Develop Reference

Exception encountered during context initialization

org.springframework.context.support.AbstractApplicationContext refresh
WARNING: Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'emp' defined in class path resource [beans.xml]: Error setting property values; nested exception is org.springframework.beans.NotWritablePropertyException: Invalid property 'id' of bean class [com.avi.spring.firstspring.employee]: Bean property 'id' is not writable or has an invalid setter method. Does the parameter type of the setter match the return type of the getter?
Exception in thread "main" org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'emp' defined in class path resource [beans.xml]: Error setting property values; nested exception is org.springframework.beans.NotWritablePropertyException: Invalid property 'id' of bean class [com.avi.spring.firstspring.employee]: Bean property 'id' is not writable or has an invalid setter method. Does the parameter type of the setter match the return type of the getter?
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1711)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1426)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:592)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:847)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:877)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:549)
at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:144)
at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:85)
at com.avi.spring.firstspring.test.main(test.java:9)
Caused by: org.springframework.beans.NotWritablePropertyException: Invalid property 'id' of bean class [com.avi.spring.firstspring.employee]: Bean property 'id' is not writable or has an invalid setter method. Does the parameter type of the setter match the return type of the getter?
at org.springframework.beans.BeanWrapperImpl.createNotWritablePropertyException(BeanWrapperImpl.java:243)
at org.springframework.beans.AbstractNestablePropertyAccessor.processLocalProperty(AbstractNestablePropertyAccessor.java:426)
at org.springframework.beans.AbstractNestablePropertyAccessor.setPropertyValue(AbstractNestablePropertyAccessor.java:278)
at org.springframework.beans.AbstractNestablePropertyAccessor.setPropertyValue(AbstractNestablePropertyAccessor.java:266)
at org.springframework.beans.AbstractPropertyAccessor.setPropertyValues(AbstractPropertyAccessor.java:97)
at org.springframework.beans.AbstractPropertyAccessor.setPropertyValues(AbstractPropertyAccessor.java:77)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1707)
... 13 more

Can you upgrade rundeck straight from 3.0.22 to 3.2.1 on Ubuntu 18.04.3 "bionic" with OpenJDK on GCP?

