You are viewing a plain text version of this content. The canonical link for it is here.
Posted to users@jena.apache.org by Damion Dooley <da...@sfu.ca> on 2023/06/28 08:26:43 UTC

In using RIOT I encounter the "64000" entity expansions error.

I’m using RIOT to parse a large food ontology in owl rdf/xml format.  Its giving me an error:



“JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; this is the limit imposed by the JDK.”



How can I increase the entityExpansionsLimit or whatever its called as a variable ? I was guessing:



riot --set ttl:entityExpansionLimit=0 --validate ../../foodon.owl



but of course that didn’t work.


I’m on a Mac powerbook btw.

Many thanks for the info,

Damion

Damion Dooley, Ontology Development Lead
Centre for Infectious Disease Genomics and One Health
Faculty of Health Sciences, SFU, Canada
Mobile 778-688-0049

Re: In using RIOT I encounter the "64000" entity expansions error.

Posted by Andy Seaborne <an...@apache.org>.
On 12/10/2023 20:20, Steve Vestal wrote:
> I couldn't resist trying https://purl.obolibrary.org/obo/foodon.owl as 
> a stress test for what we are doing.  We're on Jena 4.5.0 and I'm getting
>
> Not in RDF/XML format due to exception 
> org.apache.jena.riot.RiotException [line: 110334, col: 72] Invalid 
> byte 2 of 2-byte UTF-8 sequence.
("Not in RDF/XML format due to..." does not appear to be a Jena message)

At that location:

"...(/ˈærɪkə/ or /əˈriːkə/)..."
                         ^
(This email is UTF-8)

Line/column for encoding problems aren't always right but it looks like 
it is here.

Works for me in 3.17.0, 4.5.0, 5.0.0-dev

JVM_ARGS="-DentityExpansionLimit=2000000" riot --validate --count foodon.owl

> Could this be due to my Jena version or Eclipse or Windows or UTF-8?

Windows most likely.
It can happen if the data has been piped at the command line.

     Andy

>
> On 10/12/2023 1:42 PM, Andy Seaborne wrote:
>> Thanks. It parses OK.
>>
>> On Thu, 12 Oct 2023, 19:36 Jim Balhoff, <ba...@gmail.com> wrote:
>>
>>>> On Oct 6, 2023, at 3:46 AM, Andy Seaborne <an...@apache.org> wrote:
>>>>
>>>>
>>>> On 28/06/2023 09:26, Damion Dooley wrote:
>>>>> I’m using RIOT to parse a large food ontology in owl rdf/xml format.
>>>> Damion,
>>>>
>>>> Is that data publicly available?
>>>>
>>>> There's a new RDF/XML parser for Jena in the pipeline and I'd like to
>>> try it out on real data.
>>>
>>> Andy,
>>>
>>> Damion is active in FOODON, so that may be the ontology to try:
>>> http://obofoundry.org/ontology/foodon.html
>>>
>>> The ontology is at https://purl.obolibrary.org/obo/foodon.owl
>>>
>>> - Jim
>>>
>>>
>>>

Re: In using RIOT I encounter the "64000" entity expansions error.

Posted by Steve Vestal <st...@galois.com>.
I couldn't resist trying https://purl.obolibrary.org/obo/foodon.owl as a 
stress test for what we are doing.  We're on Jena 4.5.0 and I'm getting

Not in RDF/XML format due to exception 
org.apache.jena.riot.RiotException [line: 110334, col: 72] Invalid byte 
2 of 2-byte UTF-8 sequence.

Could this be due to my Jena version or Eclipse or Windows or UTF-8?

On 10/12/2023 1:42 PM, Andy Seaborne wrote:
> Thanks. It parses OK.
>
> On Thu, 12 Oct 2023, 19:36 Jim Balhoff, <ba...@gmail.com> wrote:
>
>>> On Oct 6, 2023, at 3:46 AM, Andy Seaborne <an...@apache.org> wrote:
>>>
>>>
>>> On 28/06/2023 09:26, Damion Dooley wrote:
>>>> I’m using RIOT to parse a large food ontology in owl rdf/xml format.
>>> Damion,
>>>
>>> Is that data publicly available?
>>>
>>> There's a new RDF/XML parser for Jena in the pipeline and I'd like to
>> try it out on real data.
>>
>> Andy,
>>
>> Damion is active in FOODON, so that may be the ontology to try:
>> http://obofoundry.org/ontology/foodon.html
>>
>> The ontology is at https://purl.obolibrary.org/obo/foodon.owl
>>
>> - Jim
>>
>>
>>

Re: In using RIOT I encounter the "64000" entity expansions error.

Posted by Andy Seaborne <an...@apache.org>.
Thanks. It parses OK.

