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Posted to users@jena.apache.org by Michael Cox <Mi...@lasp.colorado.edu> on 2012/12/05 00:01:58 UTC
Questions about Fuseki configuration with SDB and updating
Hello,
My name is Michael and I am currently working on a linked data metadata repository project for the University of Colorado's Laboratory for Atmospheric and Space Physics.
We are using a software called VIVO that implements SDB in the backend and we hope to use a Fuseki endpoint to query and update our data.
Select queries are running fine, but any update query spits errors and I wondered if you might help me work through what's causing them... I know this question has been open for a while in the VIVO community with no helpful answers as of yet.
I have installed Fuseki and a few supporting SDB libraries from the package located at http://www.adrive.com/public/UzZpq3/vivoisbyus-fuseki.tar.gz and like I mentioned select queries run fine, but update queries spit an Error 500: DatasetGraph.delete(Quad).
I posted details about log files and configuration information here as well:
Fuseki Error 500: DatasetGraph.delete(Quad)<http://stackoverflow.com/questions/13616830/fuseki-error-500-datasetgraph-deletequad>
Any suggestions on a fix would be hugely appreciated!!
-Michael
Michael Cox
-------------------------------------------------------------------
Undergraduate Assistant Database Administrator
Mission Operations and Data Systems
Laboratory for Atmospheric and Space Physics
1234 Innovation Drive
Boulder, CO 80303
Michael.Cox@lasp.colorado.edu<ma...@lasp.colorado.edu>
RE: Questions about Fuseki configuration with SDB and updating
Posted by John Fereira <ja...@cornell.edu>.
I've got version Ruby 1.8.5. I wouldn't have guessed that my version didn't support the String::start_with method either but when I replace it with
$cmd.match(/^s-/) it works.
-----Original Message-----
From: Andy Seaborne [mailto:andy.seaborne.apache@gmail.com] On Behalf Of Andy Seaborne
Sent: Thursday, December 06, 2012 11:03 AM
To: users@jena.apache.org
Subject: Re: Questions about Fuseki configuration with SDB and updating
On 06/12/12 15:10, John Fereira wrote:
> It starts up fine without any errors but when I run any query I get the following error:
>
> ../s-query:113: undefined method `start_with?' for "s-query":String
> (NoMethodError)
I have Ruby 1.8.7 and it has String::start_with? -- it hadn't occurred to me it was new in some way. Which version are you running?
It could be replaced by
$cmd.match(/^s-/)
as it's not a performance critical.
Your are right - it's so you can invoke the commands as:
soh put ....
as well as
s-put ...
(my Ruby foo runs out at this point!)
Andy
Re: Questions about Fuseki configuration with SDB and updating
Posted by Andy Seaborne <an...@apache.org>.
On 06/12/12 15:10, John Fereira wrote:
> It starts up fine without any errors but when I run any query I get the following error:
>
> ../s-query:113: undefined method `start_with?' for "s-query":String (NoMethodError)
I have Ruby 1.8.7 and it has String::start_with? -- it hadn't occurred
to me it was new in some way. Which version are you running?
It could be replaced by
$cmd.match(/^s-/)
as it's not a performance critical.
Your are right - it's so you can invoke the commands as:
soh put ....
as well as
s-put ...
(my Ruby foo runs out at this point!)
Andy
RE: Questions about Fuseki configuration with SDB and updating
Posted by John Fereira <ja...@cornell.edu>.
I had a little time before the sprint I'm working on this week (and next) so I thought I'd try to build a fuseki endpoint with SDB based on the latest fuseki-snapshot.
I grabbed the latest fuseki src with svn and ran mvn to build a distribution. I extracted that into a "jena-fuseki-0.2.6-SNAPSHOT" directory, I used the same configuration file that was working with a 0.2.4 version and copied what I believe to be the correct versions of the library necessary to run it. I started it with the following shell script:
#!/bin/sh
port=3030
java -cp ./fuseki-server.jar:lib/ReconnectingSDB-0.1-SNAPSHOT.jar:lib/jena-sdb-1.3.6-SNAPSHOT.jar:lib/mysql-connector-java-5.1.16-bin.jar:lib/jena-arq-
2.9.5-SNAPSHOT.jar -Xmx768M org.apache.jena.fuseki.FusekiCmd --desc fuseki-vivo.ttl --port=$port /ds > fuseki-0.2.6.log 2>&1 &
It starts up fine without any errors but when I run any query I get the following error:
../s-query:113: undefined method `start_with?' for "s-query":String (NoMethodError)
It looks like a difference between the 0.2.4 and 0.2.6 version of the s-query script is that some code was added to support soh queries. When I comment out those lines (113-117) my queries work fine.
