hapi-fhir-jpaserver-starter
hapi-fhir-jpaserver-starter copied to clipboard
hapifhir
Access denied to /app/target in docker
When trying to run the jpa server in docker, I get a file permission error. I'm guessing this is related to the nonroot user, although the Dockerfile looks like it is handling that appropriately. This is on an ARM mac.
2023-04-10 14:56:19.579 [main] INFO com.zaxxer.hikari.HikariDataSource [HikariDataSource.java:110] HikariPool-1 - Starting...
org.h2.message.DbException: Log file error: "/app/target/database/h2.trace.db", cause: "org.h2.message.DbException: Error while creating file ""/app/target"" [90062-214]" [90034-214]
2023-04-10 14:56:23.330 [main] ERROR com.zaxxer.hikari.pool.HikariPool [HikariPool.java:594] HikariPool-1 - Exception during pool initialization.
org.h2.jdbc.JdbcSQLNonTransientException: Error while creating file "/app/target" [90062-214]
...long stack trace...
Caused by: java.nio.file.AccessDeniedException: /app/target
Full log
. ____ _ __ _ _
/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
\\/ ___)| |_)| | | | | || (_| | ) ) ) )
' |____| .__|_| |_|_| |_\__, | / / / /
=========|_|==============|___/=/_/_/_/
:: Spring Boot :: (v2.7.5)
2023-04-10 14:56:13.555 [background-preinit] INFO o.h.validator.internal.util.Version [Version.java:21] HV000001: Hibernate Validator 6.1.5.Final
2023-04-10 14:56:13.573 [main] INFO ca.uhn.fhir.jpa.starter.Application [StartupInfoLogger.java:55] Starting Application using Java 17.0.6 on 237662c0759a with PID 1 (/app/main.war started by nonroot in /app)
2023-04-10 14:56:13.573 [main] INFO ca.uhn.fhir.jpa.starter.Application [SpringApplication.java:634] No active profile set, falling back to 1 default profile: "default"
2023-04-10 14:56:14.319 [main] INFO o.s.d.r.c.RepositoryConfigurationDelegate [RepositoryConfigurationDelegate.java:132] Bootstrapping Spring Data JPA repositories in DEFAULT mode.
2023-04-10 14:56:14.563 [main] INFO o.s.d.r.c.RepositoryConfigurationDelegate [RepositoryConfigurationDelegate.java:201] Finished Spring Data repository scanning in 231 ms. Found 52 JPA repository interfaces.
2023-04-10 14:56:15.474 [main] INFO o.s.c.s.PostProcessorRegistrationDelegate$BeanPostProcessorChecker [PostProcessorRegistrationDelegate.java:376] Bean 'ca.uhn.fhir.jpa.config.BeanPostProcessorConfig' of type [ca.uhn.fhir.jpa.config.BeanPostProcessorConfig$$EnhancerBySpringCGLIB$$ab422806] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
2023-04-10 14:56:15.738 [main] INFO o.s.b.w.e.tomcat.TomcatWebServer [TomcatWebServer.java:108] Tomcat initialized with port(s): 8080 (http)
2023-04-10 14:56:15.747 [main] INFO o.a.coyote.http11.Http11NioProtocol [DirectJDKLog.java:173] Initializing ProtocolHandler ["http-nio-8080"]
2023-04-10 14:56:15.747 [main] INFO o.a.catalina.core.StandardService [DirectJDKLog.java:173] Starting service [Tomcat]
2023-04-10 14:56:15.747 [main] INFO o.a.catalina.core.StandardEngine [DirectJDKLog.java:173] Starting Servlet engine: [Apache Tomcat/9.0.68]
2023-04-10 14:56:19.226 [main] INFO o.a.c.c.C.[Tomcat].[localhost].[/] [DirectJDKLog.java:173] Initializing Spring embedded WebApplicationContext
2023-04-10 14:56:19.226 [main] INFO o.s.b.w.s.c.ServletWebServerApplicationContext [ServletWebServerApplicationContext.java:292] Root WebApplicationContext: initialization completed in 5613 ms
2023-04-10 14:56:19.277 [main] INFO ca.uhn.fhir.util.VersionUtil [VersionUtil.java:85] HAPI FHIR version 6.4.4 - Rev 107a1bd073
2023-04-10 14:56:19.283 [main] INFO ca.uhn.fhir.context.FhirContext [FhirContext.java:211] Creating new FHIR context for FHIR version [R4]
2023-04-10 14:56:19.353 [main] INFO o.h.jpa.internal.util.LogHelper [LogHelper.java:31] HHH000204: Processing PersistenceUnitInfo [name: HAPI_PU]
2023-04-10 14:56:19.393 [main] INFO org.hibernate.Version [Version.java:44] HHH000412: Hibernate ORM core version 5.6.12.Final
2023-04-10 14:56:19.503 [main] INFO o.h.annotations.common.Version [JavaReflectionManager.java:56] HCANN000001: Hibernate Commons Annotations {5.1.2.Final}
2023-04-10 14:56:19.579 [main] INFO com.zaxxer.hikari.HikariDataSource [HikariDataSource.java:110] HikariPool-1 - Starting...
