@ -13,8 +13,8 @@ dependencies:
   - name: common
     repository: oci://registry-1.docker.io/bitnamicharts
     version: 2.31.3
-appVersion: 8.2.0
-version: 0.21.0
+appVersion: 8.6.0
+version: 0.22.0
 annotations:
   artifacthub.io/license: Apache-2.0
   artifacthub.io/containsSecurityUpdates: "false"
diff --git a/charts/hapi-fhir-jpaserver/README.md b/charts/hapi-fhir-jpaserver/README.md
@@ -1,6 +1,6 @@
 # HAPI FHIR JPA Server Starter Helm Chart
 
-![Version: 0.21.0](https://img.shields.io/badge/Version-0.21.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 8.2.0](https://img.shields.io/badge/AppVersion-8.2.0-informational?style=flat-square)
+![Version: 0.22.0](https://img.shields.io/badge/Version-0.22.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 8.6.0](https://img.shields.io/badge/AppVersion-8.6.0-informational?style=flat-square)
 
 This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
 
@@ -39,7 +39,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
 | image.pullPolicy | string | `"IfNotPresent"` | image pullPolicy to use |
 | image.registry | string | `"docker.io"` | registry where the HAPI FHIR server image is hosted |
 | image.repository | string | `"hapiproject/hapi"` | the path inside the repository |
-| image.tag | string | `"v8.2.0-1@sha256:e85ded02f60e25a66e6d9423ea71f3ebc9494e3a69bdd7d7dbfa31b8aa5b2fe9"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. |
+| image.tag | string | `"v8.6.0-1@sha256:7611e4d6601f35dd8c223ed2ed47a2807be06976f71b2e5990e6541bbc90c16f"` | the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image. |
 | imagePullSecrets | list | `[]` | image pull secrets to use when pulling the image |
 | ingress.annotations | object | `{}` | provide any additional annotations which may be required. Evaluated as a template. |
 | ingress.enabled | bool | `false` | whether to create an Ingress to expose the FHIR server HTTP endpoint |
diff --git a/charts/hapi-fhir-jpaserver/values.yaml b/charts/hapi-fhir-jpaserver/values.yaml
@@ -7,7 +7,7 @@ image:
   # -- the path inside the repository
   repository: hapiproject/hapi
   # -- the image tag. As of v5.7.0, this is the `distroless` flavor by default, add `-tomcat` to use the Tomcat-based image.
-  tag: "v8.2.0-1@sha256:e85ded02f60e25a66e6d9423ea71f3ebc9494e3a69bdd7d7dbfa31b8aa5b2fe9"
+  tag: "v8.6.0-1@sha256:7611e4d6601f35dd8c223ed2ed47a2807be06976f71b2e5990e6541bbc90c16f"
   # -- image pullPolicy to use
   pullPolicy: IfNotPresent
 
