bigdata-developers — List for bigdata developers

Re: [Bigdata-developers] trac 765: order by discarding solutions

[Bryan T. <br...@sy...>]

Excellent.

> On Aug 28, 2014, at 5:20 PM, Jeremy J Carroll <jj...@sy...> wrote:
> 
> (With some assistance) I have fixed this issue, including a change to MemorySortOp which was (incorrectly) discarding the solutions.
> 
> The motivation is documented in trac-765.
> 
> Jeremy
> 
> 
> 
> 
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[Bigdata-developers] trac 765: order by discarding solutions

[Jeremy J C. <jj...@sy...>]

(With some assistance) I have fixed this issue, including a change to MemorySortOp which was (incorrectly) discarding the solutions.

The motivation is documented in trac-765.

Jeremy

Re: [Bigdata-developers] UI improvements +1

[Bryan T. <br...@sy...>]

Many thanks to Toby and Mike for this.
Bryan

On Thu, Aug 28, 2014 at 1:19 PM, Jeremy Carroll <jj...@gm...> wrote:

>
> I have just started doing some big data work for the first time for a few
> months, and the UI is significantly improved!
>
> Jeremy
>
> ------------------------------------------------------------------------------
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>

[Bigdata-developers] UI improvements +1

[Jeremy C. <jj...@gm...>]

I have just started doing some big data work for the first time for a few months, and the UI is significantly improved!

Jeremy

Re: [Bigdata-developers] blank nodes in explorer UI

[Bryan T. <br...@sy...>]

This message was just released from the queue.  It is a duplicate of last
week's thread.
Bryan

----
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SYSTAP, LLC
4501 Tower Road
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br...@sy...
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http://mapgraph.io

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On Thu, Aug 21, 2014 at 5:23 AM, Jean-Marc Vanel <jea...@gm...>
wrote:

> Hi Bryan and all
>
> I just tried the explore feature in the Bigdata Workbench,
> from latest sources.
>
> And I saw that blank nodes, e.g. for
> foaf:knows
>
> appear as "Attributes", that is, as plain plain literals.
>
> I guess that this is due to the "work in progress" status of the  Bigdata
> Workbench ?
>
> --
> Jean-Marc Vanel
> Déductions SARL - Consulting, services, training,
> Rule-based programming, Semantic Web
> http://deductions-software.com/
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> Bigdata-developers mailing list
> Big...@li...
> https://lists.sourceforge.net/lists/listinfo/bigdata-developers
>
>

Re: [Bigdata-developers] Fwd: blank nodes in explorer UI

[Bryan T. <br...@sy...>]

Well, I have never seen stardog.  We like to rely on our own innovation rather than copying ideas from other people.  Navigational patterns based in hyperlinks are exactly as old as the web.  Nothing new there.  The whole linked open data movement is about this navigational pattern.

Further, the workbench is designed to expose some of the features of bigdata at are not in SPARQL, such as the use of the explain of a query or the analytic query mode.  

I think that you are running up against a fundamental issue with blank nodes and foaf.  Basically, the use of those blank nodes is a bad idea since SPARQL SELECT queries can not bring back the bounded description and will thus expose blank nodes that are not resolvable to their resource descriptions.  That is a fact of life arising from the relevant specifications which do not interoperate is a sensible fashion in this case.  

I suggest you try DESCRIBE and see if that provides a more appropriate navigational experience.  I make this suggestion in the spirit of open source support.  If you want to contribute, then go beyond criticism and try out my suggestion and see if it delivers a better navigational experience.  I am offering to put in time from our team to integrate the concept, but we expect people relying on open source support to get engaged and meet us half-way.

Thanks,
Bryan

> On Aug 24, 2014, at 8:37 AM, Jean-Marc Vanel <jea...@gm...> wrote:
> 
> BigData started recently developing a database console application, a bit taylored after stardog it seems.
> Anyway, this is a good thing, both as a vulgarization for non semweb aware people, and because any database needs administration tools .
> 
> Now it's up to the BigData team to offer some way of navigating through these blank node that are used  in real life, even if that may be questionable as a modeling practice.
> 
> I don't have a preference yet (by poor knowledge of the BigData vast possibilities) for one of the mechanisms you suggest. 
> As Deng Xiaoping once put it:
> "It doesn't matter whether a cat is white or black, as long as it catches mice."
> 
> 
> 
> 
> 
> 2014-08-24 13:47 GMT+02:00 Bryan Thompson <br...@sy...>:
>> Jean-Marc,
>> 
>> The point of blank nodes is that they are distinct within each context in which they are used.  How would you like us to violate that in order to provide hyperlinked navigation?
>> 
>> Really, I think that this is a problem for the foaf and the rdf data modeling community. They used a convenient mechanism for modeling complex objects, but it does not allow retrieval.  For example, if you plug in the top level uri of a foaf profile to bigdata or a web browser you will get something sensible.  You can also use bounded traversal (either concise bounded description or the RDF GASService - see the RDF GAS wiki page) to crawl the data stored in the server and navigate across those blank nodes.  But you can not navigate across blank nodes once they reach the user interface since they are no longer connected to the RDF data on the server in any useful manner.
>> 
>> This is why people use concise bounded description (CBD).  We support several variations of CBD using DESCRIBE.  I believe that the query hints page of the wiki has information on how to control the CBD behavior.  But CBD will navigate across the blank nodes to resolve the resources that they are attached to and include those within the returned resource description.
>> 
>> We certainly could make the hyperlink behavior of the workbench use CBD (via DESCRIBE), or offer it as a checkbox option for navigation. We can also expose some of the query hints used to control the DESCRIBE behavior to a little control panel to make it easier to use from the workbench.  How does that sound?
>> 
>> Thanks,
>> Bryan
>> 
>>> On Aug 24, 2014, at 5:58 AM, Jean-Marc Vanel <jea...@gm...> wrote:
>>> 
>>> 2014-08-23 23:25 GMT+02:00 Bryan Thompson <br...@sy...>:
>>>> Taking this back to the list.  The semantics of blank nodes are not supposed to provide stable identifies that can be round tripped through the database.  I really advise and prefer the use of Uris for this purpose.  Uris are intended to be stable identifiers.
>>> 
>>> Well, the problem is entirely within BigData(R) and its console explorer application.
>>> The wealth of public FOAF profiles do use blank nodes, and there is no possibility to make people rewrite them.
>>> On the other hand, the BigData(R) console explorer application must do something sensible to show blank nodes to the user.
>>> It's up to the BigData team to do something for that, and then other applications will do the same.
>>> 
>>> That being said, a possibility I see is to distinguish between 2 kinds of bnodes:
>>> - 1. the ones that come from original data like public FOAF profiles
>>> - 2.  the ones that were created by the database, as result of inference or SPARQL node creation
>>> 
>>> -- 
>>> Jean-Marc Vanel
>>> Déductions SARL - Consulting, services, training,
>>> Rule-based programming, Semantic Web
>>> http://deductions-software.com/
>>> +33 (0)6 89 16 29 52
>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> 
> 
> 
> -- 
> Jean-Marc Vanel
> Déductions SARL - Consulting, services, training,
> Rule-based programming, Semantic Web
> http://deductions-software.com/
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui

Re: [Bigdata-developers] Fwd: blank nodes in explorer UI

[Jean-Marc V. <jea...@gm...>]

BigData started recently developing a database console application, a bit
taylored after stardog it seems.
Anyway, this is a good thing, both as a vulgarization for non semweb aware
people, and because any database needs administration tools .

