Unable to get JPA up and running with PostgreSQL

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Daniel del Castillo

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Sep 10, 2018, 8:13:50 AM9/10/18

to HAPI FHIR

Hi all,

I'm new to this HAPI project.

I'm trying to get the Spring Boot JPA example up and a running with PostgesSQL, unfortunately I've not been able to so far and I wonder if anyone here could give me some hints. The stack trace is below as well as my POM. Any help will be appreciated.

Kind regards,

Daniel

POM ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

<?xml version="1.0" encoding="UTF-8"?>

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">

<groupId>com.company</groupId>

<artifactId>hapi-fhir-example</artifactId>

<version>0.0.1-SNAPSHOT</version>

<name>hapi-fhir-example</name>

<groupId>org.springframework.boot</groupId>

<artifactId>spring-boot-starter-parent</artifactId>

<version>1.5.6.RELEASE</version>

</parent>

<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

<java.version>1.8</java.version>

<hapi.fhir.version>3.4.0</hapi.fhir.version>

</properties>

<groupId>org.springframework.boot</groupId>

<artifactId>spring-boot-starter-web</artifactId>

</dependency>

<groupId>org.springframework.boot</groupId>

<artifactId>spring-boot-starter-actuator</artifactId>

</dependency>

<groupId>org.springframework.boot</groupId>

<artifactId>spring-boot-starter-data-jpa</artifactId>

</dependency>

<groupId>org.springframework.boot</groupId>

<artifactId>spring-boot-configuration-processor</artifactId>

</dependency>

<groupId>org.postgresql</groupId>

<artifactId>postgresql</artifactId>

</dependency>

<groupId>com.github.dnault</groupId>

<artifactId>xml-patch</artifactId>

</dependency>

<artifactId>hapi-fhir-spring-boot-starter</artifactId>

<version>${hapi.fhir.version}</version>

</dependency>

<artifactId>hapi-fhir-spring-boot-autoconfigure</artifactId>

<version>${hapi.fhir.version}</version>

</dependency>

<artifactId>hapi-fhir-jaxrsserver-base</artifactId>

<version>${hapi.fhir.version}</version>

</dependency>

<artifactId>hapi-fhir-jpaserver-base</artifactId>

<version>${hapi.fhir.version}</version>

</dependency>

<groupId>org.springframework.boot</groupId>

<artifactId>spring-boot-starter-test</artifactId>

</dependency>

</dependencies>

<build>

<groupId>org.springframework.boot</groupId>

<artifactId>spring-boot-maven-plugin</artifactId>

</plugin>

</plugins>

</build>

</project>

OUTPUT ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

. ____ _ __ _ _

/\\ / ___'_ __ _ _(_)_ __ __ _ \ \ \ \

( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \

\\/ ___)| |_)| | | | | || (_| | ) ) ) )

' |____| .__|_| |_|_| |_\__, | / / / /

=========|_|==============|___/=/_/_/_/

:: Spring Boot :: (v1.5.6.RELEASE)

13:01:26.162 INFO c.b.i.h.HapiFhirExampleApplication [] - Starting HapiFhirExampleApplication on B-1198.local with PID 53390 (/Users/user/ved/workspace/hapi-fhir-example/target/classes started by user in /Users/user/ved/workspace/hapi-fhir-example)

13:01:26.164 DEBUG c.b.i.h.HapiFhirExampleApplication [] - Running with Spring Boot v1.5.6.RELEASE, Spring v4.3.10.RELEASE

13:01:26.164 INFO c.b.i.h.HapiFhirExampleApplication [] - No active profile set, falling back to default profiles: default

13:01:26.225 INFO o.s.b.c.e.AnnotationConfigEmbeddedWebApplicationContext [] - Refreshing org.springframework.boot.context.embedded.AnnotationConfigEmbeddedWebApplicationContext@399c4be1: startup date [Mon Sep 10 13:01:26 BST 2018]; root of context hierarchy

13:01:26.298 INFO o.h.validator.internal.util.Version [] - HV000001: Hibernate Validator 5.3.5.Final

13:01:27.088 INFO o.s.b.f.s.DefaultListableBeanFactory [] - Overriding bean definition for bean 'propertySourcesPlaceholderConfigurer' with a different definition: replacing [Root bean: class [org.springframework.boot.autoconfigure.context.PropertyPlaceholderAutoConfiguration]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=propertySourcesPlaceholderConfigurer; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [org/springframework/boot/autoconfigure/context/PropertyPlaceholderAutoConfiguration.class]] with [Root bean: class [ca.uhn.fhir.spring.boot.autoconfigure.FhirAutoConfiguration$FhirJpaServerConfiguration$Dstu3]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=null; factoryMethodName=propertySourcesPlaceholderConfigurer; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [ca/uhn/fhir/spring/boot/autoconfigure/FhirAutoConfiguration$FhirJpaServerConfiguration$Dstu3.class]]

