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mekomsolutions / openmrs-module-initializer

The OpenMRS Initializer module is an API-only module that processes the content of the configuration folder when it is found inside OpenMRS' application data directory.
MIT License
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Add domains for FHIR Concept Source URLs and patient identifier systems #186

Closed ibacher closed 2 years ago

ibacher commented 2 years ago

Adds domains for a couple of simple mapping tables we use in the FHIR2 module.

ibacher commented 2 years ago

I've added a major refactoring of the LoadersOrderTest. Basically, the test should still have the same assertions (i.e., that each loader specifies an unequivocal order, that each loader is for a recognised domain and that every domain has an associated loader). However, this is now done in such a way that simply registering the loader as a Spring component and adding the domain to the Domain enum will enforce these checks.

mogoodrich commented 2 years ago

@ibacher we are seeing a startup error with the PIH EMR (which is running the latest snapshot of Iniz) after this commit... do things start up okay for you?

`The following error occurred at startup: Unable to start OpenMRS. Error thrown was: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'fhirPatientIdentifierSystemLineProcessor': Lookup method resolution failed; nested exception is java.lang.IllegalStateException: Failed to introspect Class [org.openmrs.module.initializer.api.fhir.pis.FhirPatientIdentifierSystemLineProcessor] from ClassLoader [{ModuleClassLoader: uid=1479380482; initializer}] org.openmrs.module.ModuleException: Unable to start OpenMRS. Error thrown was: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'fhirPatientIdentifierSystemLineProcessor': Lookup method resolution failed; nested exception is java.lang.IllegalStateException: Failed to introspect Class [org.openmrs.module.initializer.api.fhir.pis.FhirPatientIdentifierSystemLineProcessor] from ClassLoader [{ModuleClassLoader: uid=1479380482; initializer}] at org.openmrs.web.WebDaemon.startOpenmrs(WebDaemon.java:65) at org.openmrs.web.Listener.contextInitialized(Listener.java:236) at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5068) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091) at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980) at java.util.concurrent.Executors$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:750) Caused by: javax.servlet.ServletException: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'fhirPatientIdentifierSystemLineProcessor': Lookup method resolution failed; nested exception is java.lang.IllegalStateException: Failed to introspect Class [org.openmrs.module.initializer.api.fhir.pis.FhirPatientIdentifierSystemLineProcessor] from ClassLoader [{ModuleClassLoader: uid=1479380482; initializer}] at org.openmrs.web.Listener.startOpenmrs(Listener.java:308) at org.openmrs.web.WebDaemon$1.run(WebDaemon.java:42) Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'fhirPatientIdentifierSystemLineProcessor': Lookup method resolution failed; nested exception is java.lang.IllegalStateException: Failed to introspect Class [org.openmrs.module.initializer.api.fhir.pis.FhirPatientIdentifierSystemLineProcessor] from ClassLoader [{ModuleClassLoader: uid=1479380482; initializer}] at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.determineCandidateConstructors(AutowiredAnnotationBeanPostProcessor.java:289) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.determineConstructorsFromBeanPostProcessors(AbstractAutowireCapableBeanFactory.java:1290) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1205) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:556) at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:516) at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:324) at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322) at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:897) at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:879) at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:551) at org.openmrs.module.ModuleUtil.refreshApplicationContext(ModuleUtil.java:885) at org.openmrs.module.web.WebModuleUtil.refreshWAC(WebModuleUtil.java:844) at org.openmrs.web.Listener.performWebStartOfModules(Listener.java:652) at org.openmrs.web.Listener.performWebStartOfModules(Listener.java:632) at org.openmrs.web.Listener.startOpenmrs(Listener.java:300) ... 1 more Caused by: java.lang.IllegalStateException: Failed to introspect Class [org.openmrs.module.initializer.api.fhir.pis.FhirPatientIdentifierSystemLineProcessor] from ClassLoader [{ModuleClassLoader: uid=1479380482; initializer}] at org.springframework.util.ReflectionUtils.getDeclaredMethods(ReflectionUtils.java:481) at org.springframework.util.ReflectionUtils.doWithLocalMethods(ReflectionUtils.java:321) at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.determineCandidateConstructors(AutowiredAnnotationBeanPostProcessor.java:267) ... 17 more Caused by: java.lang.NoClassDefFoundError: org/openmrs/module/fhir2/model/FhirPatientIdentifierSystem at java.lang.Class.getDeclaredMethods0(Native Method) at java.lang.Class.privateGetDeclaredMethods(Class.java:2701) at java.lang.Class.getDeclaredMethods(Class.java:1975) at org.springframework.util.ReflectionUtils.getDeclaredMethods(ReflectionUtils.java:463) ... 19 more Caused by: java.lang.ClassNotFoundException: org.openmrs.module.fhir2.model.FhirPatientIdentifierSystem at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1859) at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1702) at org.openmrs.module.ModuleClassLoader.loadClass(ModuleClassLoader.java:564) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ... 23 more

See the server log for full output.`

mogoodrich commented 2 years ago

"Caused by: java.lang.ClassNotFoundException: org.openmrs.module.fhir2.model.FhirPatientIdentifierSystem" seems to be the root error

ibacher commented 2 years ago

@mogoodrich Whoops... looks like a left a critical bit out in this PR. Thanks for the quick find. Should be fixed by 3d7e174.

mogoodrich commented 2 years ago

Thanks @ibacher ! You can thank our CI for the quick find... :)