I did not, however, test the endpoint in update mode...that'll probably have to wait until tomorrow morning.
-----Original Message-----
From: Andy Seaborne [mailto:andy.seaborne.apache@gmail.com] On Behalf Of Andy Seaborne
Sent: Wednesday, December 05, 2012 4:24 AM
To: users@jena.apache.org
Subject: Re: Questions about Fuseki configuration with SDB and updating
On 04/12/12 23:01, Michael Cox wrote:
> Hello,
>
> My name is Michael and I am currently working on a linked data
> metadata repository project for the University of Colorado's
> Laboratory for Atmospheric and Space Physics.
>
> We are using a software called VIVO that implements SDB in the backend
> and we hope to use a Fuseki endpoint to query and update our data.
You may need to talk to the creators of VIVO, especially around the version of SDB used.
> Select queries are running fine, but any update query spits errors and
> I wondered if you might help me work through what's causing them... I
> know this question has been open for a while in the VIVO community
> with no helpful answers as of yet. I have installed Fuseki and a few
> supporting SDB libraries from the package located at
> http://www.adrive.com/public/UzZpq3/vivoisbyus-fuseki.tar.gz and like
> I mentioned select queries run fine, but update queries spit an Error
> 500: DatasetGraph.delete(Quad).
>
> I posted details about log files and configuration information here as
> well:
>
> Fuseki Error 500:
> DatasetGraph.delete(Quad)<http://stackoverflow.com/questions/13616830/
> fuseki-error-500-datasetgraph-deletequad>
NoSuchMethodError means there is a clash of versions which might be on SDB. Which version of SDB are you using?
>
>
> Any suggestions on a fix would be hugely appreciated!! -Michael
SDB 1.3.5 goes with Jena 2.7.3 and Fuseki 0.2.4.
The current development snapshot builds are also consistent. Check the POM for the version you have for the version requirements.
Andy
>
> Michael Cox
> -------------------------------------------------------------------
> Undergraduate Assistant Database Administrator Mission Operations and
> Data Systems Laboratory for Atmospheric and Space Physics 1234
> Innovation Drive Boulder, CO 80303
> Michael.Cox@lasp.colorado.edu<ma...@lasp.colorado.edu>
>
>
Re: Questions about Fuseki configuration with SDB and updating
Posted by Andy Seaborne <an...@apache.org>.
On 05/12/12 13:53, John Fereira wrote:
> I was the person that more or less put together recipe for the fuseki
> endpoint for VIVO that Vincent Sposato used to build the zipfile on
> the vivoisbyus site. It looks like it's using SDB-1.3.4 on that site
> and I've been using the same version for a fuseki-0.2.4 based
> endpoint (though it's not configured for updates). I've been meaning
> to build an endpoint which is based upon the fuseki-0.2.5 code but am
> not sure when I'll be able to get to it. The tricky part has always
> been to get the right mix of versions. I supposed I could try to
> build the endpoint from the fuseki-0.2.5 source (where I can look at
> the POM) but it would be nice to just use the binary release and see
> which versions of SDB, Jena, etc. documented somewhere.
Yes - it's a bit of a nuisance as you need to check the POM for the Jena
dependency of the SDB then find the version of Fuseki that does with that.
The development snapshots are built against the latest at all times so
should be consistent.
Andy
("sdbprint --version" should output the versions for you as well).
RE: Questions about Fuseki configuration with SDB and updating
Posted by John Fereira <ja...@cornell.edu>.
I was the person that more or less put together recipe for the fuseki endpoint for VIVO that Vincent Sposato used to build the zipfile on the vivoisbyus site. It looks like it's using SDB-1.3.4 on that site and I've been using the same version for a fuseki-0.2.4 based endpoint (though it's not configured for updates). I've been meaning to build an endpoint which is based upon the fuseki-0.2.5 code but am not sure when I'll be able to get to it. The tricky part has always been to get the right mix of versions. I supposed I could try to build the endpoint from the fuseki-0.2.5 source (where I can look at the POM) but it would be nice to just use the binary release and see which versions of SDB, Jena, etc. documented somewhere.
