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Posted to users@jena.apache.org by "Lebling, David (US SSA)" <da...@baesystems.com> on 2012/09/07 15:08:34 UTC

Model critical sections

I have a suite of webservices which use OWL ontologies stored as named graphs in an SDB database. I also have a set of Java objects that provide a POJO façade over ontology class instances. These instances import many or even all of the OWL ontologies, so I have an OntDocumentManager which points to cached versions of the ontologies.

When an ontology changes, I need to update it in the database, then re-cache it in the OntDocumentManager. During those operations (update ontology graph in database, update cached version in OntDocumentManager) I am within a try/finally block that (respectively) is a write lock or a read lock.

So a sketch (not the full implementation) of the code for writing and reading would be:

void update(String name, Model newModel) {
Model model = SDBFactory.connectNamedModel(store, name);
try {
                model.enterCriticalSection(false); // write
                model.removeAll();
                model.add(newModel);
}
finally {
                model.leaveCriticalSection();
}
}

void cache(OntDocumentManager mgr, String name) {
                Model model = SDBFactory.connectNamedModel(store, name);
                Model cachedModel = createModel(); // this method creates an OWL_MEM model with the doc mgr as its document manager, etc.
                try {
                                model.enterCriticalSection(true); // read
                                cachedModel.add(model);
                }
                finally {
                                model.leaveCriticalSection();
}
mgr.addModel(name, cachedModel, true);
}

What appears to happen is that these critical sections don't appear to inhibit other users (in my tests I have five) of the SDB database from modifying the stored graph. Readers of the graphs sometimes end up with empty graphs. I will sometimes end up with stored graphs that are empty, or inconsistent in some way that eventually corrupts the underlying tables in the database, requiring a complete reinitialization. I also get IllegalThreadState exceptions. Many different exceptions are thrown, with little obvious consistency.

Is critical section only good within a JVM? Do I need to use some sort of transaction instead?

Does anyone have any advice or ideas?

Dave

David Lebling
Principal Software Engineer
BAE Systems, ACDS Group

Re: using "or" in sparql

Posted by Francesco Panico <fp...@imolinfo.it>.

Hi

Your query selects all triples without  source, at first. If  the two
elements without  author have a source they will be discarded, because the
value added by "optional" clause have to respect "where clauses" anyway.

You should try to use UNION construct, because you want to retrieve a list
with
-item without a source
-item without author



2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>

> Hi,
>
> I'm having trouble with constructing a query that uses "or". I already
> tried optional, but it does not lead to the expected result. I'd be glad if
> someone could help me. I'd like to query for:
>
> all var bindings that have no author or no source.
>
> I tried:
>
> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>
> But it only computes the first part (source).
>
> If I have 3 items without a source and 2 others with no author, then I
> should get 5 results instead only the first 3. What am I doing wrong?
>
> Thanks in advance,
> Katja
>
>


-- 
ufficio:  0542 32640
mail:     fpanico@imolinfo.it
cell:      349 3508348
skype:  francies82@gmail.com

Re: using "or" in sparql

Posted by Katja Siegemund <Ka...@tu-dresden.de>.

Hi Francesco,

thanks a lot, it's working now, I also had to use SELECT DISTINCT to 
prevent duplicates.
The W3C Rec. for SPARQL is quite un-understandable in some cases ;)

Cheers,
Katja

Am 10.09.2012 12:29, schrieb Francesco Panico:
> Hi
>
> Your query selects all triples without  "source", at first. If  the two
> elements without  an "author" have a "source", they will be discarded,
> because the values added by "optional" clause have to respect "where
> clauses" anyway.
> You can check it.
>
> You can try to use UNION construct, because you want to retrieve a list
> with
> -item without a source
> -item without author
>
> SELECT ?r
> WHERE {?r a ro:FR.
>                   FILTER NOT EXISTS {?r ro:hasSource ?a}
>
> UNION{    ?r a ro:FR.
>                    FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}
>              }
> }
>
>
> I hope it is useful.
> Regards
> Francesco.
>
>
>
>
>
>
> 2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>
>
>> Hi,
>>
>> I'm having trouble with constructing a query that uses "or". I already
>> tried optional, but it does not lead to the expected result. I'd be glad if
>> someone could help me. I'd like to query for:
>>
>> all var bindings that have no author or no source.
>>
>> I tried:
>>
>> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
>> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>>
>> But it only computes the first part (source).
>>
>> If I have 3 items without a source and 2 others with no author, then I
>> should get 5 results instead only the first 3. What am I doing wrong?
>>
>> Thanks in advance,
>> Katja
>>
>>
>


