Merge branch 'master' into rel_7_1_tracking

.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/v1.11.3/helm-docs_1.11.3_Linux_x86_64.tar.gz
+ HELM_DOCS_URL: https://github.com/norwoodj/helm-docs/releases/download/v1.13.0/helm-docs_1.13.0_Linux_x86_64.tar.gz
  run: |
  curl -LSs $HELM_DOCS_URL | tar xz && \
  mv ./helm-docs /usr/local/bin/helm-docs && \

.github/workflows/stale.yaml

@@ -0,0 +1,19 @@
+name: 'Close stale issues and PRs'
+on:
+ schedule:
+ - cron: '30 1 * * *'
+
+jobs:
+ stale:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/stale@v9
+ with:
+ stale-issue-message: 'This issue is stale because it has been open 730 days with no activity. Remove stale label or comment or this will be closed in 5 days.'
+ stale-pr-message: 'This PR is stale because it has been open 45 days with no activity. Remove stale label or comment or this will be closed in 10 days.'
+ close-issue-message: 'This issue was closed because it has been stalled for 5 days with no activity.'
+ close-pr-message: 'This PR was closed because it has been stalled for 10 days with no activity.'
+ days-before-issue-stale: 730
+ days-before-pr-stale: 45
+ days-before-issue-close: 5
+ days-before-pr-close: 10

README.md

@@ -189,21 +189,32 @@ public class YourInterceptor
 
 ## Running locally
 
-The easiest way to run this server entirely depends on your environment requirements. At least, the following 4 ways are supported:
+The easiest way to run this server entirely depends on your environment requirements. The following ways are supported:
 
 ### Using jetty
 ```bash
-mvn -Pjetty jetty:run
+mvn -Pjetty spring-boot:run
 ```
 
+The Server will then be accessible at http:https://localhost:8080/fhir and the CapabilityStatement will be found at http:https://localhost:8080/fhir/metadata.
 
-If you need to run this server on a different port (using Maven), you can change the port in the run command as follows:
-
+### Using Spring Boot
 ```bash
-mvn -Pjetty -Djetty.port=8888 jetty:run
+mvn spring-boot:run
+```
+
+The Server will then be accessible at http:https://localhost:8080/fhir and the CapabilityStatement will be found at http:https://localhost:8080/fhir/metadata.
+
+If you want to run this server on a different port, you can change the port in the `src/main/resources/application.yaml` file as follows:
+
+```yaml
+server:
+# servlet:
+# context-path: /example/path
+ port: 8888
 ```
 
-Server will then be accessible at http:https://localhost:8888/ and eg. http:https://localhost:8888/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to eg.
+The Server will then be accessible at http:https://localhost:8888/fhir and the CapabilityStatement will be found at http:https://localhost:8888/fhir/metadata. Remember to adjust your overlay configuration in the `application.yaml` file to the following:
 
 ```yaml
  tester:
@@ -219,7 +230,7 @@ Server will then be accessible at http:https://localhost:8888/ and eg. http:https://localhos
 ```bash
 mvn clean spring-boot:run -Pboot
 ```
-Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to eg.
+Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust you overlay configuration in the application.yaml to the following:
 
 ```yaml
  tester:
@@ -235,7 +246,7 @@ Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhos
 ```bash
 mvn clean package spring-boot:repackage -Pboot && java -jar target/ROOT.war
 ```
-Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to eg.
+Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
 
 ```yaml
  tester:
@@ -250,7 +261,7 @@ Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhos
 ```bash
 mvn clean package com.google.cloud.tools:jib-maven-plugin:dockerBuild -Dimage=distroless-hapi && docker run -p 8080:8080 distroless-hapi
 ```
-Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to eg.
+Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
 
