hapi fhir jpaserver starter project create resources error

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Kyeoung-Vin

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Jul 28, 2020, 9:56:22 PM7/28/20

to HAPI FHIR

Hi,

I am a Korean developer who is new to HAPI FHIR this time.

So, please understand that I am not good at English.

I'm using hapi-fhir-jpaserver-starter project with my personal configuration.

And I implemented hapi fhir jpaserver starter server :)

But when I try to create patient example resource(https://www.hl7.org/fhir/patient-example.json.html) in this page,

I receive this message:

2020-07-29 10:51:41.944 [http-nio-8080-exec-2] ERROR o.h.id.enhanced.TableStructure [TableStructure.java:141] could not read a hi value - you need to populate the table: SEQ_SPIDX_STRING
2020-07-29 10:51:41.946 [http-nio-8080-exec-2] ERROR c.u.f.r.s.i.ExceptionHandlingInterceptor [ExceptionHandlingInterceptor.java:140] Failure during REST processing
ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method: org.springframework.orm.jpa.JpaSystemException: could not read a hi value - you need to populate the table: SEQ_SPIDX_STRING; nested exception is org.hibernate.id.IdentifierGenerationException: could not read a hi value - you need to populate the table: SEQ_SPIDX_STRING
	at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:250)
	at ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBinding.invokeServer(BaseOutcomeReturningMethodBinding.java:154)
	at ca.uhn.fhir.rest.server.method.CreateMethodBinding.invokeServer(CreateMethodBinding.java:41)
	at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:1029)
	at ca.uhn.fhir.rest.server.RestfulServer.doPost(RestfulServer.java:373)
	at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1728)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:733)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:690)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
	at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:373)
	at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
	at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1589)
	at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: java.lang.reflect.InvocationTargetException: null
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:245)
	... 28 common frames omitted
Caused by: org.springframework.orm.jpa.JpaSystemException: could not read a hi value - you need to populate the table: SEQ_SPIDX_STRING; nested exception is org.hibernate.id.IdentifierGenerationException: could not read a hi value - you need to populate the table: SEQ_SPIDX_STRING
	at org.springframework.orm.jpa.vendor.HibernateJpaDialect.convertHibernateAccessException(HibernateJpaDialect.java:353)
	at ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.convertHibernateAccessException(HapiFhirHibernateJpaDialect.java:105)
	at ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.convertHibernateAccessException(HapiFhirHibernateJpaDialect.java:62)
	at org.springframework.orm.jpa.vendor.HibernateJpaDialect.translateExceptionIfPossible(HibernateJpaDialect.java:255)
	at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.translateExceptionIfPossible(AbstractEntityManagerFactoryBean.java:528)
	at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:61)
	at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:242)
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:153)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:366)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:99)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
	at com.sun.proxy.$Proxy202.create(Unknown Source)
	at ca.uhn.fhir.jpa.provider.r4.JpaResourceProviderR4.create(JpaResourceProviderR4.java:71)
	... 33 common frames omitted
Caused by: org.hibernate.id.IdentifierGenerationException: could not read a hi value - you need to populate the table: SEQ_SPIDX_STRING
	at org.hibernate.id.enhanced.TableStructure$1$1.execute(TableStructure.java:142)
	at org.hibernate.id.enhanced.TableStructure$1$1.execute(TableStructure.java:126)
	at org.hibernate.jdbc.WorkExecutor.executeReturningWork(WorkExecutor.java:55)
	at org.hibernate.jdbc.AbstractReturningWork.accept(AbstractReturningWork.java:34)
	at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:57)
	at org.hibernate.id.enhanced.TableStructure$1.getNextValue(TableStructure.java:125)
	at org.hibernate.id.enhanced.PooledOptimizer.generate(PooledOptimizer.java:73)
	at org.hibernate.id.enhanced.SequenceStyleGenerator.generate(SequenceStyleGenerator.java:523)
	at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:115)
	at org.hibernate.event.internal.DefaultMergeEventListener.saveTransientEntity(DefaultMergeEventListener.java:271)
	at org.hibernate.event.internal.DefaultMergeEventListener.entityIsTransient(DefaultMergeEventListener.java:243)
	at org.hibernate.event.internal.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:175)
	at org.hibernate.event.internal.DefaultMergeEventListener.onMerge(DefaultMergeEventListener.java:70)
	at org.hibernate.event.service.internal.EventListenerGroupImpl.fireEventOnEachListener(EventListenerGroupImpl.java:102)
	at org.hibernate.internal.SessionImpl.fireMerge(SessionImpl.java:783)
	at org.hibernate.internal.SessionImpl.merge(SessionImpl.java:770)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:314)
	at com.sun.proxy.$Proxy93.merge(Unknown Source)
	at ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer.synchronize(DaoSearchParamSynchronizer.java:84)
	at ca.uhn.fhir.jpa.dao.index.DaoSearchParamSynchronizer.synchronizeSearchParamsToDatabase(DaoSearchParamSynchronizer.java:54)
	at ca.uhn.fhir.jpa.dao.BaseHapiFhirDao.updateEntity(BaseHapiFhirDao.java:1194)
	at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.doCreate(BaseHapiFhirResourceDao.java:520)
	at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.create(BaseHapiFhirResourceDao.java:221)
	at ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.create(BaseHapiFhirResourceDao.java:190)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
	at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:139)
	... 40 common frames omitted

