Hi Hugh,
The virtuoso server log does not show any error messages.
The version is Version 7.0.1-dev.3207-pthreads as of Jan 16 2014
If I use file_open instead of file_to_string_output I get a error
message (FA25 Seek error in file , which makes sense for a pipe).
i.e. DEBUG: Using script:DB.DBA.TTLP(file_open
('/tmp/virtuosoJavaCommunicationFifo7003142399157620167.ttl'),
'http://beta.sparql.uniprot.org/locations/','http://beta.sparql.uniprot.org/locations/')
2014-01-17 13:29:35 +0000
org.expasy.sesame.virtuoso.VirtuosoBulkStatementTransaction
ERROR:
virtuoso.jdbc4.VirtuosoException: FA025: Seek error in file
'/tmp/virtuosoJavaCommunicationFifo7003142399157620167.ttl', error :
Then in my code writing to the named pipe fails on the 87th triple just
as in the case with file_to_string_output. (this seems to be very close
to 4096 bytes written before failing).
However, with file_to_string_output I see the same broken pipe from the
java side. But nothing in the virtuoso.log. Just the normal start up
logging. The process also fails on the 87th triple.
Secondly as a second trial, I speed up the writing into the turtle file
then the process is successful. e.g. cat in to a named pipe or less
checks on the java side. This makes me think that the
file_to_string_output method does not correctly check if the named pipe
is finished or if it just has no bytes available at this time.
If that is the case then it would be a bug, but someone would need to
check on a code level if my idea is correct.
Regards,
Jerven
On 17/01/14 02:42, Hugh Williams wrote:
> Hi Jerven,
>
> What is the version of Virtuoso being used, please provide the output of
> running:
>
> virtuoso-t -?
>
> What are the actual errors being reported on the server side, please
> provide a copy or snippet of the virtuoso.log show these ?
>
> Are you able to provide a simple test case for recreation in-house ?
>
> Best Regards
> Hugh Williams
> Professional Services
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> On 16 Jan 2014, at 16:44, Jerven Bolleman <jerven.bolle...@isb-sib.ch
> <mailto:jerven.bolle...@isb-sib.ch>> wrote:
>
>> Hi Virtuoso Devs,
>>
>> I am trying to use file_to_string_output to read from a named pipe.
>> However, this seems to break without log message from virtuoso
>>
>> e.g.
>>
>> DB.DBA.TTLP(file_to_string_output
>> ('/tmp/virtuosoJavaCommunicationFifo7287643597025348653.ttl'),
>> 'http://beta.sparql.uniprot.org/locations/','http://beta.sparql.uniprot.org/locations/')
>>
>> Which on the other side gives me Broken Pipe IOExceptions.
>>
>> Do you know if anyone else has tried this before or if this
>> fundamentally will never work?
>>
>> The /tmp is in the DirsAllowed
>>
>> Regards,
>> Jerven
>>
>> --
>> -------------------------------------------------------------------
>> Jerven Bolleman jerven.bolle...@isb-sib.ch
>> <mailto:jerven.bolle...@isb-sib.ch>
>> SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85
>> CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58
>> 1211 Geneve 4,
>> Switzerland www.isb-sib.ch <http://www.isb-sib.ch> - www.uniprot.org
>> <http://www.uniprot.org>
>> Follow us at https://twitter.com/#!/uniprot
>> -------------------------------------------------------------------
>>
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--
-------------------------------------------------------------------
Jerven Bolleman jerven.bolle...@isb-sib.ch
SIB Swiss Institute of Bioinformatics Tel: +41 (0)22 379 58 85
CMU, rue Michel Servet 1 Fax: +41 (0)22 379 58 58
1211 Geneve 4,
Switzerland www.isb-sib.ch - www.uniprot.org
Follow us at https://twitter.com/#!/uniprot
-------------------------------------------------------------------
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