Merge pull request #27 from opensrp/feature/update_hapi_version

Feature/update hapi version

.github/workflows/chart-release.yaml

@@ -21,11 +21,6 @@ jobs:
           git config user.name "$GITHUB_ACTOR"
           git config user.email "[email protected]"
 
-      - name: Install Helm
-        uses: azure/setup-helm@v1
-        with:
-          version: v3.7.0
-
       - name: Add bitnami repo
         run: helm repo add bitnami https://charts.bitnami.com/bitnami
 

.github/workflows/chart-test.yaml

@@ -43,11 +43,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Set up Helm
-        uses: azure/setup-helm@v1
-        with:
-          version: v3.7.0
-
       - name: Set up chart-testing
         uses: helm/[email protected]
 

README.md

@@ -368,7 +368,7 @@ using the `gcr.io/distroless/java-debian10:11` base image:
 docker build --target=release-distroless -t hapi-fhir:distroless .
 ```
 
-Note that distroless images are also automatically build and pushed to the container registry,
+Note that distroless images are also automatically built and pushed to the container registry,
 see the `-distroless` suffix in the image tags.
 
 ## Adding custom operations

charts/hapi-fhir-jpaserver/Chart.yaml

@@ -18,6 +18,9 @@ annotations:
     # added, changed, deprecated, removed, fixed, and security.
     - kind: changed
       description: |
-        updated HAPI FHIR starter image to 5.5.1
-appVersion: v5.5.1
-version: 0.6.0
+        updated HAPI FHIR starter image to 5.6.0
+    - kind: added
+      description: |
+        added support for configuring PodDisruptionBudget for the server pods
+appVersion: v5.6.0
+version: 0.7.0

charts/hapi-fhir-jpaserver/README.md

@@ -1,6 +1,6 @@
 # HAPI FHIR JPA Server Starter Helm Chart
 
-![Version: 0.6.0](https://img.shields.io/badge/Version-0.6.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: v5.5.1](https://img.shields.io/badge/AppVersion-v5.5.1-informational?style=flat-square)
+![Version: 0.7.0](https://img.shields.io/badge/Version-0.7.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: v5.6.0](https://img.shields.io/badge/AppVersion-v5.6.0-informational?style=flat-square)
 
 This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
 
@@ -11,6 +11,9 @@ helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/
 helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
 ```
 
+> ⚠ By default, the included [PostgreSQL Helm chart](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)
+> auto-generates a random password for the database which may cause problems when upgrading the chart (see [here for details](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)).
+
 ## Values
 
 | Key | Type | Default | Description |
@@ -24,11 +27,12 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
 | externalDatabase.password | string | `""` | database password |
 | externalDatabase.port | int | `5432` | database port number |
 | externalDatabase.user | string | `"fhir"` | username for the external database |
+| extraEnv | list | `[]` | extra environment variables to set on the server container |
 | fullnameOverride | string | `""` | override the chart fullname |
 | image.flavor | string | `"distroless"` | the flavor or variant of the image to use. appended to the image tag by `-`. |
-| image.pullPolicy | string | `"IfNotPresent"` |  |
-| image.registry | string | `"docker.io"` |  |
-| image.repository | string | `"hapiproject/hapi"` |  |
+| 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 | `""` | defaults to `Chart.appVersion` |
 | 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. |
@@ -43,6 +47,9 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
 | networkPolicy.explicitNamespacesSelector | object | `{}` | a Kubernetes LabelSelector to explicitly select namespaces from which ingress traffic could be allowed |
 | nodeSelector | object | `{}` | node selector for the pod |
 | podAnnotations | object | `{}` | annotations applied to the server pod |
+| podDisruptionBudget.enabled | bool | `false` | Enable PodDisruptionBudget for the server pods. uses policy/v1/PodDisruptionBudget thus requiring k8s 1.21+ |
+| podDisruptionBudget.maxUnavailable | string | `""` | maximum unavailable instances |
+| podDisruptionBudget.minAvailable | int | `1` | minimum available instances |
 | podSecurityContext | object | `{}` | pod security context |
 | postgresql.containerSecurityContext.allowPrivilegeEscalation | bool | `false` |  |
 | postgresql.containerSecurityContext.capabilities.drop[0] | string | `"ALL"` |  |
@@ -61,14 +68,26 @@ helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpas
 | securityContext.readOnlyRootFilesystem | bool | `true` |  |
 | securityContext.runAsNonRoot | bool | `true` |  |
 | securityContext.runAsUser | int | `65532` |  |
-| service.port | int | `8080` |  |
-| service.type | string | `"ClusterIP"` |  |
+| service.port | int | `8080` | port where the server will be exposed at |
+| service.type | string | `"ClusterIP"` | service type |
 | startupProbe.failureThreshold | int | `10` |  |
 | startupProbe.initialDelaySeconds | int | `60` |  |
 | startupProbe.periodSeconds | int | `30` |  |
 | startupProbe.successThreshold | int | `1` |  |
 | startupProbe.timeoutSeconds | int | `30` |  |
 | tolerations | list | `[]` | pod tolerations |
 