Failed with this so I did a systemctl stop rundeckd followed by an apt-get --purge remove rundeck followed by restoring three files in /etc/rundeckd (profile, framework.properties, rundeck-config.properties which I had backed up) and restarted with systemctl start rundeckd and things are working again. Now I don't want to upgrade rundeck again due to the above experience. Can one not go directly from 3.0.22 to 3.2.1 rundeck?
The working packages are:
openjdk-8-jdk-headless/bionic-updates,bionic-security,now 8u232-b09-0ubuntu1~18.04.1 amd64 [installed]
openjdk-8-jre-headless/bionic-updates,bionic-security,now 8u232-b09-0ubuntu1~18.04.1 amd64 [installed]
rundeck/now 3.0.22.20190512-1.201905130100 all [installed,local]
The console log of the attempt to startup 3.2.1 using systemctl start rundeckd
Configuring Spring Security Core ...
... finished configuring Spring Security Core
[2020-01-16 22:53:37.436] WARN AnnotationConfigEmbeddedWebApplicationContext --- [ main] Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'requestMappingHandlerMapping' defined in org.springframework.web.servlet.config.annotation.DelegatingWebMvcConfiguration: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'grailsInterceptorMappedInterceptor': Cannot create inner bean '(inner bean)#6f12b637' of type [org.grails.plugins.web.interceptors.GrailsInterceptorHandlerInterceptorAdapter] while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name '(inner bean)#6f12b637': Unsatisfied dependency expressed through method 'setInterceptors' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'controllerBaseInterceptor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'uiPluginService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'authorizationService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configStorageService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'rundeckConfigStorageTreeFactory': Cannot resolve reference to bean 'storagePluginProviderService' while setting bean property 'storagePluginProviderService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'storagePluginProviderService': Cannot resolve reference to bean 'rundeckFramework' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkFactory': Cannot resolve reference to bean 'frameworkFilesystem' while setting bean property 'frameworkFilesystem'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkFilesystem': Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [com.dtolabs.rundeck.core.common.FilesystemFramework]: Factory method 'createFilesystemFramework' threw exception; nested exception is java.lang.IllegalArgumentException: project base directory could not be created. /var/rundeck/projects
[2020-01-16 22:53:37.538] ERROR SpringApplication --- [ main] Application startup failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'requestMappingHandlerMapping' defined in org.springframework.web.servlet.config.annotation.DelegatingWebMvcConfiguration: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'grailsInterceptorMappedInterceptor': Cannot create inner bean '(inner bean)#6f12b637' of type [org.grails.plugins.web.interceptors.GrailsInterceptorHandlerInterceptorAdapter] while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name '(inner bean)#6f12b637': Unsatisfied dependency expressed through method 'setInterceptors' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'controllerBaseInterceptor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'uiPluginService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'authorizationService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configStorageService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'rundeckConfigStorageTreeFactory': Cannot resolve reference to bean 'storagePluginProviderService' while setting bean property 'storagePluginProviderService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'storagePluginProviderService': Cannot resolve reference to bean 'rundeckFramework' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkFactory': Cannot resolve reference to bean 'frameworkFilesystem' while setting bean property 'frameworkFilesystem'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkFilesystem': Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [com.dtolabs.rundeck.core.common.FilesystemFramework]: Factory method 'createFilesystemFramework' threw exception; nested exception is java.lang.IllegalArgumentException: project base directory could not be created. /var/rundeck/projects
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:562)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:756)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:542)
at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:693)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:360)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:303)
at grails.boot.GrailsApp.run(GrailsApp.groovy:84)
at grails.boot.GrailsApp.run(GrailsApp.groovy:393)
at grails.boot.GrailsApp.run(GrailsApp.groovy:380)
at grails.boot.GrailsApp$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:116)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:136)
at rundeckapp.Application.main(Application.groovy:28)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:87)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:50)
at org.springframework.boot.loader.WarLauncher.main(WarLauncher.java:59)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'grailsInterceptorMappedInterceptor': Cannot create inner bean '(inner bean)#6f12b637' of type [org.grails.plugins.web.interceptors.GrailsInterceptorHandlerInterceptorAdapter] while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name '(inner bean)#6f12b637': Unsatisfied dependency expressed through method 'setInterceptors' parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'controllerBaseInterceptor': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'uiPluginService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'pluginService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'authorizationService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'configStorageService': Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'rundeckConfigStorageTreeFactory': Cannot resolve reference to bean 'storagePluginProviderService' while setting bean property 'storagePluginProviderService'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'storagePluginProviderService': Cannot resolve reference to bean 'rundeckFramework' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkFactory': Cannot resolve reference to bean 'frameworkFilesystem' while setting bean property 'frameworkFilesystem'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'frameworkFilesystem': Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [com.dtolabs.rundeck.core.common.FilesystemFramework]: Factory method 'createFilesystemFramework' threw exception; nested exception is java.lang.IllegalArgumentException: project base directory could not be created. /var/rundeck/projects
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveInnerBean(BeanDefinitionValueResolver.java:313)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:129)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:648)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:145)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1197)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1099)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:511)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeansOfType(DefaultListableBeanFactory.java:519)
at org.springframework.context.support.AbstractApplicationContext.getBeansOfType(AbstractApplicationContext.java:1198)
at org.springframework.beans.factory.BeanFactoryUtils.beansOfTypeIncludingAncestors(BeanFactoryUtils.java:289)
at org.springframework.web.servlet.handler.AbstractHandlerMapping.detectMappedInterceptors(AbstractHandlerMapping.java:272)
at org.springframework.web.servlet.handler.AbstractHandlerMapping.initApplicationContext(AbstractHandlerMapping.java:247)
at org.springframework.context.support.ApplicationObjectSupport.initApplicationContext(ApplicationObjectSupport.java:120)
at org.springframework.web.context.support.WebApplicationObjectSupport.initApplicationContext(WebApplicationObjectSupport.java:76)
at org.springframework.context.support.ApplicationObjectSupport.setApplicationContext(ApplicationObjectSupport.java:74)
at org.springframework.context.support.ApplicationContextAwareProcessor.invokeAwareInterfaces(ApplicationContextAwareProcessor.java:121)
at org.springframework.context.support.ApplicationContextAwareProcessor.postProcessBeforeInitialization(ApplicationContextAwareProcessor.java:97)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:407)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1622)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
... 28 common frames omitted