-- 
Dipl.-Medieninf. Katja Siegemund
Research Assistant

Technische Universität Dresden
Department of Computer Science

Phone +49 (0)40 572 44 55 1
Email Katja.Siegemund@tu-dresden.de
WWW   http://st.inf.tu-dresden.de/

Re: using "or" in sparql

Posted by Francesco Panico <fp...@imolinfo.it>.

Yes, you can use multiple  "Union" in a sparql query.



2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>

> Hm, well, but how can I use UNION for multiple times? I have a lot of
> "or's" in my query :(
>
>
>
> Am 10.09.2012 12:29, schrieb Francesco Panico:
>
>> Hi
>>
>>
>> Your query selects all triples without  "source", at first. If  the two
>> elements without  an "author" have a "source", they will be discarded,
>> because the values added by "optional" clause have to respect "where
>> clauses" anyway.
>> You can check it.
>>
>> You can try to use UNION construct, because you want to retrieve a list
>> with
>> -item without a source
>> -item without author
>>
>> SELECT ?r
>> WHERE {?r a ro:FR.
>>                   FILTER NOT EXISTS {?r ro:hasSource ?a}
>>
>> UNION{    ?r a ro:FR.
>>                    FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}
>>              }
>> }
>>
>>
>> I hope it is useful.
>> Regards
>> Francesco.
>>
>>
>>
>>
>>
>>
>> 2012/9/10 Katja Siegemund <Katja.Siegemund@tu-dresden.de**>
>>
>>  Hi,
>>>
>>> I'm having trouble with constructing a query that uses "or". I already
>>> tried optional, but it does not lead to the expected result. I'd be glad
>>> if
>>> someone could help me. I'd like to query for:
>>>
>>> all var bindings that have no author or no source.
>>>
>>> I tried:
>>>
>>> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
>>> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>>>
>>> But it only computes the first part (source).
>>>
>>> If I have 3 items without a source and 2 others with no author, then I
>>> should get 5 results instead only the first 3. What am I doing wrong?
>>>
>>> Thanks in advance,
>>> Katja
>>>
>>>
>>>
>>
>
> --
> Dipl.-Medieninf. Katja Siegemund
> Research Assistant
>
> Technische Universität Dresden
> Department of Computer Science
>
> Phone +49 (0)40 572 44 55 1
> Email Katja.Siegemund@tu-dresden.de
> WWW   http://st.inf.tu-dresden.de/
>
>


-- 
ufficio:  0542 32640
mail:     fpanico@imolinfo.it
cell:      349 3508348
skype:  francies82@gmail.com

Re: using "or" in sparql

Posted by Katja Siegemund <Ka...@tu-dresden.de>.

Oh that's good! Thanks, I'll try this out. Especially "minus" seems more 
convenient :)

