Sync 6.2.2

.github/workflows/chart-test.yaml

@@ -15,7 +15,7 @@ jobs:
       - name: Install helm-docs
         working-directory: /tmp
         env:
-          HELM_DOCS_URL: https://github.com/norwoodj/helm-docs/releases/download/v1.9.1/helm-docs_1.9.1_Linux_x86_64.tar.gz
+          HELM_DOCS_URL: https://github.com/norwoodj/helm-docs/releases/download/v1.11.0/helm-docs_1.11.0_Linux_x86_64.tar.gz
         run: |
           curl -LSs $HELM_DOCS_URL | tar xz && \
           mv ./helm-docs /usr/local/bin/helm-docs && \

.github/workflows/maven.yml

@@ -5,10 +5,14 @@ name: Java CI with Maven
 
 on:
   push:
-    branches: 
-      - '**' 
+    branches:
+      - '**'
+    paths-ignore:
+      - "charts/**"
   pull_request:
     branches: [ master ]
+    paths-ignore:
+      - "charts/**"
 
 jobs:
   build:

Dockerfile

@@ -1,24 +1,26 @@
 FROM maven:3.8-openjdk-17-slim as build-hapi
-WORKDIR /usr/app/hapi-fhir-jpaserver-starter
+WORKDIR /usr/app//hapi-fhir-jpaserver-starter
+
+ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.17.0
+RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar
 
 COPY pom.xml .
 COPY server.xml .
 RUN mvn -ntp dependency:go-offline
 
-COPY src/ /usr/app/hapi-fhir-jpaserver-starter/src/
+COPY src/ /usr/app//hapi-fhir-jpaserver-starter/src/
 RUN mvn clean install -DskipTests -Djdk.lang.Process.launchMechanism=vfork
 
 FROM build-hapi AS build-distroless
 RUN mvn package spring-boot:repackage -Pboot
-RUN mkdir /app && cp /usr/app/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
+RUN mkdir /app && cp /usr/app//hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.war
 
 
 ########### bitnami tomcat version is suitable for debugging and comes with a shell
 ########### it can be built using eg. `docker build --target tomcat .`
 FROM bitnami/tomcat:9.0 as tomcat
 
 RUN rm -rf /opt/bitnami/tomcat/webapps/ROOT && \
-    rm -rf /opt/bitnami/tomcat/webapps_default/ROOT && \
     mkdir -p /opt/bitnami/hapi/data/hapi/lucenefiles && \
     chmod 775 /opt/bitnami/hapi/data/hapi/lucenefiles
 
@@ -28,16 +30,20 @@ USER 1001
 
 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 /usr/app/hapi-fhir-jpaserver-starter/target/ROOT.war /opt/bitnami/tomcat/webapps_default/ROOT.war
+COPY --from=build-hapi --chown=1001:1001 /usr/app//hapi-fhir-jpaserver-starter/target/ROOT.war /opt/bitnami/tomcat/webapps/ROOT.war
+COPY --from=build-hapi --chown=1001:1001 /usr/app//hapi-fhir-jpaserver-starter/opentelemetry-javaagent.jar /app
 
 ENV ALLOW_EMPTY_PASSWORD=yes
 
 ########### distroless brings focus on security and runs on plain spring boot - this is the default image
-FROM gcr.io/distroless/java17:nonroot as default
-COPY --chown=nonroot:nonroot --from=build-distroless /app /app
+FROM gcr.io/distroless/java17-debian11: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.
 USER 65532:65532
 WORKDIR /app
+
+COPY --chown=nonroot:nonroot --from=build-distroless /app /app
+COPY --chown=nonroot:nonroot --from=build-hapi /usr/app//hapi-fhir-jpaserver-starter/opentelemetry-javaagent.jar /app
+
 CMD ["/app/main.war"]

README.md

@@ -17,9 +17,9 @@ In order to use this sample, you should have:
  - Apache Maven build tool (newest version)
 
 ### or
- - Docker, as the entire project can be built using multistage docker (with both JDK and maven wrapped in docker) or used directly from [Docker Hub](https://hub.docker.com/repository/docker/hapiproject/hapi)
+ - Docker, as the entire project can be built using multistage docker (with both JDK and maven wrapped in docker) or used directly from [Docker Hub](https://hub.docker.com/r/hapiproject/hapi)
 
-## Running via [Docker Hub](https://hub.docker.com/repository/docker/hapiproject/hapi)
+## Running via [Docker Hub](https://hub.docker.com/r/hapiproject/hapi)
 
 Each tagged/released version of `hapi-fhir-jpaserver` is built as a Docker image and published to Docker hub. To run the published Docker image from DockerHub:
 
