Deploy WAR file to Tomcat 8.5 and got PersistenceException

[James REN]

Dear all,

I have build a hapi-fhir-jpaserver with MySQL locally (based on your hapi-fhir-jpaserver-example fromhttps://github.com/jamesagnew/hapi-fhir/tree/master/hapi-fhir-jpaserver-example). I can successfully run the server by using command mvn jetty:run ; however, after I deployed the WAR file to Apache Tomcat/8.5.5, the server cannot be started and I got the following error in the log file:

04-Nov-2016 15:17:31.881 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart 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 'entityManagerFactory' defined in ca.uhn.fhir.jpa.demo.FhirServerConfig: Invocation of init method failed; nested exception is javax.persistence.PersistenceException: [PersistenceUnit: HAPI_PU] Unable to build Hibernate SessionFactory

Please see localhost_2016-11-04.txt for the complete log. Thank you.

Best,
Ren

[Kevin Mayfield]

Your fault is further down the log. It's a problem with your lucene directory. It can create the target folder (within tomcat folders), change it to point to another location or change permissions?

	... 42 more
Caused by: org.hibernate.search.exception.SearchException: Unable to create index directory: target/lucenefiles for index ca.uhn.fhir.jpa.entity.ResourceTable
	at 

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[James REN]

I did not see that. Nice catch! Thanks a lot!

[ansuman.bes...@gmail.com]

Hii, 

I am facing the same issue ; but how to exactly fix this issue. 

Caused by: org.hibernate.search.exception.SearchException: Unable to create index directory: target/lucenefiles for index ca.uhn.fhir.jpa.entity.TermConcept

[Kevin Mayfield]

You need to alter your JPA config. Mine is in a file called FhirServerConfigStu3 - it will have a properties section like this

private Properties jpaProperties() {

Properties extraProperties = new Properties();

extraProperties.put("hibernate.dialect",  env.getProperty("hibernate.dialect"));

//extraProperties.put("hibernate.dialect", org.hibernate.dialect.SQLServerDialect.class.getName());

extraProperties.put("hibernate.format_sql", "true");

extraProperties.put("hibernate.show_sql", env.getProperty("hibernate.show_sql"));

extraProperties.put("hibernate.hbm2ddl.auto", "update");

extraProperties.put("hibernate.jdbc.batch_size", "20");

extraProperties.put("hibernate.cache.use_query_cache", "false");

extraProperties.put("hibernate.cache.use_second_level_cache", "false");

extraProperties.put("hibernate.cache.use_structured_entries", "false");

extraProperties.put("hibernate.cache.use_minimal_puts", "false");

extraProperties.put("hibernate.search.default.directory_provider", "filesystem");

// needed to set properties of this directory sudo chmod -R 777 .

extraProperties.put("hibernate.search.default.indexBase", "/Development/lucene/stu3/indexes");

extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");

//extraProperties.put("hibernate.connection.driver.class",

// env.getProperty("jdbc.Driver"));

return extraProperties;

}

You either need to change the folder location or change the permissions of this folder.

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[ansuman.bes...@gmail.com]

Do I have to create a directory like root/Development/lucene/stu3/indexes manually and add the properties

[Kevin Mayfield]

If you've used the git hub version. It's this file you'd need to alter on your version

https://github.com/jamesagnew/hapi-fhir/blob/master/hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/FhirServerConfigDstu3.java

Where you place the lucene index is upto you.

Alternatively you can change the permissions of the directory 

On 30 November 2016 at 09:42, <ansuman.bes...@gmail.com> wrote:

Do I have to create a directory like root/Development/lucene/stu3/indexes manually and add the properties

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[ansuman.bes...@gmail.com]

extraProperties.put("hibernate.search.default.indexBase", "target/lucenefiles");

This is what i have originally from hapi-fhir jpa server example; how i could give access to it

 sudo chmod -R 777 target/lucenefiles
It is showing that no directory exists

[ansuman.bes...@gmail.com]

And when I change the directory it is throwing this error

Caused by: org.hibernate.search.exception.SearchException: Unable to initialize index: ca.uhn.fhir.jpa.entity.TermConcept: /root/lucene/indexes is a file.

but this root/lucene/indexes is a directory

 

[James Agnew]

Try deleting the indexes directory, but ensuring that the parent directory exists and is writeable by your tomcat user.

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[ansuman.bes...@gmail.com]

It's working after setting the path like 

extraProperties.put("hibernate.search.default.indexBase", "/var/lib/tomcat7/webapps/hapi-fhir-jpaserver-example/indexes");