Am 10.09.2012 13:53, schrieb Andy Seaborne:
> On 10/09/12 12:16, Magnus Stuhr wrote:
>> Hi,
>>
>> I just mocked up a template really quick, but something like this 
>> should work:
>>
>> SELECT ?s WHERE {
>> {
>> { ?s ?p ?o. FILTER NOT EXISTS {?s ?p ?o}}
>> UNION
>> {?s ?p ?o.  FILTER NOT EXISTS {?s ?p ?o}}
>> UNION
>> {?s ?p ?o.  FILTER NOT EXISTS {?s ?p ?o}}
>> }
>> UNION
>> {?s ?p ?o. FILTER NOT EXISTS {?s ?p ?o}}
>> }
>>
>> On top of this you can add even more UNION clauses. Obviously, you 
>> have to replace the triple-patterns and solution variables with 
>> whatever you want to find in your query.
>>
>> Regards,
>> Magnus Stuhr
>
> Alternatives which are similar:
>
> 1/
>
> SELECT ?r
>    {?r a ro:FR.
>     ?r ?p ?a
>     FILTER ( ?p NOT IN (ro:hasSource, ro:isAuthoredBy) )
> }
>
> This has limited applicability -- it's using the fact you have only 
> one triple pattern in the NOT EXISTS clause.
>
> 2/
>
> SELECT ?r
> { ?r a ro:FR.
>     MINUS { ?r ro:hasSource ?a }
>     MINUS { ?r ro:isAuthoredBy ?a }
> }
>
> Which style is best depends on how you think about the query and the 
> shape of the data.
>
>     Andy
>
>
>
>>
>> -----Original Message-----
>> From: Katja Siegemund [mailto:Katja.Siegemund@tu-dresden.de]
>> Sent: 10. september 2012 13:03
>> To: users@jena.apache.org
>> Subject: Re: using "or" in sparql
>>
>> Hm, well, but how can I use UNION for multiple times? I have a lot of 
>> "or's" in my query :(
>>
>>
>> Am 10.09.2012 12:29, schrieb Francesco Panico:
>>> Hi
>>>
>>> Your query selects all triples without  "source", at first. If  the two
>>> elements without  an "author" have a "source", they will be discarded,
>>> because the values added by "optional" clause have to respect "where
>>> clauses" anyway.
>>> You can check it.
>>>
>>> You can try to use UNION construct, because you want to retrieve a list
>>> with
>>> -item without a source
>>> -item without author
>>>
>>> SELECT ?r
>>> WHERE {?r a ro:FR.
>>>                    FILTER NOT EXISTS {?r ro:hasSource ?a}
>>>
>>> UNION{    ?r a ro:FR.
>>>                     FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}
>>>               }
>>> }
>>>
>>>
>>> I hope it is useful.
>>> Regards
>>> Francesco.
>>>
>>>
>>>
>>>
>>>
>>>
>>> 2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>
>>>
>>>> Hi,
>>>>
>>>> I'm having trouble with constructing a query that uses "or". I already
>>>> tried optional, but it does not lead to the expected result. I'd be 
>>>> glad if
>>>> someone could help me. I'd like to query for:
>>>>
>>>> all var bindings that have no author or no source.
>>>>
>>>> I tried:
>>>>
>>>> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
>>>> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>>>>
>>>> But it only computes the first part (source).
>>>>
>>>> If I have 3 items without a source and 2 others with no author, then I
>>>> should get 5 results instead only the first 3. What am I doing wrong?
>>>>
>>>> Thanks in advance,
>>>> Katja
>>>>
>>>>
>>>
>>
>>
>


-- 
Dipl.-Medieninf. Katja Siegemund
Research Assistant

Technische Universität Dresden
Department of Computer Science

Phone +49 (0)40 572 44 55 1
Email Katja.Siegemund@tu-dresden.de
WWW   http://st.inf.tu-dresden.de/

Re: using "or" in sparql

Posted by Andy Seaborne <an...@apache.org>.

On 10/09/12 12:16, Magnus Stuhr wrote:
> Hi,
>
> I just mocked up a template really quick, but something like this should work:
>
> SELECT ?s WHERE {
> {
> { ?s ?p ?o. FILTER NOT EXISTS {?s ?p ?o}}
> UNION
> {?s ?p ?o.  FILTER NOT EXISTS {?s ?p ?o}}
> UNION
> {?s ?p ?o.  FILTER NOT EXISTS {?s ?p ?o}}
> }
> UNION
> {?s ?p ?o. FILTER NOT EXISTS {?s ?p ?o}}
> }
>
> On top of this you can add even more UNION clauses. Obviously, you have to replace the triple-patterns and solution variables with whatever you want to find in your query.
>
> Regards,
> Magnus Stuhr

Alternatives which are similar:

1/

SELECT ?r
    {?r a ro:FR.
     ?r ?p ?a
     FILTER ( ?p NOT IN (ro:hasSource, ro:isAuthoredBy) )
}

This has limited applicability -- it's using the fact you have only one 
triple pattern in the NOT EXISTS clause.