Please help me how to fix this problem.

Thanks in advance.

Kyeoung vin (a.k.a Penny)

Keerthivasan Ramanathan

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Jul 29, 2020, 12:51:04 AM7/29/20

to HAPI FHIR

Are you using your own id? Looks like its a problem with id generation

org.hibernate.id.IdentifierGenerationException: could not read a hi value - you need to populate the table ?

KyeoungVin

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Jul 29, 2020, 1:43:06 AM7/29/20

to HAPI FHIR

I am using MySQL as a DB and accessing it using my own ID.

Nothing has been touched except hapi.properties.

What ID are you talking about?

I only touched here:

datasource.driver=com.mysql.jdbc.Driver

datasource.url=jdbc:mysql://localhost:9000/dbhapi

datasource.username=root

datasource.password=1234

hibernate.dialect=org.hibernate.dialect.MySQL5InnoDBDialect

2020년 7월 29일 수요일 오후 1시 51분 4초 UTC+9, Keerthivasan Ramanathan 님의 말:

Keerthivasan Ramanathan

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Jul 29, 2020, 1:53:28 AM7/29/20

to HAPI FHIR

Hi, I am talking about the Patient resource id, Can you post the full resource 'Patient', you are trying to create?

KyeoungVin

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Jul 29, 2020, 2:15:31 AM7/29/20

to HAPI FHIR

Oh...

This is the full resource I used :

{
  "resourceType": "Patient",
  "id": "example",
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n\t\t\t<table>\n\t\t\t\t<tbody>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Name</td>\n\t\t\t\t\t\t<td>Peter James \n              <b>Chalmers</b> (&quot;Jim&quot;)\n            </td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Address</td>\n\t\t\t\t\t\t<td>534 Erewhon, Pleasantville, Vic, 3999</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Contacts</td>\n\t\t\t\t\t\t<td>Home: unknown. Work: (03) 5555 6473</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Id</td>\n\t\t\t\t\t\t<td>MRN: 12345 (Acme Healthcare)</td>\n\t\t\t\t\t</tr>\n\t\t\t\t</tbody>\n\t\t\t</table>\n\t\t</div>"
  },
  "identifier": [
    {
      "use": "usual",
      "type": {
        "coding": [
          {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
            "code": "MR"
          }
        ]
      },
      "system": "urn:oid:1.2.36.146.595.217.0.1",
      "value": "12345",
      "period": {
        "start": "2001-05-06"
      },
      "assigner": {
        "display": "Acme Healthcare"
      }
    }
  ],
  "active": true,
  "name": [
    {
      "use": "official",
      "family": "Chalmers",
      "given": [
        "Peter",
        "James"
      ]
    },
    {
      "use": "usual",
      "given": [
        "Jim"
      ]
    },
    {
      "use": "maiden",
      "family": "Windsor",
      "given": [
        "Peter",
        "James"
      ],
      "period": {
        "end": "2002"
      }
    }
  ],
  "telecom": [
    {
      "use": "home"
    },
    {
      "system": "phone",
      "value": "(03) 5555 6473",
      "use": "work",
      "rank": 1
    },
    {
      "system": "phone",
      "value": "(03) 3410 5613",
      "use": "mobile",
      "rank": 2
    },
    {
      "system": "phone",
      "value": "(03) 5555 8834",
      "use": "old",
      "period": {
        "end": "2014"
      }
    }
  ],
  "gender": "male",
  "birthDate": "1974-12-25",
  "_birthDate": {
    "extension": [
      {
        "url": "http://hl7.org/fhir/StructureDefinition/patient-birthTime",
        "valueDateTime": "1974-12-25T14:35:45-05:00"
      }
    ]
  },
  "deceasedBoolean": false,
  "address": [
    {
      "use": "home",
      "type": "both",
      "text": "534 Erewhon St PeasantVille, Rainbow, Vic  3999",
      "line": [
        "534 Erewhon St"
      ],
      "city": "PleasantVille",
      "district": "Rainbow",
      "state": "Vic",
      "postalCode": "3999",
      "period": {
        "start": "1974-12-25"
      }
    }
  ],
  "contact": [
    {
      "relationship": [
        {
          "coding": [
            {
              "system": "http://terminology.hl7.org/CodeSystem/v2-0131",
              "code": "N"
            }
          ]
        }
      ],
      "name": {
        "family": "du Marché",
        "_family": {
          "extension": [
            {
              "url": "http://hl7.org/fhir/StructureDefinition/humanname-own-prefix",
              "valueString": "VV"
            }
          ]
        },
        "given": [
          "Bénédicte"
        ]
      },
      "telecom": [
        {
          "system": "phone",
          "value": "+33 (237) 998327"
        }
      ],
      "address": {
        "use": "home",
        "type": "both",
        "line": [
          "534 Erewhon St"
        ],
        "city": "PleasantVille",
        "district": "Rainbow",
        "state": "Vic",
        "postalCode": "3999",
        "period": {
          "start": "1974-12-25"
        }
      },
      "gender": "female",
      "period": {
        "start": "2012"
      }
    }
  ],
  "managingOrganization": {
    "reference": "Organization/1"
  }
}

