v7.2.0

.github/workflows/python-pre-release.yml

@@ -29,6 +29,10 @@ jobs:
         with:
           java-version: 17
           distribution: "zulu"
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.8'
       - name: Cache local Maven repository
         uses: actions/cache@v4
         with:

.github/workflows/release.yml

@@ -76,6 +76,10 @@ jobs:
         with:
           java-version: 17
           distribution: "zulu"
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.8'
       - name: Cache local Maven repository
         uses: actions/cache@v4
         with:

.github/workflows/test.yml

@@ -483,7 +483,7 @@ jobs:
           restore-keys: |-
             ${{ runner.os }}-maven-
       - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         id: pythoninstall
         with:
           python-version: 3.8

CONTRIBUTING.md

@@ -75,8 +75,14 @@ production environments such as the Pathling website and sandbox instance.
 
 ### Coding conventions
 
-This repository uses [EditorConfig](https://editorconfig.org/), please use it to
-reformat your code before pushing.
+This repository uses multiple code formatters:
+- Prettier for JavaScript code
+- Black for Python code  
+- EditorConfig for all other languages
+
+Please use the appropriate formatter to reformat your code before pushing.
+
+Please terminate all line comments with a period.
 
 ## Code of conduct
 

LICENSE

@@ -183,65 +183,66 @@ agree to comply with the licence terms for these components as part of
 accessing the Software. Other third party software may also be identified in
 separate files distributed with the Software.
 