2/

SELECT ?r
{ ?r a ro:FR.
     MINUS { ?r ro:hasSource ?a }
     MINUS { ?r ro:isAuthoredBy ?a }
}

Which style is best depends on how you think about the query and the 
shape of the data.

	Andy



>
> -----Original Message-----
> From: Katja Siegemund [mailto:Katja.Siegemund@tu-dresden.de]
> Sent: 10. september 2012 13:03
> To: users@jena.apache.org
> Subject: Re: using "or" in sparql
>
> Hm, well, but how can I use UNION for multiple times? I have a lot of "or's" in my query :(
>
>
> Am 10.09.2012 12:29, schrieb Francesco Panico:
>> Hi
>>
>> Your query selects all triples without  "source", at first. If  the two
>> elements without  an "author" have a "source", they will be discarded,
>> because the values added by "optional" clause have to respect "where
>> clauses" anyway.
>> You can check it.
>>
>> You can try to use UNION construct, because you want to retrieve a list
>> with
>> -item without a source
>> -item without author
>>
>> SELECT ?r
>> WHERE {?r a ro:FR.
>>                    FILTER NOT EXISTS {?r ro:hasSource ?a}
>>
>> UNION{    ?r a ro:FR.
>>                     FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}
>>               }
>> }
>>
>>
>> I hope it is useful.
>> Regards
>> Francesco.
>>
>>
>>
>>
>>
>>
>> 2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>
>>
>>> Hi,
>>>
>>> I'm having trouble with constructing a query that uses "or". I already
>>> tried optional, but it does not lead to the expected result. I'd be glad if
>>> someone could help me. I'd like to query for:
>>>
>>> all var bindings that have no author or no source.
>>>
>>> I tried:
>>>
>>> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
>>> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>>>
>>> But it only computes the first part (source).
>>>
>>> If I have 3 items without a source and 2 others with no author, then I
>>> should get 5 results instead only the first 3. What am I doing wrong?
>>>
>>> Thanks in advance,
>>> Katja
>>>
>>>
>>
>
>

RE: using "or" in sparql

Posted by Magnus Stuhr <Ma...@computas.com>.

Hi,

I just mocked up a template really quick, but something like this should work:

SELECT ?s WHERE {
{
{ ?s ?p ?o. FILTER NOT EXISTS {?s ?p ?o}}
UNION 
{?s ?p ?o.  FILTER NOT EXISTS {?s ?p ?o}} 
UNION 
{?s ?p ?o.  FILTER NOT EXISTS {?s ?p ?o}}
}
UNION 
{?s ?p ?o. FILTER NOT EXISTS {?s ?p ?o}}
}

On top of this you can add even more UNION clauses. Obviously, you have to replace the triple-patterns and solution variables with whatever you want to find in your query.

Regards,
Magnus Stuhr

-----Original Message-----
From: Katja Siegemund [mailto:Katja.Siegemund@tu-dresden.de] 
Sent: 10. september 2012 13:03
To: users@jena.apache.org
Subject: Re: using "or" in sparql

Hm, well, but how can I use UNION for multiple times? I have a lot of "or's" in my query :(


Am 10.09.2012 12:29, schrieb Francesco Panico:
> Hi
>
> Your query selects all triples without  "source", at first. If  the two
> elements without  an "author" have a "source", they will be discarded,
> because the values added by "optional" clause have to respect "where
> clauses" anyway.
> You can check it.
>
> You can try to use UNION construct, because you want to retrieve a list
> with
> -item without a source
> -item without author
>
> SELECT ?r
> WHERE {?r a ro:FR.
>                   FILTER NOT EXISTS {?r ro:hasSource ?a}
>
> UNION{    ?r a ro:FR.
>                    FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}
>              }
> }
>
>
> I hope it is useful.
> Regards
> Francesco.
>
>
>
>
>
>
> 2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>
>
>> Hi,
>>
>> I'm having trouble with constructing a query that uses "or". I already
>> tried optional, but it does not lead to the expected result. I'd be glad if
>> someone could help me. I'd like to query for:
>>
>> all var bindings that have no author or no source.
>>
>> I tried:
>>
>> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
>> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>>
>> But it only computes the first part (source).
>>
>> If I have 3 items without a source and 2 others with no author, then I
>> should get 5 results instead only the first 3. What am I doing wrong?
>>
>> Thanks in advance,
>> Katja
>>
>>
>


