Petascope_Cannot load GDAL JNI on Centos 7 with SELinux enabled

[Bang Pham Huu]

On Centos 7 VM with SELinux enabled, Petascope cannot connect to rasserver and cannot load GDAL Java JNI. Because of this error, then, Petascope doesn't continue with try to create new petascopedb when it doesn't exist and it leads to the error with Hibernate.

Real problem comes from the check for loading GDAL Java JNI after loading it in Petascope. However, because of SELinux, it returns this error

Caused by: java.lang.UnsatisfiedLinkError: org.gdal.osr.osrJNI.new_SpatialReference__SWIG_1()J
	at org.gdal.osr.osrJNI.new_SpatialReference__SWIG_1(Native Method)
	at org.gdal.osr.SpatialReference.<init>(SpatialReference.java:117)
	at petascope.util.CrsProjectionUtil.transform(CrsProjectionUtil.java:126)

Full stack trace (old):

ApplicationMain@178: Failed initializing type registry from rasdaman.
org.odmg.ODMGRuntimeException: RasManager Error: Could not connect to RasServer .
	at org.rasdaman.rasnet.communication.RasRasnetImplementation.connectClient(RasRasnetImplementation.java:385)
	at org.rasdaman.rasnet.communication.RasRasnetImplementation.setUserIdentification(RasRasnetImplementation.java:364)
	at rasj.RasImplementation.setUserIdentification(RasImplementation.java:306)
	at petascope.util.ras.RasUtil.executeRasqlQuery(RasUtil.java:95)
	at petascope.util.ras.RasUtil.executeRasqlQuery(RasUtil.java:243)
	at petascope.util.ras.RasUtil.executeRasqlQuery(RasUtil.java:77)
	at petascope.util.ras.TypeRegistry.initializeStructRegistry(TypeRegistry.java:277)
	at petascope.util.ras.TypeRegistry.initializeRegistry(TypeRegistry.java:198)
	at petascope.util.ras.TypeRegistry.getInstance(TypeRegistry.java:57)
	at org.rasdaman.ApplicationMain.initConfigurations(ApplicationMain.java:176)
	at org.rasdaman.ApplicationMain.init(ApplicationMain.java:95)
	at org.rasdaman.ApplicationMain.placeholderConfigurer(ApplicationMain.java:126)
	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.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162)
	at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1173)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1067)
	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)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202)
	at org.springframework.context.support.PostProcessorRegistrationDelegate.invokeBeanFactoryPostProcessors(PostProcessorRegistrationDelegate.java:149)
	at org.springframework.context.support.AbstractApplicationContext.invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:686)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:524)
	at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122)
	at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:737)
	at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:370)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)
	at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:151)
	at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:131)
	at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:86)
	at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5623)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
	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:1092)
	at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
	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)
  WARN [2018-04-13 14:11:58] JdbcEnvironmentInitiator@132: HHH000342: Could not obtain connection to query metadata : FATAL: database "petascopedb" does not exist
  WARN [2018-04-13 14:11:58] AnnotationConfigEmbeddedWebApplicationContext@550: Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaAutoConfiguration.class]: Invocation of init method failed; nested exception is org.hibernate.service.spi.ServiceException: Unable to create requested service [org.hibernate.engine.jdbc.env.spi.JdbcEnvironment]
 ERROR [2018-04-13 14:11:58] SpringApplication@815: Application startup failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaAutoConfiguration.class]: Invocation of init method failed; nested exception is org.hibernate.service.spi.ServiceException: Unable to create requested service [org.hibernate.engine.jdbc.env.spi.JdbcEnvironment]
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1628)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
	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.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1081)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:856)
	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:737)
	at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:370)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)
	at org.springframework.boot.web.support.SpringBootServletInitializer.run(SpringBootServletInitializer.java:151)
	at org.springframework.boot.web.support.SpringBootServletInitializer.createRootApplicationContext(SpringBootServletInitializer.java:131)
	at org.springframework.boot.web.support.SpringBootServletInitializer.onStartup(SpringBootServletInitializer.java:86)
	at org.springframework.web.SpringServletContainerInitializer.onStartup(SpringServletContainerInitializer.java:169)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5623)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
	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:1092)
	at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
	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.hibernate.service.spi.ServiceException: Unable to create requested service [org.hibernate.engine.jdbc.env.spi.JdbcEnvironment]
	at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:264)
	at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:228)
	at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:207)
	at org.hibernate.engine.jdbc.internal.JdbcServicesImpl.configure(JdbcServicesImpl.java:51)
	at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.configureService(StandardServiceRegistryImpl.java:94)
	at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:237)
	at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:207)
	at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.handleTypes(MetadataBuildingProcess.java:352)
	at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.complete(MetadataBuildingProcess.java:111)
	at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.metadata(EntityManagerFactoryBuilderImpl.java:847)
	at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:874)
	at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:60)
	at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:353)
	at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:370)
	at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:359)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1687)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1624)
	... 29 more
Caused by: org.hibernate.HibernateException: Access to DialectResolutionInfo cannot be null when 'hibernate.dialect' not set
	at org.hibernate.engine.jdbc.dialect.internal.DialectFactoryImpl.determineDialect(DialectFactoryImpl.java:100)
	at org.hibernate.engine.jdbc.dialect.internal.DialectFactoryImpl.buildDialect(DialectFactoryImpl.java:54)
	at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:137)
	at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:35)
	at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.initiateService(StandardServiceRegistryImpl.java:88)
	at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:254)
	... 45 more

[Bang Pham Huu]

Rasdaman needs SELinux disabled as with it enabled, Petascope cannot connect to rasmgr as well as GDAL Java JNI cannot be loaded.