+## Development
+
+To update the Helm chart when a new version of the `hapiproject/hapi` image is released, the [Chart.yaml](Chart.yaml)'s
+`appVersion` and `version` fields need to be updated accordingly. Afterwards, re-generate the [README.md](README.md)
+by running:
+
+```sh
+$ helm-docs
+INFO[2021-11-20T12:38:04Z] Found Chart directories [charts/hapi-fhir-jpaserver]
+INFO[2021-11-20T12:38:04Z] Generating README Documentation for chart /usr/src/app/charts/hapi-fhir-jpaserver
+```
+
 ----------------------------------------------
 Autogenerated from chart metadata using [helm-docs v1.5.0](https://github.com/norwoodj/helm-docs/releases/v1.5.0)

charts/hapi-fhir-jpaserver/README.md.gotmpl

@@ -11,6 +11,21 @@ helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/
 helm install --render-subchart-notes hapi-fhir-jpaserver hapifhir/hapi-fhir-jpaserver
 ```
 
+> ⚠ By default, the included [PostgreSQL Helm chart](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)
+> auto-generates a random password for the database which may cause problems when upgrading the chart (see [here for details](https://github.com/bitnami/charts/tree/master/bitnami/postgresql#upgrading)).
+
 {{ template "chart.valuesSection" . }}
 
+## Development
+
+To update the Helm chart when a new version of the `hapiproject/hapi` image is released, the [Chart.yaml](Chart.yaml)'s
+`appVersion` and `version` fields need to be updated accordingly. Afterwards, re-generate the [README.md](README.md)
+by running:
+
+```sh
+$ helm-docs
+INFO[2021-11-20T12:38:04Z] Found Chart directories [charts/hapi-fhir-jpaserver]
+INFO[2021-11-20T12:38:04Z] Generating README Documentation for chart /usr/src/app/charts/hapi-fhir-jpaserver
+```
+
 {{ template "helm-docs.versionFooter" . }}

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

@@ -0,0 +1,18 @@
+{{- if .Values.podDisruptionBudget.enabled }}
+kind: PodDisruptionBudget
+apiVersion: policy/v1
+metadata:
+  name: {{ include "hapi-fhir-jpaserver.fullname" . }}
+  labels:
+    {{- include "hapi-fhir-jpaserver.labels" . | nindent 4 }}
+spec:
+  {{- if .Values.podDisruptionBudget.minAvailable }}
+  minAvailable: {{ .Values.podDisruptionBudget.minAvailable }}
+  {{- end }}
+  {{- if .Values.podDisruptionBudget.maxUnavailable }}
+  maxUnavailable: {{ .Values.podDisruptionBudget.maxUnavailable }}
+  {{- end }}
+  selector:
+    matchLabels:
+      {{- include "hapi-fhir-jpaserver.selectorLabels" . | nindent 6 }}
+{{- end }}

charts/hapi-fhir-jpaserver/values.yaml

@@ -2,13 +2,16 @@
 replicaCount: 1
 
 image:
+  # -- registry where the HAPI FHIR server image is hosted
   registry: docker.io
+  # -- the path inside the repository
   repository: hapiproject/hapi
   # -- defaults to `Chart.appVersion`
   tag: ""
   # -- the flavor or variant of the image to use.
   # appended to the image tag by `-`.
   flavor: "distroless"
+  # -- image pullPolicy to use
   pullPolicy: IfNotPresent
 
 # -- image pull secrets to use when pulling the image
@@ -42,7 +45,9 @@ securityContext:
 
 # service to expose the server
 service:
+  # -- service type
   type: ClusterIP
+  # -- port where the server will be exposed at
   port: 8080
 
 ingress:
@@ -157,3 +162,18 @@ networkPolicy:
   #       matchLabels:
   #         app.kubernetes.io/name: {{ $.Release.Name }}
   allowedFrom: []
+
+# -- extra environment variables to set on the server container
+extraEnv:
+  []
+  # - name: SPRING_FLYWAY_BASELINE_ON_MIGRATE
+  #   value: "true"
+
+podDisruptionBudget:
+  # -- Enable PodDisruptionBudget for the server pods.
+  # uses policy/v1/PodDisruptionBudget thus requiring k8s 1.21+
+  enabled: false
+  # -- minimum available instances
+  minAvailable: 1
+  # -- maximum unavailable instances
