Re: Cypher installation problem

[Sherman Monroe]

Hi JP,

Thanks for your interest in Cypher! I'm sorry to hear you're having problems, I hope I can be of some help.

As a start, could you please attach your config.ini file, it's difficult to read in the email. Also, what are the specs of the server you're running Cypher on? Are you running the standalone app, or the Web Services app also?

Thanks,
-sherman

On Thu, Jun 4, 2009 at 11:23 PM, jp <jpez...@gmail.com> wrote:

Hello,
I am trying to install cypher 1.9 on Ubuntu, java1.6, tomcat6.0.18.
When I run cypher.sh it hangs after 3-4 minutes and 1000s of log
messages; it does not finish.
These are the last lines before it hangs:

23:59:04.041 [main] DEBUG o.a.c.httpclient.HttpMethodBase - Resorting
to protocol version default close connection policy
23:59:04.041 [main] DEBUG o.a.c.httpclient.HttpMethodBase - Should NOT
close connection, using HTTP/1.1
23:59:04.041 [main] DEBUG o.a.c.httpclient.HttpConnection - Releasing
connection back to connection manager.
23:59:04.041 [main] DEBUG o.a.c.h.MultiThreadedHttpConnectionManager -
Freeing connection, hostConfig=HostConfiguration[host=http://
ec2-75-101-243-131.compute-1.amazonaws.com:8890]
23:59:04.041 [main] DEBUG o.a.c.h.util.IdleConnectionHandler - Adding
connection at: 1244174344041
23:59:04.041 [main] DEBUG o.a.c.h.MultiThreadedHttpConnectionManager -
Notifying no-one, there are no waiting threads

I have created 4 repositories in sesame as described and it gets
connected (I get 200).
this is my config.ini (the top part of it):

## The Monrai Cypher start up properties
## For a comprehensive description of these properties, visit
http://docs.monrai.com

rdf.repository.output=org.openrdf.repository.http.HTTPRepository,http://
ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-
sesame,semantic-output
rdf.repository.lexicon=org.openrdf.repository.http.HTTPRepository,http://
ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-sesame,lexicon
rdf.repository.dictionary=org.openrdf.repository.http.HTTPRepository,http://
ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-
sesame,dictionary
rdf.repository.internal=org.openrdf.repository.http.HTTPRepository,http://
ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-
sesame,internal
rdf.repository.grammar=org.openrdf.repository.http.HTTPRepository,http://
ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-sesame,grammar
rdf.repository.dbpedia=com.monrai.rdbc.driver.RDBCRepository,http://
dbpedia.org:8890/sparql
##rdf.repository.northwind=com.monrai.rdbc.driver.RDBCRepository,http://
demo.openlinksw.com/sparql
##rdf.repository.myopenlink=com.monrai.rdbc.driver.RDBCRepository,http://
myopenlink.net:8890/sparql
##rdf.repository.linkedmdb=com.monrai.rdbc.driver.RDBCRepository,http://
data.linkedmdb.org/sparql

## RDF triple stores used by Cypher
## the format is [java classname],[constructor args...]
## constructore args must be of type java.lang.String
rdf.repository.lexicon=org.openrdf.repository.http.HTTPRepository,http://
localhost:8080/openrdf-sesame,lexicon
rdf.repository.output=org.openrdf.repository.http.HTTPRepository,http://
localhost:8080/openrdf-sesame,semantic-output
rdf.repository.dictionary=org.openrdf.repository.http.HTTPRepository,http://
localhost:8080/openrdf-sesame,framenet
rdf.repository.internal=org.openrdf.repository.http.HTTPRepository,http://
localhost:8080/openrdf-sesame,internal
#rdf.repository.grammar=org.openrdf.repository.http.HTTPRepository,http://
localhost:8890/openrdf-sesame,grammar

## whether to clear the repository
rdf.repository.lexicon.purge=f
rdf.repository.dictionary.purge=f
rdf.repository.output.purge=t
rdf.repository.internal.purge=t
rdf.repository.grammar.purge=f

rdf.mso.schema.url=http://mlo.monrai.com\#
rdf.mso.instance.url=http://mlo.monrai.com\#

I would greatly appreciate any help.

