hapi-fhir-jpaserver-starter
hapi-fhir-jpaserver-starter copied to clipboard
hapifhir
(Auth)Interceptor
Hello, I started using the fhir server a couple of days ago. At the moment I succesfully deployed the project with a postgres db using docker and the helm chart. I now face some uncertainty on how I can develope an Interceptor for the fhir server. Unfortunatelly the documentation on the official hapi fhir page is kinda unclear. Is anybody able to give a more comprehensive walkthrough of how it would be possible to develop an (auth)interceptor?
@michael-gvdw Here is details steps
-
Create file inside (HAPI_FHIR_SERVER/src/main/java/ca/uhn/fhir/jpa/starter): BasicSecurityInterceptor.java I am attaching BasicSecurityInterceptor.java file. dont forget to change ext to java BasicSecurityInterceptor.txt
-
In application.yml update interceptor put this in 186 line number and you are good to go. custom-interceptor-classes: ca.uhn.fhir.jpa.starter.BasicSecurityInterceptor,
For any request, it will check if jwt token is valid or not. You can pass jwt secret using environment variable or hard code. Make sure jwt secret have 128 char length at least.
@aakashkag
Hey, I have been trying to apply the help you provided by (trying to) implementing the example interceptor code provided in the project docs in src/main/java/ca/uhn/fhir/jpa/starter/MyInterceptor.java. Unfortunately when in register the interceptor in file src/main/resources/application.yaml in line 180 custom-interceptor-classes: ca.uhn.fhir.jpa.starter.MyInterceptor, I try to run the project using docker compose up --build but it seems it is unable to find my new class. Here I provide the complete stack trace:
hapi-fhir-jpaserver-start | hapi-fhir-jpaserver-start | . ____ _ __ _ _ hapi-fhir-jpaserver-start | /\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \ hapi-fhir-jpaserver-start | ( ( )\___ | '_ | '_| | '_ \/ _ | \ \ \
hapi-fhir-jpaserver-start | \/ )| |)| | | | | || (| | ) ) ) )
hapi-fhir-jpaserver-start | ' || .__|| ||| |_, | / / / /
hapi-fhir-jpaserver-start | =========||==============|/=////
hapi-fhir-jpaserver-start | :: Spring Boot :: (v3.2.0)
hapi-fhir-jpaserver-start |
hapi-fhir-jpaserver-start | 2024-04-06 11:32:31.080 [background-preinit] INFO o.h.validator.internal.util.Version [Version.java:21] HV000001: Hibernate Validator 8.0.0.Final
hapi-fhir-jpaserver-start | 2024-04-06 11:32:31.240 [main] INFO ca.uhn.fhir.jpa.starter.Application [StartupInfoLogger.java:50] Starting Application using Java 17.0.10 with PID 1 (/app/main.war started by nonroot in /app)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:31.241 [main] INFO ca.uhn.fhir.jpa.starter.Application [SpringApplication.java:653] No active profile set, falling back to 1 default profile: "default"
hapi-fhir-jpaserver-start | 2024-04-06 11:32:32.855 [main] INFO o.s.d.r.c.RepositoryConfigurationDelegate [RepositoryConfigurationDelegate.java:139] Bootstrapping Spring Data JPA repositories in DEFAULT mode.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:33.153 [main] INFO o.s.d.r.c.RepositoryConfigurationDelegate [RepositoryConfigurationDelegate.java:208] Finished Spring Data repository scanning in 286 ms. Found 53 JPA repository interfaces.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:35.701 [main] WARN o.s.c.s.PostProcessorRegistrationDelegate$BeanPostProcessorChecker [PostProcessorRegistrationDelegate.java:429] Bean 'ca.uhn.fhir.jpa.config.BeanPostProcessorConfig' of type [ca.uhn.fhir.jpa.config.BeanPostProcessorConfig$$SpringCGLIB$$0] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying). The currently created BeanPostProcessor [persistenceExceptionTranslationPostProcessor] is declared through a non-static factory method on that class; consider declaring it as static instead.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.154 [main] INFO o.s.b.w.e.tomcat.TomcatWebServer [TomcatWebServer.java:108] Tomcat initialized with port 8080 (http)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.163 [main] INFO o.a.coyote.http11.Http11NioProtocol [DirectJDKLog.java:173] Initializing ProtocolHandler ["http-nio-8080"]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.166 [main] INFO o.a.catalina.core.StandardService [DirectJDKLog.java:173] Starting service [Tomcat]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.166 [main] INFO o.a.catalina.core.StandardEngine [DirectJDKLog.java:173] Starting Servlet engine: [Apache Tomcat/10.1.16]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.276 [main] INFO o.a.c.c.C.[Tomcat].[localhost].[/] [DirectJDKLog.java:173] Initializing Spring embedded WebApplicationContext
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.276 [main] INFO o.s.b.w.s.c.ServletWebServerApplicationContext [ServletWebServerApplicationContext.java:296] Root WebApplicationContext: initialization completed in 4966 ms
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.361 [main] INFO ca.uhn.fhir.util.VersionUtil [VersionUtil.java:84] HAPI FHIR version 7.0.2 - Rev 95beaec894
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.367 [main] INFO ca.uhn.fhir.context.FhirContext [FhirContext.java:226] Creating new FHIR context for FHIR version [R4]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.394 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:39] Server configured to allow contains searches
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.394 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:41] Server configured to deny multiple deletes
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.395 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:43] Server configured to deny external references
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.395 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:45] Server configured to enable DAO scheduling
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.395 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:47] Server configured to disable delete expunges
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.395 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:49] Server configured to enable expunges
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.395 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:51] Server configured to allow overriding default search params
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.396 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:54] Server configured to disable auto-creating placeholder references
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.396 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:57] Server configured to auto-version references at paths []
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.436 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:122] Server configured to have a maximum fetch size of 'unlimited'
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.436 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:127] Server configured to cache search results for 60000 milliseconds
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.437 [main] INFO c.u.f.j.s.c.FhirServerConfigCommon [FhirServerConfigCommon.java:178] Server configured to use 'ALPHANUMERIC' Client ID Strategy
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.567 [main] INFO o.h.jpa.internal.util.LogHelper [LogHelper.java:31] HHH000204: Processing PersistenceUnitInfo [name: HAPI_PU]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:36.706 [main] INFO org.hibernate.Version [Version.java:44] HHH000412: Hibernate ORM core version 6.4.1.Final
^[[1;2A^[[1;2Ahapi-fhir-jpaserver-start | 2024-04-06 11:32:42.528 [main] INFO o.h.c.i.RegionFactoryInitiator [RegionFactoryInitiator.java:50] HHH000026: Second-level cache disabled
hapi-fhir-jpaserver-start | 2024-04-06 11:32:42.705 [main] INFO o.h.e.b.internal.EnversServiceImpl [EnversServiceImpl.java:76] Envers integration enabled? : true
hapi-fhir-jpaserver-start | 2024-04-06 11:32:42.967 [main] INFO o.s.o.j.p.SpringPersistenceUnitInfo [SpringPersistenceUnitInfo.java:87] No LoadTimeWeaver setup: ignoring JPA class transformer
hapi-fhir-jpaserver-start | 2024-04-06 11:32:43.019 [main] INFO com.zaxxer.hikari.HikariDataSource [HikariDataSource.java:110] HikariPool-1 - Starting...
hapi-fhir-jpaserver-start | 2024-04-06 11:32:43.373 [main] INFO com.zaxxer.hikari.pool.HikariPool [HikariPool.java:565] HikariPool-1 - Added connection conn0: url=jdbc:h2:mem:test_mem user=SA
hapi-fhir-jpaserver-start | 2024-04-06 11:32:43.375 [main] INFO com.zaxxer.hikari.HikariDataSource [HikariDataSource.java:123] HikariPool-1 - Start completed.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:44.245 [main] INFO o.h.s.m.o.b.i.HibernateSearchPreIntegrationService [HibernateSearchPreIntegrationService.java:101] HSEARCH000034: Hibernate Search version 7.0.0.Final
hapi-fhir-jpaserver-start | 2024-04-06 11:32:44.417 [main] INFO o.h.e.c.i.m.AuditMetadataGenerator [AuditMetadataGenerator.java:322] Adding properties for entity: ca.uhn.fhir.jpa.entity.MdmLink
hapi-fhir-jpaserver-start | 2024-04-06 11:32:46.276 [main] INFO o.h.e.t.j.p.i.JtaPlatformInitiator [JtaPlatformInitiator.java:58] HHH000489: No JTA platform available (set 'hibernate.transaction.jta.platform' to enable JTA platform integration)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:47.677 [main] INFO c.u.f.j.c.HapiFhirLocalContainerEntityManagerFactoryBean [AbstractEntityManagerFactoryBean.java:437] Initialized JPA EntityManagerFactory for persistence unit 'HAPI_PU'
hapi-fhir-jpaserver-start | 2024-04-06 11:32:48.390 [main] INFO c.u.f.c.s.DefaultProfileValidationSupport [DefaultProfileValidationSupportBundleStrategy.java:368] Loading structure definitions from classpath: /org/hl7/fhir/r4/model/profile/profiles-resources.xml
hapi-fhir-jpaserver-start | Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
hapi-fhir-jpaserver-start | NOT STARTED.
hapi-fhir-jpaserver-start | Currently in standby mode.
hapi-fhir-jpaserver-start | Number of jobs executed: 0
hapi-fhir-jpaserver-start | Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 4 threads.
hapi-fhir-jpaserver-start | Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.
hapi-fhir-jpaserver-start |
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.391 [main] INFO org.quartz.impl.StdSchedulerFactory [StdSchedulerFactory.java:1374] Quartz scheduler 'hapi-fhir-jpa-scheduler' initialized from an externally provided properties instance.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.391 [main] INFO org.quartz.impl.StdSchedulerFactory [StdSchedulerFactory.java:1378] Quartz scheduler version: 2.3.2
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.391 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:2293] JobFactory set to: ca.uhn.fhir.jpa.sched.AutowiringSpringBeanJobFactory@4bf6ce64
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.392 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:585] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED paused.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.812 [main] INFO ca.uhn.fhir.context.FhirContext [FhirContext.java:226] Creating new FHIR context for FHIR version [R4]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:53.040 [main] INFO c.u.f.j.s.common.StarterJpaConfig [StarterJpaConfig.java:222] CORS is enabled on this server
hapi-fhir-jpaserver-start | 2024-04-06 11:32:53.042 [main] INFO c.u.f.j.s.common.StarterJpaConfig [StarterJpaConfig.java:235] CORS allows the following origins: *
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.304 [main] INFO ca.uhn.fhir.context.FhirContext [FhirContext.java:226] Creating new FHIR context for FHIR version [R4]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.424 [main] ERROR o.s.b.w.e.tomcat.TomcatStarter [TomcatStarter.java:60] Error starting Tomcat context. Exception: org.springframework.beans.factory.UnsatisfiedDependencyException. Message: Error creating bean with name 'hapiServletRegistration' defined in ca.uhn.fhir.jpa.starter.Application: Unsatisfied dependency expressed through method 'hapiServletRegistration' parameter 0: Error creating bean with name 'restfulServer' defined in class path resource [ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.class]: Failed to instantiate [ca.uhn.fhir.rest.server.RestfulServer]: Factory method 'restfulServer' threw exception with message: Interceptor class was not found on classpath:
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.467 [main] INFO o.a.catalina.core.StandardService [DirectJDKLog.java:173] Stopping service [Tomcat]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.471 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [HikariPool-1 housekeeper] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1182)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:899)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
hapi-fhir-jpaserver-start | [email protected]/java.lang.Thread.run(Thread.java:840)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.479 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [Hibernate Search - Engine - Timing thread - 0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1182)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:899)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
hapi-fhir-jpaserver-start | Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
hapi-fhir-jpaserver-start | NOT STARTED.
hapi-fhir-jpaserver-start | Currently in standby mode.
hapi-fhir-jpaserver-start | Number of jobs executed: 0
hapi-fhir-jpaserver-start | Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 4 threads.
hapi-fhir-jpaserver-start | Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.
hapi-fhir-jpaserver-start |
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.391 [main] INFO org.quartz.impl.StdSchedulerFactory [StdSchedulerFactory.java:1374] Quartz scheduler 'hapi-fhir-jpa-scheduler' initialized from an externally provided properties instance.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.391 [main] INFO org.quartz.impl.StdSchedulerFactory [StdSchedulerFactory.java:1378] Quartz scheduler version: 2.3.2
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.391 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:2293] JobFactory set to: ca.uhn.fhir.jpa.sched.AutowiringSpringBeanJobFactory@4bf6ce64
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.392 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:585] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED paused.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:52.812 [main] INFO ca.uhn.fhir.context.FhirContext [FhirContext.java:226] Creating new FHIR context for FHIR version [R4]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:53.040 [main] INFO c.u.f.j.s.common.StarterJpaConfig [StarterJpaConfig.java:222] CORS is enabled on this server
hapi-fhir-jpaserver-start | 2024-04-06 11:32:53.042 [main] INFO c.u.f.j.s.common.StarterJpaConfig [StarterJpaConfig.java:235] CORS allows the following origins: *
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.304 [main] INFO ca.uhn.fhir.context.FhirContext [FhirContext.java:226] Creating new FHIR context for FHIR version [R4]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.424 [main] ERROR o.s.b.w.e.tomcat.TomcatStarter [TomcatStarter.java:60] Error starting Tomcat context. Exception: org.springframework.beans.factory.UnsatisfiedDependencyException. Message: Error creating bean with name 'hapiServletRegistration' defined in ca.uhn.fhir.jpa.starter.Application: Unsatisfied dependency expressed through method 'hapiServletRegistration' parameter 0: Error creating bean with name 'restfulServer' defined in class path resource [ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.class]: Failed to instantiate [ca.uhn.fhir.rest.server.RestfulServer]: Factory method 'restfulServer' threw exception with message: Interceptor class was not found on classpath:
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.467 [main] INFO o.a.catalina.core.StandardService [DirectJDKLog.java:173] Stopping service [Tomcat]
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.471 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [HikariPool-1 housekeeper] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1182)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:899)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
hapi-fhir-jpaserver-start | [email protected]/java.lang.Thread.run(Thread.java:840)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.479 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [Hibernate Search - Engine - Timing thread - 0] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/jdk.internal.misc.Unsafe.park(Native Method)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:252)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(AbstractQueuedSynchronizer.java:1672)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1182)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:899)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1062)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1122)
hapi-fhir-jpaserver-start | [email protected]/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-local-3] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-local-4] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-2] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-3] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-4] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler_QuartzSchedulerThread] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.core.QuartzSchedulerThread.run(QuartzSchedulerThread.java:254)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler_QuartzSchedulerThread] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.core.QuartzSchedulerThread.run(QuartzSchedulerThread.java:254)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.508 [main] WARN o.s.b.w.s.c.AnnotationConfigServletWebServerApplicationContext [AbstractApplicationContext.java:632] Exception encountered during context initialization - cancelling refresh attempt: org.springframework.context.ApplicationContextException: Unable to start web server
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.533 [main] INFO c.u.f.j.s.BaseSchedulerServiceImpl [BaseSchedulerServiceImpl.java:182] Shutting down task scheduler...
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.534 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:666] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED shutting down.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.534 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:585] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED paused.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.874 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:740] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED shutdown complete.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.874 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:666] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED shutting down.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.874 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:585] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED paused.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.893 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:740] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED shutdown complete.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.904 [main] INFO c.u.f.j.c.HapiFhirLocalContainerEntityManagerFactoryBean [AbstractEntityManagerFactoryBean.java:650] Closing JPA EntityManagerFactory for persistence unit 'HAPI_PU
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-local-3] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-local-4] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-1] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.505 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-2] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-3] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler-clustered-4] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:568)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler_QuartzSchedulerThread] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.core.QuartzSchedulerThread.run(QuartzSchedulerThread.java:254)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.506 [main] WARN o.a.c.loader.WebappClassLoaderBase [DirectJDKLog.java:173] The web application [ROOT] appears to have started a thread named [hapi-fhir-jpa-scheduler_QuartzSchedulerThread] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
hapi-fhir-jpaserver-start | [email protected]/java.lang.Object.wait(Native Method)
hapi-fhir-jpaserver-start | org.quartz.core.QuartzSchedulerThread.run(QuartzSchedulerThread.java:254)
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.508 [main] WARN o.s.b.w.s.c.AnnotationConfigServletWebServerApplicationContext [AbstractApplicationContext.java:632] Exception encountered during context initialization - cancelling refresh attempt: org.springframework.context.ApplicationContextException: Unable to start web server
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.533 [main] INFO c.u.f.j.s.BaseSchedulerServiceImpl [BaseSchedulerServiceImpl.java:182] Shutting down task scheduler...
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.534 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:666] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED shutting down.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.534 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:585] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED paused.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.874 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:740] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED shutdown complete.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.874 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:666] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED shutting down.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.874 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:585] Scheduler hapi-fhir-jpa-scheduler$NON_CLUSTERED paused.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.893 [main] INFO org.quartz.core.QuartzScheduler [QuartzScheduler.java:740] Scheduler hapi-fhir-jpa-scheduler$_NON_CLUSTERED shutdown complete.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.904 [main] INFO c.u.f.j.c.HapiFhirLocalContainerEntityManagerFactoryBean [AbstractEntityManagerFactoryBean.java:650] Closing JPA EntityManagerFactory for persistence unit 'HAPI_PU'
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.916 [main] INFO com.zaxxer.hikari.HikariDataSource [HikariDataSource.java:350] HikariPool-1 - Shutdown initiated...
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.918 [main] INFO com.zaxxer.hikari.HikariDataSource [HikariDataSource.java:352] HikariPool-1 - Shutdown completed.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.937 [main] INFO o.s.b.a.l.ConditionEvaluationReportLogger [ConditionEvaluationReportLogger.java:82]
hapi-fhir-jpaserver-start |
hapi-fhir-jpaserver-start | Error starting ApplicationContext. To display the condition evaluation report re-run your application with 'debug' enabled.
hapi-fhir-jpaserver-start | 2024-04-06 11:32:58.966 [main] ERROR o.s.boot.SpringApplication [SpringApplication.java:839] Application run failed
hapi-fhir-jpaserver-start | org.springframework.context.ApplicationContextException: Unable to start web server
hapi-fhir-jpaserver-start | at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:165)
hapi-fhir-jpaserver-start | at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:618)
hapi-fhir-jpaserver-start | at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:146)
hapi-fhir-jpaserver-start | at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:753)
hapi-fhir-jpaserver-start | at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:455)
hapi-fhir-jpaserver-start | at org.springframework.boot.SpringApplication.run(SpringApplication.java:323)
hapi-fhir-jpaserver-start | at org.springframework.boot.SpringApplication.run(SpringApplication.java:1342)
hapi-fhir-jpaserver-start | at org.springframework.boot.SpringApplication.run(SpringApplication.java:1331)
hapi-fhir-jpaserver-start | at ca.uhn.fhir.jpa.starter.Application.main(Application.java:46)
hapi-fhir-jpaserver-start | at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
hapi-fhir-jpaserver-start | at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
hapi-fhir-jpaserver-start | at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
hapi-fhir-jpaserver-start | at java.base/java.lang.reflect.Method.invoke(Method.java:568)
hapi-fhir-jpaserver-start | at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
hapi-fhir-jpaserver-start | at org.springframework.boot.loader.Launcher.launch(Launcher.java:95)
hapi-fhir-jpaserver-start | at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
hapi-fhir-jpaserver-start | at org.springframework.boot.loader.PropertiesLauncher.main(PropertiesLauncher.java:466)
hapi-fhir-jpaserver-start | Caused by: org.springframework.boot.web.server.WebServerException: Unable to start embedded Tomcat
hapi-fhir-jpaserver-start | at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.initialize(TomcatWebServer.java:142)
hapi-fhir-jpaserver-start | at org.springframework.boot.web.embedded.tomcat.TomcatWebServer.
It's not finding your interceptor class on the classpath: [ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.class]: Failed to instantiate [ca.uhn.fhir.rest.server.RestfulServer]: Factory method 'restfulServer' threw exception with message: Interceptor class was not found on classpath:
There are two common ways to make your interceptor available:
-
clone the project, add your interceptor to it, and re-build it with your custom interceptor included. This would assume you are going to package/deploy your modified server yourself and not use the published docker image from dockerhub.
-
compile your interceptor and add it to the stock HAPI Docker container using the hapi-extra-classes config, as per: https://github.com/hapifhir/hapi-fhir-jpaserver-starter?tab=readme-ov-file#example-running-custom-interceptor-using-docker-compose
@michael-gvdw I am attaching a code for you That includes "BasicSecurityInterceptor.java" HAPI_FHIR_SERVER.zip
It's not finding your interceptor class on the classpath: [ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.class]: Failed to instantiate [ca.uhn.fhir.rest.server.RestfulServer]: Factory method 'restfulServer' threw exception with message: Interceptor class was not found on classpath:
There are two common ways to make your interceptor available:
- clone the project, add your interceptor to it, and re-build it with your custom interceptor included. This would assume you are going to package/deploy your modified server yourself and not use the published docker image from dockerhub.
- compile your interceptor and add it to the stock HAPI Docker container using the hapi-extra-classes config, as per: https://github.com/hapifhir/hapi-fhir-jpaserver-starter?tab=readme-ov-file#example-running-custom-interceptor-using-docker-compose
How do I manually compile the Interceptor? Since hapi-fhir-jpa-started is running under docker environment
How do I manually compile the Interceptor? Since hapi-fhir-jpa-started is running under docker environment
I've never tried to use the hapi-extra-classes config, so I won't be of too much help.. but I assume you'd need to set up a Java project to compile your interceptor, then take the compiled artifact and inject it into the container. I don't know the precise steps though. I'd personally rather do (1) and have my own clone of the project with my interceptor added so that when there are updates to HAPI I'd know if anything breaks with my interceptor when I compile the new versions. You can still use the Dockerfile in the project to build the image - you'd just be compiling HAPI yourself, and running the docker build yourself.