 ```yaml
  tester:
@@ -266,7 +277,7 @@ Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhos
 ```bash
 ./build-docker-image.sh && docker run -p 8080:8080 hapi-fhir/hapi-fhir-jpaserver-starter:latest
 ```
-Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to eg.
+Server will then be accessible at http:https://localhost:8080/ and eg. http:https://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
 
 ```yaml
  tester:

charts/hapi-fhir-jpaserver/Chart.lock

@@ -1,6 +1,6 @@
 dependencies:
 - name: postgresql
  repository: oci:https://registry-1.docker.io/bitnamicharts
- version: 13.2.27
-digest: sha256:6374f6f32d32adbe6763c48e2d817d85ec20a1784b2aea1fb0312c658f8e58e9
-generated: "2024-01-10T17:56:36.521957926+01:00"
+ version: 14.3.1
+digest: sha256:fb1d56a00b544bb2ad5691553cadf6384f499652acb9ff5ad625ef36a1b8979e
+generated: "2024-03-10T14:43:22.395381351+01:00"

charts/hapi-fhir-jpaserver/Chart.yaml

@@ -7,11 +7,11 @@ sources:
  - https://github.com/hapifhir/hapi-fhir-jpaserver-starter
 dependencies:
  - name: postgresql
- version: 13.2.27
+ version: 14.3.1
  repository: oci:https://registry-1.docker.io/bitnamicharts
  condition: postgresql.enabled
-appVersion: 6.10.1
-version: 0.15.0
+appVersion: 7.0.3
+version: 0.16.0
 annotations:
  artifacthub.io/license: Apache-2.0
  artifacthub.io/containsSecurityUpdates: "false"
@@ -24,8 +24,8 @@ annotations:
  # When using the list of objects option the valid supported kinds are
  # added, changed, deprecated, removed, fixed, and security.
  - kind: changed
- description: updated starter image to 6.10.1
+ description: updated starter image to v7.0.3
  - kind: changed
- description: updated curlimages/curl to 8.5.0
+ description: updated curlimages/curl to 8.6.0
  - kind: changed
- description: "updated postgresql sub-chart to 13.2.27. ⚠️: this updates the used PostgreSQL image from v15 to v16."
+ description: "updated postgresql sub-chart to 14.3.1."

charts/hapi-fhir-jpaserver/README.md

@@ -1,6 +1,6 @@
 # HAPI FHIR JPA Server Starter Helm Chart
 
-![Version: 0.15.0](https://img.shields.io/badge/Version-0.15.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 6.10.1](https://img.shields.io/badge/AppVersion-6.10.1-informational?style=flat-square)
+![Version: 0.16.0](https://img.shields.io/badge/Version-0.16.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 7.0.3](https://img.shields.io/badge/AppVersion-7.0.3-informational?style=flat-square)
 
 This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
 
@@ -15,7 +15,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
 
 | Repository | Name | Version |
 |------------|------|---------|
-| oci:https://registry-1.docker.io/bitnamicharts | postgresql | 13.2.27 |
+| oci:https://registry-1.docker.io/bitnamicharts | postgresql | 14.3.1 |
 
 ## Values
 
@@ -36,7 +36,7 @@ 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 | `"v6.10.1@sha256:4eac1b3481180b028616d1fab7e657e368538063d75f7ed3be2032e34c657dd4"` | 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 | `"v7.0.3@sha256:73ff82fec42e5cbb7e66338d47af09ba91c140e98beeaee41a5459572d5ae1ce"` | 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 |
@@ -57,6 +57,7 @@ helm install hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
 | postgresql.auth.database | string | `"fhir"` | name for a custom database to create |
 | postgresql.auth.existingSecret | string | `""` | Name of existing secret to use for PostgreSQL credentials `auth.postgresPassword`, `auth.password`, and `auth.replicationPassword` will be ignored and picked up from this secret The secret must contain the keys `postgres-password` (which is the password for "postgres" admin user), `password` (which is the password for the custom user to create when `auth.username` is set), and `replication-password` (which is the password for replication user). The secret might also contains the key `ldap-password` if LDAP is enabled. `ldap.bind_password` will be ignored and picked from this secret in this case. The value is evaluated as a template. |
 | postgresql.enabled | bool | `true` | enable an included PostgreSQL DB. see <https://github.com/bitnami/charts/tree/master/bitnami/postgresql> for details if set to `false`, the values under `externalDatabase` are used |
+| postgresql.primary.containerSecurityContext.readOnlyRootFilesystem | bool | `true` | |
 | replicaCount | int | `1` | number of replicas to deploy |
 | resources | object | `{}` | configure the FHIR server's resource requests and limits |
 | securityContext.allowPrivilegeEscalation | bool | `false` | |
@@ -139,4 +140,4 @@ kubectl port-forward -n observability service/simplest-query 16686:16686
 and opening <http:https://localhost:16686/> in your browser.
 
 ----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.11.3](https://github.com/norwoodj/helm-docs/releases/v1.11.3)
+Autogenerated from chart metadata using [helm-docs v1.13.0](https://github.com/norwoodj/helm-docs/releases/v1.13.0)