On Thu, 12 Oct 2023, 19:36 Jim Balhoff, <ba...@gmail.com> wrote:

> > On Oct 6, 2023, at 3:46 AM, Andy Seaborne <an...@apache.org> wrote:
> >
> >
> > On 28/06/2023 09:26, Damion Dooley wrote:
> >> I’m using RIOT to parse a large food ontology in owl rdf/xml format.
> >
> > Damion,
> >
> > Is that data publicly available?
> >
> > There's a new RDF/XML parser for Jena in the pipeline and I'd like to
> try it out on real data.
>
> Andy,
>
> Damion is active in FOODON, so that may be the ontology to try:
> http://obofoundry.org/ontology/foodon.html
>
> The ontology is at https://purl.obolibrary.org/obo/foodon.owl
>
> - Jim
>
>
>

Re: In using RIOT I encounter the "64000" entity expansions error.

Posted by Jim Balhoff <ba...@gmail.com>.
> On Oct 6, 2023, at 3:46 AM, Andy Seaborne <an...@apache.org> wrote:
> 
> 
> On 28/06/2023 09:26, Damion Dooley wrote:
>> I’m using RIOT to parse a large food ontology in owl rdf/xml format.
> 
> Damion,
> 
> Is that data publicly available?
> 
> There's a new RDF/XML parser for Jena in the pipeline and I'd like to try it out on real data.

Andy,

Damion is active in FOODON, so that may be the ontology to try: http://obofoundry.org/ontology/foodon.html

The ontology is at https://purl.obolibrary.org/obo/foodon.owl

- Jim

Re: In using RIOT I encounter the "64000" entity expansions error.

Posted by Andy Seaborne <an...@apache.org>.
On 28/06/2023 09:26, Damion Dooley wrote:
> I’m using RIOT to parse a large food ontology in owl rdf/xml format.

Damion,

Is that data publicly available?

There's a new RDF/XML parser for Jena in the pipeline and I'd like to 
try it out on real data.

     Andy

Re: In using RIOT I encounter the "64000" entity expansions error.

Posted by Damion Dooley <da...@sfu.ca>.
Thanks, that worked perfectly!  Very helpful!

Cheers,

Damion

On 2023-06-28, 1:57 AM, "Lorenz Buehmann" <bu...@informatik.uni-leipzig.de> wrote:

    it is not a Jena specific parameter, thus, you have to set if via 
    standard Java JVM arguments:
    
    riot does make use of the system var JVM_ARGS, so you can use that
    
    
    export JVM_ARGS="$JVM_ARGS  -DentityExpansionLimit=250000"
    
    
    or just prepend your call
    
    
    JVM_ARGS="$JVM_ARGS  -DentityExpansionLimit=2500000" riot --set 
    ttl:entityExpansionLimit=0 --validate ../../foodon.owl
    
    
    On 28.06.23 10:26, Damion Dooley wrote:
    > I’m using RIOT to parse a large food ontology in owl rdf/xml format.  Its giving me an error:
    >
    >
    >
    > “JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; this is the limit imposed by the JDK.”
    >
    >
    >
    > How can I increase the entityExpansionsLimit or whatever its called as a variable ? I was guessing:
    >
    >
    >
    > riot --set ttl:entityExpansionLimit=0 --validate ../../foodon.owl
    >
    >
    >
    > but of course that didn’t work.
    >
    >
    > I’m on a Mac powerbook btw.
    >
    > Many thanks for the info,
    >
    > Damion
    >
    > Damion Dooley, Ontology Development Lead
    > Centre for Infectious Disease Genomics and One Health
    > Faculty of Health Sciences, SFU, Canada
    > Mobile 778-688-0049
    >
    -- 
    Lorenz Bühmann
    Research Associate/Scientific Developer
    
    Email buehmann@infai.org
    
    Institute for Applied Informatics e.V. (InfAI) | Goerdelerring 9 | 04109 Leipzig | Germany

Re: In using RIOT I encounter the "64000" entity expansions error.

Posted by Lorenz Buehmann <bu...@informatik.uni-leipzig.de>.
it is not a Jena specific parameter, thus, you have to set if via 
standard Java JVM arguments:

riot does make use of the system var JVM_ARGS, so you can use that


export JVM_ARGS="$JVM_ARGS  -DentityExpansionLimit=250000"


or just prepend your call


JVM_ARGS="$JVM_ARGS  -DentityExpansionLimit=2500000" riot --set 
ttl:entityExpansionLimit=0 --validate ../../foodon.owl


On 28.06.23 10:26, Damion Dooley wrote:
> I’m using RIOT to parse a large food ontology in owl rdf/xml format.  Its giving me an error:
>
>
>
> “JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; this is the limit imposed by the JDK.”
>
>
>
> How can I increase the entityExpansionsLimit or whatever its called as a variable ? I was guessing:
>
>
>
> riot --set ttl:entityExpansionLimit=0 --validate ../../foodon.owl
>
>
>
> but of course that didn’t work.
>
>
> I’m on a Mac powerbook btw.
>
> Many thanks for the info,
>
> Damion
>
> Damion Dooley, Ontology Development Lead
> Centre for Infectious Disease Genomics and One Health
> Faculty of Health Sciences, SFU, Canada
> Mobile 778-688-0049
>
-- 
Lorenz Bühmann
Research Associate/Scientific Developer

Email buehmann@infai.org

Institute for Applied Informatics e.V. (InfAI) | Goerdelerring 9 | 04109 Leipzig | Germany