4.0.0 au.csiro.pathling pathling 7.2.0 fhir-server jar Pathling Server A server that exposes Pathling functionality through a FHIR API. aehrc/pathling latest arm64 1.37 amazoncorretto:17 file://${project.basedir}/src/test/resources/test-data parquet 1 5 au.csiro.pathling terminology au.csiro.pathling fhirpath org.apache.spark spark-core_${pathling.scalaVersion} org.apache.spark spark-sql_${pathling.scalaVersion} org.apache.spark spark-kubernetes_${pathling.scalaVersion} io.delta delta-spark_${pathling.scalaVersion} org.apache.hadoop hadoop-aws com.fasterxml.jackson.core jackson-core javax.servlet javax.servlet-api ca.uhn.hapi.fhir hapi-fhir-base ca.uhn.hapi.fhir hapi-fhir-structures-r4 ca.uhn.hapi.fhir hapi-fhir-server ca.uhn.hapi.fhir hapi-fhir-client com.fasterxml.woodstox woodstox-core org.springframework.boot spring-boot-configuration-processor true org.springframework.boot spring-boot-starter-aop org.springframework.boot spring-boot-starter-security org.springframework.security spring-security-oauth2-resource-server org.springframework.security spring-security-oauth2-jose org.springframework.boot spring-boot-starter-web org.springframework.boot spring-boot-starter-jetty org.springframework.boot spring-boot-starter-actuator org.springframework.security spring-security-test test org.antlr antlr4 org.slf4j slf4j-api com.auth0 java-jwt 4.5.0 com.auth0 jwks-rsa 0.22.1 com.google.code.gson gson com.amazonaws aws-java-sdk-bundle io.sentry sentry org.hibernate.validator hibernate-validator com.google.guava guava io.micrometer micrometer-registry-prometheus 1.14.4 au.csiro.pathling utilities test-jar test au.csiro.pathling terminology test-jar test au.csiro.pathling fhirpath test-jar test org.springframework.boot spring-boot-starter-test test org.junit.vintage junit-vintage-engine com.github.docker-java docker-java test com.github.docker-java docker-java-transport-okhttp test com.github.tomakehurst wiremock-jre8-standalone test org.awaitility awaitility test org.projectlombok lombok com.google.code.findbugs jsr305 commons-beanutils commons-beanutils org.json json ch.qos.logback logback-classic org.scala-lang scala-library org.openjdk.jmh jmh-core ${jmh.version} test org.openjdk.jmh jmh-generator-annprocess ${jmh.version} test org.apache.maven.plugins maven-source-plugin org.apache.maven.plugins maven-javadoc-plugin org.apache.maven.plugins maven-clean-plugin ${project.basedir}/src/test/resources/test-data/parquet **/* org.apache.maven.plugins maven-surefire-plugin default-test test UnitTest unit-test true file://${project.basedir}/src/test/resources/test-data parquet integration-test test IntegrationTest 1 core,server,integration-test file://${project.basedir}/src/test/resources/test-data parquet org.jacoco jacoco-maven-plugin au/csiro/pathling/fhirpath/parser/generated/* au/csiro/pathling/terminology/mock/* com.google.cloud.tools jib-maven-plugin 3.4.4 ${pathling.dockerBaseImage} ${pathling.dockerArchitecture} linux ${pathling.fhirServerDockerRepo} ${pathling.fhirServerDockerTag} ${project.version} ${project.majorVersion} ${git.commit.id} ${project.version} -Xmx2g -XX:MaxMetaspaceSize=400m -XX:ReservedCodeCacheSize=240m -Xss1m -Duser.timezone=UTC --add-exports=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED Copyright © 2018-2023, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230. Licensed under the CSIRO Open Source Software Licence Agreement. John Grimes <John.Grimes@csiro.au> 8080 8081 4040 7077 /usr/bin/entrypoint.sh src/main/jib /usr/bin/entrypoint.sh 755 maven_central Maven Central https://repo.maven.apache.org/maven2/ runBenchmark org.codehaus.mojo exec-maven-plugin run-benchmark test exec java -classpath -Xmx6g -XX:MaxMetaspaceSize=400m -XX:ReservedCodeCacheSize=240m -Xss1m -Duser.timezone=UTC --add-exports=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED -Dspring.profiles.active=unit-test -Dpathling.storage.warehouseUrl=${pathling.benchmark.warehouseUrl} -Dpathling.storage.databaseName=${pathling.benchmark.databaseName} -Dbenchmark.test.iterations=${pathling.benchmark.testIterations} -Dbenchmark.warmup.iterations=${pathling.benchmark.warmupIterations} au.csiro.pathling.test.benchmark.PathlingBenchmarkRunner ${project.build.directory}/benchmark test importTestData !skipTests org.codehaus.mojo exec-maven-plugin import-test-data process-test-classes exec java -classpath -Xmx4g -Duser.timezone=UTC --add-exports=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED -Dspring.profiles.active=spark,fhir,import,cli -Dpathling.version=${project.version} -Dpathling.terminology.enabled=false -Dpathling.storage.warehouseUrl=file://${project.basedir}/src/test/resources/test-data -Dpathling.storage.databaseName=parquet -Dspark.master=local[1] au.csiro.pathling.test.TestDataImporter ${project.basedir}/src/test/resources/test-data/fhir test docker org.apache.maven.plugins maven-failsafe-plugin system-test integration-test verify ${project.build.outputDirectory} **/*.java SystemTest ${git.commit.id} https://auth.ontoserver.csiro.au/auth/realms/aehrc pathling-test openid user/*.* https://tx.ontoserver.csiro.au/fhir ${pathling.fhirServerDockerRepo} system-test com.google.cloud.tools jib-maven-plugin build package dockerBuild deploy deploy build ${pathling.dockerBaseImage} amd64 linux arm64 linux ${pathling.fhirServerDockerRepo} ${pathling.fhirServerDockerTag} ${project.version} ${project.majorVersion} dockerPreRelease com.google.cloud.tools jib-maven-plugin deploy deploy build ${pathling.dockerBaseImage} amd64 linux arm64 linux ${pathling.fhirServerDockerRepo}:${pathling.fhirServerDockerTag}-develop testTranche1 org.apache.maven.plugins maven-surefire-plugin default-test test UnitTest & Tranche1 unit-test true integration-test test IntegrationTest & Tranche1 1 core,server,integration-test file://${project.basedir}/src/test/resources/test-data parquet testTranche2 org.apache.maven.plugins maven-surefire-plugin default-test test UnitTest & Tranche2 unit-test true integration-test test IntegrationTest & Tranche2 1 core,server,integration-test file://${project.basedir}/src/test/resources/test-data parquet testTranche3 org.apache.maven.plugins maven-surefire-plugin default-test test UnitTest & !Tranche1 & !Tranche2 unit-test true integration-test test IntegrationTest & !Tranche1 & !Tranche2 1 core,server,integration-test file://${project.basedir}/src/test/resources/test-data parquet