diff --git a/docker-build.bat b/docker-build.bat
@@ -1 +1 @@
-docker build --tag hapiproject/hapi:latest --tag hapiproject/hapi:4.1 -m 4g .
+docker build --tag hapiproject/hapi:latest --tag hapiproject/hapi:8.6.1 -m 4g .
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,4 +1,3 @@
-version: "3"
 services:
   hapi-fhir-jpaserver-start:
     build: .
@@ -8,18 +7,29 @@ services:
       SPRING_DATASOURCE_URL: "jdbc:postgresql://hapi-fhir-postgres:5432/hapi"
       SPRING_DATASOURCE_USERNAME: "admin"
       SPRING_DATASOURCE_PASSWORD: "admin"
-      SPRING_DATASOURCE_DRIVERCLASSNAME: "org.postgresql.Driver"
+      SPRING_DATASOURCE_DRIVER_CLASS_NAME: "org.postgresql.Driver"
+      SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
     ports:
       - "8080:8080"
+    depends_on:
+      hapi-fhir-postgres:
+        condition: service_healthy
   hapi-fhir-postgres:
-    image: postgres:15-alpine
+    image: postgres:16-alpine
     container_name: hapi-fhir-postgres
     restart: always
     environment:
       POSTGRES_DB: "hapi"
       POSTGRES_USER: "admin"
       POSTGRES_PASSWORD: "admin"
+    healthcheck:
+      test: ["CMD-SHELL", "sh -c 'pg_isready -U admin -d hapi' || exit 1"]
+      interval: 10s
+      timeout: 5s
+      start_period: 5s
+      retries: 5
     volumes:
       - hapi-fhir-postgres:/var/lib/postgresql/data
+
 volumes:
   hapi-fhir-postgres:
diff --git a/pom.xml b/pom.xml
@@ -7,6 +7,20 @@
         <java.version>17</java.version>
         <hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision>
         <clinical-reasoning.version>4.0.0</clinical-reasoning.version>
+
+        <!-- Plugins Versions -->
+        <maven.failsafe.version>3.5.4</maven.failsafe.version>
+        <maven.fire.version>${maven.failsafe.version}</maven.fire.version>
+        <maven.dependency.version>3.9.0</maven.dependency.version>
+        <maven.compiler.version>3.14.1</maven.compiler.version>
+
+        <!-- Dependencies Versions -->
+        <spring.ai.version>1.1.2</spring.ai.version>
+        <awaitility.version>4.3.0</awaitility.version>
+        <micrometer.version>1.16.2</micrometer.version>
+        <commons.logging.version>1.3.5</commons.logging.version>
+        <spring_boot_version>3.5.9</spring_boot_version>
+        <postgresql.version>42.7.9</postgresql.version>
     </properties>
 
     <!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
@@ -20,7 +34,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-        <version>8.6.0</version>
+        <version>8.6.1</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -73,6 +87,7 @@
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
+            <version>${postgresql.version}</version>
         </dependency>
         <dependency>
           <groupId>com.microsoft.sqlserver</groupId>
@@ -222,7 +237,7 @@
         <dependency>
             <groupId>commons-logging</groupId>
             <artifactId>commons-logging</artifactId>
-            <version>1.2</version>
+            <version>${commons.logging.version}</version>
             <scope>provided</scope>
         </dependency>
 
@@ -344,7 +359,7 @@
         <dependency>
             <groupId>org.awaitility</groupId>
             <artifactId>awaitility</artifactId>
-            <version>4.2.0</version>
+            <version>${awaitility.version}</version>
             <scope>test</scope>
         </dependency>
 
@@ -364,41 +379,41 @@
         <dependency>
             <groupId>io.micrometer</groupId>
             <artifactId>micrometer-core</artifactId>
-            <version>1.13.3</version>
+            <version>${micrometer.version}</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus -->
         <dependency>
             <groupId>io.micrometer</groupId>
             <artifactId>micrometer-registry-prometheus</artifactId>
-            <version>1.13.3</version>
+            <version>${micrometer.version}</version>
         </dependency>
 
         <!-- https://mvnrepository.com/artifact/io.micrometer/micrometer-registry-prometheus-simpleclient -->
         <dependency>
             <groupId>io.micrometer</groupId>
             <artifactId>micrometer-registry-prometheus-simpleclient</artifactId>
-            <version>1.13.3</version>
+            <version>${micrometer.version}</version>
         </dependency>
 
 
         <dependency>
             <groupId>com.zaxxer</groupId>
             <artifactId>HikariCP</artifactId>
-            <version>5.0.1</version>
+            <version>5.1.0</version>
         </dependency>
 
         <dependency>
             <groupId>org.springframework.ai</groupId>
             <artifactId>spring-ai-mcp</artifactId>
-            <version>1.1.0-M2</version>
+            <version>${spring.ai.version}</version>
         </dependency>
 