This resource was taken from https://www.hl7.org/fhir/patient-examples.html

2020년 7월 29일 수요일 오후 2시 53분 28초 UTC+9, Keerthivasan Ramanathan 님의 말:

James Agnew

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Jul 29, 2020, 6:00:54 AM7/29/20

to KyeoungVin, HAPI FHIR

Hibernate uses a table called "hibernate_sequences" to manage ID generation on MySQL (as it doesn't support native sequences for some reason).

That error looks like the sequence table is missing or didn't get initialized properly by the system. If by chance you are upgrading and didn't run the migrator, that might cause this. If you are starting fresh, I might recommend trying deleting your database entirely and starting with an empty schema so that it will recreate everything it needs.

Cheers,

James

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KyeoungVin

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Jul 30, 2020, 2:32:45 AM7/30/20

to HAPI FHIR

OMG It works!!

This is so helpful, thanks a lot XD

Thanks,

Penny

2020년 7월 29일 수요일 오후 7시 0분 54초 UTC+9, James Agnew 님의 말:

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revathi vadlamudi

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Feb 10, 2021, 7:27:21 AM2/10/21

to HAPI FHIR

Hi,

Me too facing the same issue. I am starting hapi fhir project by creating new spring boot project and adding dependencies related to hapi fhir. I would like to use MySQL database.

@WebServlet("/*")

public class HapiRestfulServer extends RestfulServer{

@Override

protected void initialize()throws ServletException{

super.initialize();

setFhirContext(FhirContext.forR5());

registerProvider(new PatientResourceProvider() { });

}

package com.hapifhir;

import org.springframework.beans.factory.annotation.Autowired;

import org.springframework.beans.factory.config.AutowireCapableBeanFactory;

import org.springframework.boot.SpringApplication;

import org.springframework.boot.autoconfigure.SpringBootApplication;

import org.springframework.boot.autoconfigure.elasticsearch.ElasticsearchRestClientAutoConfiguration;

import org.springframework.boot.web.servlet.ServletComponentScan;

import org.springframework.context.annotation.Bean;

import org.springframework.data.jpa.repository.config.EnableJpaRepositories;

import ca.uhn.fhir.context.FhirContext;

import ca.uhn.fhir.jpa.api.config.DaoConfig;

@ServletComponentScan(basePackageClasses = {

HapiRestfulServer.class})

@SpringBootApplication(exclude = {ElasticsearchRestClientAutoConfiguration.class})

@EnableJpaRepositories

public class HapiFhirApplication {

public static void main(String[] args) {

SpringApplication.run(HapiFhirApplication.class, args);

}

@Bean

public FhirContext fhirContext() {

return FhirContext.forR5();

}

@Bean

public DaoConfig daoConfig() {

DaoConfig retVal = new DaoConfig();

retVal.getTreatBaseUrlsAsLocal().add("http://localhost:8080/");

return retVal;

}

@Autowired

AutowireCapableBeanFactory beanFactory;

}

application.properties

spring.jpa.hibernate.ddl-auto=update

spring.h2.console.enabled=true

spring.datasource.url=jdbc:mysql://localhost:3307/test

spring.datasource.username=root

spring.datasource.password=mysql

spring.jpa.database-platform=org.hibernate.dialect.MySQL5Dialect

spring.jpa.show-sql=false

spring.jpa.properties.hibernate.dialect=org.hibernate.dialect.MySQL5Dialect

server.error.whitelabel.enabled=false

POM.XML

<?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 https://maven.apache.org/xsd/maven-4.0.0.xsd">

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

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

</parent>

<version>0.0.1-SNAPSHOT</version>

<name>HapiFhir</name>

<description>Hapi FHIR project for Spring Boot</description>

<java.version>8</java.version>

<hibernate_version>5.4.26.Final</hibernate_version>

<hibernate_search_version>6.0.0.Final</hibernate_search_version>

<elastic_apm_version>1.13.0</elastic_apm_version>

</properties>

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

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

</dependency>

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

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

</dependency>

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

<artifactId>spring-boot-starter-jdbc</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.springframework.boot</groupId>

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

</dependency>

<!-- <dependency>

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

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

</dependency> -->

<groupId>mysql</groupId>

<artifactId>mysql-connector-java</artifactId>

<scope>runtime</scope>

</dependency>

<groupId>org.apache.lucene</groupId>

<artifactId>lucene-analyzers</artifactId>

</dependency>

<version>5.3.0-SNAPSHOT</version>

</dependency>

<artifactId>hapi-fhir-structures-r5</artifactId>

<version>5.3.0-SNAPSHOT</version>

</dependency>

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

<version>5.3.0-SNAPSHOT</version>

</dependency>

<!-- <dependency>

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

<version>5.3.0-SNAPSHOT</version>

</dependency>

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

</dependency> -->

<groupId>org.apache.commons</groupId>

<artifactId>commons-dbcp2</artifactId>

</dependency>

</dependencies>

<build>

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

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

</plugin>

</plugins>

</build>

</project>

Console

. ____ _ __ _ _

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

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

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

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

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

:: Spring Boot :: (v2.4.1)

2021-02-10 17:13:47.940 INFO 5212 --- [ main] com.hapifhir.HapiFhirApplication : Starting HapiFhirApplication using Java 1.8.0_151 on Sekhar with PID 5212 (C:\Users\revathi\Downloads\hapi-fhir (1)\hapi-fhir\target\classes started by revathi in C:\Users\revathi\Downloads\hapi-fhir (1)\hapi-fhir)

2021-02-10 17:13:47.947 INFO 5212 --- [ main] com.hapifhir.HapiFhirApplication : No active profile set, falling back to default profiles: default

2021-02-10 17:13:50.027 INFO 5212 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Multiple Spring Data modules found, entering strict repository configuration mode!

2021-02-10 17:13:50.028 INFO 5212 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data JPA repositories in DEFAULT mode.

2021-02-10 17:13:50.091 INFO 5212 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 44 ms. Found 0 JPA repository interfaces.

2021-02-10 17:13:50.481 INFO 5212 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Multiple Spring Data modules found, entering strict repository configuration mode!

2021-02-10 17:13:50.481 INFO 5212 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Bootstrapping Spring Data JDBC repositories in DEFAULT mode.

2021-02-10 17:13:50.489 INFO 5212 --- [ main] .s.d.r.c.RepositoryConfigurationDelegate : Finished Spring Data repository scanning in 7 ms. Found 0 JDBC repository interfaces.

2021-02-10 17:13:51.841 INFO 5212 --- [ main] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat initialized with port(s): 8080 (http)

2021-02-10 17:13:51.871 INFO 5212 --- [ main] o.apache.catalina.core.StandardService : Starting service [Tomcat]

2021-02-10 17:13:51.871 INFO 5212 --- [ main] org.apache.catalina.core.StandardEngine : Starting Servlet engine: [Apache Tomcat/9.0.41]

2021-02-10 17:13:52.141 INFO 5212 --- [ main] o.a.c.c.C.[Tomcat].[localhost].[/] : Initializing Spring embedded WebApplicationContext

2021-02-10 17:13:52.141 INFO 5212 --- [ main] w.s.c.ServletWebServerApplicationContext : Root WebApplicationContext: initialization completed in 4004 ms