The value of framework.projects.dir in the default install of Rundeck 3.2 in the config file framework.properties has changed to:
framework.projects.dir=/var/lib/rundeck/projects
Please follow the instructions: Upgrading to Rundeck 3.2

Spring Security SAML error logging throws an error

I am new to SAML as well as spring security. I have configured the sample app to connect to an ADFS server following the documentation. When I access the app, I get redirected to the ADFS server appropriately, but one I enter my username and password, I get an error back in the app stating that there was an error validating the SAML message.
In an attempt to see why this is happening, I enabled the message logging according to the documentation (enabling the three properties in the samlLogger bean). When I do that, I get the following stacktrace on startup:
Sep 17, 2018 11:56:25 AM org.apache.catalina.core.StandardContext
listenerStart SEVERE: Exception sending context initialized event to
listener instance of class
[org.springframework.web.context.ContextLoaderListener]
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'org.springframework.security.filterChains':
Cannot resolve reference to bean
'org.springframework.security.web.DefaultSecurityFilterChain#4' while
setting bean property 'sourceList' with key [4]; nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name
'org.springframework.security.web.DefaultSecurityFilterChain#4':
Cannot resolve reference to bean 'metadataGeneratorFilter' while
setting constructor argument with key [0]; nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'metadataGeneratorFilter' defined in
ServletContext resource [/WEB-INF/securityContext.xml]: Cannot create
inner bean
'org.springframework.security.saml.metadata.MetadataGenerator#3aca2643'
of type [org.springframework.security.saml.metadata.MetadataGenerator]
while setting constructor argument; nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name
'org.springframework.security.saml.metadata.MetadataGenerator#3aca2643':
Injection of autowired dependencies failed; nested exception is
org.springframework.beans.factory.BeanCreationException: Could not
autowire method: public void
org.springframework.security.saml.metadata.MetadataGenerator.setSamlEntryPoint(org.springframework.security.saml.SAMLEntryPoint);
nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'samlEntryPoint': Injection of autowired
dependencies failed; nested exception is
org.springframework.beans.factory.BeanCreationException: Could not
autowire method: public void
org.springframework.security.saml.SAMLEntryPoint.setSamlLogger(org.springframework.security.saml.log.SAMLLogger);
nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'samlLogger' defined in ServletContext
resource [/WEB-INF/securityContext.xml]: Error setting property
values; nested exception is
org.springframework.beans.NotWritablePropertyException: Invalid
property 'logAllMessages' of bean class
[org.springframework.security.saml.log.SAMLDefaultLogger]: Bean
property 'logAllMessages' is not writable or has an invalid setter
method. Does the parameter type of the setter match the return type of
the getter?
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:353)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:153)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:591)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:383)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:283)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:111)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4745)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5207)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:988)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1860)
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) Caused by: org.springframework.beans.factory.BeanCreationException: Error
creating bean with name
'org.springframework.security.web.DefaultSecurityFilterChain#4':
Cannot resolve reference to bean 'metadataGeneratorFilter' while
setting constructor argument with key [0]; nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'metadataGeneratorFilter' defined in
ServletContext resource [/WEB-INF/securityContext.xml]: Cannot create
inner bean
'org.springframework.security.saml.metadata.MetadataGenerator#3aca2643'
of type [org.springframework.security.saml.metadata.MetadataGenerator]
while setting constructor argument; nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name
'org.springframework.security.saml.metadata.MetadataGenerator#3aca2643':
Injection of autowired dependencies failed; nested exception is
org.springframework.beans.factory.BeanCreationException: Could not
autowire method: public void
org.springframework.security.saml.metadata.MetadataGenerator.setSamlEntryPoint(org.springframework.security.saml.SAMLEntryPoint);
nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'samlEntryPoint': Injection of autowired
dependencies failed; nested exception is
org.springframework.beans.factory.BeanCreationException: Could not
autowire method: public void
org.springframework.security.saml.SAMLEntryPoint.setSamlLogger(org.springframework.security.saml.log.SAMLLogger);
nested exception is
org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'samlLogger' defined in ServletContext
resource [/WEB-INF/securityContext.xml]: Error setting property
values; nested exception is
org.springframework.beans.NotWritablePropertyException: Invalid
property 'logAllMessages' of bean class
[org.springframework.security.saml.log.SAMLDefaultLogger]: Bean
property 'logAllMessages' is not writable or has an invalid setter
method. Does the parameter type of the setter match the return type of
the getter?
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:353)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:153)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:616)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:148)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1035)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:939)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
... 30 more
<!-- Logger for SAML messages and events -->
<bean id="samlLogger" class="org.springframework.security.saml.log.SAMLDefaultLogger">
<!-- Enable these to see the actual SAML Messages in logs -->
<property name="logAllMessages" value="true"/>
<property name="logErrors" value="true"/>
<property name="logMessagesOnException" value="true"/>
</bean>
Any help please.
Thanks
Shaun