         <!--implementation("org.springframework.ai:spring-ai-starter-mcp-server-webmvc:1.1.0-M1")-->
         <dependency>
             <groupId>org.springframework.ai</groupId>
             <artifactId>spring-ai-starter-mcp-server</artifactId>
-            <version>1.1.0-M2</version>
+            <version>${spring.ai.version}</version>
         </dependency>
 
         <dependency>
@@ -433,12 +448,12 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-dependency-plugin</artifactId>
-                    <version>3.6.0</version>
+                    <version>${maven.dependency.version}</version>
                 </plugin>
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-surefire-plugin</artifactId>
-                    <version>3.4.0</version>
+                    <artifactId>maven-fire-plugin</artifactId>
+                    <version>${maven.fire.version}</version>
                 </plugin>
             </plugins>
         </pluginManagement>
@@ -474,7 +489,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.13.0</version>
+                <version>${maven.compiler.version}</version>
                 <configuration>
                     <release>${java.version}</release>
                 </configuration>
@@ -505,7 +520,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
-                <version>3.4.0</version>
+                <version>${maven.failsafe.version}</version>
                 <configuration>
                     <redirectTestOutputToFile>true</redirectTestOutputToFile>
                 </configuration>
@@ -677,62 +692,6 @@
                 </dependency>
             </dependencies>
         </profile>
-        <profile>
-            <id>ossrh-repo</id>
-            <activation>
-                <activeByDefault>false</activeByDefault>
-                <property>
-                    <name>deployToSonatype</name>
-                </property>
-            </activation>
-            <distributionManagement>
-                <snapshotRepository>
-                    <id>ossrh</id>
-                    <url>https://oss.sonatype.org/content/repositories/snapshots</url>
-                </snapshotRepository>
-                <repository>
-                    <id>ossrh</id>
-                    <url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
-                </repository>
-            </distributionManagement>
-            <build>
-                <plugins>
-                    <plugin>
-                        <groupId>org.sonatype.plugins</groupId>
-                        <artifactId>nexus-staging-maven-plugin</artifactId>
-                        <version>1.6.13</version>
-                        <extensions>true</extensions>
-                        <configuration>
-                            <serverId>ossrh</serverId>
-                            <nexusUrl>https://oss.sonatype.org/</nexusUrl>
-                            <autoReleaseAfterClose>true</autoReleaseAfterClose>
-                        </configuration>
-                    </plugin>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-gpg-plugin</artifactId>
-                        <version>1.6</version>
-                        <executions>
-                            <execution>
-                                <id>sign-artifacts</id>
-                                <phase>verify</phase>
-                                <goals>
-                                    <goal>sign</goal>
-                                </goals>
-                                <configuration>
-                                    <keyname>${gpg.keyname}</keyname>
-                                    <passphraseServerId>${gpg.keyname}</passphraseServerId>
-                                    <gpgArguments>
-                                        <arg>--pinentry-mode</arg>
-                                        <arg>loopback</arg>
-                                    </gpgArguments>
-                                </configuration>
-                            </execution>
-                        </executions>
-                    </plugin>
-                </plugins>
-            </build>
-        </profile>
         <!-- For connecting to GCP CloudSQL Postgres instances:
         https://github.com/GoogleCloudPlatform/cloud-sql-jdbc-socket-factory/blob/main/docs/jdbc.md#postgres-1
         Needs 'boot' profile as well. -->
@@ -742,7 +701,7 @@
                 <dependency>
                     <groupId>com.google.cloud.sql</groupId>
                     <artifactId>postgres-socket-factory</artifactId>
-                    <version>1.17.0</version>
+                    <version>1.28.0</version>
                 </dependency>
             </dependencies>
         </profile>       

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-docker build --tag hapiproject/hapi:latest --tag hapiproject/hapi:4.1 -m 4g .`
	`1`	`+docker build --tag hapiproject/hapi:latest --tag hapiproject/hapi:8.6.1 -m 4g .`