org.h2.message.DbException: Log file error: "/app/target/database/h2.trace.db", cause: "org.h2.message.DbException: Error while creating file ""/app/target"" [90062-214]" [90034-214]
2023-04-10 14:56:23.330 [main] ERROR com.zaxxer.hikari.pool.HikariPool [HikariPool.java:594] HikariPool-1 - Exception during pool initialization.
org.h2.jdbc.JdbcSQLNonTransientException: Error while creating file "/app/target" [90062-214]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:554)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:477)
at org.h2.message.DbException.get(DbException.java:212)
at org.h2.store.fs.disk.FilePathDisk.createDirectory(FilePathDisk.java:356)
at org.h2.store.fs.FileUtils.createDirectory(FileUtils.java:85)
at org.h2.store.fs.FileUtils.createDirectories(FileUtils.java:382)
at org.h2.store.fs.FileUtils.createDirectories(FileUtils.java:381)
at org.h2.mvstore.db.Store.<init>(Store.java:109)
at org.h2.engine.Database.<init>(Database.java:324)
at org.h2.engine.Engine.openSession(Engine.java:92)
at org.h2.engine.Engine.openSession(Engine.java:222)
at org.h2.engine.Engine.createSession(Engine.java:201)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:338)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:122)
at org.h2.Driver.connect(Driver.java:59)
at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138)
at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:359)
at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:201)
at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:470)
at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561)
at com.zaxxer.hikari.pool.HikariPool.<init>(HikariPool.java:100)
at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112)
at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator$ConnectionProviderJdbcConnectionAccess.obtainConnection(JdbcEnvironmentInitiator.java:181)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:68)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:35)
at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.initiateService(StandardServiceRegistryImpl.java:101)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:263)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:237)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:214)
at org.hibernate.id.factory.internal.DefaultIdentifierGeneratorFactory.injectServices(DefaultIdentifierGeneratorFactory.java:175)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.injectDependencies(AbstractServiceRegistryImpl.java:286)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:243)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:214)
at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.<init>(InFlightMetadataCollectorImpl.java:173)
at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.complete(MetadataBuildingProcess.java:127)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.metadata(EntityManagerFactoryBuilderImpl.java:1460)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:1494)
at org.hibernate.jpa.HibernatePersistenceProvider.createContainerEntityManagerFactory(HibernatePersistenceProvider.java:141)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:365)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:409)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:396)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.afterPropertiesSet(LocalContainerEntityManagerFactoryBean.java:341)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1863)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1800)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:620)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:233)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveNamedBean(DefaultListableBeanFactory.java:1284)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveNamedBean(DefaultListableBeanFactory.java:1245)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveNamedBean(DefaultListableBeanFactory.java:1213)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.findDefaultEntityManagerFactory(PersistenceAnnotationBeanPostProcessor.java:565)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.findEntityManagerFactory(PersistenceAnnotationBeanPostProcessor.java:528)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor$PersistenceElement.resolveEntityManager(PersistenceAnnotationBeanPostProcessor.java:696)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor$PersistenceElement.getResourceToInject(PersistenceAnnotationBeanPostProcessor.java:669)
at org.springframework.beans.factory.annotation.InjectionMetadata$InjectedElement.inject(InjectionMetadata.java:228)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:119)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.postProcessProperties(PersistenceAnnotationBeanPostProcessor.java:348)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1431)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:619)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208)
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1391)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1311)
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887)
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791)
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:541)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1352)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1195)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208)
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1391)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1311)
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887)
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791)
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:541)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1352)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1195)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:213)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.getOrderedBeansOfType(ServletContextInitializerBeans.java:212)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.getOrderedBeansOfType(ServletContextInitializerBeans.java:203)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.addServletContextInitializerBeans(ServletContextInitializerBeans.java:97)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.<init>(ServletContextInitializerBeans.java:86)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.getServletContextInitializerBeans(ServletWebServerApplicationContext.java:262)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.selfInitialize(ServletWebServerApplicationContext.java:236)