Update Hibernate gives an error

I have an Java project and I'm upgrading to the latest version of Hibernate (from hibernate 3 to hibernate 5).
When I startup the tomcat (tomcat7) gives me the following error:
2017-06-28 22:57:01,330 ERROR [_ ()] [] [org.springframework.web.context.ContextLoader] Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.security.filterChains': Cannot resolve reference to bean 'org.springframework.security.web.DefaultSecurityFilterChain#3' while setting bean property 'sourceList' with key [3]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.security.web.DefaultSecurityFilterChain#3': Cannot create inner bean '(inner bean)#261fa193' of type [org.springframework.security.web.session.ConcurrentSessionFilter] while setting constructor argument with key [2]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#261fa193': Cannot resolve reference to bean 'org.springframework.security.web.authentication.rememberme.PersistentTokenBasedRememberMeServices#0' while setting bean property 'logoutHandlers' with key [2]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.security.web.authentication.rememberme.PersistentTokenBasedRememberMeServices#0': Cannot create inner bean '(inner bean)#5435998e' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#5435998e': Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.security.core.userdetails.UserDetailsService]: Factory method 'cachingUserDetailsService' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'loginService': Unsatisfied dependency expressed through field 'registeredUserServiceDAO'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'registeredUserServiceDAO': Unsatisfied dependency expressed through field 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in ServletContext resource [/WEB-INF/application-context.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.hibernate.integrator.internal.IntegratorServiceImpl.<init>(Ljava/util/LinkedHashSet;Lorg/hibernate/boot/registry/classloading/spi/ClassLoaderService;)V
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:359)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1531)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1276)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:742)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4939)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5434)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:983)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1660)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.security.web.DefaultSecurityFilterChain#3': Cannot create inner bean '(inner bean)#261fa193' of type [org.springframework.security.web.session.ConcurrentSessionFilter] while setting constructor argument with key [2]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#261fa193': Cannot resolve reference to bean 'org.springframework.security.web.authentication.rememberme.PersistentTokenBasedRememberMeServices#0' while setting bean property 'logoutHandlers' with key [2]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.security.web.authentication.rememberme.PersistentTokenBasedRememberMeServices#0': Cannot create inner bean '(inner bean)#5435998e' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#5435998e': Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.springframework.security.core.userdetails.UserDetailsService]: Factory method 'cachingUserDetailsService' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'loginService': Unsatisfied dependency expressed through field 'registeredUserServiceDAO'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'registeredUserServiceDAO': Unsatisfied dependency expressed through field 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in ServletContext resource [/WEB-INF/application-context.xml]: Invocation of init method failed; nested exception is java.lang.NoSuchMethodError: org.hibernate.integrator.internal.IntegratorServiceImpl.<init>(Ljava/util/LinkedHashSet;Lorg/hibernate/boot/registry/classloading/spi/ClassLoaderService;)V
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveInnerBean(BeanDefinitionValueResolver.java:313)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:129)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveManagedList(BeanDefinitionValueResolver.java:382)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:157)
at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:634)
at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:145)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1193)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1095)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:513)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
What I need to do now? I did try to find for the first error on Google and nothing helped me.
Thanks

