As a Java Developer, facing error(s) when trying to run the `controller` locally via `mvn spring-boot:run`.

[muhammad-levi]

GIVEN:

• Default configurations,
• mvn clean install on the other modules besides controller,
• Commenting usage of APIs from jdk.internal package (as suggested in this comment),
• Java 17,
• Apache Maven 3.9.8.

WHEN:

• Executing mvn spring-boot:run on pipelines/controller (as instructed in the wiki "Try out the FHIR Pipelines Controller").

THEN:

• Encountered error along this line: "Unsatisfied dependency",
• In the bottom of this issue description is the stack trace.

What thing(s) are missing to run the controller locally via mvn spring-boot:run?

levi@Axolotl:/mnt/d/SourceCodes/google/fhir-data-pipes/pipelines/controller$ mvn spring-boot:run
[INFO] Scanning for projects...
[INFO]
[INFO] ----------------< com.google.fhir.analytics:controller >----------------
[INFO] Building controller 0.2.7-SNAPSHOT
[INFO]   from pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] >>> spring-boot:3.2.2:run (default-cli) > test-compile @ controller >>>
[WARNING] 1 problem was encountered while building the effective model for org.apache.hadoop:hadoop-annotations:jar:2.6.0
[WARNING] 2 problems were encountered while building the effective model for org.apache.yetus:audience-annotations:jar:0.5.0
[INFO]
[INFO] --- directory:1.0:highest-basedir (directories) @ controller ---
[INFO] Highest basedir set to: /mnt/d/SourceCodes/google/fhir-data-pipes
[INFO]
[INFO] --- jacoco:0.8.12:prepare-agent (default) @ controller ---
[INFO] argLine set to -javaagent:/home/levi/.m2/repository/org/jacoco/org.jacoco.agent/0.8.12/org.jacoco.agent-0.8.12-runtime.jar=destfile=/mnt/d/SourceCodes/google/fhir-data-pipes/pipelines/controller/target/jacoco.exec
[INFO]
[INFO] --- license:4.5:format (add-license) @ controller ---
[WARNING]  Parameter 'legacyConfigExcludes' (user property 'license.excludes') is deprecated: use LicenseSet.excludes
[WARNING]  Parameter 'legacyConfigHeader' (user property 'license.header') is deprecated: use LicenseSet.header
[WARNING]  Parameter 'legacyConfigIncludes' (user property 'license.includes') is deprecated: use LicenseSet.includes
[INFO] Updating license headers...
[INFO]
[INFO] --- resources:3.3.1:resources (default-resources) @ controller ---
[INFO] Copying 6 resources from src/main/resources to target/classes
[INFO]
[INFO] --- compiler:3.13.0:compile (default-compile) @ controller ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] --- spotless:2.43.0:apply (default) @ controller ---
[INFO] Spotless.Format is keeping 1 files clean - 0 were changed to be clean, 0 were already clean, 1 were skipped because caching determined they were already clean
[INFO] Spotless.Format is keeping 1 files clean - 0 were changed to be clean, 0 were already clean, 1 were skipped because caching determined they were already clean
[INFO] Spotless.Java is keeping 22 files clean - 0 were changed to be clean, 0 were already clean, 22 were skipped because caching determined they were already clean
[INFO] Spotless.Pom is keeping 1 files clean - 0 were changed to be clean, 0 were already clean, 1 were skipped because caching determined they were already clean
[INFO]
[INFO] --- resources:3.3.1:testResources (default-testResources) @ controller ---
[INFO] Copying 3 resources from src/test/resources to target/test-classes
[INFO]
[INFO] --- compiler:3.13.0:testCompile (default-testCompile) @ controller ---
[INFO] Nothing to compile - all classes are up to date.
[INFO]
[INFO] <<< spring-boot:3.2.2:run (default-cli) < test-compile @ controller <<<
[INFO]
[INFO]
[INFO] --- spring-boot:3.2.2:run (default-cli) @ controller ---
[INFO] Attaching agents: []

  .   ____          _            __ _ _
 /\\ / ___'_ __ _ _(_)_ __  __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
 \\/  ___)| |_)| | | | | || (_| |  ) ) ) )
  '  |____| .__|_| |_|_| |_\__, | / / / /
 =========|_|==============|___/=/_/_/_/
 :: Spring Boot ::                (v3.2.2)

13:39:43.901 [restartedMain] INFO  c.g.f.a.ControlPanelApplication org.springframework.boot.StartupInfoLogger.logStarting:50 - Starting ControlPanelApplication using Java 17.0.12 with PID 76996 (/mnt/d/SourceCodes/google/fhir-data-pipes/pipelines/controller/target/classes started by levi in /mnt/d/SourceCodes/google/fhir-data-pipes/pipelines/controller)
13:39:43.908 [restartedMain] INFO  c.g.f.a.ControlPanelApplication org.springframework.boot.SpringApplication.logStartupProfileInfo:654 - No active profile set, falling back to 1 default profile: "default"
Aug 21, 2024 1:39:52 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["http-nio-8080"]
Aug 21, 2024 1:39:52 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service [Tomcat]
Aug 21, 2024 1:39:52 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet engine: [Apache Tomcat/10.1.18]
Aug 21, 2024 1:39:52 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring embedded WebApplicationContext
13:39:53.245 [restartedMain] WARN  o.s.boot.actuate.endpoint.EndpointId o.springframework.boot.actuate.endpoint.EndpointId.logWarning:155 - Endpoint ID 'pipeline-metrics' contains invalid characters, please migrate to a valid format.
13:39:53.923 [restartedMain] INFO  c.g.f.analytics.FlinkConfiguration com.google.fhir.analytics.FlinkConfiguration.initialiseFlinkConfiguration:107 - Creating Flink temporary configuration directory at
/tmp/tmp-flink-conf15747916679248383578
13:39:53.994 [restartedMain] INFO  c.g.f.analytics.FlinkConfiguration com.google.fhir.analytics.FlinkConfiguration.validateAndCreateConfFile:138 - Network memory : 12845056
13:39:54.016 [restartedMain] WARN  o.s.b.w.s.c.AnnotationConfigServletWebServerApplicationContext o.s.context.support.AbstractApplicationContext.refresh:632 - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'apiController': Unsatisfied dependency expressed through field 'pipelineManager': Error creating bean with name 'pipelineManager': Invocation of init method failed
Aug 21, 2024 1:39:54 PM org.apache.catalina.core.StandardService stopInternal
INFO: Stopping service [Tomcat]
13:39:54.352 [restartedMain] ERROR o.s.boot.SpringApplication org.springframework.boot.SpringApplication.reportFailure:851 - Application run failed
org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'apiController': Unsatisfied dependency expressed through field 'pipelineManager': Error creating bean with name 'pipelineManager': Invocation of init method failed
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:787)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:767)
        at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:145)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessProperties(AutowiredAnnotationBeanPostProcessor.java:508)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1418)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:598)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:975)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:959)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:624)
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:146)
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:754)
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:456)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:334)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1354)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343)
        at com.google.fhir.analytics.ControlPanelApplication.main(ControlPanelApplication.java:25)
        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:569)
        at org.springframework.boot.devtools.restart.RestartLauncher.run(RestartLauncher.java:50)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pipelineManager': Invocation of init method failed
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:222)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:421)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1765)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:599)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521)
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:325)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:323)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1443)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1353)
        at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.resolveFieldValue(AutowiredAnnotationBeanPostProcessor.java:784)
        ... 25 common frames omitted
Caused by: java.lang.IllegalAccessError: class com.google.fhir.analytics.PipelineManager tried to access method 'com.google.fhir.analytics.AvroConversionUtil com.google.fhir.analytics.AvroConversionUtil.getInstance(ca.uhn.fhir.context.FhirVersionEnum, java.lang.String, int)' (com.google.fhir.analytics.PipelineManager is in unnamed module of loader org.springframework.boot.devtools.restart.classloader.RestartClassLoader @69e1e8d; com.google.fhir.analytics.AvroConversionUtil is in unnamed module of loader 'app')
        at com.google.fhir.analytics.PipelineManager.initDwhStatus(PipelineManager.java:176)
        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:569)
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMethod.invoke(InitDestroyAnnotationBeanPostProcessor.java:457)
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:401)
        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:219)
        ... 37 common frames omitted
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  51.437 s
[INFO] Finished at: 2024-08-21T13:39:54+07:00
[INFO] ------------------------------------------------------------------------

[bashir2]

@muhammad-levi you need to comment out the actual usage of jdk.internal.misc as shown in PR #1161. I also realized that after doing that there is another issue which can be fixed by removing spring-boot-devtools (shown in the same PR).

Just to emphasize: You need to use spring-boot:run only if you intend to create a dev env. for controller changes. Otherwise you can simply use the uber jar controller-bundled.jar or just the docker image created from the Dockerfile.

[muhammad-levi]

Okay, thank you, @bashir2.

Yes, I intend to set up a dev env for the controller in case there are some things that I can contribute. Thank you. 🙇🏻

[bashir2]

Okay, great, looking forward to your contributions. I am going to close this issue for now but I agree we should make setting up the dev env easier.