Merge branch 'master' into rel_7_3_tracking

Author: dotasek

Dockerfile

@@ -1,7 +1,7 @@
-FROM docker.io/library/maven:3.9.4-eclipse-temurin-17 AS build-hapi
+FROM docker.io/library/maven:3.9.7-eclipse-temurin-17 AS build-hapi
 WORKDIR /tmp/hapi-fhir-jpaserver-starter
 
-ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.31.0
+ARG OPENTELEMETRY_JAVA_AGENT_VERSION=1.33.3
 RUN curl -LSsO https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases/download/v${OPENTELEMETRY_JAVA_AGENT_VERSION}/opentelemetry-javaagent.jar
 
 COPY pom.xml .
@@ -18,7 +18,7 @@ RUN mkdir /app && cp /tmp/hapi-fhir-jpaserver-starter/target/ROOT.war /app/main.
 
 ########### 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
+FROM bitnami/tomcat:10.1 AS tomcat
 
 RUN rm -rf /opt/bitnami/tomcat/webapps/ROOT && \
     mkdir -p /opt/bitnami/hapi/data/hapi/lucenefiles && \
@@ -36,7 +36,7 @@ COPY --from=build-hapi --chown=1001:1001 /tmp/hapi-fhir-jpaserver-starter/opente
 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-debian11:nonroot AS default
+FROM gcr.io/distroless/java17-debian12: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.

README.md

@@ -13,7 +13,7 @@ In order to use this sample, you should have:
 - [This project](https://github.com/hapifhir/hapi-fhir-jpaserver-starter) checked out. You may wish to create a GitHub Fork of the project and check that out instead so that you can customize the project and save the results to GitHub.
 
 ### and either
- - Oracle Java (JDK) installed: Minimum JDK8 or newer.
+ - Oracle Java (JDK) installed: Minimum JDK17 or newer.
  - Apache Maven build tool (newest version)
 
