Hi Osma!
does thin mean that Fuseki loads the entire data into memory first?
Dataset is bigger than installed memory on the server. Tried 3Gb which
got it further but not to the finish line so trying bigger value tomorrow.
Br,
Mikael
On 24.3.2016 17:19, Osma Suominen wrote:
Hi Mikael!
Please check the Fuseki log, you're likely to find the problem over
there. s-put/SOH is just reporting that the connection to Fuseki was
broken for some reason.
One probable cause is that Fuseki has run out of memory while
processing the upload. In that case you will need to increase the
memory allocated to Fuseki by setting JAVA_OPTS to a value such as
"-Xmx4G". The default setting of 1.2 GB doesn't allow for particularly
large files to be uploaded.
-Osma
On 24/03/16 15:08, Mikael Pesonen wrote:
Hi again!
I got now further, but at some point when loading a fairly lage XML file
I get this:
/usr/lib/ruby/1.9.1/net/protocol.rb:199:in `write': Broken pipe
(Errno::EPIPE)
from /usr/lib/ruby/1.9.1/net/protocol.rb:199:in `write0'
from /usr/lib/ruby/1.9.1/net/protocol.rb:173:in `block in
write'
from /usr/lib/ruby/1.9.1/net/protocol.rb:190:in `writing'
from /usr/lib/ruby/1.9.1/net/protocol.rb:172:in `write'
from /usr/lib/ruby/1.9.1/net/http.rb:1956:in
`send_request_with_body_stream'
from /usr/lib/ruby/1.9.1/net/http.rb:1922:in `exec'
from /usr/lib/ruby/1.9.1/net/http.rb:1318:in `block in
transport_request'
from /usr/lib/ruby/1.9.1/net/http.rb:1317:in `catch'
from /usr/lib/ruby/1.9.1/net/http.rb:1317:in
`transport_request'
from /usr/lib/ruby/1.9.1/net/http.rb:1294:in `request'
from bin/s-put:221:in `response_no_body'
from bin/s-put:208:in `send_body'
from bin/s-put:164:in `PUT'
from bin/s-put:424:in `cmd_soh'
from bin/s-put:703:in `<main>'
Do you have any idea whether it is because of big file or malformed XML
or something else?
Br,
Mikael
On 24.3.2016 13:25, Osma Suominen wrote:
Hi Mikael!
Try renaming the file to .rdf instead of .xml. It's likely that s-put
doesn't recognize the file extension .xml - after all, it could be any
kind of XML, not just RDF/XML.
-Osma
On 24/03/16 11:31, Mikael Pesonen wrote:
Hi,
sorry for missing info. So I'm trying to:
/apache-jena-fuseki-2.3.1$ bin/s-put http://localhost:3030/ds/data
http://www.lingsoft.fi/geonames/ ./tmp.xml
tmp.xml is a geonames entry:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<rdf:RDF xmlns:cc="http://creativecommons.org/ns#";
xmlns:dcterms="http://purl.org/dc/terms/";
xmlns:foaf="http://xmlns.com/foaf/0.1/";
xmlns:gn="http://www.geonames.org/ontology#";
xmlns:owl="http://www.w3.org/2002/07/owl#";
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#";
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#";
xmlns:wgs84_pos="http://www.w3.org/2003/01/geo/wgs84_pos#";>
<gn:Feature rdf:about="http://sws.geonames.org/3/";><rdfs:isDefinedBy
rdf:resource="http://sws.geonames.org/3/about.rdf"/>
<gn:name>Zamīn Sūkhteh</gn:name><gn:alternateName xml:lang="fa">زمين
سوخته</gn:alternateName>
<gn:alternateName xml:lang="fa">Zamīn
Sūkhteh</gn:alternateName><gn:featureClass
rdf:resource="http://www.geonames.org/ontology#S"/>
<gn:featureCode
rdf:resource="http://www.geonames.org/ontology#S.CRRL"/>
<gn:countryCode>IR</gn:countryCode>
<wgs84_pos:lat>32.45831</wgs84_pos:lat>
<wgs84_pos:long>48.96335</wgs84_pos:long>
<gn:parentFeature rdf:resource="http://sws.geonames.org/127082/"/>
<gn:parentCountry rdf:resource="http://sws.geonames.org/130758/"/>
<gn:parentADM1 rdf:resource="http://sws.geonames.org/127082/"/>
<gn:nearbyFeatures
rdf:resource="http://sws.geonames.org/3/nearby.rdf"/>
<gn:locationMap
rdf:resource="http://www.geonames.org/3/zamin-sukhteh.html"/>
</gn:Feature>
</rdf:RDF>
And error comes from Ruby:
/usr/lib/ruby/1.9.1/net/http.rb:1436:in `block in
initialize_http_header': undefined method `strip' for nil:NilClass
(NoMethodError)
from /usr/lib/ruby/1.9.1/net/http.rb:1434:in `each'
from /usr/lib/ruby/1.9.1/net/http.rb:1434:in
`initialize_http_header'
from bin/s-put:205:in `send_body'
from bin/s-put:164:in `PUT'
from bin/s-put:424:in `cmd_soh'
from bin/s-put:703:in `<main>'
XML looks like valid, but is s-put missing some info on what that XML
is?