13:01:27.598 INFO o.s.b.f.s.DefaultListableBeanFactory [] - Overriding bean definition for bean 'hapiJpaTaskExecutor' with a different definition: replacing [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=ca.uhn.fhir.spring.boot.autoconfigure.FhirAutoConfiguration$FhirJpaServerConfiguration$Dstu3; factoryMethodName=taskScheduler; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [ca/uhn/fhir/spring/boot/autoconfigure/FhirAutoConfiguration$FhirJpaServerConfiguration$Dstu3.class]] with [Root bean: class [null]; scope=; abstract=false; lazyInit=false; autowireMode=3; dependencyCheck=0; autowireCandidate=true; primary=false; factoryBeanName=ca.uhn.fhir.spring.boot.autoconfigure.FhirAutoConfiguration$FhirJpaServerConfiguration; factoryMethodName=taskScheduler; initMethodName=null; destroyMethodName=(inferred); defined in class path resource [ca/uhn/fhir/spring/boot/autoconfigure/FhirAutoConfiguration$FhirJpaServerConfiguration.class]]

13:01:28.392 INFO o.s.b.c.e.t.TomcatEmbeddedServletContainer [] - Tomcat initialized with port(s): 9000 (http)

13:01:28.399 INFO o.a.catalina.core.StandardService [] - Starting service [Tomcat]

13:01:28.399 INFO o.a.catalina.core.StandardEngine [] - Starting Servlet Engine: Apache Tomcat/8.5.16

13:01:28.505 INFO o.a.c.c.C.[Tomcat].[localhost].[/] [] - Initializing Spring embedded WebApplicationContext

13:01:28.505 INFO o.s.web.context.ContextLoader [] - Root WebApplicationContext: initialization completed in 2285 ms

13:01:28.735 INFO ca.uhn.fhir.util.VersionUtil [] - HAPI FHIR version is: 3.4.0

13:01:28.737 INFO ca.uhn.fhir.context.FhirContext [] - Creating new FHIR context for FHIR version [DSTU3]

13:01:29.141 INFO o.s.o.j.LocalContainerEntityManagerFactoryBean [] - Building JPA container EntityManagerFactory for persistence unit 'default'

13:01:29.148 INFO o.h.jpa.internal.util.LogHelper [] - HHH000204: Processing PersistenceUnitInfo [

name: default

...]

13:01:29.191 INFO org.hibernate.Version [] - HHH000412: Hibernate Core {5.0.12.Final}

13:01:29.192 INFO org.hibernate.cfg.Environment [] - HHH000206: hibernate.properties not found

13:01:29.192 INFO org.hibernate.cfg.Environment [] - HHH000021: Bytecode provider name : javassist

13:01:29.218 INFO o.h.annotations.common.Version [] - HCANN000001: Hibernate Commons Annotations {5.0.1.Final}

13:01:29.379 INFO org.hibernate.dialect.Dialect [] - HHH000400: Using dialect: org.hibernate.dialect.PostgreSQLDialect

13:01:29.621 INFO o.h.e.j.e.i.LobCreatorBuilderImpl [] - HHH000424: Disabling contextual LOB creation as createClob() method threw error : java.lang.reflect.InvocationTargetException

13:01:29.622 INFO org.hibernate.type.BasicTypeRegistry [] - HHH000270: Type registration [java.util.UUID] overrides previous : org.hibernate.type.UUIDBinaryType@5c56d3d

13:01:29.784 WARN org.hibernate.orm.deprecation [] - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

13:01:29.786 WARN org.hibernate.orm.deprecation [] - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

13:01:29.787 WARN org.hibernate.orm.deprecation [] - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

13:01:29.788 WARN org.hibernate.orm.deprecation [] - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

13:01:29.789 WARN org.hibernate.orm.deprecation [] - HHH90000014: Found use of deprecated [org.hibernate.id.SequenceGenerator] sequence-based id generator; use org.hibernate.id.enhanced.SequenceStyleGenerator instead. See Hibernate Domain Model Mapping Guide for details.

13:01:29.986 INFO org.hibernate.search.engine.Version [] - HSEARCH000034: Hibernate Search 5.7.1.Final

13:01:30.274 INFO o.h.tool.hbm2ddl.SchemaUpdate [] - HHH000228: Running hbm2ddl schema update

13:01:32.031 INFO o.h.s.s.impl.DirectoryProviderHelper [] - HSEARCH000041: Index directory not found, creating: 'target/lucenefiles'

13:01:32.032 INFO o.h.s.s.impl.DirectoryProviderHelper [] - HSEARCH000041: Index directory not found, creating: 'target/lucenefiles/ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString'

13:01:32.153 INFO o.h.s.s.impl.DirectoryProviderHelper [] - HSEARCH000041: Index directory not found, creating: 'target/lucenefiles/ca.uhn.fhir.jpa.entity.ResourceTable'

13:01:32.162 INFO o.h.s.s.impl.DirectoryProviderHelper [] - HSEARCH000041: Index directory not found, creating: 'target/lucenefiles/ca.uhn.fhir.jpa.entity.TermConcept'

13:01:32.235 INFO o.s.o.j.LocalContainerEntityManagerFactoryBean [] - Initialized JPA EntityManagerFactory for persistence unit 'default'

13:01:32.506 INFO o.h.h.i.QueryTranslatorFactoryInitiator [] - HHH000397: Using ASTQueryTranslatorFactory

13:01:32.969 ERROR o.h.hql.internal.ast.ErrorCounter [] - Path expected for join!

