From steffen.ryll at student.hpi.uni-potsdam.de  Mon Jul  7 12:09:45 2008
From: steffen.ryll at student.hpi.uni-potsdam.de (Steffen Ryll)
Date: Mon, 07 Jul 2008 12:09:45 +0200
Subject: [Rdf2go-devel] [Patch] Jena model implementation's readFrom(Reader)
Message-ID: <4871EB69.1080307@student.hpi.uni-potsdam.de>

Hi all,

I discovered a problem recently, when using RDF2Go's Jena backend. When 
you pass a Reader and a base URI to readFrom(), it ignored the baseURI, 
and the underlying Jena classes complained heavily.

For clarification:
This call works smoothly, where rdfStream is an InputStream:

this.rdfModel.readFrom(rdfStream, Syntax.RdfXml, baseURI);


But, this call makes Jena complain about an empty namespace:

this.rdfModel.readFrom(rdfReader, Syntax.RdfXml, baseURI);

I've attached a patch that fixes this issue. I wasn't sure how your test 
cases are structured, nor how I could test this problem. The only 
manifestation was log messages from Jena...

Cheers,

Steffen
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From mariusz.cygan at deri.org  Mon Jul 21 11:50:40 2008
From: mariusz.cygan at deri.org (Mariusz Cygan)
Date: Mon, 21 Jul 2008 10:50:40 +0100
Subject: [Rdf2go-devel] adding two models
Message-ID: <48845BF0.9080705@deri.org>

Hi,

I was investigating Model.addModel(Model) implementation in the 
AbstractModel class.

	/** subclasses should overwrite this for performance reasons */
	public void addModel(Model model) {
		ClosableIterator<Statement> it = model.iterator();
		Set<Statement> statements = new HashSet<Statement>();
		while (it.hasNext()) {
			Statement stmt = it.next();
			statements.add(stmt);
		}
		it.close();
		for( Statement stmt : statements) {
			this.addStatement( stmt.getSubject(), stmt.getPredicate(), 
stmt.getObject());
		}
	}

In the Sesame plugin implementation it takes a lot of time to add two 
models because every addStatement is a separate transaction. The 
comments suggest though to use Model.addAll(Iterator). Don't you think 
it would be a good idea to rewrite the addModel in the abstract 
implementation or at least override this method in Sesame plugin?

Best,

-- 
Mariusz Cygan
Research Assistant, DERI
National University of Ireland, Galway


From gunnar.grimnes at dfki.de  Mon Jul 21 13:05:13 2008
From: gunnar.grimnes at dfki.de (Gunnar Aastrand Grimnes)
Date: Mon, 21 Jul 2008 13:05:13 +0200
Subject: [Rdf2go-devel] adding two models
In-Reply-To: <48845BF0.9080705@deri.org>
References: <48845BF0.9080705@deri.org>
Message-ID: <48846D69.2070003@dfki.de>

This method is strangely awkward. I guess the reason is that you want to 
be able to have do this:

ModelSet ms= ...

m1=ms.getModel(uri1);

m2=ms.getModel(uri2);

m2.addModel(m1);

and this strange caching of all statements in a hashset is required for 
some implementations not to deadlock?

Anyway - this special case should be detectable by the implementation 
and handled separately.

Have you checked if the sesame plugin does not override this method?

If not can you try to write such a method? :)

Cheers,

- Gunnar

Mariusz Cygan wrote:
> Hi,
> 
> I was investigating Model.addModel(Model) implementation in the 
> AbstractModel class.
> 
> 	/** subclasses should overwrite this for performance reasons */
> 	public void addModel(Model model) {
> 		ClosableIterator<Statement> it = model.iterator();
> 		Set<Statement> statements = new HashSet<Statement>();
> 		while (it.hasNext()) {
> 			Statement stmt = it.next();
> 			statements.add(stmt);
> 		}
> 		it.close();
> 		for( Statement stmt : statements) {
> 			this.addStatement( stmt.getSubject(), stmt.getPredicate(), 
> stmt.getObject());
> 		}
> 	}
> 
> In the Sesame plugin implementation it takes a lot of time to add two 
> models because every addStatement is a separate transaction. The 
> comments suggest though to use Model.addAll(Iterator). Don't you think 
> it would be a good idea to rewrite the addModel in the abstract 
> implementation or at least override this method in Sesame plugin?
> 
> Best,
> 



From mariusz.cygan at deri.org  Mon Jul 21 13:16:30 2008
From: mariusz.cygan at deri.org (Mariusz Cygan)
Date: Mon, 21 Jul 2008 12:16:30 +0100
Subject: [Rdf2go-devel] adding two models
In-Reply-To: <48846D69.2070003@dfki.de>
References: <48845BF0.9080705@deri.org> <48846D69.2070003@dfki.de>
Message-ID: <4884700E.30004@deri.org>