Now it's up to the BigData team to offer *some* way of navigating through
these blank node that are used  in real life, even if that may be
questionable as a modeling practice.

I don't have a preference yet (by poor knowledge of the BigData vast
possibilities) for one of the mechanisms you suggest.
As Deng Xiaoping once put it:
"It doesn't matter whether a cat is white or black, as long as it catches
mice."





2014-08-24 13:47 GMT+02:00 Bryan Thompson <br...@sy...>:

> Jean-Marc,
>
> The point of blank nodes is that they are distinct within each context in
> which they are used.  How would you like us to violate that in order to
> provide hyperlinked navigation?
>
> Really, I think that this is a problem for the foaf and the rdf data
> modeling community. They used a convenient mechanism for modeling complex
> objects, but it does not allow retrieval.  For example, if you plug in the
> top level uri of a foaf profile to bigdata or a web browser you will get
> something sensible.  You can also use bounded traversal (either concise
> bounded description or the RDF GASService - see the RDF GAS wiki page) to
> crawl the data stored in the server and navigate across those blank nodes.
>  But you can not navigate across blank nodes once they reach the user
> interface since they are no longer connected to the RDF data on the server
> in any useful manner.
>
> This is why people use concise bounded description (CBD).  We support
> several variations of CBD using DESCRIBE.  I believe that the query hints
> page of the wiki has information on how to control the CBD behavior.  But
> CBD will navigate across the blank nodes to resolve the resources that they
> are attached to and include those within the returned resource description.
>
> We certainly could make the hyperlink behavior of the workbench use CBD
> (via DESCRIBE), or offer it as a checkbox option for navigation. We can
> also expose some of the query hints used to control the DESCRIBE behavior
> to a little control panel to make it easier to use from the workbench.  How
> does that sound?
>
> Thanks,
> Bryan
>
> On Aug 24, 2014, at 5:58 AM, Jean-Marc Vanel <jea...@gm...>
> wrote:
>
> 2014-08-23 23:25 GMT+02:00 Bryan Thompson <br...@sy...>:
>
>> Taking this back to the list.  The semantics of blank nodes are not
>> supposed to provide stable identifies that can be round tripped through the
>> database.  I really advise and prefer the use of Uris for this purpose.
>>  Uris are intended to be stable identifiers.
>>
>
> Well, the problem is entirely within BigData(R) and its console explorer
> application.
> The wealth of public FOAF profiles do use blank nodes, and there is no
> possibility to make people rewrite them.
> On the other hand, the BigData(R) console explorer application must do
> something sensible to show blank nodes to the user.
> It's up to the BigData team to do something for that, and then other
> applications will do the same.
>
> That being said, a possibility I see is to distinguish between 2 kinds of
> bnodes:
> - 1. the ones that come from original data like public FOAF profiles
> - 2.  the ones that were created by the database, as result of inference
> or SPARQL node creation
>
> --
> Jean-Marc Vanel
> Déductions SARL - Consulting, services, training,
> Rule-based programming, Semantic Web
> http://deductions-software.com/
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
>
>


-- 
Jean-Marc Vanel
Déductions SARL - Consulting, services, training,
Rule-based programming, Semantic Web
http://deductions-software.com/
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui

Re: [Bigdata-developers] Fwd: blank nodes in explorer UI

[Bryan T. <br...@sy...>]

Jean-Marc,

The point of blank nodes is that they are distinct within each context in which they are used.  How would you like us to violate that in order to provide hyperlinked navigation?

Really, I think that this is a problem for the foaf and the rdf data modeling community. They used a convenient mechanism for modeling complex objects, but it does not allow retrieval.  For example, if you plug in the top level uri of a foaf profile to bigdata or a web browser you will get something sensible.  You can also use bounded traversal (either concise bounded description or the RDF GASService - see the RDF GAS wiki page) to crawl the data stored in the server and navigate across those blank nodes.  But you can not navigate across blank nodes once they reach the user interface since they are no longer connected to the RDF data on the server in any useful manner.

This is why people use concise bounded description (CBD).  We support several variations of CBD using DESCRIBE.  I believe that the query hints page of the wiki has information on how to control the CBD behavior.  But CBD will navigate across the blank nodes to resolve the resources that they are attached to and include those within the returned resource description.

We certainly could make the hyperlink behavior of the workbench use CBD (via DESCRIBE), or offer it as a checkbox option for navigation. We can also expose some of the query hints used to control the DESCRIBE behavior to a little control panel to make it easier to use from the workbench.  How does that sound?

Thanks,
Bryan

> On Aug 24, 2014, at 5:58 AM, Jean-Marc Vanel <jea...@gm...> wrote:
> 
> 2014-08-23 23:25 GMT+02:00 Bryan Thompson <br...@sy...>:
>> Taking this back to the list.  The semantics of blank nodes are not supposed to provide stable identifies that can be round tripped through the database.  I really advise and prefer the use of Uris for this purpose.  Uris are intended to be stable identifiers.
> 
> Well, the problem is entirely within BigData(R) and its console explorer application.
> The wealth of public FOAF profiles do use blank nodes, and there is no possibility to make people rewrite them.
> On the other hand, the BigData(R) console explorer application must do something sensible to show blank nodes to the user.
> It's up to the BigData team to do something for that, and then other applications will do the same.
> 
> That being said, a possibility I see is to distinguish between 2 kinds of bnodes:
> - 1. the ones that come from original data like public FOAF profiles
> - 2.  the ones that were created by the database, as result of inference or SPARQL node creation
> 
> -- 
> Jean-Marc Vanel
> Déductions SARL - Consulting, services, training,
> Rule-based programming, Semantic Web
> http://deductions-software.com/
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui

Re: [Bigdata-developers] Fwd: blank nodes in explorer UI

[Jean-Marc V. <jea...@gm...>]

2014-08-23 23:25 GMT+02:00 Bryan Thompson <br...@sy...>:

> Taking this back to the list.  The semantics of blank nodes are not
> supposed to provide stable identifies that can be round tripped through the
> database.  I really advise and prefer the use of Uris for this purpose.
>  Uris are intended to be stable identifiers.
>

Well, the problem is entirely within BigData(R) and its console explorer
application.
The wealth of public FOAF profiles do use blank nodes, and there is no
possibility to make people rewrite them.
On the other hand, the BigData(R) console explorer application must do
something sensible to show blank nodes to the user.
It's up to the BigData team to do something for that, and then other
applications will do the same.