JP

--

Thanks,
-sherman

I pray that you may prosper in all things and be healthy, even as your soul prospers
(3 John 1:2)

[Sherman Monroe]

Hi JP,

Sorry for the delay.

Are you running Sesame on port 8080? If not, either change the port number of the repositories in the config.ini file to the one Sesame runs on, or change the Sesame port number to 8080.

Also, please comment out the first 5 lines which set up default repositories at the Monrai server, those meant to be as examples only. Next, be sure that the following repositories point to the ones you set up in Sesame:

## RDF triple stores used by Cypher
## the format is [java classname],[constructor args...]
## constructore args must be of type java.lang.String

rdf.repository.lexicon=org.openrdf.repository.http.HTTPRepository,http://localhost:[your-port]/openrdf-sesame,[your-lexicon-repo-name]
rdf.repository.output=org.openrdf.repository.http.HTTPRepository,http://localhost:[your-port]/openrdf-sesame,[your-sem-repo-name]
rdf.repository.dictionary=org.openrdf.repository.http.HTTPRepository,http://localhost:[your-port]/openrdf-sesame,[your-dict-repo-name]
rdf.repository.internal=org.openrdf.repository.http.HTTPRepository,http://localhost:[your-port]/openrdf-sesame,[your-intern-repo-name]
#rdf.repository.grammar=org.openrdf.repository.http.HTTPRepository,http://localhost:[your-port]/openrdf-sesame,[your-grammar-repo-name]


In addition, the last line there should be uncommented.

So let's give that a try and see if that helps.

[jp]

Hello Sherman,

Thank you for response.
Great to know that I have something configured well.
Now, I have just remembered that a week ago I have updated the lib/
sesame-libs with the newest jars from open-rdf. That was generating
the mysterious errors from HttpClient.
I figured that was not the best idea and I have just copied back the
original jars. This is all the output cypher.sh generates now:

STRING_FILE.GETFILE: java.io.FileNotFoundException: /home/jakub/cypher/
data/repository/internal/frames.rdfs (No such file or directory)
Jun 9, 2009 11:21:47 PM info.aduna.lang.service.ServiceRegistry <init>
INFO: Registered service class
org.openrdf.query.resultio.binary.BinaryQueryResultParserFactory
Jun 9, 2009 11:21:47 PM info.aduna.lang.service.ServiceRegistry <init>
INFO: Registered service class
org.openrdf.query.resultio.sparqlxml.SPARQLResultsXMLParserFactory

This file (frames.rdfs) is configured in two places:

data/repository/internal/index.xml: <load file="frames.rdfs"/>
data/repository/dictonary/index.xml: <load file="frames.rdfs"/>

I tried to run the program after removing the two lines but program
did not run either.
Appreciate any advice on that.

Sincerely,
Jakub

> > sesame,semantic-output<http://ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-%0Ases...>

> > rdf.repository.lexicon=org.openrdf.repository.http.HTTPRepository,http://
> > ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-sesame,lexicon
>
> > rdf.repository.dictionary=org.openrdf.repository.http.HTTPRepository,http://
> > ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-

> > sesame,dictionary<http://ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-%0Ases...>
> > rdf.repository.internal=org.openrdf.repository.http.HTTPRepository,http://
> > ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-
> > sesame,internal<http://ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-%0Ases...>

> > rdf.repository.grammar=org.openrdf.repository.http.HTTPRepository,http://
> > ec2-75-101-243-131.compute-1.amazonaws.com:8890/openrdf-sesame,grammar
> > rdf.repository.dbpedia=com.monrai.rdbc.driver.RDBCRepository,http://
> > dbpedia.org:8890/sparql