/**
  * Implementation of the RDF2Go model interface for an OpenRDF Repository.
  *
  * Note that RepositoryModel and RepositoryModelSet only work well together
  * because they both keep their RepositoryConnections in auto-commit 
mode. This
  * cannot be changed by the user. Do mass-updates using {@link 
#update(Diff)},
  * {@link #addAll(Iterator)} or {@link #removeAll(Iterator)}, then the 
current
  * connection will be used in non-autocommit mode and commited, including a
  * rollback when it fails.
  */
public class RepositoryModel extends AbstractLockingModel implements Model {


The sesame plugin doesn't override the addModel method. Of course I can 
use model.addAll(model.iterator()) as it is done in one transaction and 
is much faster. As for now I'm not using any ModelSets.

I should be able to find some time and fix this in sesame patch, but I 
was thinking that maybe it would be better if you rewrite the addModel 
in AbstractModel using model.addAll(model.iterator()).

Cheers,

Mariusz Cygan
Research Assistant, DERI
National University of Ireland, Galway


Gunnar Aastrand Grimnes wrote:
> This method is strangely awkward. I guess the reason is that you want to 
> be able to have do this:
> 
> ModelSet ms= ...
> 
> m1=ms.getModel(uri1);
> 
> m2=ms.getModel(uri2);
> 
> m2.addModel(m1);
> 
> and this strange caching of all statements in a hashset is required for 
> some implementations not to deadlock?
> 
> Anyway - this special case should be detectable by the implementation 
> and handled separately.
> 
> Have you checked if the sesame plugin does not override this method?
> 
> If not can you try to write such a method? :)
> 
> Cheers,
> 
> - Gunnar
> 
> Mariusz Cygan wrote:
>> Hi,
>>
>> I was investigating Model.addModel(Model) implementation in the 
>> AbstractModel class.
>>
>>     /** subclasses should overwrite this for performance reasons */
>>     public void addModel(Model model) {
>>         ClosableIterator<Statement> it = model.iterator();
>>         Set<Statement> statements = new HashSet<Statement>();
>>         while (it.hasNext()) {
>>             Statement stmt = it.next();
>>             statements.add(stmt);
>>         }
>>         it.close();
>>         for( Statement stmt : statements) {
>>             this.addStatement( stmt.getSubject(), stmt.getPredicate(), 
>> stmt.getObject());
>>         }
>>     }
>>
>> In the Sesame plugin implementation it takes a lot of time to add two 
>> models because every addStatement is a separate transaction. The 
>> comments suggest though to use Model.addAll(Iterator). Don't you think 
>> it would be a good idea to rewrite the addModel in the abstract 
>> implementation or at least override this method in Sesame plugin?
>>
>> Best,
>>


From voelkel at fzi.de  Tue Jul 22 14:59:01 2008
From: voelkel at fzi.de (Max Voelkel)
Date: Tue, 22 Jul 2008 14:59:01 +0200
Subject: [Rdf2go-devel] RDFTool and SimpleDataFormat
Message-ID: <1157399385.20080722145901@fzi.de>

Hi,  today  is  RDF2Go clean-up day. I stumbled over a very old email from Grant
Ingersoll <grant.ingersoll at gmail.com>.

He  noticed  that  RDFTool  (maintained  by  Leo)  has an issue with Threads and
SimpleDataFormat.  I  was  surprised  and  Googled,  until I found a huge heated
debate about just how bad SimpleDataFormat is.

http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4228335

The  discussion  seems  to conclude, that there is no good fix in general an the
solution from Grant (using ThreadLocal) was also discouraged by some.
Now  I am overwhelmed around the complexity of the issue (has nothing to do with
RDF at all).

Leo, Grant can you help to resolve & explain the issue?

Grants proposal in brief:

1)
        private static DateFormat dateTimeFormat = null;
-->
        private static ThreadLocal<DateFormat> dateTimeFormatTL = new ThreadLocal<DateFormat>();

2)

        public static DateFormat getDateFormat() {
                if (dateFormat == null) {
                        dateFormat = new SimpleDateFormat("yyyy-MM-dd");
                }
                return dateFormat;
        }
-->
        public static DateFormat getDateFormat() {
               DateFormat dateFormat = dateFormatTL.get();
               if (dateFormat == null) {
                        dateFormat = new SimpleDateFormat("yyyy-MM-dd");
                        dateFormatTL.set(dateFormat);
               }
               return dateFormat;
        }
        
Lots more infos are here
http://blogs.atlassian.com/developer/2007/07/dateformat_objects_and_threads.html


Btw, the current code of the class is here
http://semweb4j.googlecode.com/svn/trunk/org.semweb4j.rdf2go.impl.util/src/main/java/org/ontoware/rdf2go/util/RDFTool.java

There are so many options, which way should we go?
Does using ThreadLocals solves all problems you have, Grant?