That being said, a possibility I see is to distinguish between 2 kinds of
bnodes:
- 1. the ones that come from original data like public FOAF profiles
- 2.  the ones that were created by the database, as result of inference or
SPARQL node creation

-- 
Jean-Marc Vanel
Déductions SARL - Consulting, services, training,
Rule-based programming, Semantic Web
http://deductions-software.com/
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui

Re: [Bigdata-developers] Fwd: blank nodes in explorer UI

[Bryan T. <br...@sy...>]

Taking this back to the list.  The semantics of blank nodes are not supposed to provide stable identifies that can be round tripped through the database.  I really advise and prefer the use of Uris for this purpose.  Uris are intended to be stable identifiers.

Bigdata does support stable blank node identifiers as an option.  Look at the AbstractTripleStore.Options interface.  There is an option that you can specify when you create the triple or quad store instance to have stable blank node identifiers.  I believe that this is named something like "told bnodes mode".

If that were enabled, then it would be possible to hyperlink the bnodes back to a select query against the kb.  However, we would have to have out of band information in the SPARQL response indicating that the database supported that stable blank nodes mode.  Or we would have to just recognize the syntactic form of the blank node when that mode was in use.

Is that what you are looking for? Stable blank node identifiers?  Or do you normally use the correct semantics for blank nodes, in which case they SHOULD NOT be stable.

Thanks,
Bryan 

> On Aug 23, 2014, at 4:39 PM, Jean-Marc Vanel <jea...@gm...> wrote:
> 
> Yeah, I was suspecting such a problem from my tiny knowledge of BigData ...
> 
> Note that with Jena TDB it is possible to reuse the bnode label , like
> 7b968435:1479bb52912:-7ffd
> 
> to be part of a SPARQL query as 
> _:7b968435:1479bb52912:-7ffd
> 
> cf
> http://mail-archives.apache.org/mod_mbox/jena-users/201408.mbox/%3C5...@ap...%3E
> 
> 
> 
> 
> 
> 
> 2014-08-23 22:21 GMT+02:00 Bryan Thompson <br...@sy...>:
>> Actually, how would we hyperlink the blank node?  We are not storing blank node identifiers in a durable fashion in the database (not unless you turn on the told bnodes mode).  So the value of the blank node in a query response can not be used to readily query the database for the same blank node.
>> 
>> What behavior did you have in mind?
>> 
>> Thanks,
>> Bryan
>> 
>>> On Aug 23, 2014, at 4:16 PM, Bryan Thompson <br...@sy...> wrote:
>>> 
>>> Ok. I have been traveling and not yet had time to check this out myself.  I will pass along that clarification. 
>>> 
>>> Of course, we could hyperlink Literals also and reverse them to statements in which they appear.
>>> 
>>> Bryan
>>> 
>>>> On Aug 23, 2014, at 4:14 PM, Jean-Marc Vanel <jea...@gm...> wrote:
>>>> 
>>>> No quotes around , just :
>>>> t53
>>>> 
>>>> Literals do not have quotes either.
>>>> 
>>>> Blanks nodes should be displayed as hyperlinks just like URI's .
>>>> 
>>>> 
>>>> 
>>>> 2014-08-23 21:43 GMT+02:00 Bryan Thompson <br...@sy...>:
>>>>> I am talking with Toby about this.  We will clear it up.  What are you seeing, quotes around the bnode? Bryan
>>>>> 
>>>>>> On Aug 22, 2014, at 6:45 AM, Jean-Marc Vanel <jea...@gm...> wrote:
>>>>>> 
>>>>>> Hi Bryan and all
>>>>>> 
>>>>>> I just tried the explore feature in the Bigdata Workbench,
>>>>>> from latest sources.
>>>>>> 
>>>>>> And I saw that blank nodes, e.g. for 
>>>>>> foaf:knows
>>>>>> 
>>>>>> appear as "Attributes", that is, as plain literals.
>>>>>> 
>>>>>> I guess that this is due to the "work in progress" status of the  Bigdata Workbench ?
>>>>>> 
>>>>>> -- 
>>>>>> Jean-Marc Vanel
>>>>>> Déductions SARL - Consulting, services, training,
>>>>>> Rule-based programming, Semantic Web
>>>>>> http://deductions-software.com/
>>>>>> +33 (0)6 89 16 29 52
>>>>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> -- 
>>>>>> Jean-Marc Vanel
>>>>>> Déductions SARL - Consulting, services, training,
>>>>>> Rule-based programming, Semantic Web
>>>>>> http://deductions-software.com/
>>>>>> +33 (0)6 89 16 29 52
>>>>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
>>>>>> ------------------------------------------------------------------------------
>>>>>> Slashdot TV.  
>>>>>> Video for Nerds.  Stuff that matters.
>>>>>> http://tv.slashdot.org/
>>>>>> _______________________________________________
>>>>>> Bigdata-developers mailing list
>>>>>> Big...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/bigdata-developers
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Jean-Marc Vanel
>>>> Déductions SARL - Consulting, services, training,
>>>> Rule-based programming, Semantic Web
>>>> http://deductions-software.com/
>>>> +33 (0)6 89 16 29 52
>>>> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> 
> 
> 
> -- 
> Jean-Marc Vanel
> Déductions SARL - Consulting, services, training,
> Rule-based programming, Semantic Web
> http://deductions-software.com/
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui

Re: [Bigdata-developers] Fwd: blank nodes in explorer UI

[Bryan T. <br...@sy...>]

I am talking with Toby about this.  We will clear it up.  What are you seeing, quotes around the bnode? Bryan

> On Aug 22, 2014, at 6:45 AM, Jean-Marc Vanel <jea...@gm...> wrote:
> 
> Hi Bryan and all
> 
> I just tried the explore feature in the Bigdata Workbench,
> from latest sources.
> 
> And I saw that blank nodes, e.g. for 
> foaf:knows
> 
> appear as "Attributes", that is, as plain literals.
> 
> I guess that this is due to the "work in progress" status of the  Bigdata Workbench ?
> 
> -- 
> Jean-Marc Vanel
> Déductions SARL - Consulting, services, training,
> Rule-based programming, Semantic Web
> http://deductions-software.com/
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> 
> 
> 
> -- 
> Jean-Marc Vanel
> Déductions SARL - Consulting, services, training,
> Rule-based programming, Semantic Web
> http://deductions-software.com/
> +33 (0)6 89 16 29 52
> Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui
> ------------------------------------------------------------------------------
> Slashdot TV.  
> Video for Nerds.  Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> Bigdata-developers mailing list
> Big...@li...
> https://lists.sourceforge.net/lists/listinfo/bigdata-developers

[Bigdata-developers] Fwd: blank nodes in explorer UI

[Jean-Marc V. <jea...@gm...>]

Hi Bryan and all

I just tried the explore feature in the Bigdata Workbench,
from latest sources.

And I saw that blank nodes, e.g. for
foaf:knows

appear as "Attributes", that is, as plain literals.

I guess that this is due to the "work in progress" status of the  Bigdata
Workbench ?

-- 
Jean-Marc Vanel
Déductions SARL - Consulting, services, training,
Rule-based programming, Semantic Web
http://deductions-software.com/
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui



-- 
Jean-Marc Vanel
Déductions SARL - Consulting, services, training,
Rule-based programming, Semantic Web
http://deductions-software.com/
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui

[Bigdata-developers] blank nodes in explorer UI

[Jean-Marc V. <jea...@gm...>]

Hi Bryan and all

I just tried the explore feature in the Bigdata Workbench,
from latest sources.

