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