2021-02-10 17:13:52.313 INFO 5212 --- [ main] ca.uhn.fhir.util.VersionUtil : HAPI FHIR version 5.3.0-SNAPSHOT - Rev 7f127f75f9/2021-02-09

2021-02-10 17:13:53.053 INFO 5212 --- [ main] o.hibernate.jpa.internal.util.LogHelper : HHH000204: Processing PersistenceUnitInfo [name: default]

2021-02-10 17:13:53.371 INFO 5212 --- [ main] org.hibernate.Version : HHH000412: Hibernate ORM core version 5.4.25.Final

2021-02-10 17:13:53.764 INFO 5212 --- [ main] o.hibernate.annotations.common.Version : HCANN000001: Hibernate Commons Annotations {5.1.2.Final}

2021-02-10 17:13:54.132 INFO 5212 --- [ main] com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Starting...

2021-02-10 17:13:54.560 INFO 5212 --- [ main] com.zaxxer.hikari.HikariDataSource : HikariPool-1 - Start completed.

2021-02-10 17:13:54.611 INFO 5212 --- [ main] org.hibernate.dialect.Dialect : HHH000400: Using dialect: org.hibernate.dialect.MySQL5Dialect

2021-02-10 17:13:55.616 INFO 5212 --- [ main] o.h.s.m.o.b.i.HibernateSearchIntegrator : HSEARCH000034: Hibernate Search version 6.0.0.Final

2021-02-10 17:13:56.290 INFO 5212 --- [ main] o.h.e.t.j.p.i.JtaPlatformInitiator : HHH000490: Using JtaPlatform implementation: [org.hibernate.engine.transaction.jta.platform.internal.NoJtaPlatform]

2021-02-10 17:13:56.740 INFO 5212 --- [ main] j.LocalContainerEntityManagerFactoryBean : Initialized JPA EntityManagerFactory for persistence unit 'default'

2021-02-10 17:13:56.879 INFO 5212 --- [ main] ca.uhn.fhir.context.FhirContext : Creating new FHIR context for FHIR version [R5]

2021-02-10 17:13:57.096 WARN 5212 --- [ main] JpaBaseConfiguration$JpaWebConfiguration : spring.jpa.open-in-view is enabled by default. Therefore, database queries may be performed during view rendering. Explicitly configure spring.jpa.open-in-view to disable this warning

2021-02-10 17:13:57.384 INFO 5212 --- [ main] o.s.s.concurrent.ThreadPoolTaskExecutor : Initializing ExecutorService 'applicationTaskExecutor'

2021-02-10 17:13:57.690 INFO 5212 --- [ main] o.s.b.a.w.s.WelcomePageHandlerMapping : Adding welcome page: class path resource [static/index.html]

2021-02-10 17:13:57.873 WARN 5212 --- [ main] ion$DefaultTemplateResolverConfiguration : Cannot find template location: classpath:/templates/ (please add some templates or check your Thymeleaf configuration)

2021-02-10 17:13:58.327 INFO 5212 --- [ main] org.quartz.impl.StdSchedulerFactory : Using default implementation for ThreadExecutor

2021-02-10 17:13:58.396 INFO 5212 --- [ main] org.quartz.core.SchedulerSignalerImpl : Initialized Scheduler Signaller of type: class org.quartz.core.SchedulerSignalerImpl

2021-02-10 17:13:58.397 INFO 5212 --- [ main] org.quartz.core.QuartzScheduler : Quartz Scheduler v.2.3.2 created.

2021-02-10 17:13:58.399 INFO 5212 --- [ main] org.quartz.simpl.RAMJobStore : RAMJobStore initialized.

2021-02-10 17:13:58.402 INFO 5212 --- [ main] org.quartz.core.QuartzScheduler : Scheduler meta-data: Quartz Scheduler (v2.3.2) 'quartzScheduler' with instanceId 'NON_CLUSTERED'

Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.

NOT STARTED.

Currently in standby mode.

Number of jobs executed: 0

Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 10 threads.

Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.

2021-02-10 17:13:58.403 INFO 5212 --- [ main] org.quartz.impl.StdSchedulerFactory : Quartz scheduler 'quartzScheduler' initialized from an externally provided properties instance.