-- 
Dipl.-Medieninf. Katja Siegemund
Research Assistant

Technische Universität Dresden
Department of Computer Science

Phone +49 (0)40 572 44 55 1
Email Katja.Siegemund@tu-dresden.de
WWW   http://st.inf.tu-dresden.de/

Re: using "or" in sparql

Posted by Katja Siegemund <Ka...@tu-dresden.de>.

Hm, well, but how can I use UNION for multiple times? I have a lot of 
"or's" in my query :(


Am 10.09.2012 12:29, schrieb Francesco Panico:
> Hi
>
> Your query selects all triples without  "source", at first. If  the two
> elements without  an "author" have a "source", they will be discarded,
> because the values added by "optional" clause have to respect "where
> clauses" anyway.
> You can check it.
>
> You can try to use UNION construct, because you want to retrieve a list
> with
> -item without a source
> -item without author
>
> SELECT ?r
> WHERE {?r a ro:FR.
>                   FILTER NOT EXISTS {?r ro:hasSource ?a}
>
> UNION{    ?r a ro:FR.
>                    FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}
>              }
> }
>
>
> I hope it is useful.
> Regards
> Francesco.
>
>
>
>
>
>
> 2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>
>
>> Hi,
>>
>> I'm having trouble with constructing a query that uses "or". I already
>> tried optional, but it does not lead to the expected result. I'd be glad if
>> someone could help me. I'd like to query for:
>>
>> all var bindings that have no author or no source.
>>
>> I tried:
>>
>> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
>> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>>
>> But it only computes the first part (source).
>>
>> If I have 3 items without a source and 2 others with no author, then I
>> should get 5 results instead only the first 3. What am I doing wrong?
>>
>> Thanks in advance,
>> Katja
>>
>>
>


-- 
Dipl.-Medieninf. Katja Siegemund
Research Assistant

Technische Universität Dresden
Department of Computer Science

Phone +49 (0)40 572 44 55 1
Email Katja.Siegemund@tu-dresden.de
WWW   http://st.inf.tu-dresden.de/

Re: using "or" in sparql

Posted by Francesco Panico <fp...@imolinfo.it>.

Hi

Your query selects all triples without  "source", at first. If  the two
elements without  an "author" have a "source", they will be discarded,
because the values added by "optional" clause have to respect "where
clauses" anyway.
You can check it.

You can try to use UNION construct, because you want to retrieve a list
with
-item without a source
-item without author

SELECT ?r
WHERE {?r a ro:FR.
                 FILTER NOT EXISTS {?r ro:hasSource ?a}

UNION{    ?r a ro:FR.
                  FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}
            }
}


I hope it is useful.
Regards
Francesco.






2012/9/10 Katja Siegemund <Ka...@tu-dresden.de>

> Hi,
>
> I'm having trouble with constructing a query that uses "or". I already
> tried optional, but it does not lead to the expected result. I'd be glad if
> someone could help me. I'd like to query for:
>
> all var bindings that have no author or no source.
>
> I tried:
>
> SELECT ?r WHERE {?r a ro:FR. FILTER NOT EXISTS {?r ro:hasSource ?a}
> OPTIONAL {FILTER NOT EXISTS {?r ro:isAuthoredBy ?a}}}";
>
> But it only computes the first part (source).
>
> If I have 3 items without a source and 2 others with no author, then I
> should get 5 results instead only the first 3. What am I doing wrong?
>
> Thanks in advance,
> Katja
>
>


-- 
ufficio:  0542 32640
mail:     fpanico@imolinfo.it
cell:      349 3508348
skype:  francies82@gmail.com