Kind Regards,
Max
--
       Max V?lkel
       voelkel at fzi.de | www.Xam.de
       office     +49 721 96 54-854
       mobile     +49 171 83 59 678
--
FZI Forschungszentrum Informatik an der Universit?t Karlsruhe
Haid-und-Neu-Str. 10-14, D-76131 Karlsruhe
Tel.: +49-721-9654-0, Fax: +49-721-9654-959
Stiftung des b?rgerlichen Rechts, Az: 14-0563.1 Regierungspr?sidium Karlsruhe.
Vorstand: Prof. Dr.-Ing. R?diger Dillmann, Dipl. Wi.-Ing. Michael Flor
Prof. Dr. Dr.-Ing. Jivka Ovtcharova, Prof. Dr. rer. nat. Rudi Studer
Vorsitzender des Kuratoriums: Ministerialdirigent G?nther Le?nerkraus



From leo.sauermann at dfki.de  Tue Jul 22 15:12:15 2008
From: leo.sauermann at dfki.de (Leo Sauermann)
Date: Tue, 22 Jul 2008 15:12:15 +0200
Subject: [Rdf2go-devel] RDFTool and SimpleDataFormat
In-Reply-To: <1157399385.20080722145901@fzi.de>
References: <1157399385.20080722145901@fzi.de>
Message-ID: <4885DCAF.6000705@dfki.de>

It was Max Voelkel who said at the right time 22.07.2008 14:59 the 
following words:
> Hi,  today  is  RDF2Go clean-up day. I stumbled over a very old email from Grant
> Ingersoll <grant.ingersoll at gmail.com>.
>
> He  noticed  that  RDFTool  (maintained  by  Leo)  has an issue with Threads and
> SimpleDataFormat.  I  was  surprised  and  Googled,  until I found a huge heated
> debate about just how bad SimpleDataFormat is.
>
> http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4228335
>
> The  discussion  seems  to conclude, that there is no good fix in general an the
> solution from Grant (using ThreadLocal) was also discouraged by some.
> Now  I am overwhelmed around the complexity of the issue (has nothing to do with
> RDF at all).
>
> Leo, Grant can you help to resolve & explain the issue?
>
> Grants proposal in brief:
>
> 1)
>         private static DateFormat dateTimeFormat = null;
> -->
>         private static ThreadLocal<DateFormat> dateTimeFormatTL = new ThreadLocal<DateFormat>();
>
> 2)
>
>         public static DateFormat getDateFormat() {
>                 if (dateFormat == null) {
>                         dateFormat = new SimpleDateFormat("yyyy-MM-dd");
>                 }
>                 return dateFormat;
>         }
> -->
>         public static DateFormat getDateFormat() {
>                DateFormat dateFormat = dateFormatTL.get();
>                if (dateFormat == null) {
>                         dateFormat = new SimpleDateFormat("yyyy-MM-dd");
>                         dateFormatTL.set(dateFormat);
>                }
>                return dateFormat;
>         }
>         
> Lots more infos are here
> http://blogs.atlassian.com/developer/2007/07/dateformat_objects_and_threads.html
>
>
> Btw, the current code of the class is here
> http://semweb4j.googlecode.com/svn/trunk/org.semweb4j.rdf2go.impl.util/src/main/java/org/ontoware/rdf2go/util/RDFTool.java
>
> There are so many options, which way should we go?
> Does using ThreadLocals solves all problems you have, Grant?
>   
I think ThreadLocal is ok.

it leaves a bit of clutter at the end, but who cares....

best
Leo



> Kind Regards,
> Max
> --
>        Max V?lkel
>        voelkel at fzi.de | www.Xam.de
>        office     +49 721 96 54-854
>        mobile     +49 171 83 59 678
> --
> FZI Forschungszentrum Informatik an der Universit?t Karlsruhe
> Haid-und-Neu-Str. 10-14, D-76131 Karlsruhe
> Tel.: +49-721-9654-0, Fax: +49-721-9654-959
> Stiftung des b?rgerlichen Rechts, Az: 14-0563.1 Regierungspr?sidium Karlsruhe.
> Vorstand: Prof. Dr.-Ing. R?diger Dillmann, Dipl. Wi.-Ing. Michael Flor
> Prof. Dr. Dr.-Ing. Jivka Ovtcharova, Prof. Dr. rer. nat. Rudi Studer
> Vorsitzender des Kuratoriums: Ministerialdirigent G?nther Le?nerkraus
>
>
>   