2021-02-10 17:13:58.404 INFO 5212 --- [ main] org.quartz.impl.StdSchedulerFactory : Quartz scheduler version: 2.3.2

2021-02-10 17:13:58.404 INFO 5212 --- [ main] org.quartz.core.QuartzScheduler : JobFactory set to: org.springframework.scheduling.quartz.SpringBeanJobFactory@31859960

2021-02-10 17:13:58.618 INFO 5212 --- [ main] o.s.b.w.embedded.tomcat.TomcatWebServer : Tomcat started on port(s): 8080 (http) with context path ''

2021-02-10 17:13:58.626 INFO 5212 --- [ main] o.s.s.quartz.SchedulerFactoryBean : Starting Quartz Scheduler now

2021-02-10 17:13:58.630 INFO 5212 --- [ main] org.quartz.core.QuartzScheduler : Scheduler quartzScheduler_$_NON_CLUSTERED started.

2021-02-10 17:13:58.767 INFO 5212 --- [ main] com.hapifhir.HapiFhirApplication : Started HapiFhirApplication in 12.157 seconds (JVM running for 15.56)

2021-02-10 17:14:04.857 INFO 5212 --- [nio-8080-exec-1] ca.uhn.fhir.context.FhirContext : Creating new FHIR context for FHIR version [R5]

2021-02-10 17:14:47.047 INFO 5212 --- [nio-8080-exec-1] ca.uhn.fhir.rest.server.RestfulServer : Initializing HAPI FHIR restful server running in R5 mode

2021-02-10 17:14:57.747 INFO 5212 --- [nio-8080-exec-1] ca.uhn.fhir.rest.server.RestfulServer : Added 1 resource provider(s). Total 1

2021-02-10 17:15:20.821 INFO 5212 --- [nio-8080-exec-1] ca.uhn.fhir.rest.server.RestfulServer : A FHIR has been lit on this server

2021-02-10 17:15:54.447 ERROR 5212 --- [nio-8080-exec-1] c.u.f.r.s.i.ExceptionHandlingInterceptor : Failure during REST processing

ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method: java.lang.NullPointerException

at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:250) ~[hapi-fhir-server-5.3.0-SNAPSHOT.jar:na]

at ca.uhn.fhir.rest.server.method.BaseOutcomeReturningMethodBinding.invokeServer(BaseOutcomeReturningMethodBinding.java:154) ~[hapi-fhir-server-5.3.0-SNAPSHOT.jar:na]

at ca.uhn.fhir.rest.server.method.CreateMethodBinding.invokeServer(CreateMethodBinding.java:41) ~[hapi-fhir-server-5.3.0-SNAPSHOT.jar:na]

at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:1068) [hapi-fhir-server-5.3.0-SNAPSHOT.jar:na]

at ca.uhn.fhir.rest.server.RestfulServer.doPost(RestfulServer.java:387) [hapi-fhir-server-5.3.0-SNAPSHOT.jar:na]

at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1765) [hapi-fhir-server-5.3.0-SNAPSHOT.jar:na]

at javax.servlet.http.HttpServlet.service(HttpServlet.java:733) [tomcat-embed-core-9.0.41.jar:4.0.FR]

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) [tomcat-embed-websocket-9.0.41.jar:9.0.41]

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100) [spring-web-5.3.2.jar:5.3.2]

at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) [spring-web-5.3.2.jar:5.3.2]

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.springframework.web.filter.FormContentFilter.doFilterInternal(FormContentFilter.java:93) [spring-web-5.3.2.jar:5.3.2]

at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) [spring-web-5.3.2.jar:5.3.2]

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) [spring-web-5.3.2.jar:5.3.2]

at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) [spring-web-5.3.2.jar:5.3.2]

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:542) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:143) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:374) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:888) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1597) [tomcat-embed-core-9.0.41.jar:9.0.41]

at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat-embed-core-9.0.41.jar:9.0.41]

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_151]

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_151]

at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-embed-core-9.0.41.jar:9.0.41]

at java.lang.Thread.run(Thread.java:748) [na:1.8.0_151]

Caused by: java.lang.reflect.InvocationTargetException: null

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_151]

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_151]

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_151]

at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_151]

at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:245) ~[hapi-fhir-server-5.3.0-SNAPSHOT.jar:na]

... 39 common frames omitted

Caused by: java.lang.NullPointerException: null

at ca.uhn.fhir.jpa.provider.r5.JpaResourceProviderR5.create(JpaResourceProviderR5.java:71) ~[hapi-fhir-jpaserver-base-5.3.0-SNAPSHOT.jar:na]

... 44 common frames omitted

2021-02-10 17:27:52.973 ERROR 5212 --- [nio-8080-exec-2] c.u.f.r.s.i.ExceptionHandlingInterceptor : Failure during REST processing