-----Original Message-----
From: Andy Seaborne [mailto:andy.seaborne.apache@gmail.com] On Behalf Of Andy Seaborne
Sent: Wednesday, December 05, 2012 4:24 AM
To: users@jena.apache.org
Subject: Re: Questions about Fuseki configuration with SDB and updating
On 04/12/12 23:01, Michael Cox wrote:
> Hello,
>
> My name is Michael and I am currently working on a linked data
> metadata repository project for the University of Colorado's
> Laboratory for Atmospheric and Space Physics.
>
> We are using a software called VIVO that implements SDB in the backend
> and we hope to use a Fuseki endpoint to query and update our data.
You may need to talk to the creators of VIVO, especially around the version of SDB used.
> Select queries are running fine, but any update query spits errors and
> I wondered if you might help me work through what's causing them... I
> know this question has been open for a while in the VIVO community
> with no helpful answers as of yet. I have installed Fuseki and a few
> supporting SDB libraries from the package located at
> http://www.adrive.com/public/UzZpq3/vivoisbyus-fuseki.tar.gz and like
> I mentioned select queries run fine, but update queries spit an Error
> 500: DatasetGraph.delete(Quad).
>
> I posted details about log files and configuration information here as
> well:
>
> Fuseki Error 500:
> DatasetGraph.delete(Quad)<http://stackoverflow.com/questions/13616830/
> fuseki-error-500-datasetgraph-deletequad>
NoSuchMethodError means there is a clash of versions which might be on SDB. Which version of SDB are you using?
>
>
> Any suggestions on a fix would be hugely appreciated!! -Michael
SDB 1.3.5 goes with Jena 2.7.3 and Fuseki 0.2.4.
The current development snapshot builds are also consistent. Check the POM for the version you have for the version requirements.
Andy
>
> Michael Cox
> -------------------------------------------------------------------
> Undergraduate Assistant Database Administrator Mission Operations and
> Data Systems Laboratory for Atmospheric and Space Physics 1234
> Innovation Drive Boulder, CO 80303
> Michael.Cox@lasp.colorado.edu<ma...@lasp.colorado.edu>
>
>
Re: Questions about Fuseki configuration with SDB and updating
Posted by Andy Seaborne <an...@apache.org>.
On 04/12/12 23:01, Michael Cox wrote:
> Hello,
>
> My name is Michael and I am currently working on a linked data
> metadata repository project for the University of Colorado's
> Laboratory for Atmospheric and Space Physics.
>
> We are using a software called VIVO that implements SDB in the
> backend and we hope to use a Fuseki endpoint to query and update our
> data.
You may need to talk to the creators of VIVO, especially around the
version of SDB used.
> Select queries are running fine, but any update query spits errors
> and I wondered if you might help me work through what's causing
> them... I know this question has been open for a while in the VIVO
> community with no helpful answers as of yet. I have installed Fuseki
> and a few supporting SDB libraries from the package located at
> http://www.adrive.com/public/UzZpq3/vivoisbyus-fuseki.tar.gz and like
> I mentioned select queries run fine, but update queries spit an Error
> 500: DatasetGraph.delete(Quad).
>
> I posted details about log files and configuration information here
> as well:
>
> Fuseki Error 500:
> DatasetGraph.delete(Quad)<http://stackoverflow.com/questions/13616830/fuseki-error-500-datasetgraph-deletequad>
NoSuchMethodError means there is a clash of versions which might be on
SDB. Which version of SDB are you using?
>
>
> Any suggestions on a fix would be hugely appreciated!! -Michael
SDB 1.3.5 goes with Jena 2.7.3 and Fuseki 0.2.4.
The current development snapshot builds are also consistent. Check the
POM for the version you have for the version requirements.
Andy
>
> Michael Cox
> -------------------------------------------------------------------
> Undergraduate Assistant Database Administrator Mission Operations and
> Data Systems Laboratory for Atmospheric and Space Physics 1234
> Innovation Drive Boulder, CO 80303
> Michael.Cox@lasp.colorado.edu<ma...@lasp.colorado.edu>
>
>