-- 
____________________________________________________
DI Leo Sauermann       http://www.dfki.de/~sauermann 

Deutsches Forschungszentrum fuer 
Kuenstliche Intelligenz DFKI GmbH
Trippstadter Strasse 122
P.O. Box 2080           Fon:   +49 631 20575-116
D-67663 Kaiserslautern  Fax:   +49 631 20575-102
Germany                 Mail:  leo.sauermann at dfki.de

Geschaeftsfuehrung:
Prof.Dr.Dr.h.c.mult. Wolfgang Wahlster (Vorsitzender)
Dr. Walter Olthoff
Vorsitzender des Aufsichtsrats:
Prof. Dr. h.c. Hans A. Aukes
Amtsgericht Kaiserslautern, HRB 2313
____________________________________________________



From mariusz.cygan at deri.org  Thu Jul 24 14:15:24 2008
From: mariusz.cygan at deri.org (Mariusz Cygan)
Date: Thu, 24 Jul 2008 13:15:24 +0100
Subject: [Rdf2go-devel] Fwd: JIRA [keks] Commented: (RTGO-53) Sesame
 ModelSet should support other query languages
In-Reply-To: <57aa22380807220919p3895433cte50a2935f8d0d8d5@mail.gmail.com>
References: <28331719.1216737671851.JavaMail.SYSTEM@octopus13>
	<18567634.1216737791351.JavaMail.SYSTEM@octopus13>
	<57aa22380807220919p3895433cte50a2935f8d0d8d5@mail.gmail.com>
Message-ID: <4888725C.3000904@deri.org>

What do you mean by 'This cannot be fixed on the level ob 
AbstractModels. ' ?



Mariusz Cygan
Research Assistant, DERI
National University of Ireland, Galway


Sebastian Kruk wrote:
> ---------- Forwarded message ----------
> From: "Max V?lkel (JIRA)" <jira at octopus13.fzi.de>
> Date: Tue, 22 Jul 2008 16:43:11 +0200 (CEST)
> Subject: JIRA [keks] Commented: (RTGO-53) Sesame ModelSet should
> support other query languages
> To: Sebastian, Kruk, sebastian.kruk at gmail.com
> 
> 
>     [ 
> http://octopus13.fzi.de:8080/browse/RTGO-53?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#action_12015
> ]
> 
> Max V?lkel commented on RTGO-53:
> --------------------------------
> 
> This cannot be fixed on the level ob AbstractModels.
> 
>  > Sesame ModelSet should support other query languages
>  > ----------------------------------------------------
>  >
>  >                 Key: RTGO-53
>  >                 URL: http://octopus13.fzi.de:8080/browse/RTGO-53
>  >             Project: RDF2Go
>  >          Issue Type: Improvement
>  >    Affects Versions: 4.6.*
>  >            Reporter: Sebastian Kruk
>  >            Assignee: Max V?lkel
>  >            Priority: Minor
>  >             Fix For: 4.6.*
>  >
>  >
>  > I got
>  > org.ontoware.rdf2go.exception.QueryLanguageNotSupportedException:
>  > Unsupported query language: SeRQL ... see developer mailing list
> 
> --
> This message is automatically generated by JIRA.
> -
> If you think it was sent incorrectly contact one of the
> administrators:
> http://octopus13.fzi.de:8080/secure/Administrators.jspa
> -
> For more information on JIRA, see: http://www.atlassian.com/software/jira
> 
> 
> 
> 
> 
> --
> --
> --------------------------------------------
> --   Sebastian Ryszard Kruk
> --   Lead Researcher, Project Manager
> --   Digital Enterprise Research Institute
> --   National University of Ireland, Galway
> --   mailto: sebastian.kruk at gmail.com
> --   GG: 335067, Jabber: sebastian.kruk at gmail.com
> --   Skype: sebastiankruk
> --   WWW: http://www.sebastiankruk.com/
> --   mobile (IRL): +353 85 7126591
> --   VoIP   (PL):  +48  52 5110114
> --------------------------------------------
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From venkatesh88 at gmail.com  Thu Jul 31 12:15:43 2008
From: venkatesh88 at gmail.com (Venkatesh Nandakumar)
Date: Thu, 31 Jul 2008 12:15:43 +0200
Subject: [Rdf2go-devel] Validation in RDF2GO
Message-ID: <4986ffac0807310315l2fad751cyc36f3cdf02b0bbae@mail.gmail.com>

Hi,

I'm pretty new to RDF2G0...
I wanted to know if there is some abstraction that you have made in
the lines of ValidityReport of Jena, for RDFS Reasoner?
Or is there any other way to do it? My aim is to feed into the RDF2G0
model an rdf interpretation of the CommonWikiSyntax and find if it is
Valid.

Thanking you,
Venkatesh Nandakumar