at org.springframework.boot.web.embedded.tomcat.TomcatStarter.onStartup(TomcatStarter.java:53)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5220)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1396)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1386)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:145)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:919)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:835)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1396)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1386)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:145)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:919)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:265)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:432)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.startup.Tomcat.start(Tomcat.java:486)
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.initialize(TomcatWebServer.java:123)
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.<init>(TomcatWebServer.java:104)
at org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory.getTomcatWebServer(TomcatServletWebServerFactory.java:479)
at org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory.getWebServer(TomcatServletWebServerFactory.java:211)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.createWebServer(ServletWebServerApplicationContext.java:184)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:162)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:577)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:147)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:734)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:408)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:308)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1306)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1295)
at ca.uhn.fhir.jpa.starter.Application.main(Application.java:44)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
at org.springframework.boot.loader.PropertiesLauncher.main(PropertiesLauncher.java:467)
Caused by: java.nio.file.AccessDeniedException: /app/target
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:397)
at java.base/java.nio.file.Files.createDirectory(Files.java:700)
at org.h2.store.fs.disk.FilePathDisk.createDirectory(FilePathDisk.java:347)
... 144 common frames omitted
2023-04-10 14:56:23.339 [main] WARN o.h.e.j.e.i.JdbcEnvironmentInitiator [JdbcEnvironmentInitiator.java:133] HHH000342: Could not obtain connection to query metadata
org.h2.jdbc.JdbcSQLNonTransientException: Error while creating file "/app/target" [90062-214]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:554)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:477)
at org.h2.message.DbException.get(DbException.java:212)
at org.h2.store.fs.disk.FilePathDisk.createDirectory(FilePathDisk.java:356)
at org.h2.store.fs.FileUtils.createDirectory(FileUtils.java:85)
at org.h2.store.fs.FileUtils.createDirectories(FileUtils.java:382)
at org.h2.store.fs.FileUtils.createDirectories(FileUtils.java:381)
at org.h2.mvstore.db.Store.<init>(Store.java:109)
at org.h2.engine.Database.<init>(Database.java:324)
at org.h2.engine.Engine.openSession(Engine.java:92)
at org.h2.engine.Engine.openSession(Engine.java:222)
at org.h2.engine.Engine.createSession(Engine.java:201)
at org.h2.engine.SessionRemote.connectEmbeddedOrServer(SessionRemote.java:338)
at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:122)
at org.h2.Driver.connect(Driver.java:59)
at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:138)
at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:359)
at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:201)
at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:470)
at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561)
at com.zaxxer.hikari.pool.HikariPool.<init>(HikariPool.java:100)
at com.zaxxer.hikari.HikariDataSource.getConnection(HikariDataSource.java:112)
at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:122)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator$ConnectionProviderJdbcConnectionAccess.obtainConnection(JdbcEnvironmentInitiator.java:181)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:68)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:35)
at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.initiateService(StandardServiceRegistryImpl.java:101)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:263)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:237)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:214)
at org.hibernate.id.factory.internal.DefaultIdentifierGeneratorFactory.injectServices(DefaultIdentifierGeneratorFactory.java:175)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.injectDependencies(AbstractServiceRegistryImpl.java:286)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:243)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:214)
at org.hibernate.boot.internal.InFlightMetadataCollectorImpl.<init>(InFlightMetadataCollectorImpl.java:173)
at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.complete(MetadataBuildingProcess.java:127)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.metadata(EntityManagerFactoryBuilderImpl.java:1460)
at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:1494)
at org.hibernate.jpa.HibernatePersistenceProvider.createContainerEntityManagerFactory(HibernatePersistenceProvider.java:141)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:365)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:409)
at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:396)