 ### or
@@ -102,7 +102,7 @@ spring:
     driverClassName: org.postgresql.Driver
   jpa:
     properties:
-      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
+      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
       hibernate.search.enabled: false
 ```
 
@@ -155,7 +155,7 @@ spring:
     driverClassName: org.postgresql.Driver
   jpa:
     properties:
-      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
+      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
       hibernate.search.enabled: false
 hapi:
   fhir:
@@ -244,7 +244,7 @@ Server will then be accessible at http://localhost:8080/ and eg. http://localhos
 
 ### Using Spring Boot
 ```bash
-mvn clean package spring-boot:repackage -Pboot && java -jar target/ROOT.war
+mvn clean package spring-boot:repackage -DskipTests=true -Pboot && java -jar target/ROOT.war
 ```
 Server will then be accessible at http://localhost:8080/ and eg. http://localhost:8080/fhir/metadata. Remember to adjust your overlay configuration in the application.yaml to the following:
 
@@ -312,7 +312,7 @@ spring:
     driverClassName: org.postgresql.Driver
   jpa:
     properties:
-      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
+      hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
       hibernate.search.enabled: false
 
       # Then comment all hibernate.search.backend.*
@@ -430,7 +430,7 @@ spring:
     driverClassName: org.postgresql.Driver
 jpa:
   properties:
-    hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
+    hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
     hibernate.search.enabled: false
 
     # Then comment all hibernate.search.backend.*

charts/hapi-fhir-jpaserver/Chart.yaml

@@ -10,8 +10,8 @@ dependencies:
     version: 14.3.1
     repository: oci://registry-1.docker.io/bitnamicharts
     condition: postgresql.enabled
-appVersion: 7.0.3
-version: 0.16.0
+appVersion: 7.2.0
+version: 0.17.0
 annotations:
   artifacthub.io/license: Apache-2.0
   artifacthub.io/containsSecurityUpdates: "false"
@@ -24,7 +24,7 @@ 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 v7.0.3
+      description: updated starter image to v7.2.0
     - kind: changed
       description: updated curlimages/curl to 8.6.0
     - kind: changed

charts/hapi-fhir-jpaserver/README.md

@@ -1,6 +1,6 @@
 # HAPI FHIR JPA Server Starter Helm Chart
 
-![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)
+![Version: 0.17.0](https://img.shields.io/badge/Version-0.17.0-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 7.2.0](https://img.shields.io/badge/AppVersion-7.2.0-informational?style=flat-square)
 
 This helm chart will help you install the HAPI FHIR JPA Server in a Kubernetes environment.
 
@@ -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 | `"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. |
+| image.tag | string | `"v7.2.0@sha256:9bcafa8342b572eee248cb7c48c496863d352bbd0347e1d98ea238d09620e89b"` | 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 |

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: "v7.0.3@sha256:73ff82fec42e5cbb7e66338d47af09ba91c140e98beeaee41a5459572d5ae1ce"
+  tag: "v7.2.0@sha256:9bcafa8342b572eee248cb7c48c496863d352bbd0347e1d98ea238d09620e89b"
   # -- image pullPolicy to use
   pullPolicy: IfNotPresent
 

docker-compose.yml

@@ -4,10 +4,15 @@ services:
     build: .
     container_name: hapi-fhir-jpaserver-start
     restart: on-failure
+    environment:
+      SPRING_DATASOURCE_URL: "jdbc:postgresql://hapi-fhir-postgres:5432/hapi"
+      SPRING_DATASOURCE_USERNAME: "admin"
+      SPRING_DATASOURCE_PASSWORD: "admin"
+      SPRING_DATASOURCE_DRIVERCLASSNAME: "org.postgresql.Driver"
     ports:
       - "8080:8080"
   hapi-fhir-postgres:
-    image: postgres:13-alpine
+    image: postgres:14-alpine
     container_name: hapi-fhir-postgres
     restart: always
     environment:

pom.xml

@@ -21,7 +21,7 @@
     <packaging>war</packaging>
 
     <properties>
-        <java.version>11</java.version>
+        <java.version>17</java.version>
     </properties>
 
     <prerequisites>
@@ -77,13 +77,13 @@
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-base</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
         </dependency>
         <!-- This dependency includes the EmailSenderImpl we will be using instead of standard javamail.-->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-jpaserver-subscription</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>com.zaxxer</groupId>
@@ -96,7 +96,7 @@
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-jpaserver-base</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.springframework</groupId>
@@ -112,13 +112,13 @@
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-storage-cr</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
         </dependency>
         <!-- This dependency includes the JPA MDM Server -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-jpaserver-mdm</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
         </dependency>
         <dependency>
             <groupId>org.springframework</groupId>
@@ -128,13 +128,13 @@
         <dependency>
           <groupId>ca.uhn.hapi.fhir</groupId>
           <artifactId>hapi-fhir-server-cds-hooks</artifactId>
-          <version>${project.version}</version>
+          <version>${project.parent.version}</version>
         </dependency>
         <!-- This dependency includes the OpenAPI Server -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-server-openapi</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.yaml</groupId>
@@ -146,21 +146,21 @@
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-testpage-overlay</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
             <type>war</type>
             <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-testpage-overlay</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
