Message: JAXP00010001: The parser has encountered more than "64000" entity expansions

[Roman Sova]

I am trying to load an ontology (owl file) into a stardog's database and getting this error:

 Message: JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; 

After a quick research it looks like this has something to do with with bug in Java JDK and the workaround is recommended as the following steps:

The workaround is to disable FPS or entity expansion limit (be careful now your code can be vulnerable to denial of service attack, see replies on Bug ID: JDK-4843787 org.xml.sax.SAXException was thrown when parsing large file ) 

1. set system property jdk.xml.entityExpansionLimit to 0
   
2. disable FPS in XMLSecurityManager for XMLInputFactory: 
   

        XMLInputFactory factory = XMLInputFactory.newInstance();

        XMLSecurityManager securityManager = new XMLSecurityManager(false);

        factory.setProperty("http://apache.org/xml/properties/security-manager", securityManager);

(here is a link to the source: https://community.oracle.com/thread/2594170)

Any suggestion how I can change the startup script to make this change?

My other option is to chop the owl file to peaces to load it in, but this would not be cool :)

Hope to hear from you soon, and thanks for all you hard work.

Cheers,

Roman  

[Mike Grove]

On Fri, Jun 13, 2014 at 6:47 PM, Roman Sova <sova....@gmail.com> wrote:

I am trying to load an ontology (owl file) into a stardog's database and getting this error:

 Message: JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; 

After a quick research it looks like this has something to do with with bug in Java JDK and the workaround is recommended as the following steps:

The workaround is to disable FPS or entity expansion limit (be careful now your code can be vulnerable to denial of service attack, see replies on Bug ID: JDK-4843787 org.xml.sax.SAXException was thrown when parsing large file ) 

1. set system property jdk.xml.entityExpansionLimit to 0
   
2. disable FPS in XMLSecurityManager for XMLInputFactory: 
   

        XMLInputFactory factory = XMLInputFactory.newInstance();

        XMLSecurityManager securityManager = new XMLSecurityManager(false);

        factory.setProperty("http://apache.org/xml/properties/security-manager", securityManager);

(here is a link to the source: https://community.oracle.com/thread/2594170)

Any suggestion how I can change the startup script to make this change?

You can try setting the system property for the Java XML parser (-DentityExpansionLimit=1000000) as part of the STARDOG_JAVA_ARGS environment variable.

Cheers,

Mike 

My other option is to chop the owl file to peaces to load it in, but this would not be cool :)

Hope to hear from you soon, and thanks for all you hard work.

Cheers,

Roman  

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[Roman Sova]

Thanks Mike,

I will give it a try.

I ended up splitting the ontologies into smaller subfiles.

You help is greatly appreciated.

Roman