+  maxUnavailable: ""

pom.xml

@@ -14,16 +14,17 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-		  <version>5.5.1</version>
+		  <version>5.6.0</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
     <groupId>org.smartregister</groupId>
-    <version>5.5.3-SNAPSHOT</version>
+    <version>5.6.0-SNAPSHOT</version>
 
     <properties>
         <java.version>8</java.version>
-        <hapi.fhir.version>5.5.1</hapi.fhir.version>
+        <hapi.fhir.version>5.6.0</hapi.fhir.version>
+        <spring_boot_version>2.5.6</spring_boot_version>
     </properties>
 
     <prerequisites>
@@ -72,6 +73,7 @@
         <dependency>
             <groupId>com.sun.mail</groupId>
             <artifactId>javax.mail</artifactId>
+            <version>1.6.2</version>
             <exclusions>
                 <exclusion>
                     <groupId>javax.activation</groupId>
@@ -115,6 +117,12 @@
             <artifactId>hapi-fhir-jpaserver-mdm</artifactId>
             <version>${hapi.fhir.version}</version>
         </dependency>
+        <!-- This dependency includes the OpenAPI Server -->
+        <dependency>
+            <groupId>ca.uhn.hapi.fhir</groupId>
+            <artifactId>hapi-fhir-server-openapi</artifactId>
+            <version>${hapi.fhir.version}</version>
+        </dependency>
         <!-- This dependency is used for the "FHIR Tester" web app overlay -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>

src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java

@@ -22,6 +22,7 @@
 public class AppProperties {
 
   private Boolean cql_enabled = false;
+  private Boolean openapi_enabled = false;
   private Boolean mdm_enabled = false;
   private Boolean allow_cascading_deletes = false;
   private Boolean allow_contains_searches = true;
@@ -75,6 +76,14 @@ public class AppProperties {
   private Boolean use_apache_address_strategy = false;
   private Boolean use_apache_address_strategy_https = false;
 
+	public Boolean getOpenapi_enabled() {
+		return openapi_enabled;
+	}
+
+	public void setOpenapi_enabled(Boolean openapi_enabled) {
+		this.openapi_enabled = openapi_enabled;
+	}
+
 	public Boolean getUse_apache_address_strategy() {
     return use_apache_address_strategy;
   }

src/main/java/ca/uhn/fhir/jpa/starter/Application.java

@@ -32,16 +32,6 @@ public class Application extends SpringBootServletInitializer {
 
   public static void main(String[] args) {
 
-  	 /*
-  	 * https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/246
-  	 * This will be allowed for a short period until we know how MDM should be configured
-  	 * or don't have multiple equal bean instantiations.
-  	 *
-  	 * This will require changes in the main project as stated in the Github comment
-  	 * */
-  	 System.setProperty("spring.main.allow-bean-definition-overriding","true");
-
-    System.setProperty("spring.batch.job.enabled", "false");
     SpringApplication.run(Application.class, args);
 
     //Server is now accessible at eg. http://localhost:8080/fhir/metadata

src/main/java/ca/uhn/fhir/jpa/starter/BaseJpaRestfulServer.java

@@ -22,12 +22,14 @@
 import ca.uhn.fhir.jpa.provider.SubscriptionTriggeringProvider;
 import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
 import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
+import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
 import ca.uhn.fhir.jpa.search.DatabaseBackedPagingProvider;
 import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
 import ca.uhn.fhir.mdm.provider.MdmProviderLoader;
 import ca.uhn.fhir.narrative.DefaultThymeleafNarrativeGenerator;
 import ca.uhn.fhir.narrative.INarrativeGenerator;
 import ca.uhn.fhir.narrative2.NullNarrativeGenerator;
+import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
 import ca.uhn.fhir.rest.server.ApacheProxyAddressStrategy;
 import ca.uhn.fhir.rest.server.ETagSupportEnum;
 import ca.uhn.fhir.rest.server.HardcodedServerAddressStrategy;
@@ -91,6 +93,8 @@ public class BaseJpaRestfulServer extends RestfulServer {
   @Autowired
   PartitionManagementProvider partitionManagementProvider;
   @Autowired
+  ValueSetOperationProvider valueSetOperationProvider;
+  @Autowired
   BinaryStorageInterceptor binaryStorageInterceptor;
   @Autowired
   IPackageInstallerSvc packageInstallerSvc;
@@ -357,11 +361,18 @@ protected void initialize() throws ServletException {
 
     daoConfig.setDeferIndexingForCodesystemsOfSize(appProperties.getDefer_indexing_for_codesystems_of_size());
 
+	 if (appProperties.getOpenapi_enabled()) {
+		registerInterceptor(new OpenApiInterceptor());
+	}
+
     // Bulk Export
     if (appProperties.getBulk_export_enabled()) {
       registerProvider(bulkDataExportProvider);
     }
 
+    // valueSet Operations i.e $expand
+    registerProvider(valueSetOperationProvider);
+
     // Partitioning
     if (appProperties.getPartitioning() != null) {
       registerInterceptor(new RequestTenantPartitionInterceptor());

src/main/java/ca/uhn/fhir/jpa/starter/EnvironmentHelper.java

@@ -14,6 +14,7 @@
 import org.hibernate.search.mapper.orm.automaticindexing.session.AutomaticIndexingSynchronizationStrategyNames;
 import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
 import org.hibernate.search.mapper.orm.schema.management.SchemaManagementStrategyName;
+import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
 import org.springframework.boot.orm.jpa.hibernate.SpringImplicitNamingStrategy;
 import org.springframework.boot.orm.jpa.hibernate.SpringPhysicalNamingStrategy;
 import org.springframework.core.env.CompositePropertySource;
@@ -25,7 +26,8 @@
 
 public class EnvironmentHelper {
 
-	public static Properties getHibernateProperties(ConfigurableEnvironment environment) {
+	public static Properties getHibernateProperties(ConfigurableEnvironment environment,
+		ConfigurableListableBeanFactory myConfigurableListableBeanFactory) {
 		Properties properties = new Properties();
 		Map<String, Object> jpaProps = getPropertiesStartingWith(environment, "spring.jpa.properties");
 		for (Map.Entry<String, Object> entry : jpaProps.entrySet()) {
@@ -41,7 +43,7 @@ public static Properties getHibernateProperties(ConfigurableEnvironment environm
 		//properties.putIfAbsent(AvailableSettings.BEAN_CONTAINER, new SpringBeanContainer(beanFactory));
 
 		//hapi-fhir-jpaserver-base "sensible defaults"
-		Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean().getJpaPropertyMap();
+		Map<String, Object> hapiJpaPropertyMap = new HapiFhirLocalContainerEntityManagerFactoryBean(myConfigurableListableBeanFactory).getJpaPropertyMap();
 		hapiJpaPropertyMap.forEach(properties::putIfAbsent);
 
 		//hapi-fhir-jpaserver-starter defaults
@@ -73,7 +75,7 @@ public static Properties getHibernateProperties(ConfigurableEnvironment environm
 				ElasticsearchHibernatePropertiesBuilder builder = new ElasticsearchHibernatePropertiesBuilder();
 				IndexStatus requiredIndexStatus = environment.getProperty("elasticsearch.required_index_status", IndexStatus.class);
 				builder.setRequiredIndexStatus(requireNonNullElse(requiredIndexStatus, IndexStatus.YELLOW));
-				builder.setRestUrl(getElasticsearchServerUrl(environment));
+				builder.setHosts(getElasticsearchServerUrl(environment));
 				builder.setUsername(getElasticsearchServerUsername(environment));
 				builder.setPassword(getElasticsearchServerPassword(environment));
 				builder.setProtocol(getElasticsearchServerProtocol(environment));