And I saw that blank nodes, e.g. for
foaf:knows

appear as "Attributes", that is, as plain plain literals.

I guess that this is due to the "work in progress" status of the  Bigdata
Workbench ?

-- 
Jean-Marc Vanel
Déductions SARL - Consulting, services, training,
Rule-based programming, Semantic Web
http://deductions-software.com/
+33 (0)6 89 16 29 52
Twitter: @jmvanel , @jmvanel_fr ; chat: irc://irc.freenode.net#eulergui

[Bigdata-developers] Syapse Selects SYSTAP’s Bigdata® as Semantic Database for Precision Medicine Data Platform

[Bigdata by S. L. <bi...@sy...>]

Syapse Selects SYSTAP’s Bigdata® as Semantic Database for Precision Medicine Data Platform

View this email in your browser (http://us8.campaign-archive2.com/?u=807fe42a6d19f97994387207d&id=1a88df7886&e=085d8ae40c)

Syapse Selects SYSTAP’s Bigdata® as Semantic Database for Precision Medicine Data Platform


** WASHINGTON, D.C. and PALO ALTO, Calif., Aug. 19, 2014 -- For Immediate Release
------------------------------------------------------------
SYSTAP, LLC today announced that Syapse, the leading provider of software for enabling precision medicine, has selected Bigdata® as its backend semantic database. Syapse, which launched the Precision Medicine Data Platform in 2011, will use the Bigdata® database as a key element of its semantic platform. The Syapse Precision Medicine Data Platform integrates medical data, omics data, and biomedical knowledge for use in the clinic. Syapse software is delivered as a cloud-based SaaS, enabling access from anywhere with an internet connection, regular software updates and new features, and online collaboration and delivery of results, with minimal IT resources required. Syapse applications comply with HIPAA/HITECH, and data in the Syapse platform are protected according to industry standards.

Syapse's Precision Medicine Data Platform features a semantic layer that provides powerful data modeling, query, and integration functionality. According to Syapse CTO and Co-Founder, Tony Loeser, Ph.D., “We have adopted SYSTAP's graph database, Bigdata®, as our RDF store. Bigdata's exceptional scalability, query performance, and high-availability architecture make it an enterprise-class foundation for our semantic technology stack.”

SYSTAP’s flagship product, Bigdata®, has been a market leader since 2006 in providing high performance, scalable solutions for graphs. The Bigdata® platform supports both Semantic Web (RDF/SPARQL) and Graph Database (tinkerpop, blueprints, vertex-centric) APIs. It features robust, scalable, fault-tolerant, enterprise-class storage and query, and high-availability with online backup, failover and self-healing. Bigdata® powers many high profile enterprise applications for customers including Syapse, EMC, AutoDesk, and Yahoo!7. Learn more at http://bigdata.us8.list-manage.com/track/click?u=807fe42a6d19f97994387207d&id=e37b3d92a7&e=085d8ae40c.

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About Syapse

Syapse is a software company enabling healthcare providers to deploy precision medicine programs. Leading academic and community healthcare providers use the Syapse Precision Medicine Data Platform to integrate complex genomic and clinical data to provide clinicians with actionable insights at point of care, enabling diagnosis, treatment, and outcomes tracking. Headquartered in Palo Alto, California, Syapse is backed by Safeguard Scientifics (http://bigdata.us8.list-manage.com/track/click?u=807fe42a6d19f97994387207d&id=08a3dc9216&e=085d8ae40c)  (NYSE:SFE) and The Social+Capital Partnership (http://bigdata.us8.list-manage1.com/track/click?u=807fe42a6d19f97994387207d&id=0d73e9eae3&e=085d8ae40c) . For more information, please visit www.syapse.com (http://bigdata.us8.list-manage1.com/track/click?u=807fe42a6d19f97994387207d&id=e3e577570b&e=085d8ae40c) .

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SYSTAP, LLC was founded in 2006 with vision of building high quality, highly scalable, open-source software solutions for big graphs. While graph problems may look similar to other big data challenges from the outside, they have very different computational workloads and scaling requirements. Techniques that work on a small scale will often fail to deliver on larger graphs.   SYSTAP’s solutions fill the gap created by this “big graph anti-pattern”. We believe the only way to get scaling and high throughput for graph traversal and graph mining is to get the architecture, the software, and the hardware right. Helping customers achieve their business objectives with graph data is our vision, mission, and the essence of our software solutions.

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Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Bryan T. <br...@sy...>]

Pretty much. The truth maintenance is the minimal work required to keep the
materialized entailments in sync with the  add/drop of explicit statements.
Bryan
On Aug 18, 2014 8:54 AM, "Antoni Mylka" <ant...@qu...> wrote:

> Hi,
>
> Thanks for the answer. I'll see what I can do about the test.
>
> What is really "truth maintenance" from the user point of view?
>
> I understand it as follows, please confirm:
>
> There are two kinds of statements in the triple store: explicit and
> entailed ones.
>
> Truth maintenance means automatic, synchronous recomputation of all
> entailments after each modification of the explicit statements.
>
> When this feature is turned on, every SPARQL UPDATE or LOAD will recompute
> the inferred statements synchronously, so that after the modification
> operation finishes - I can count on the inferred statements being there.
> Both the modification and inference are a single transaction. Other clients
> don't ever see the state between the modification and the inference.
>
> When it's turned off - the set of inferred statements is not modified
> after I modify the explicit statements. New entailments will not appear in
> the dataset, old entailments will not be removed. Inference must be
> triggered explicitly, on a whole graph. It's possible to do both in one
> transaction but it's also possible to do them in two transactions. In the
> second case, the intermediate, inconsistent state will be visible to anyone
> for a while, unless it's prevented by other means.
>
> Truth maintenance is a server-side feature. No temporary data is kept in
> the client-side connection object. It's not affected by my using one
> RepositoryConnection for all updates and queries in the application or
> creating a connection for each query and update and then closing it. It's
> also orthogonal to the client-side autoCommit flag. I can have autocommit
> or not, with or without truth maintenance. I'll get the same behavior by
> using curl and POSTing SPARQL queries.
>
> --
> Antoni Myłka
> Software Engineer
>
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
>
> ----- Ursprüngliche Mail -----
> Von: "Bryan Thompson" <br...@sy...>
> An: "Antoni Mylka" <ant...@qu...>
> CC: "Big...@li..." <
> big...@li...>
> Gesendet: Montag, 18. August 2014 14:14:08
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a
> given set of resources
>
>
> This has been tested without truth maintenance, so I suspect that the
> truth maintenance is the problem. The GASEngine tunnels some abstractions
> and some of those assumptions might be violated in this case.
>
>
> Can you create a simple test case that fails, attach it to a ticket, and
> send me a link to the ticket?
>
>
> Thanks,
> Bryan
>
>
>
>
> ----
> Bryan Thompson
>
> Chief Scientist & Founder
> SYSTAP, LLC
>
> 4501 Tower Road
> Greensboro, NC 27410
>
> br...@sy...
>
> http://bigdata.com
>
> http://mapgraph.io
>
>
> CONFIDENTIALITY NOTICE: This email and its contents and attachments are
> for the sole use of the intended recipient(s) and are confidential or
> proprietary to SYSTAP. Any unauthorized review, use, disclosure,
> dissemination or copying of this email or its contents or attachments is
> prohibited. If you have received this communication in error, please notify
> the sender by reply email and permanently delete all copies of the email
> and its contents and attachments.
>
>
> On Mon, Aug 18, 2014 at 8:09 AM, Antoni Mylka < ant...@qu...
> > wrote:
>
>
> Hi,
>
> Thanks for your answer.
>
> Our RWStore.properties file doesn't contain any entries for
> com.bigdata.rdf.sail.truthMaintenance nor
> com.bigdata.rdf.sail.isolatableIndices. AFAIU this means that the default
> values are used, which is true for truth maintenance and false for
> isolatable indices.
>
> I'll try to do another attempt without truth maintenance. AFAIU the
> inference closure is always computed when transaction is committed. If I
> need to write and then read within the same transaction - I need to call
> BigdataSailConnection.computeClosure. I don't, so in my case this change
> won't have any influence on the application code. I can just flip the
> switch in the configuration and the app won't notice.
>
> You seem to say, that "full read/write transaction support" is only
> available with the "isolatableIndices" configuration property. We don't use
> it, but we thought that calling setAutoCommit(false) and then commit() on
> the RepositoryConnection gives us transaction isolation "out of the box".
> Doesn't it?
>
> --
> Antoni Myłka
> Software Engineer
>
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
>
> ----- Ursprüngliche Mail -----
> Von: "Bryan Thompson" < br...@sy... >
> An: "Antoni Mylka" < ant...@qu... >
> CC: big...@li...
> Gesendet: Montag, 18. August 2014 13:45:41
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a
> given set of resources
>
> The RWStore.properties is used by the war under a variety of deployment
> models. The GraphStore,properties is used by a single ant target and could
> probably be replaced by the use of the RWStore.properties file.
>
> Are you configuring the kb instance with full read/write transaction
> support or incremental truth maintenance? Both of those use a temporary
> store and might account for the exception. Try using unisolated indices (do
> not specify the bigdata sail option ISOLATABLE_INDICES) and try turning off
> incremental truth maintenance. Let us know which one is responsible for the
> issue and then we can file a ticket for this.
>
> Bryan
>
> > On Aug 18, 2014, at 7:25 AM, Antoni Mylka < ant...@qu...
> > wrote:
> >
> > Hi,
> >
> > Yet another update. I still get the exceptions. It doesn't seem to
> depend on the JVM.
> >
> > The query works, but only if I load data, restart the server and then do
> the query. Then, after the first update, I start getting the exceptions.
> That's why it started working with curl after a restart of Tomcat with a
> different JVM. The moment I fired up my app, which started writing stuff to
> the store and doing queries - the exceptions reappeared.
> >
> > Is it a bug? Do I need to do anything between loading data and doing GAS
> queries?
> >
> > Best regards,
> >
> > --
> > Antoni Myłka
> > Software Engineer
> >
> > Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> > http://www.quantinum.com - Bee for Business
> >
> > ----- Ursprüngliche Mail -----
> > Von: "Antoni Myłka" < ant...@qu... >
> > An: big...@li...
> > Gesendet: Montag, 18. August 2014 11:34:46
> > Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a
> given set of resources
> >
> > Hi,
> >
> > The exception doesn't appear when I switch from JRE 8 to JRE 7. The
> query seems to work.
> >
> > Best Regards,
> >
> > --
> > Antoni Myłka
> > Software Engineer
> >
> > Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> > http://www.quantinum.com - Bee for Business
> >
> > ----- Ursprüngliche Mail -----
> > Von: "Antoni Myłka" < ant...@qu... >
> > An: big...@li...
> > Gesendet: Montag, 18. August 2014 10:37:17
> > Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a
> given set of resources
> >
> > Hi
> >
> > I'm trying to experiment with the BFS program. The example "BFS with
> extracted subgraph" seems most interesting to me. I do this:
> >
> > curl -X POST '
> http://localhost:28080/bigdata/namespace/our.namespace/sparql ' -o
> out.xml \
> > --data-urlencode 'query=PREFIX gas: < http://www.bigdata.com/rdf/gas# >
> > SELECT ?depth ?out ?p ?o
> > WHERE {
> > SERVICE gas:service {
> > gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
> > gas:program gas:in <my-starting-point> .
> > gas:program gas:out ?out .
> > gas:program gas:out1 ?depth .
> > gas:program gas:maxIterations 1 .
> > }
> > ?out ?p ?o .
> > }'
> >
> >
> > But the out.xml file contains an exception where the root cause is (Full
> stack trace below):
> >
> > Caused by: java.lang.ClassCastException:
> com.bigdata.journal.TemporaryStore cannot be cast to
> com.bigdata.journal.Journal
> > at
> com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
> > ... 15 more
> >
> > It seems like some configuration issue. Is there anything I must or
> can't put in the configuration files before I can use GAS? I also don't
> quite understand why there are two configuration files: RWStore.properties
> and GraphStore.properties. What is the relation between them? Is a "graph
> store" something separate from a normal RDF store?
> >
> > --
> > Antoni Myłka
> > Software Engineer
> >
> > Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> > http://www.quantinum.com - Bee for Business
> >
> >
> > PREFIX gas: < http://www.bigdata.com/rdf/gas# >
> > SELECT ?depth ?out ?p ?o
> > WHERE {
> > SERVICE gas:service {
> > gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
> > gas:program gas:in <my-starting-point> .
> > gas:program gas:out ?out .
> > gas:program gas:out1 ?depth .
> > gas:program gas:out2 ?predecessor .
> > gas:program gas:maxIterations 1 .
> > }
> > ?out ?p ?o .
> > }
> > java.util.concurrent.ExecutionException: java.lang.Exception:
> org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at java.util.concurrent.FutureTask.report(Unknown Source)
> > at java.util.concurrent.FutureTask.get(Unknown Source)
> > at
> com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625)
> > at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182)
> > at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237)
> > at
> com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
> > at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
> > at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> > at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> > at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> > at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> > at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
> > at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
> > at
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
> > at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
> > at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
> > at
> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
> > at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
> > at
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
> > at
> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
> > at
> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
> > at
> org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
> > at
> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
> > at java.lang.Thread.run(Unknown Source)
> > Caused by: java.lang.Exception:
> org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191)
> > at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500)
> > at java.util.concurrent.FutureTask.run(Unknown Source)
> > at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
> > at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
> > ... 1 more
> > Caused by: org.openrdf.query.QueryEvaluationException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at
> com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
> > at
> org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90)
> > at org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52)
> > at
> org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63)
> > at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310)
> > at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164)
> > ... 5 more
> > Caused by: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
> > at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
> > at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
> > at
> com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
> > at
> com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
> > at
> com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
> > ... 10 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at java.util.concurrent.FutureTask.report(Unknown Source)
> > at java.util.concurrent.FutureTask.get(Unknown Source)
> > at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
> > ... 15 more
> > Caused by: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
> > at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
> > at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82)
> > at
> com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197)
> > at
> com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222)
> > at
> com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
> > ... 4 more
> > Caused by: java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
> > at
> com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477)
> > at
> com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
> > at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
> > ... 9 more
> > Caused by: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335)
> > at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894)
> > at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
> > at java.util.concurrent.FutureTask.run(Unknown Source)
> > at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
> > at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789)
> > ... 3 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at java.util.concurrent.FutureTask.report(Unknown Source)
> > at java.util.concurrent.FutureTask.get(Unknown Source)
> > at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315)
> > ... 8 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: Could not instantiate relation:
> java.lang.reflect.InvocationTargetException
> > at java.util.concurrent.FutureTask.report(Unknown Source)
> > at java.util.concurrent.FutureTask.get(Unknown Source)
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341)
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293)
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205)
> > at java.util.concurrent.FutureTask.run(Unknown Source)
> > at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314)
> > ... 8 more
> > Caused by: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743)
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606)
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542)
> > at java.util.concurrent.FutureTask.run(Unknown Source)
> > ... 3 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: Could not instantiate relation:
> java.lang.reflect.InvocationTargetException
> > at java.util.concurrent.FutureTask.report(Unknown Source)
> > at java.util.concurrent.FutureTask.get(Unknown Source)
> > at
> com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329)
> > at
> com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236)
> > at
> com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604)
> > at com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391)
> > at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240)
> > at
> com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837)
> > at
> com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414)
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756)
> > at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697)
> > ... 6 more
> > Caused by: java.lang.RuntimeException: Could not instantiate relation:
> java.lang.reflect.InvocationTargetException
> > at
> com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982)
> > at
> com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464)
> > at
> com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333)
> > at
> com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301)
> > at
> com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272)
> > at
> com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687)
> > at
> com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744)
> > at
> com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700)
> > ... 4 more
> > Caused by: java.lang.reflect.InvocationTargetException
> > at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
> > at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
> Source)
> > at java.lang.reflect.Constructor.newInstance(Unknown Source)
> > at
> com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963)
> > ... 11 more
> > Caused by: java.lang.ClassCastException:
> com.bigdata.journal.TemporaryStore cannot be cast to
> com.bigdata.journal.Journal
> > at
> com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
> > ... 15 more
> >
> >
> >
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>

Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Antoni M. <ant...@qu...>]

Hi,

Thanks for the answer. I'll see what I can do about the test.

What is really "truth maintenance" from the user point of view?

I understand it as follows, please confirm:

There are two kinds of statements in the triple store: explicit and entailed ones.

Truth maintenance means automatic, synchronous recomputation of all entailments after each modification of the explicit statements. 

When this feature is turned on, every SPARQL UPDATE or LOAD will recompute the inferred statements synchronously, so that after the modification operation finishes - I can count on the inferred statements being there. Both the modification and inference are a single transaction. Other clients don't ever see the state between the modification and the inference.

When it's turned off - the set of inferred statements is not modified after I modify the explicit statements. New entailments will not appear in the dataset, old entailments will not be removed. Inference must be triggered explicitly, on a whole graph. It's possible to do both in one transaction but it's also possible to do them in two transactions. In the second case, the intermediate, inconsistent state will be visible to anyone for a while, unless it's prevented by other means. 

Truth maintenance is a server-side feature. No temporary data is kept in the client-side connection object. It's not affected by my using one RepositoryConnection for all updates and queries in the application or creating a connection for each query and update and then closing it. It's also orthogonal to the client-side autoCommit flag. I can have autocommit or not, with or without truth maintenance. I'll get the same behavior by using curl and POSTing SPARQL queries.

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business

----- Ursprüngliche Mail -----
Von: "Bryan Thompson" <br...@sy...>
An: "Antoni Mylka" <ant...@qu...>
CC: "Big...@li..." <big...@li...>
Gesendet: Montag, 18. August 2014 14:14:08
Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources


This has been tested without truth maintenance, so I suspect that the truth maintenance is the problem. The GASEngine tunnels some abstractions and some of those assumptions might be violated in this case. 


Can you create a simple test case that fails, attach it to a ticket, and send me a link to the ticket? 


Thanks, 
Bryan 




---- 
Bryan Thompson 

Chief Scientist & Founder 
SYSTAP, LLC 

4501 Tower Road 
Greensboro, NC 27410 

br...@sy... 

http://bigdata.com 

http://mapgraph.io 


CONFIDENTIALITY NOTICE: This email and its contents and attachments are for the sole use of the intended recipient(s) and are confidential or proprietary to SYSTAP. Any unauthorized review, use, disclosure, dissemination or copying of this email or its contents or attachments is prohibited. If you have received this communication in error, please notify the sender by reply email and permanently delete all copies of the email and its contents and attachments. 


On Mon, Aug 18, 2014 at 8:09 AM, Antoni Mylka < ant...@qu... > wrote: 


Hi, 

Thanks for your answer. 

Our RWStore.properties file doesn't contain any entries for com.bigdata.rdf.sail.truthMaintenance nor com.bigdata.rdf.sail.isolatableIndices. AFAIU this means that the default values are used, which is true for truth maintenance and false for isolatable indices. 

I'll try to do another attempt without truth maintenance. AFAIU the inference closure is always computed when transaction is committed. If I need to write and then read within the same transaction - I need to call BigdataSailConnection.computeClosure. I don't, so in my case this change won't have any influence on the application code. I can just flip the switch in the configuration and the app won't notice. 

You seem to say, that "full read/write transaction support" is only available with the "isolatableIndices" configuration property. We don't use it, but we thought that calling setAutoCommit(false) and then commit() on the RepositoryConnection gives us transaction isolation "out of the box". Doesn't it? 

-- 
Antoni Myłka 
Software Engineer 

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40 
http://www.quantinum.com - Bee for Business 

----- Ursprüngliche Mail ----- 
Von: "Bryan Thompson" < br...@sy... > 
An: "Antoni Mylka" < ant...@qu... > 
CC: big...@li... 
Gesendet: Montag, 18. August 2014 13:45:41 
Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources 

The RWStore.properties is used by the war under a variety of deployment models. The GraphStore,properties is used by a single ant target and could probably be replaced by the use of the RWStore.properties file. 

Are you configuring the kb instance with full read/write transaction support or incremental truth maintenance? Both of those use a temporary store and might account for the exception. Try using unisolated indices (do not specify the bigdata sail option ISOLATABLE_INDICES) and try turning off incremental truth maintenance. Let us know which one is responsible for the issue and then we can file a ticket for this. 