13:01:32.970 ERROR o.h.hql.internal.ast.ErrorCounter [] - Path expected for join!

antlr.SemanticException: Path expected for join!

at org.hibernate.hql.internal.ast.HqlSqlWalker.createFromJoinElement(HqlSqlWalker.java:368)

at org.hibernate.hql.internal.antlr.HqlSqlBaseWalker.joinElement(HqlSqlBaseWalker.java:3912)

at org.hibernate.hql.internal.antlr.HqlSqlBaseWalker.fromElement(HqlSqlBaseWalker.java:3698)

at org.hibernate.hql.internal.antlr.HqlSqlBaseWalker.fromElementList(HqlSqlBaseWalker.java:3576)

at org.hibernate.hql.internal.antlr.HqlSqlBaseWalker.fromClause(HqlSqlBaseWalker.java:716)

at org.hibernate.hql.internal.antlr.HqlSqlBaseWalker.query(HqlSqlBaseWalker.java:572)

at org.hibernate.hql.internal.antlr.HqlSqlBaseWalker.selectStatement(HqlSqlBaseWalker.java:309)

at org.hibernate.hql.internal.antlr.HqlSqlBaseWalker.statement(HqlSqlBaseWalker.java:257)

at org.hibernate.hql.internal.ast.QueryTranslatorImpl.analyze(QueryTranslatorImpl.java:262)

at org.hibernate.hql.internal.ast.QueryTranslatorImpl.doCompile(QueryTranslatorImpl.java:190)

at org.hibernate.hql.internal.ast.QueryTranslatorImpl.compile(QueryTranslatorImpl.java:142)

at org.hibernate.engine.query.spi.HQLQueryPlan.<init>(HQLQueryPlan.java:115)

at org.hibernate.engine.query.spi.HQLQueryPlan.<init>(HQLQueryPlan.java:76)

at org.hibernate.engine.query.spi.QueryPlanCache.getHQLQueryPlan(QueryPlanCache.java:150)

at org.hibernate.internal.AbstractSessionImpl.getHQLQueryPlan(AbstractSessionImpl.java:302)

at org.hibernate.internal.AbstractSessionImpl.createQuery(AbstractSessionImpl.java:240)

at org.hibernate.internal.SessionImpl.createQuery(SessionImpl.java:1894)

at org.hibernate.jpa.spi.AbstractEntityManagerImpl.createQuery(AbstractEntityManagerImpl.java:291)

at sun.reflect.GeneratedMethodAccessor48.invoke(Unknown Source)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.springframework.orm.jpa.ExtendedEntityManagerCreator$ExtendedEntityManagerInvocationHandler.invoke(ExtendedEntityManagerCreator.java:347)

at com.sun.proxy.$Proxy124.createQuery(Unknown Source)

at org.springframework.data.jpa.repository.query.SimpleJpaQuery.validateQuery(SimpleJpaQuery.java:86)

at org.springframework.data.jpa.repository.query.SimpleJpaQuery.<init>(SimpleJpaQuery.java:62)

at org.springframework.data.jpa.repository.query.JpaQueryFactory.fromMethodWithQueryString(JpaQueryFactory.java:72)

at org.springframework.data.jpa.repository.query.JpaQueryFactory.fromQueryAnnotation(JpaQueryFactory.java:53)

at org.springframework.data.jpa.repository.query.JpaQueryLookupStrategy$DeclaredQueryLookupStrategy.resolveQuery(JpaQueryLookupStrategy.java:144)

at org.springframework.data.jpa.repository.query.JpaQueryLookupStrategy$CreateIfNotFoundQueryLookupStrategy.resolveQuery(JpaQueryLookupStrategy.java:212)

at org.springframework.data.jpa.repository.query.JpaQueryLookupStrategy$AbstractQueryLookupStrategy.resolveQuery(JpaQueryLookupStrategy.java:77)

at org.springframework.data.repository.core.support.RepositoryFactorySupport$QueryExecutorMethodInterceptor.<init>(RepositoryFactorySupport.java:436)

at org.springframework.data.repository.core.support.RepositoryFactorySupport.getRepository(RepositoryFactorySupport.java:221)

at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.initAndReturn(RepositoryFactoryBeanSupport.java:277)

at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.afterPropertiesSet(RepositoryFactoryBeanSupport.java:263)

at org.springframework.data.jpa.repository.support.JpaRepositoryFactoryBean.afterPropertiesSet(JpaRepositoryFactoryBean.java:101)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1687)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1624)

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:202)

at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:208)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1138)

at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1066)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:585)

at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88)

at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:366)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1264)

at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:553)