Configuration JOOQ in JHipster

I have a problem with the configuration of JOOQ in JHipster. I'm trying to use petrikainulainen.net configuration in my testing app, but when I compile I have many errors. I'm using jooq-jhipster-generator.
My plugin generator
<plugin>
<!-- Specify the maven code generator plugin -->
<groupId>org.jooq</groupId>
<artifactId>jooq-codegen-maven</artifactId>
<version>${jooq.version}</version>
<!-- The plugin should hook into the generate goal -->
<executions>
<execution>
<goals>
<goal>generate</goal>
</goals>
</execution>
</executions>
<!-- Manage the plugin's dependency. In this example, we'll use a PostgreSQL database -->
<dependencies>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgresql.version}</version>
</dependency>
</dependencies>
<!-- Specify the plugin configuration.
The configuration format is the same as for the standalone code generator -->
<configuration>
<!-- JDBC connection parameters -->
<jdbc>
<driver>${jdbcDriverClass}</driver>
<url>${env.DATABASE_SHORT_URL}</url>
<user>${env.DATABASE_USER}</user>
<password>${env.DATABASE_PASS}</password>
</jdbc>
<!-- Generator parameters -->
<generator>
<generate>
<daos>true</daos>
<records>true</records>
</generate>
<name>com.app3.jjg.JooqJhipsterGenerator</name>
<database>
<name>org.jooq.util.postgres.PostgresDatabase</name>
<includes>.*</includes>
<excludes />
<inputSchema>public</inputSchema>
</database>
<target>
<packageName>com.mycompany.myapp.jooq.todo.db</packageName>
<directory>target/generated-sources/jooq</directory>
</target>
</generator>
</configuration>
</plugin>
JooqConfiguration.java
package com.mycompany.myapp.config;
import com.jolbox.bonecp.BoneCPDataSource;
import com.mycompany.myapp.todo.JOOQToSpringExceptionTransformer;
import org.jooq.SQLDialect;
import org.jooq.impl.DataSourceConnectionProvider;
import org.jooq.impl.DefaultConfiguration;
import org.jooq.impl.DefaultDSLContext;
import org.jooq.impl.DefaultExecuteListenerProvider;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.jdbc.datasource.DataSourceTransactionManager;
import org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy;
import org.springframework.jdbc.datasource.TransactionAwareDataSourceProxy;
import org.springframework.jdbc.datasource.init.DataSourceInitializer;
import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.sql.DataSource;
#Configuration
#EnableTransactionManagement
public class JooqConfuguration {
#Bean
public DataSource source(){
BoneCPDataSource ds = new BoneCPDataSource();
ds.setDriverClass("org.postgresql.ds.PGSimpleDataSource");
ds.setJdbcUrl("jdbc:postgresql://localhost:5432/test");
ds.setUsername("user");
ds.setPassword("password");
return ds;
}
#Bean
public DefaultConfiguration configuration(){
DefaultConfiguration jooqConfiguration = new DefaultConfiguration();
jooqConfiguration.set(connectionProvider());
jooqConfiguration.set(new DefaultExecuteListenerProvider(jooqToSpringExceptionTransformer()));
SQLDialect dialect = SQLDialect.valueOf(String.valueOf(SQLDialect.POSTGRES));
jooqConfiguration.set(dialect);
return jooqConfiguration;
}
#Bean
public LazyConnectionDataSourceProxy lazyConnectionDataSource() {
return new LazyConnectionDataSourceProxy(source());
}
#Bean
public TransactionAwareDataSourceProxy transactionAwareDataSource() {
return new TransactionAwareDataSourceProxy(lazyConnectionDataSource());
}
#Bean
public DataSourceTransactionManager transactionManager() {
return new DataSourceTransactionManager(lazyConnectionDataSource());
}
#Bean
public DataSourceConnectionProvider connectionProvider() {
return new DataSourceConnectionProvider(transactionAwareDataSource());
}
#Bean
public JOOQToSpringExceptionTransformer jooqToSpringExceptionTransformer() {
return new JOOQToSpringExceptionTransformer();
}
#Bean
public DefaultDSLContext dsl() {
return new DefaultDSLContext(configuration());
}
#Bean
public DataSourceInitializer dataSourceInitializer() {
DataSourceInitializer initializer = new DataSourceInitializer();
initializer.setDataSource(source());
return initializer;
}
}
Stack Trace
2016-02-29 21:34:06.930 ERROR 3053 --- [ost-startStop-1] o.a.c.c.C.[Tomcat].[localhost].[/] : Exception starting filter springSecurityFilterChain
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.security.config.annotation.web.configuration.WebSecurityConfiguration': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire method: public void org.springframework.security.config.annotation.web.configuration.WebSecurityConfiguration.setFilterChainProxySecurityConfigurer(org.springframework.security.config.annotation.ObjectPostProcessor,java.util.List) throws java.lang.Exception; nested exception is org.springframework.beans.factory.BeanExpressionException: Expression parsing failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'securityConfiguration': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private org.springframework.security.core.userdetails.UserDetailsService com.mycompany.myapp.config.SecurityConfiguration.userDetailsService; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'userDetailsService': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.mycompany.myapp.repository.UserRepository com.mycompany.myapp.security.UserDetailsService.userRepository; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'userRepository': Cannot create inner bean '(inner bean)#242533b6' 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)#242533b6': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'liquibase' defined in class path resource [com/mycompany/myapp/config/DatabaseConfiguration.class]: Unsatisfied dependency expressed through constructor argument with index 0 of type [javax.sql.DataSource]: : Error creating bean with name 'dataSource' defined in class path resource [com/mycompany/myapp/config/DatabaseConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSourceInitializer': Invocation of init method failed; nested exception is org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type [javax.sql.DataSource] is defined: expected single matching bean but found 4: transactionAwareDataSource,source,lazyConnectionDataSource,dataSource; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSource' defined in class path resource [com/mycompany/myapp/config/DatabaseConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSourceInitializer': Invocation of init method failed; nested exception is org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type [javax.sql.DataSource] is defined: expected single matching bean but found 4: transactionAwareDataSource,source,lazyConnectionDataSource,dataSource
at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:334) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1214) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:543) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:368) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1123) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1018) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:510) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) ~[spring-beans-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1060) ~[spring-context-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.initDelegate(DelegatingFilterProxy.java:326) ~[spring-web-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.initFilterBean(DelegatingFilterProxy.java:235) ~[spring-web-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.springframework.web.filter.GenericFilterBean.init(GenericFilterBean.java:199) ~[spring-web-4.2.4.RELEASE.jar:4.2.4.RELEASE]
at org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279) ~[tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:109) ~[tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4659) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5281) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1408) [tomcat-embed-core-8.0.30.jar:8.0.30]
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1398) [tomcat-embed-core-8.0.30.jar:8.0.30]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_72]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_72]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_72]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_72]
Caused by: org.springframework.beans.factory.BeanCreationException: Could not autowire method: public void org.springframework.security.config.annotation.web.configuration.WebSecurityConfiguration.setFilterChainProxySecurityConfigurer(org.springframework.security.config.annotation.ObjectPostProcessor,java.util.List) throws java.lang.Exception; nested exception is org.springframework.beans.factory.BeanExpressionException: Expression parsing failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'securityConfiguration': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private org.springframework.security.core.userdetails.UserDetailsService com.mycompany.myapp.config.SecurityConfiguration.userDetailsService; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'userDetailsService': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.mycompany.myapp.repository.UserRepository com.mycompany.myapp.security.UserDetailsService.userRepository; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'userRepository': Cannot create inner bean '(inner bean)#242533b6' 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)#242533b6': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'liquibase' defined in class path resource [com/mycompany/myapp/config/DatabaseConfiguration.class]: Unsatisfied dependency expressed through constructor argument with index 0 of type [javax.sql.DataSource]: : Error creating bean with name 'dataSource' defined in class path resource [com/mycompany/myapp/config/DatabaseConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSourceInitializer': Invocation of init method failed; nested exception is org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type [javax.sql.DataSource] is defined: expected single matching bean but found 4: transactionAwareDataSource,source,lazyConnectionDataSource,dataSource; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSource' defined in class path resource [com/mycompany/myapp/config/DatabaseConfiguration.class]: Initialization of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSourceInitializer': Invocation of init method failed; nested exception is org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type [javax.sql.DataSource] is defined: expected single matching bean but found 4: transactionAwareDataSource,source,lazyConnectionDataSource,dataSource
I don't know what I'm doing wrong.