-* (Apache License, Version 2.0) HAPI FHIR - Core Library (ca.uhn.hapi.fhir:hapi-fhir-base:7.0.2 - http://jamesagnew.github.io/hapi-fhir/)
-* (Apache License, Version 2.0) HAPI FHIR - Client Framework (ca.uhn.hapi.fhir:hapi-fhir-client:7.0.2 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-client)
-* (Apache License, Version 2.0) HAPI FHIR - Server Framework (ca.uhn.hapi.fhir:hapi-fhir-server:7.0.2 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-server)
-* (Apache License, Version 2.0) HAPI FHIR Structures - FHIR R4 (ca.uhn.hapi.fhir:hapi-fhir-structures-r4:7.0.2 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-structures-r4)
-* (Eclipse Public License 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.4.14 - http://logback.qos.ch/logback-classic)
-* (Apache License, Version 2.0) AWS SDK for Java - Bundle (com.amazonaws:aws-java-sdk-bundle:1.12.603 - https://aws.amazon.com/sdkforjava)
-* (MIT License) java jwt (com.auth0:java-jwt:4.4.0 - https://github.com/auth0/java-jwt)
+* (Apache License, Version 2.0) FHIR Bulk Client (au.csiro.fhir:bulk-export:1.0.2 - https://github.com/aehrc/fhir-bulk-java)
+* (Apache License, Version 2.0) HAPI FHIR - Core Library (ca.uhn.hapi.fhir:hapi-fhir-base:7.6.1 - http://jamesagnew.github.io/hapi-fhir/)
+* (Apache License, Version 2.0) HAPI FHIR - Client Framework (ca.uhn.hapi.fhir:hapi-fhir-client:7.6.1 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-client)
+* (Apache License, Version 2.0) HAPI FHIR - Server Framework (ca.uhn.hapi.fhir:hapi-fhir-server:7.6.1 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-server)
+* (Apache License, Version 2.0) HAPI FHIR Structures - FHIR R4 (ca.uhn.hapi.fhir:hapi-fhir-structures-r4:7.6.1 - https://hapifhir.io/hapi-deployable-pom/hapi-fhir-structures-r4)
+* (Eclipse Public License 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.5.11 - http://logback.qos.ch/logback-classic)
+* (Apache License, Version 2.0) AWS SDK for Java - Bundle (com.amazonaws:aws-java-sdk-bundle:1.12.782 - https://aws.amazon.com/sdkforjava)
+* (MIT License) java jwt (com.auth0:java-jwt:4.5.0 - https://github.com/auth0/java-jwt)
 * (MIT License) jwks-rsa (com.auth0:jwks-rsa:0.22.1 - https://github.com/auth0/jwks-rsa-java)
-* (Apache License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.16.1 - https://github.com/FasterXML/jackson-core)
+* (Apache License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.17.2 - https://github.com/FasterXML/jackson-core)
 * (Apache License, Version 2.0) Woodstox (com.fasterxml.woodstox:woodstox-core:6.4.0 - https://github.com/FasterXML/woodstox)
 * (Apache License, Version 2.0) docker-java (com.github.docker-java:docker-java:3.3.4 - https://github.com/docker-java/docker-java)
 * (Apache License, Version 2.0) docker-java-transport-okhttp (com.github.docker-java:docker-java-transport-okhttp:3.3.4 - https://github.com/docker-java/docker-java)
 * (Apache License, Version 2.0) WireMock (com.github.tomakehurst:wiremock-jre8-standalone:2.35.2 - http://wiremock.org)
 * (Apache License, Version 2.0) FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.2 - http://findbugs.sourceforge.net/)
 * (Apache License, Version 2.0) Gson (com.google.code.gson:gson:2.10 - https://github.com/google/gson/gson)
 * (Apache License, Version 2.0) Guava: Google Core Libraries for Java (com.google.guava:guava:32.1.3-jre - https://github.com/google/guava)
-* (Apache License, Version 2.0) Apache Commons BeanUtils (commons-beanutils:commons-beanutils:1.9.4 - https://commons.apache.org/proper/commons-beanutils/)
-* (Apache License, Version 2.0) Apache Commons IO (commons-io:commons-io:2.16.1 - https://commons.apache.org/proper/commons-io/)
+* (Apache License, Version 2.0) Apache Commons BeanUtils (commons-beanutils:commons-beanutils:1.10.1 - https://commons.apache.org/proper/commons-beanutils)
+* (Apache License, Version 2.0) Apache Commons IO (commons-io:commons-io:2.18.0 - https://commons.apache.org/proper/commons-io/)
 * (Apache License, Version 2.0) Commons Lang (commons-lang:commons-lang:2.6 - http://commons.apache.org/lang/)
-* (Apache License, Version 2.0) delta-spark (io.delta:delta-spark_2.12:3.2.0 - https://delta.io/)
-* (Apache License, Version 2.0) micrometer-registry-prometheus (io.micrometer:micrometer-registry-prometheus:1.13.0 - https://github.com/micrometer-metrics/micrometer)
+* (Apache License, Version 2.0) delta-spark (io.delta:delta-spark_2.12:3.3.0 - https://delta.io/)
+* (Apache License, Version 2.0) micrometer-registry-prometheus (io.micrometer:micrometer-registry-prometheus:1.14.4 - https://github.com/micrometer-metrics/micrometer)
 * (MIT License) Sentry SDK (io.sentry:sentry:6.6.0 - https://github.com/getsentry/sentry-java)
 * (Apache License, Version 2.0) Jakarta Bean Validation API (jakarta.validation:jakarta.validation-api:3.0.2 - https://beanvalidation.org)