Br,
Mikael
On 18.3.2016 13:32, Andy Seaborne wrote:
> No idea? I need to update data to either running database or make
> a new db.
(to a message 3 days ago ...)
"this does not work" is a bit minimal.
What does work? Other s-* commands? Other files?
I'd guess that ".xml" is not recognized as RDF. It's not the right
file extension. The MIME type must be for the request. There's some
kind of determination in the soh script.
When trying to start another server to port 3031 server complains
org.apache.jena.tdb.TDBException: Can't open database at location
/home/text/tools/apache-jena-fuseki-2.3.1/run/system/
You can't have two servers running on the same TDB files at the same
time. (For that matter, you can't do that with MySQL either - you
need
a server process to mediate requests).
Andy
Mikael
On 15.3.2016 13:40, Mikael Pesonen wrote:
Hi,
okay thats good to know. I tried with s-put
apache-jena-fuseki-2.3.1$ bin/s-put http://localhost:3030/ds/data
http://www.lingsoft.fi/geonames/ tmp.xml
/usr/lib/ruby/1.9.1/net/http.rb:1436:in `block in
initialize_http_header': undefined method `strip' for nil:NilClass
(NoMethodError)
from /usr/lib/ruby/1.9.1/net/http.rb:1434:in `each'
from /usr/lib/ruby/1.9.1/net/http.rb:1434:in
`initialize_http_header'
from bin/s-put:205:in `send_body'
from bin/s-put:164:in `PUT'
from bin/s-put:424:in `cmd_soh'
from bin/s-put:703:in `<main>'
tmp.xml contains one entry from Geonames dump:
<?xml version="1.0" encoding="UTF-8" standalone="no"?><rdf:RDF
xmlns:cc="http://creativecommons.org/ns#";
xmlns:dcterms="http://purl.org/dc/terms/";
xmlns:foaf="http://xmlns.com/foaf/0.1/";
xmlns:gn="http://www.geonames.org/ontology#";
xmlns:owl="http://www.w3.org/2002/07/owl#";
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#";
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#";
xmlns:wgs84_pos="http://www.w3.org/2003/01/geo/wgs84_pos#";><gn:Feature
rdf:about="http://sws.geonames.org/3/";><rdfs:isDefinedBy
rdf:resource="http://sws.geonames.org/3/about.rdf"/><gn:name>Zamīn
Sūkhteh</gn:name><gn:alternateName xml:lang="fa">زمين
سوخته</gn:alternateName><gn:alternateName xml:lang="fa">Zamīn
Sūkhteh</gn:alternateName><gn:featureClass
rdf:resource="http://www.geonames.org/ontology#S"/><gn:featureCode
rdf:resource="http://www.geonames.org/ontology#S.CRRL"/><gn:countryCode>IR</gn:countryCode><wgs84_pos:lat>32.45831</wgs84_pos:lat><wgs84_pos:long>48.96335</wgs84_pos:long><gn:parentFeature
rdf:resource="http://sws.geonames.org/127082/"/><gn:parentCountry
rdf:resource="http://sws.geonames.org/130758/"/><gn:parentADM1
rdf:resource="http://sws.geonames.org/127082/"/><gn:nearbyFeatures
rdf:resource="http://sws.geonames.org/3/nearby.rdf"/><gn:locationMap
rdf:resource="http://www.geonames.org/3/zamin-sukhteh.html"/></gn:Feature></rdf:RDF>
Br,
Mikael
On 15.3.2016 13:21, Andy Seaborne wrote:
On 15/03/16 10:40, Mikael Pesonen wrote:
Hi,
is it possible to add content to graph from RDF XML with command
line
tools? s-put requires SPARQL and tdbloader says
org.apache.jena.tdb.TDBException: Can't open database at location
/home/text/tools/apache-jena-3.0.1/DB/ as it is already locked
by the
process with PID 7672. TDB databases do not permit concurrent
usage
across JVMs so in order to prevent possible data corruption you
cannot
open this location from the JVM that does not own the lock for
the
dataset
Br,
Mikael
Yes - use s-put or s-post.
These are the SPARQL Graph Store Protocol - no query language, no
update language.
All they do is HTTP PUT or POST to the right graph name and the
right
content type.
You can PUT and POST to the dataset itself as well using curl or
wget
or any HTTP tool. You need to set the Content-type header.
Andy
--
www.lingsoft.fi
Speech Applications - Language Management - Translation - Reader's and Writer's
Tools - Text Tools - E-books and M-books
Mikael Pesonen
System Engineer
e-mail: [email protected]
Tel. +358 2 279 3300
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