> > ##rdf.repository.northwind=com.monrai.rdbc.driver.RDBCRepository,http://<http://dbpedia.org:8890/sparql%0A##rdf.repository.northwind=com.monra...>
> > demo.openlinksw.com/sparql
> > ##rdf.repository.myopenlink=com.monrai.rdbc.driver.RDBCRepository,http://<http://demo.openlinksw.com/sparql%0A##rdf.repository.myopenlink=com.m...>
> > myopenlink.net:8890/sparql
> > ##rdf.repository.linkedmdb=com.monrai.rdbc.driver.RDBCRepository,http://<http://myopenlink.net:8890/sparql%0A##rdf.repository.linkedmdb=com.mo...>

[Sherman Monroe]

Hi JP,

Great news! I'm glad you finally got it to work. Yes, Cypher 1.9 should only use the Sesame 1.2 libs.

original jars. This is all the output cypher.sh generates now:

STRING_FILE.GETFILE: java.io.FileNotFoundException: /home/jakub/cypher/
data/repository/internal/frames.rdfs (No such file or directory)
Jun 9, 2009 11:21:47 PM info.aduna.lang.service.ServiceRegistry <init>
INFO: Registered service class
org.openrdf.query.resultio.binary.BinaryQueryResultParserFactory
Jun 9, 2009 11:21:47 PM info.aduna.lang.service.ServiceRegistry <init>
INFO: Registered service class
org.openrdf.query.resultio.sparqlxml.SPARQLResultsXMLParserFactory

This file (frames.rdfs) is configured in two places:

data/repository/internal/index.xml:      <load file="frames.rdfs"/>
data/repository/dictonary/index.xml: <load file="frames.rdfs"/>

I tried to run the program after removing the two lines but program
did not run either.
Appreciate any advice on that.

The <load/> element will search for files in the xml:base attribute value of the <cypher/> element. Please be sure that the base points to the directory on your system which contains the files specified by the <load/> elements. Check this for all the files under the .../repository directory. Also, the frame.rdfs is a file that is not included with the standard distribution, so yes, you should remove that one.
 

[jp]

That's great advises. Thank you very much.

Unfortunately, I have a new problem:

jakub@jakub-laptop:~/cypher$ ./cypher.sh
Jun 11, 2009 10:13:32 PM info.aduna.lang.service.ServiceRegistry

<init>
INFO: Registered service class
org.openrdf.query.resultio.binary.BinaryQueryResultParserFactory

Jun 11, 2009 10:13:32 PM info.aduna.lang.service.ServiceRegistry

<init>
INFO: Registered service class
org.openrdf.query.resultio.sparqlxml.SPARQLResultsXMLParserFactory

..and hanging.

basically it stops on openrdf. No error, no exception. I will test my
openrdf server more.
However, When I remove the lib/sesame-lib/* and copy the newest jars
from openrdf distribution I get connected to the repos. I also see
some rdf being created. Multiple connection succeed; then app hangs
on:

22:55:41.310 [main] DEBUG o.a.c.httpclient.HttpMethodBase - Resorting

to protocol version default close connection policy

22:55:41.310 [main] DEBUG o.a.c.httpclient.HttpMethodBase - Should NOT
close connection, using HTTP/1.1
22:55:41.311 [main] DEBUG o.a.c.httpclient.HttpConnection - Releasing

connection back to connection manager.

22:55:41.311 [main] DEBUG o.a.c.h.MultiThreadedHttpConnectionManager -
Freeing connection, hostConfig=HostConfiguration[host=http://localhost:
8080]
22:55:41.311 [main] DEBUG o.a.c.h.util.IdleConnectionHandler - Adding
connection at: 1244775341311
22:55:41.316 [main] DEBUG o.a.c.h.MultiThreadedHttpConnectionManager -

Notifying no-one, there are no waiting threads

.. and hanging.

which basically tells me something about httpclient which doesn't work
well with the cypher 1.9.
So although cypher with original sesame packages stops on openrdf info
logs openrdf works with the newest jars.

Any suggestions on that? Can some jars be not compatibile with open-
rdf-2.2.4? Is Ubuntu bad system to try cypher in?

Thank you,
Jakub