 * (CDDL + GPLv2 with classpath exception) Java Servlet API (javax.servlet:javax.servlet-api:4.0.1 - https://javaee.github.io/servlet-spec/)
-* (Apache License, Version 2.0) Joda-Time (joda-time:joda-time:2.12.7 - https://www.joda.org/joda-time/)
+* (Apache License, Version 2.0) Joda-Time (joda-time:joda-time:2.13.1 - https://www.joda.org/joda-time/)
 * (BSD License) ANTLR 4 Tool (org.antlr:antlr4:4.9.3 - http://www.antlr.org)
 * (Apache License, Version 2.0) Apache Commons Lang (org.apache.commons:commons-lang3:3.14.0 - https://commons.apache.org/proper/commons-lang/)
-* (Apache License, Version 2.0) Apache Derby Tools (org.apache.derby:derbytools:10.14.2.0 - http://db.apache.org/derby/)
+* (Apache License, Version 2.0) Apache Derby Tools (org.apache.derby:derbytools:10.16.1.1 - http://db.apache.org/derby/)
 * (Apache License, Version 2.0) Apache Hadoop Amazon Web Services support (org.apache.hadoop:hadoop-aws:3.3.4 - no url defined)
 * (Apache License, Version 2.0) Apache Hadoop Client API (org.apache.hadoop:hadoop-client-api:3.3.4 - no url defined)
-* (Apache License, Version 2.0) Spark Project Catalyst (org.apache.spark:spark-catalyst_2.12:3.5.0 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project Core (org.apache.spark:spark-core_2.12:3.5.0 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project Hive (org.apache.spark:spark-hive_2.12:3.5.0 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project Kubernetes (org.apache.spark:spark-kubernetes_2.12:3.5.0 - https://spark.apache.org/spark-kubernetes_2.12/)
-* (Apache License, Version 2.0) Spark Project SQL (org.apache.spark:spark-sql_2.12:3.5.0 - https://spark.apache.org/)
-* (Apache License, Version 2.0) Spark Project Unsafe (org.apache.spark:spark-unsafe_2.12:3.5.0 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Catalyst (org.apache.spark:spark-catalyst_2.12:3.5.5 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Core (org.apache.spark:spark-core_2.12:3.5.5 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Hive (org.apache.spark:spark-hive_2.12:3.5.5 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Kubernetes (org.apache.spark:spark-kubernetes_2.12:3.5.5 - https://spark.apache.org/spark-kubernetes_2.12/)
+* (Apache License, Version 2.0) Spark Project SQL (org.apache.spark:spark-sql_2.12:3.5.5 - https://spark.apache.org/)
+* (Apache License, Version 2.0) Spark Project Unsafe (org.apache.spark:spark-unsafe_2.12:3.5.5 - https://spark.apache.org/)
 * (Apache License, Version 2.0) Awaitility (org.awaitility:awaitility:4.2.0 - http://awaitility.org)
 * (Apache License, Version 2.0) Hibernate Validator Engine (org.hibernate.validator:hibernate-validator:8.0.1.Final - http://hibernate.org/validator/hibernate-validator)
-* (Apache License, Version 2.0) Infinispan Commons (org.infinispan:infinispan-commons:15.0.3.Final - http://www.infinispan.org)
-* (Apache License, Version 2.0) Infinispan Component Annotations (org.infinispan:infinispan-component-annotations:15.0.3.Final - http://www.infinispan.org)
-* (Apache License, Version 2.0) Infinispan Core (org.infinispan:infinispan-core:15.0.3.Final - http://www.infinispan.org)
-* (Public Domain) JSON in Java (org.json:json:20240303 - https://github.com/douglascrockford/JSON-java)
-* (Eclipse Public License v2.0) JUnit Jupiter API (org.junit.jupiter:junit-jupiter-api:5.10.1 - https://junit.org/junit5/)
-* (Eclipse Public License v2.0) JUnit Jupiter Engine (org.junit.jupiter:junit-jupiter-engine:5.10.1 - https://junit.org/junit5/)
-* (Eclipse Public License v2.0) JUnit Jupiter Params (org.junit.jupiter:junit-jupiter-params:5.10.1 - https://junit.org/junit5/)
-* (MIT License) mockito-core (org.mockito:mockito-core:5.8.0 - https://github.com/mockito/mockito)
+* (Apache License, Version 2.0) Infinispan Commons (org.infinispan:infinispan-commons:15.0.10.Final - http://www.infinispan.org)
+* (Apache License, Version 2.0) Infinispan Component Annotations (org.infinispan:infinispan-component-annotations:15.0.10.Final - http://www.infinispan.org)
+* (Apache License, Version 2.0) Infinispan Core (org.infinispan:infinispan-core:15.0.10.Final - http://www.infinispan.org)
+* (Public Domain) JSON in Java (org.json:json:20250107 - https://github.com/douglascrockford/JSON-java)
+* (Eclipse Public License v2.0) JUnit Jupiter API (org.junit.jupiter:junit-jupiter-api:5.10.5 - https://junit.org/junit5/)
+* (Eclipse Public License v2.0) JUnit Jupiter Engine (org.junit.jupiter:junit-jupiter-engine:5.10.5 - https://junit.org/junit5/)
+* (Eclipse Public License v2.0) JUnit Jupiter Params (org.junit.jupiter:junit-jupiter-params:5.10.5 - https://junit.org/junit5/)
+* (MIT License) mockito-core (org.mockito:mockito-core:5.11.0 - https://github.com/mockito/mockito)