charts/hapi-fhir-jpaserver/templates/deployment.yaml

@@ -31,7 +31,7 @@ spec:
  {{- toYaml .Values.podSecurityContext | nindent 8 }}
  initContainers:
  - name: wait-for-db-to-be-ready
- image: docker.io/bitnami/postgresql:16.1.0-debian-11-r18@sha256:06f1f2297f6241a02bd8e8c025b31625254ca66784ac75a4a62e945fa611d045
+ image: docker.io/bitnami/postgresql:16.2.0-debian-12-r6@sha256:ea55532b6f75afbc97f617d91ec5efae17609c8eb825a31845fa9cb9e4aa13e1
  imagePullPolicy: IfNotPresent
  {{- with .Values.restrictedContainerSecurityContext }}
  securityContext:

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: "v6.10.1@sha256:4eac1b3481180b028616d1fab7e657e368538063d75f7ed3be2032e34c657dd4"
+ tag: "v7.0.3@sha256:73ff82fec42e5cbb7e66338d47af09ba91c140e98beeaee41a5459572d5ae1ce"
  # -- image pullPolicy to use
  pullPolicy: IfNotPresent
 
@@ -109,6 +109,9 @@ postgresql:
  # see <https://github.com/bitnami/charts/tree/master/bitnami/postgresql> for details
  # if set to `false`, the values under `externalDatabase` are used
  enabled: true
+ primary:
+ containerSecurityContext:
+ readOnlyRootFilesystem: true
  auth:
  # -- name for a custom database to create
  database: "fhir"

pom.xml

@@ -596,9 +596,20 @@
  </dependency>
  </dependencies>
  </profile>
- <!-- examples of how to start the server using the default profile-->
- <!-- mvn clean package jetty:run -->
- <!-- java -jar jetty-runner.jar target/hapi-fhir-jpaserver.war -->
+ <!-- -->
+ <!-- Examples of how to run the server: -->
+ <!-- -->
+ <!-- For Spring Boot use: -->
+ <!-- mvn spring-boot:run -->
+ <!-- -->
+ <!-- For JETTY use: -->
+ <!-- mvn -Pjetty spring-boot:run -->
+ <!-- -->
+ <!-- For the Tomcat WAR approach use: -->
+ <!-- mvn clean package -DskipTests && java -jar ./target/ROOT.war -->
+ <!-- -->
+ <!-- NEXT: Browse to http:https://localhost:8080/fhir -->
+ <!-- -->
  <profile>
  <id>jetty</id>
  <dependencies>
@@ -676,5 +687,18 @@
  </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. -->
+ <profile>
+ <id>cloudsql-postgres</id>
+ <dependencies>
+ <dependency>
+ <groupId>com.google.cloud.sql</groupId>
+ <artifactId>postgres-socket-factory</artifactId>
+ <version>1.17.0</version>
+ </dependency>
+ </dependencies>
+ </profile> 
  </profiles>
 </project>

src/main/java/ca/uhn/fhir/jpa/starter/web/JobController.java

@@ -0,0 +1,42 @@
+package ca.uhn.fhir.jpa.starter.web;
+
+import ca.uhn.fhir.batch2.api.IJobCoordinator;
+import ca.uhn.fhir.batch2.api.JobOperationResultJson;
+import ca.uhn.fhir.batch2.model.JobInstance;
+import ca.uhn.fhir.batch2.model.StatusEnum;
+import ca.uhn.fhir.batch2.models.JobInstanceFetchRequest;
+import jakarta.validation.constraints.Min;
+import org.springframework.data.domain.Sort;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.*;
+
+import java.util.List;
+
+@RestController
+@RequestMapping("control")
+public class JobController {
+ private final IJobCoordinator theJobCoordinator;
+
+ public JobController(IJobCoordinator theJobCoordinator) {
+ this.theJobCoordinator = theJobCoordinator;
+ }
+
+ @RequestMapping(value = JobController.JOBS, method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
+ public List<JobInstance> getAllJobs(@RequestParam(name = "pageStart") @Min(0) int pageStart, @RequestParam(name = "batchSize") int batchSize, @RequestParam(name = "jobStatus", required = false) StatusEnum jobStatus) {
+ JobInstanceFetchRequest jobInstanceFetchRequest = new JobInstanceFetchRequest();
+ jobInstanceFetchRequest.setPageStart(pageStart);
+ jobInstanceFetchRequest.setBatchSize(batchSize);
+ jobInstanceFetchRequest.setJobStatus(jobStatus != null ? jobStatus.toString() : "");
+ jobInstanceFetchRequest.setSort(Sort.by(Sort.Direction.DESC, JobController.MY_CREATE_TIME));
+
+ return theJobCoordinator.fetchAllJobInstances(jobInstanceFetchRequest).getContent();
+ }
+
+ @RequestMapping(value = JobController.JOBS, method = RequestMethod.DELETE, produces = MediaType.APPLICATION_JSON_VALUE)
+ public JobOperationResultJson cancelInstance(@RequestParam(name = "instanceId") String instanceId) {
+ return theJobCoordinator.cancelInstance(instanceId);
+ }
+
+ public static final String JOBS = "jobs";
+ public static final String MY_CREATE_TIME = "myCreateTime";
+}

src/main/resources/application.yaml

@@ -1,7 +1,8 @@
-#Uncomment the following lines to enable the fhir endpoint to be available at /example/path/fhir instead of /fhir
-#server:
+#Uncomment the "servlet" and "context-path" lines below to make the fhir endpoint available at /example/path/fhir instead of the default value of /fhir
+server:
 # servlet:
 # context-path: /example/path
+ port: 8080
 #Adds the option to go to eg. http:https://localhost:8080/actuator/health for seeing the running configuration
 #see https://docs.spring.io/spring-boot/docs/current/reference/html/actuator.html#actuator.endpoints
 management: