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Trying to set webapi


(simon white) #1

Hi,
I am running a POC to see if we can get our own EHR data into CDM and run Atlas and the other tools.
I have a basic ETL to get our data into a CDM schema but setting up the webapi is proving difficult.
I have tomcat running and the .war file gets loaded and it connects to the webapi schema and starts making tables but then falls over with some incompatibility I don’t understand.

2020-07-17 03:35:01.880 WARN localhost-startStop-1 rg.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext -  - Exception encountered during context initialization - cancelling refresh attempt: org.springframework.context.ApplicationContextException: Unable to start embedded container; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'cacheFilter': Unsatisfied dependency expressed through field 'permissionManager'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'permissionManager': Unsatisfied dependency expressed through field 'userRepository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'userRepository': Cannot create inner bean '(inner bean)#5b861914' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#5b861914': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/ohdsi/webapi/DataAccessConfig.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [javax.persistence.EntityManagerFactory]: Factory method 'entityManagerFactory' threw exception; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'hibernate.dialect' in value "${hibernate.dialect}"
    2020-07-17 03:35:01.890 INFO localhost-startStop-1 org.springframework.boot.autoconfigure.logging.AutoConfigurationReportLoggingInitializer -  - 

Error starting ApplicationContext. To display the auto-configuration report re-run your application with 'debug' enabled.
2020-07-17 03:35:01.895 ERROR localhost-startStop-1 org.springframework.boot.SpringApplication -  - Application startup failed
org.springframework.context.ApplicationContextException: Unable to start embedded container; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'cacheFilter': Unsatisfied dependency expressed through field 'permissionManager'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'permissionManager': Unsatisfied dependency expressed through field 'userRepository'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'userRepository': Cannot create inner bean '(inner bean)#5b861914' of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#5b861914': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/ohdsi/webapi/DataAccessConfig.class]: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [javax.persistence.EntityManagerFactory]: Factory method 'entityManagerFactory' threw exception; nested exception is java.lang.IllegalArgumentException: Could not resolve placeholder 'hibernate.dialect' in value "${hibernate.dialect}"
        at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.onRefresh(EmbeddedWebApplicationContext.java:139)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:536)
        at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:124)
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:693)
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:360)
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:303)
        at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:156)
        at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:136)
        at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:91)
        at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5144)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:743)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:719)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:705)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:970)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1840)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)

I am using apache-tomcat-8.5.57 and openjdk-8-jdk with WebAPI v2.7.7
Any suggestions would be welcome.

Thanks,
Simon


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