 * (GNU General Public License (GPL), version 2, with the Classpath exception) JMH Core (org.openjdk.jmh:jmh-core:1.37 - http://openjdk.java.net/projects/code-tools/jmh/jmh-core/)
 * (GNU General Public License (GPL), version 2, with the Classpath exception) JMH Generators: Annotation Processors (org.openjdk.jmh:jmh-generator-annprocess:1.37 - http://openjdk.java.net/projects/code-tools/jmh/jmh-generator-annprocess/)
-* (MIT License) Project Lombok (org.projectlombok:lombok:1.18.32 - https://projectlombok.org)
+* (MIT License) Project Lombok (org.projectlombok:lombok:1.18.34 - https://projectlombok.org)
 * (Apache License, Version 2.0) Scala Library (org.scala-lang:scala-library:2.12.17 - https://www.scala-lang.org/)
 * (Apache License, Version 2.0) JSONassert (org.skyscreamer:jsonassert:1.5.1 - https://github.com/skyscreamer/JSONassert)
-* (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.9 - http://www.slf4j.org)
-* (Apache License, Version 2.0) spring-boot-configuration-processor (org.springframework.boot:spring-boot-configuration-processor:3.2.0 - https://spring.io/projects/spring-boot)
-* (Apache License, Version 2.0) spring-boot-starter-actuator (org.springframework.boot:spring-boot-starter-actuator:3.2.0 - https://spring.io/projects/spring-boot)
-* (Apache License, Version 2.0) spring-boot-starter-aop (org.springframework.boot:spring-boot-starter-aop:3.2.0 - https://spring.io/projects/spring-boot)
-* (Apache License, Version 2.0) spring-boot-starter-jetty (org.springframework.boot:spring-boot-starter-jetty:3.2.0 - https://spring.io/projects/spring-boot)
-* (Apache License, Version 2.0) spring-boot-starter-security (org.springframework.boot:spring-boot-starter-security:3.2.0 - https://spring.io/projects/spring-boot)
-* (Apache License, Version 2.0) spring-boot-starter-test (org.springframework.boot:spring-boot-starter-test:3.2.0 - https://spring.io/projects/spring-boot)
-* (Apache License, Version 2.0) spring-boot-starter-web (org.springframework.boot:spring-boot-starter-web:3.2.0 - https://spring.io/projects/spring-boot)
-* (Apache License, Version 2.0) spring-security-oauth2-jose (org.springframework.security:spring-security-oauth2-jose:6.2.0 - https://spring.io/projects/spring-security)
-* (Apache License, Version 2.0) spring-security-oauth2-resource-server (org.springframework.security:spring-security-oauth2-resource-server:6.2.0 - https://spring.io/projects/spring-security)
-* (Apache License, Version 2.0) spring-security-test (org.springframework.security:spring-security-test:6.2.0 - https://spring.io/projects/spring-security)
+* (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.16 - http://www.slf4j.org)
+* (Apache License, Version 2.0) spring-boot-configuration-processor (org.springframework.boot:spring-boot-configuration-processor:3.3.5 - https://spring.io/projects/spring-boot)
+* (Apache License, Version 2.0) spring-boot-starter-actuator (org.springframework.boot:spring-boot-starter-actuator:3.3.5 - https://spring.io/projects/spring-boot)
+* (Apache License, Version 2.0) spring-boot-starter-aop (org.springframework.boot:spring-boot-starter-aop:3.3.5 - https://spring.io/projects/spring-boot)
+* (Apache License, Version 2.0) spring-boot-starter-jetty (org.springframework.boot:spring-boot-starter-jetty:3.3.5 - https://spring.io/projects/spring-boot)
+* (Apache License, Version 2.0) spring-boot-starter-security (org.springframework.boot:spring-boot-starter-security:3.3.5 - https://spring.io/projects/spring-boot)
+* (Apache License, Version 2.0) spring-boot-starter-test (org.springframework.boot:spring-boot-starter-test:3.3.5 - https://spring.io/projects/spring-boot)
+* (Apache License, Version 2.0) spring-boot-starter-web (org.springframework.boot:spring-boot-starter-web:3.3.5 - https://spring.io/projects/spring-boot)
+* (Apache License, Version 2.0) spring-security-oauth2-jose (org.springframework.security:spring-security-oauth2-jose:6.3.4 - https://spring.io/projects/spring-security)
+* (Apache License, Version 2.0) spring-security-oauth2-resource-server (org.springframework.security:spring-security-oauth2-resource-server:6.3.4 - https://spring.io/projects/spring-security)
+* (Apache License, Version 2.0) spring-security-test (org.springframework.security:spring-security-test:6.3.4 - https://spring.io/projects/spring-security)

deployment/helm/pom.xml

@@ -24,7 +24,7 @@
   <parent>
     <groupId>au.csiro.pathling</groupId>
     <artifactId>pathling</artifactId>
-    <version>7.1.0</version>
+    <version>7.2.0-SNAPSHOT</version>
     <relativePath>../../pom.xml</relativePath>
   </parent>
   <artifactId>helm</artifactId>

encoders/pom.xml

@@ -30,7 +30,7 @@
   <parent>
     <groupId>au.csiro.pathling</groupId>
     <artifactId>pathling</artifactId>
-    <version>7.1.0</version>
+    <version>7.2.0-SNAPSHOT</version>
   </parent>
   <artifactId>encoders</artifactId>
   <packaging>jar</packaging>