@@ -184,6 +184,57 @@ volumes:
         external: true
 ```
 
+## Running via [Docker Hub](https://hub.docker.com/repository/docker/hapiproject/hapi)
+
+Each tagged/released version of `hapi-fhir-jpaserver` is built as a Docker image and published to Docker hub. To run the published Docker image from DockerHub:
+
+```
+docker pull hapiproject/hapi:latest
+docker run -p 8080:8080 hapiproject/hapi:tagname
+```
+
+This will run the docker image with the default configuration, mapping port 8080 from the container to port 8080 in the host. Once running, you can access `http://localhost:8080/hapi-fhir-jpaserver/fhir` in the browser to access the HAPI FHIR server's UI.
+
+If you change the mapped port, you need to change the configuration used by HAPI to have the correct `server_address` property/value.
+
+### Configuration via environment variables
+
+You can customize HAPI directly from the `run` command using environment variables. For example:
+
+`docker run -p 8090:8080 -e server_address=http://localhost:8090/hapi-fhir-jpaserver/fhir hapiproject/hapi:tagname`
+
+HAPI looks in the environment variables for properties in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file.
+
+### Configuration via overridden hapi.properties file
+
+You can customize HAPI by telling HAPI to look for the `hapi.properties` file in a different location:
+
+`docker run -p 8090:8080 -e hapi.properties=/some/directory/with/hapi.properties hapiproject/hapi:tagname`
+
+### Example docker-compose.yml
+
+```
+version: '3.7'
+services:
+  web:
+    image: "hapiproject/hapi:tagname"
+    ports:
+      - "8090:8080"
+    configs:
+      - source: hapi
+        target: /data/hapi/hapi.properties
+    volumes:
+      - hapi-data:/data/hapi
+    environment:
+      JAVA_OPTS: '-Dhapi.properties=/data/hapi/hapi.properties'
+configs:
+  hapi:
+     external: true
+volumes:
+    hapi-data:
+        external: true
+```
+
 ## Running locally
 
 The easiest way to run this server entirely depends on your environment requirements. At least, the following 4 ways are supported:
@@ -323,7 +374,7 @@ Also, make sure you are not setting the Hibernate dialect explicitly, in other w
 hibernate.dialect: {some none MySQL dialect}
 ```
 
-On some systems, it might be necessary to override hibernate's default naming strategy. The naming strategy must be set using spring.jpa.hibernate.physical_naming_strategy. 
+On some systems, it might be necessary to override hibernate's default naming strategy. The naming strategy must be set using spring.jpa.hibernate.physical_naming_strategy.
 
 ```yaml
 spring:
@@ -345,6 +396,9 @@ spring:
     username: admin
     password: admin
     driverClassName: org.postgresql.Driver
+  jpa:
+    properties:
+      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
 ```
 
 Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicity skip the integration tests during the build process, i.e., `mvn install -DskipTests`, or delete the tests altogether. Failure to skip or delete the tests once you've configured PostgreSQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure.
@@ -362,12 +416,18 @@ spring:
     driverClassName: com.microsoft.sqlserver.jdbc.SQLServerDriver
 ```
 
+Also, make sure you are not setting the Hibernate dialect explicitly, in other words remove any lines similar to:
+
+```
+hibernate.dialect: {some none Microsoft SQL dialect}
+```
+
 
 Because the integration tests within the project rely on the default H2 database configuration, it is important to either explicity skip the integration tests during the build process, i.e., `mvn install -DskipTests`, or delete the tests altogether. Failure to skip or delete the tests once you've configured PostgreSQL for the datasource.driver, datasource.url, and hibernate.dialect as outlined above will result in build errors and compilation failure.
 
 
-NOTE: MS SQL Server by default uses a case-insensitive codepage. This will cause errors with some operations - such as when expanding case-sensitive valuesets (UCUM) as there are unique indexes defined on the terminology tables for codes. 
-It is recommended to deploy a case-sensitive database prior to running HAPI FHIR when using MS SQL Server to avoid these and potentially other issues. 
+NOTE: MS SQL Server by default uses a case-insensitive codepage. This will cause errors with some operations - such as when expanding case-sensitive valuesets (UCUM) as there are unique indexes defined on the terminology tables for codes.
+It is recommended to deploy a case-sensitive database prior to running HAPI FHIR when using MS SQL Server to avoid these and potentially other issues.
 
 ## Customizing The Web Testpage UI
 
@@ -495,6 +555,14 @@ Set `hapi.fhir.mdm_enabled=true` in the [application.yaml](https://github.com/ha
 Set `empi.enabled=true` in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file to enable EMPI on this server.  The EMPI matching rules are configured in [empi-rules.json](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/empi-rules.json).  The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that EMPI relies on subscriptions, so for EMPI to work, subscriptions must be enabled. 
 
 
+## Enabling EMPI
+
+Set `empi.enabled=true` in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file to enable EMPI on this server.  The EMPI matching rules are configured in [empi-rules.json](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/empi-rules.json).  The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that EMPI relies on subscriptions, so for EMPI to work, subscriptions must be enabled. 
+
+## Enabling EMPI
+
+Set `empi.enabled=true` in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file to enable EMPI on this server.  The EMPI matching rules are configured in [empi-rules.json](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/empi-rules.json).  The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that EMPI relies on subscriptions, so for EMPI to work, subscriptions must be enabled. 
+
 ## Enabling EMPI
 
 Set `empi.enabled=true` in the [hapi.properties](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/hapi.properties) file to enable EMPI on this server.  The EMPI matching rules are configured in [empi-rules.json](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/empi-rules.json).  The rules in this example file should be replaced with actual matching rules appropriate to your data. Note that EMPI relies on subscriptions, so for EMPI to work, subscriptions must be enabled. 
@@ -526,7 +594,7 @@ Set `hapi.fhir.store_resource_in_lucene_index_enabled` in the [application.yaml]
 ## Changing cached search results time
 
 It is possible to change the cached search results time. The option `reuse_cached_search_results_millis` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) is 6000 miliseconds by default.
-Set `reuse_cached_search_results_millis: -1` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to ignore the cache time every search. 
+Set `reuse_cached_search_results_millis: -1` in the [application.yaml](https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/resources/application.yaml) file to ignore the cache time every search.
 
 ## Build the distroless variant of the image (for lower footprint and improved security)
 
@@ -545,3 +613,20 @@ see the `-distroless` suffix in the image tags.
 To add a custom operation, refer to the documentation in the core hapi-fhir libraries [here](https://hapifhir.io/hapi-fhir/docs/server_plain/rest_operations_operations.html).
 
 Within `hapi-fhir-jpaserver-starter`, create a generic class (that does not extend or implement any classes or interfaces), add the `@Operation` as a method within the generic class, and then register the class as a provider using `RestfulServer.registerProvider()`.
+
+## Enable OpenTelemetry auto-instrumentation
+
+The container image includes the [OpenTelemetry Java auto-instrumentation](https://github.com/open-telemetry/opentelemetry-java-instrumentation)
+Java agent JAR which can be used to export telemetry data for the HAPI FHIR JPA Server. You can enable it by specifying the `-javaagent` flag,
+for example by overriding the `JAVA_TOOL_OPTIONS` environment variable:
+
+```sh
+docker run --rm -it -p 8080:8080 \
+  -e JAVA_TOOL_OPTIONS="-javaagent:/app/opentelemetry-javaagent.jar" \
+  -e OTEL_TRACES_EXPORTER="jaeger" \
+  -e OTEL_SERVICE_NAME="hapi-fhir-server" \
+  -e OTEL_EXPORTER_JAEGER_ENDPOINT="http://jaeger:14250" \
+  docker.io/hapiproject/hapi:latest
+```
+
+You can configure the agent using environment variables or Java system properties, see <https://opentelemetry.io/docs/instrumentation/java/automatic/agent-config/> for details.

charts/hapi-fhir-jpaserver/Chart.lock

@@ -1,6 +1,6 @@
 dependencies:
 - name: postgresql
   repository: https://charts.bitnami.com/bitnami
-  version: 11.6.2
-digest: sha256:1b96efc47b5dbe28bf34bcb694697325f3d2755a39ce2f1c371b2c9de9fac9d3
-generated: "2022-06-03T11:48:19.1684784+02:00"
+  version: 12.1.2
+digest: sha256:525689611a29f90b0bc8cd674df5d97024c99eda8104216390f6747904fd0208
+generated: "2022-11-21T22:55:45.1699395+01:00"

charts/hapi-fhir-jpaserver/Chart.yaml

@@ -7,39 +7,21 @@ sources:
   - https://github.com/hapifhir/hapi-fhir-jpaserver-starter
 dependencies:
   - name: postgresql
-    version: 11.6.2
+    version: 12.1.2
     repository: https://charts.bitnami.com/bitnami
     condition: postgresql.enabled
-appVersion: v6.0.1
-version: 0.9.0
+appVersion: 6.2.1
+version: 0.11.0
 annotations:
   artifacthub.io/license: Apache-2.0
   artifacthub.io/changes: |
     # When using the list of objects option the valid supported kinds are
     # added, changed, deprecated, removed, fixed, and security.
     - kind: changed
-      description: |
-        BREAKING CHANGE: updated HAPI FHIR starter image to v6.0.1.
-        See <https://github.com/hapifhir/hapi-fhir/releases/tag/v6.0.0> for all application changes.
+      description: updated HAPI FHIR JPA Server app image version to v6.2.1
     - kind: changed
       description: |
-        updated included PostgreSQL-subchart to v11.6.2
-    - kind: fixed
-      description: |
-        use a fixed image for the wait-for-database container (docker.io/bitnami/postgresql:14.3.0-debian-10-r20)
-        instead of relying on the PostgreSQL sub-chart values
-    - kind: changed
-      description: |
-        expose actuator/metrics endpoint on a separate port (8081)
-    - kind: added
-      description: |
-        support for monitoring metrics using ServiceMonitor CRDs
+        Reduced `startupProbe.initialDelaySeconds` to a more realistic `30` from `60`.
+        This should allow the server to become ready quicker and recover from failures faster.
     - kind: changed
-      description: |
-        switched liveness and readiness probes to Spring Boot actuator endpoints
-    - kind: changed
-      description: |
-        BREAKING CHANGE: removed included `NetworkPolicy`, which is subject to more thorough rework
-    - kind: added
-      description: |
-        allow configuring `topologySpreadConstraints` for the deployment
+      description: "⚠️ BREAKING CHANGE: updated included postgresql chart to v12, which is based on PostgreSQL 15.1"