at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.afterPropertiesSet(LocalContainerEntityManagerFactoryBean.java:341)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1863)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1800)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:620)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:233)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveNamedBean(DefaultListableBeanFactory.java:1284)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveNamedBean(DefaultListableBeanFactory.java:1245)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveNamedBean(DefaultListableBeanFactory.java:1213)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.findDefaultEntityManagerFactory(PersistenceAnnotationBeanPostProcessor.java:565)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.findEntityManagerFactory(PersistenceAnnotationBeanPostProcessor.java:528)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor$PersistenceElement.resolveEntityManager(PersistenceAnnotationBeanPostProcessor.java:696)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor$PersistenceElement.getResourceToInject(PersistenceAnnotationBeanPostProcessor.java:669)
at org.springframework.beans.factory.annotation.InjectionMetadata$InjectedElement.inject(InjectionMetadata.java:228)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:119)
at org.springframework.orm.jpa.support.PersistenceAnnotationBeanPostProcessor.postProcessProperties(PersistenceAnnotationBeanPostProcessor.java:348)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1431)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:619)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208)
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1391)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1311)
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887)
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791)
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:541)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1352)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1195)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208)
at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1391)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1311)
at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887)
at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791)
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:541)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1352)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1195)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:213)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.getOrderedBeansOfType(ServletContextInitializerBeans.java:212)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.getOrderedBeansOfType(ServletContextInitializerBeans.java:203)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.addServletContextInitializerBeans(ServletContextInitializerBeans.java:97)
at org.springframework.boot.web.servlet.ServletContextInitializerBeans.<init>(ServletContextInitializerBeans.java:86)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.getServletContextInitializerBeans(ServletWebServerApplicationContext.java:262)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.selfInitialize(ServletWebServerApplicationContext.java:236)
at org.springframework.boot.web.embedded.tomcat.TomcatStarter.onStartup(TomcatStarter.java:53)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5220)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1396)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1386)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:145)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:919)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:835)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1396)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1386)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:145)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:919)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:265)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:432)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.startup.Tomcat.start(Tomcat.java:486)
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.initialize(TomcatWebServer.java:123)
at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.<init>(TomcatWebServer.java:104)
at org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory.getTomcatWebServer(TomcatServletWebServerFactory.java:479)
at org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory.getWebServer(TomcatServletWebServerFactory.java:211)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.createWebServer(ServletWebServerApplicationContext.java:184)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:162)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:577)
at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:147)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:734)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:408)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:308)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1306)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1295)
at ca.uhn.fhir.jpa.starter.Application.main(Application.java:44)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
at org.springframework.boot.loader.PropertiesLauncher.main(PropertiesLauncher.java:467)
Caused by: java.nio.file.AccessDeniedException: /app/target
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:106)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:397)
at java.base/java.nio.file.Files.createDirectory(Files.java:700)
at org.h2.store.fs.disk.FilePathDisk.createDirectory(FilePathDisk.java:347)
... 144 common frames omitted
OK, so the weird thing is that I am seeing this same issue but ONLY for running it a AWS service. The AWS service image is built purely from the dockerfile.
However, I ended up building my working local image with the docker compose file and docker compose v2 so there could be some delta there. Using that, my local version runs perfectly within docker.
How did you build it?
I'm building it locally. The docker-compose file doesn't alter the way that it's built, so it shouldn't matter if you build it using docker-compose or not.
I have the same problem deploying on GCP. What is weird, it worked with the 6.6 branch before. I didn't found out yet what changed, keep u posted!
@jkiddo any idea why changing the run command / entrypoint is affecting the directory access? https://github.com/hapifhir/hapi-fhir-jpaserver-starter/commit/7e0fb80dac478dee882ecf23e9590aff557acb4d
Nope - but it sort of relates to https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/591