You don't want all those DataSource to be beans. If you read the exception and look at the Java doc for those DataSource decorators it will tell you not to create beans from except the most outer one.
So the trick is to remove #Bean from all but the outer DataSource.
//remove #Bean
public DataSource source(){
BoneCPDataSource ds = new BoneCPDataSource();
ds.setDriverClass("org.postgresql.ds.PGSimpleDataSource");
ds.setJdbcUrl("jdbc:postgresql://localhost:5432/test");
ds.setUsername("user");
ds.setPassword("password");
return ds;
}
#Bean
public DefaultConfiguration configuration(){
DefaultConfiguration jooqConfiguration = new DefaultConfiguration();
jooqConfiguration.set(connectionProvider());
jooqConfiguration.set(new DefaultExecuteListenerProvider(jooqToSpringExceptionTransformer()));
SQLDialect dialect = SQLDialect.valueOf(String.valueOf(SQLDialect.POSTGRES));
jooqConfiguration.set(dialect);
return jooqConfiguration;
}
//remove #Bean
public LazyConnectionDataSourceProxy lazyConnectionDataSource() {
return new LazyConnectionDataSourceProxy(source());
}
#Bean
public TransactionAwareDataSourceProxy transactionAwareDataSource() {
return new TransactionAwareDataSourceProxy(lazyConnectionDataSource());
}
#Bean
public DataSourceTransactionManager transactionManager() {
return new DataSourceTransactionManager(transactionAwareDataSource());
}
#Bean
public DataSourceConnectionProvider connectionProvider() {
return new DataSourceConnectionProvider(transactionAwareDataSource());
}
#Bean
public JOOQToSpringExceptionTransformer jooqToSpringExceptionTransformer() {
return new JOOQToSpringExceptionTransformer();
}
#Bean
public DefaultDSLContext dsl() {
return new DefaultDSLContext(configuration());
}
You probably don't even need the LazyConnectionDataSourceProxy as I believe BoneCP does something to this effect.

The error message is clear: you have defined 4 beans of type datasource. userRepository requires one datasource and so Spring does not know which one to inject.
No qualifying bean of type [javax.sql.DataSource] is defined:
expected single matching bean but found 4:
transactionAwareDataSource,source,lazyConnectionDataSource,dataSource
From what I see you expose all of them as beans but source and lazyConnectionDataSource are used to build transactionAwareDataSource so they should not be annotated with #Bean.
Then there is dataSource bean which seems to be created by spring boot maybe from your application properties.
Why using BoneCP when JHipster uses Hikari?