             <classifier>classes</classifier>
         </dependency>
         <!-- This dependency is used to include the IPS Base Implementation -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-jpaserver-ips</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
         </dependency>
 
         <!-- HAPI-FHIR uses Logback for logging support. The logback library is included automatically by Maven as a part of the hapi-fhir-base dependency, but you also need to include a logging library. Logback
@@ -261,7 +261,7 @@
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-jpaserver-test-utilities</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
             <scope>test</scope>
             <exclusions>
                 <exclusion>
@@ -300,7 +300,7 @@
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-test-utilities</artifactId>
-            <version>${project.version}</version>
+            <version>${project.parent.version}</version>
             <scope>test</scope>
             <exclusions>
                 <exclusion>
@@ -393,7 +393,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-surefire-plugin</artifactId>
-                    <version>3.1.2</version>
+                    <version>3.2.5</version>
                 </plugin>
             </plugins>
         </pluginManagement>
@@ -429,9 +429,9 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.11.0</version>
+                <version>3.13.0</version>
                 <configuration>
-                    <release>11</release>
+                    <release>${java.version}</release>
                 </configuration>
             </plugin>
 

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

@@ -37,6 +37,7 @@ public class AppProperties {
   private Boolean allow_multiple_delete = false;
   private Boolean allow_override_default_search_params = true;
   private Boolean auto_create_placeholder_reference_targets = false;
+  private Boolean mass_ingestion_mode_enabled = false;
   private final Set<String> auto_version_reference_at_paths = new HashSet<>();
   private Boolean language_search_parameter_enabled = false;
   private Boolean dao_scheduling_enabled = true;
@@ -324,6 +325,14 @@ public void setAllow_override_default_search_params(
     this.allow_override_default_search_params = allow_override_default_search_params;
   }
 
+  public Boolean getMass_ingestion_mode_enabled() {
+    return mass_ingestion_mode_enabled;
+  }
+
+  public void setMass_ingestion_mode_enabled(Boolean mass_ingestion_mode_enabled) {
+    this.mass_ingestion_mode_enabled = mass_ingestion_mode_enabled;
+  }
+
   public Boolean getAuto_create_placeholder_reference_targets() {
     return auto_create_placeholder_reference_targets;
   }
@@ -913,4 +922,4 @@ public Boolean getResource_dbhistory_enabled() {
 public void setResource_dbhistory_enabled(Boolean resource_dbhistory_enabled) {
 	this.resource_dbhistory_enabled = resource_dbhistory_enabled;
 }
-}
+}

src/main/java/ca/uhn/fhir/jpa/starter/common/FhirServerConfigCommon.java

@@ -135,6 +135,8 @@ public JpaStorageSettings jpaStorageSettings(AppProperties appProperties) {
 						: StorageSettings.IndexEnabledEnum.DISABLED);
 		jpaStorageSettings.setAutoCreatePlaceholderReferenceTargets(
 				appProperties.getAuto_create_placeholder_reference_targets());
+		jpaStorageSettings.setMassIngestionMode(
+				appProperties.getMass_ingestion_mode_enabled());
 		jpaStorageSettings.setAutoVersionReferenceAtPaths(appProperties.getAuto_version_reference_at_paths());
 		jpaStorageSettings.setEnforceReferentialIntegrityOnWrite(
 				appProperties.getEnforce_referential_integrity_on_write());

src/main/resources/application.yaml

@@ -6,10 +6,26 @@ server:
 #Adds the option to go to eg. http://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:
-  endpoints:
-    web:
-      exposure:
-        include: "health,prometheus"
+  endpoint:
+    endpoints:
+      enabled-by-default: false
+      web:
+        exposure:
+          include: health,prometheus
+    health:
+      enabled: true
+      probes:
+        enabled: true
+      livenessState:
+        enabled: true
+      readinessState:
+        enabled: true
+    prometheus:
+      enabled: true
+      metrics:
+        export:
+          enabled: true
+
 spring:
   main:
     allow-circular-references: true
@@ -36,7 +52,7 @@ spring:
 
       #Hibernate dialect is automatically detected except Postgres and H2.
       #If using H2, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
-      #If using postgres, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgres94Dialect
+      #If using postgres, then supply the value of ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
       hibernate.dialect: ca.uhn.fhir.jpa.model.dialect.HapiFhirH2Dialect
   #      hibernate.hbm2ddl.auto: update
   #      hibernate.jdbc.batch_size: 20
@@ -46,7 +62,7 @@ spring:
   #      hibernate.cache.use_minimal_puts: false
 
   ###    These settings will enable fulltext search with lucene or elastic
-      hibernate.search.enabled: true
+      hibernate.search.enabled: false
   ### lucene parameters
 #      hibernate.search.backend.type: lucene
 #      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiHSearchAnalysisConfigurers$HapiLuceneAnalysisConfigurer
@@ -116,6 +132,7 @@ hapi:
     #    allow_multiple_delete: true
     #    allow_override_default_search_params: true
     #    auto_create_placeholder_reference_targets: false
+    #    mass_ingestion_mode_enabled: false
     ### tells the server to automatically append the current version of the target resource to references at these paths
     #    auto_version_reference_at_paths: Device.patient, Device.location, Device.parent, DeviceMetric.parent, DeviceMetric.source, Observation.device, Observation.subject
     #    ips_enabled: false