Bryan 

> On Aug 18, 2014, at 7:25 AM, Antoni Mylka < ant...@qu... > wrote: 
> 
> Hi, 
> 
> Yet another update. I still get the exceptions. It doesn't seem to depend on the JVM. 
> 
> The query works, but only if I load data, restart the server and then do the query. Then, after the first update, I start getting the exceptions. That's why it started working with curl after a restart of Tomcat with a different JVM. The moment I fired up my app, which started writing stuff to the store and doing queries - the exceptions reappeared. 
> 
> Is it a bug? Do I need to do anything between loading data and doing GAS queries? 
> 
> Best regards, 
> 
> -- 
> Antoni Myłka 
> Software Engineer 
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40 
> http://www.quantinum.com - Bee for Business 
> 
> ----- Ursprüngliche Mail ----- 
> Von: "Antoni Myłka" < ant...@qu... > 
> An: big...@li... 
> Gesendet: Montag, 18. August 2014 11:34:46 
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources 
> 
> Hi, 
> 
> The exception doesn't appear when I switch from JRE 8 to JRE 7. The query seems to work. 
> 
> Best Regards, 
> 
> -- 
> Antoni Myłka 
> Software Engineer 
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40 
> http://www.quantinum.com - Bee for Business 
> 
> ----- Ursprüngliche Mail ----- 
> Von: "Antoni Myłka" < ant...@qu... > 
> An: big...@li... 
> Gesendet: Montag, 18. August 2014 10:37:17 
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources 
> 
> Hi 
> 
> I'm trying to experiment with the BFS program. The example "BFS with extracted subgraph" seems most interesting to me. I do this: 
> 
> curl -X POST ' http://localhost:28080/bigdata/namespace/our.namespace/sparql ' -o out.xml \ 
> --data-urlencode 'query=PREFIX gas: < http://www.bigdata.com/rdf/gas# > 
> SELECT ?depth ?out ?p ?o 
> WHERE { 
> SERVICE gas:service { 
> gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" . 
> gas:program gas:in <my-starting-point> . 
> gas:program gas:out ?out . 
> gas:program gas:out1 ?depth . 
> gas:program gas:maxIterations 1 . 
> } 
> ?out ?p ?o . 
> }' 
> 
> 
> But the out.xml file contains an exception where the root cause is (Full stack trace below): 
> 
> Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal 
> at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163) 
> ... 15 more 
> 
> It seems like some configuration issue. Is there anything I must or can't put in the configuration files before I can use GAS? I also don't quite understand why there are two configuration files: RWStore.properties and GraphStore.properties. What is the relation between them? Is a "graph store" something separate from a normal RDF store? 
> 
> -- 
> Antoni Myłka 
> Software Engineer 
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40 
> http://www.quantinum.com - Bee for Business 
> 
> 
> PREFIX gas: < http://www.bigdata.com/rdf/gas# > 
> SELECT ?depth ?out ?p ?o 
> WHERE { 
> SERVICE gas:service { 
> gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" . 
> gas:program gas:in <my-starting-point> . 
> gas:program gas:out ?out . 
> gas:program gas:out1 ?depth . 
> gas:program gas:out2 ?predecessor . 
> gas:program gas:maxIterations 1 . 
> } 
> ?out ?p ?o . 
> } 
> java.util.concurrent.ExecutionException: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at java.util.concurrent.FutureTask.report(Unknown Source) 
> at java.util.concurrent.FutureTask.get(Unknown Source) 
> at com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625) 
> at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182) 
> at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237) 
> at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135) 
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:646) 
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:727) 
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) 
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) 
> at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) 
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) 
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) 
> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) 
> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) 
> at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501) 
> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) 
> at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) 
> at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950) 
> at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) 
> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408) 
> at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040) 
> at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607) 
> at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314) 
> at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) 
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) 
> at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) 
> at java.lang.Thread.run(Unknown Source) 
> Caused by: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191) 
> at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500) 
> at java.util.concurrent.FutureTask.run(Unknown Source) 
> at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) 
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) 
> ... 1 more 
> Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188) 
> at org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90) 
> at org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52) 
> at org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63) 
> at com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310) 
> at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164) 
> ... 5 more 
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523) 
> at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710) 
> at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563) 
> at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365) 
> at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341) 
> at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134) 
> ... 10 more 
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at java.util.concurrent.FutureTask.report(Unknown Source) 
> at java.util.concurrent.FutureTask.get(Unknown Source) 
> at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454) 
> ... 15 more 
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59) 
> at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73) 
> at com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82) 
> at com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197) 
> at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222) 
> at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197) 
> ... 4 more 
> Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273) 
> at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477) 
> at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104) 
> at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46) 
> ... 9 more 
> Caused by: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335) 
> at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894) 
> at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) 
> at java.util.concurrent.FutureTask.run(Unknown Source) 
> at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63) 
> at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789) 
> ... 3 more 
> Caused by: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at java.util.concurrent.FutureTask.report(Unknown Source) 
> at java.util.concurrent.FutureTask.get(Unknown Source) 
> at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315) 
> ... 8 more 
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at java.util.concurrent.FutureTask.report(Unknown Source) 
> at java.util.concurrent.FutureTask.get(Unknown Source) 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341) 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293) 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205) 
> at java.util.concurrent.FutureTask.run(Unknown Source) 
> at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314) 
> ... 8 more 
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743) 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606) 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542) 
> at java.util.concurrent.FutureTask.run(Unknown Source) 
> ... 3 more 
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at java.util.concurrent.FutureTask.report(Unknown Source) 
> at java.util.concurrent.FutureTask.get(Unknown Source) 
> at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329) 
> at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236) 
> at com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604) 
> at com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391) 
> at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240) 
> at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837) 
> at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414) 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756) 
> at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697) 
> ... 6 more 
> Caused by: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException 
> at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982) 
> at com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464) 
> at com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333) 
> at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301) 
> at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272) 
> at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687) 
> at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744) 
> at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700) 
> ... 4 more 
> Caused by: java.lang.reflect.InvocationTargetException 
> at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source) 
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) 
> at java.lang.reflect.Constructor.newInstance(Unknown Source) 
> at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963) 
> ... 11 more 
> Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal 
> at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163) 
> ... 15 more 
> 
> 
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Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Bryan T. <br...@sy...>]

This has been tested without truth maintenance, so I suspect that the truth
maintenance is the problem. The GASEngine tunnels some abstractions and
some of those assumptions might be violated in this case.

Can you create a simple test case that fails, attach it to a ticket, and
send me a link to the ticket?

Thanks,
Bryan

----
Bryan Thompson
Chief Scientist & Founder
SYSTAP, LLC
4501 Tower Road
Greensboro, NC 27410
br...@sy...
http://bigdata.com
http://mapgraph.io

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On Mon, Aug 18, 2014 at 8:09 AM, Antoni Mylka <ant...@qu...>
wrote:

> Hi,
>
> Thanks for your answer.
>
> Our RWStore.properties file doesn't contain any entries for
> com.bigdata.rdf.sail.truthMaintenance nor
> com.bigdata.rdf.sail.isolatableIndices. AFAIU this means that the default
> values are used, which is true for truth maintenance and false for
> isolatable indices.
>
> I'll try to do another attempt without truth maintenance. AFAIU the
> inference closure is always computed when transaction is committed. If I
> need to write and then read within the same transaction - I need to call
> BigdataSailConnection.computeClosure. I don't, so in my case this change
> won't have any influence on the application code. I can just flip the
> switch in the configuration and the app won't notice.
>
> You seem to say, that "full read/write transaction support" is only
> available with the "isolatableIndices" configuration property. We don't use
> it, but we thought that calling setAutoCommit(false) and then commit() on
> the RepositoryConnection gives us transaction isolation "out of the box".
> Doesn't it?
>
> --
> Antoni Myłka
> Software Engineer
>
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
>
> ----- Ursprüngliche Mail -----
> Von: "Bryan Thompson" <br...@sy...>
> An: "Antoni Mylka" <ant...@qu...>
> CC: big...@li...
> Gesendet: Montag, 18. August 2014 13:45:41
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a
> given set of resources
>
> The RWStore.properties is used by the war under a variety of deployment
> models. The GraphStore,properties is used by a single ant target and could
> probably be replaced by the use of the RWStore.properties file.
>
> Are you configuring the kb instance with full read/write transaction
> support or incremental truth maintenance? Both of those use a temporary
> store and might account for the exception. Try using unisolated indices (do
> not specify the bigdata sail option ISOLATABLE_INDICES) and try turning off
> incremental truth maintenance.  Let us know which one is responsible for
> the issue and then we can file a ticket for this.
>
> Bryan
>
> > On Aug 18, 2014, at 7:25 AM, Antoni Mylka <ant...@qu...>
> wrote:
> >
> > Hi,
> >
> > Yet another update. I still get the exceptions. It doesn't seem to
> depend on the JVM.
> >
> > The query works, but only if I load data, restart the server and then do
> the query. Then, after the first update, I start getting the exceptions.
> That's why it started working with curl after a restart of Tomcat with a
> different JVM. The moment I fired up my app, which started writing stuff to
> the store and doing queries - the exceptions reappeared.
> >
> > Is it a bug? Do I need to do anything between loading data and doing GAS
> queries?
> >
> > Best regards,
> >
> > --
> > Antoni Myłka
> > Software Engineer
> >
> > Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> > http://www.quantinum.com - Bee for Business
> >
> > ----- Ursprüngliche Mail -----
> > Von: "Antoni Myłka" <ant...@qu...>
> > An: big...@li...
> > Gesendet: Montag, 18. August 2014 11:34:46
> > Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a
> given set of resources
> >
> > Hi,
> >
> > The exception doesn't appear when I switch from JRE 8 to JRE 7. The
> query seems to work.
> >
> > Best Regards,
> >
> > --
> > Antoni Myłka
> > Software Engineer
> >
> > Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> > http://www.quantinum.com - Bee for Business
> >
> > ----- Ursprüngliche Mail -----
> > Von: "Antoni Myłka" <ant...@qu...>
> > An: big...@li...
> > Gesendet: Montag, 18. August 2014 10:37:17
> > Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a
> given set of resources
> >
> > Hi
> >
> > I'm trying to experiment with the BFS program. The example "BFS with
> extracted subgraph" seems most interesting to me. I do this:
> >
> > curl -X POST '
> http://localhost:28080/bigdata/namespace/our.namespace/sparql' -o out.xml
> \
> > --data-urlencode 'query=PREFIX gas: <http://www.bigdata.com/rdf/gas#>
> > SELECT ?depth ?out ?p ?o
> > WHERE {
> >    SERVICE gas:service {
> >     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
> >     gas:program gas:in <my-starting-point> .
> >     gas:program gas:out ?out .
> >     gas:program gas:out1 ?depth .
> >     gas:program gas:maxIterations 1 .
> >  }
> >  ?out ?p ?o .
> > }'
> >
> >
> > But the out.xml file contains an exception where the root cause is (Full
> stack trace below):
> >
> > Caused by: java.lang.ClassCastException:
> com.bigdata.journal.TemporaryStore cannot be cast to
> com.bigdata.journal.Journal
> >        at
> com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
> >        ... 15 more
> >
> > It seems like some configuration issue. Is there anything I must or
> can't put in the configuration files before I can use GAS? I also don't
> quite understand why there are two configuration files: RWStore.properties
> and GraphStore.properties. What is the relation between them? Is a "graph
> store" something separate from a normal RDF store?
> >
> > --
> > Antoni Myłka
> > Software Engineer
> >
> > Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> > http://www.quantinum.com - Bee for Business
> >
> >
> > PREFIX gas: <http://www.bigdata.com/rdf/gas#>
> > SELECT ?depth ?out ?p ?o
> > WHERE {
> >    SERVICE gas:service {
> >     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
> >     gas:program gas:in <my-starting-point> .
> >     gas:program gas:out ?out .
> >     gas:program gas:out1 ?depth .
> >     gas:program gas:out2 ?predecessor .
> >     gas:program gas:maxIterations 1 .
> >  }
> >  ?out ?p ?o .
> > }
> > java.util.concurrent.ExecutionException: java.lang.Exception:
> org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at java.util.concurrent.FutureTask.report(Unknown Source)
> >        at java.util.concurrent.FutureTask.get(Unknown Source)
> >        at
> com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625)
> >        at
> com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182)
> >        at
> com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237)
> >        at
> com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135)
> >        at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
> >        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
> >        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
> >        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> >        at
> org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> >        at
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
> >        at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
> >        at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
> >        at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
> >        at
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
> >        at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
> >        at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
> >        at
> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
> >        at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
> >        at
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
> >        at
> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
> >        at
> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
> >        at
> org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
> >        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown
> Source)
> >        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
> Source)
> >        at
> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
> >        at java.lang.Thread.run(Unknown Source)
> > Caused by: java.lang.Exception:
> org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191)
> >        at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500)
> >        at java.util.concurrent.FutureTask.run(Unknown Source)
> >        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown
> Source)
> >        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
> Source)
> >        ... 1 more
> > Caused by: org.openrdf.query.QueryEvaluationException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at
> com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
> >        at
> org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90)
> >        at
> org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52)
> >        at
> org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63)
> >        at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310)
> >        at
> com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164)
> >        ... 5 more
> > Caused by: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
> >        at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
> >        at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
> >        at
> com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
> >        at
> com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
> >        at
> com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
> >        ... 10 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at java.util.concurrent.FutureTask.report(Unknown Source)
> >        at java.util.concurrent.FutureTask.get(Unknown Source)
> >        at
> com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
> >        ... 15 more
> > Caused by: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
> >        at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
> >        at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82)
> >        at
> com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197)
> >        at
> com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222)
> >        at
> com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
> >        ... 4 more
> > Caused by: java.util.concurrent.ExecutionException: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
> >        at
> com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477)
> >        at
> com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
> >        at
> com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
> >        ... 9 more
> > Caused by: java.lang.Exception:
> task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null},
> cause=java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335)
> >        at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894)
> >        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown
> Source)
> >        at java.util.concurrent.FutureTask.run(Unknown Source)
> >        at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
> >        at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789)
> >        ... 3 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at java.util.concurrent.FutureTask.report(Unknown Source)
> >        at java.util.concurrent.FutureTask.get(Unknown Source)
> >        at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315)
> >        ... 8 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: Could not instantiate relation:
> java.lang.reflect.InvocationTargetException
> >        at java.util.concurrent.FutureTask.report(Unknown Source)
> >        at java.util.concurrent.FutureTask.get(Unknown Source)
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341)
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293)
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205)
> >        at java.util.concurrent.FutureTask.run(Unknown Source)
> >        at
> com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314)
> >        ... 8 more
> > Caused by: java.lang.RuntimeException:
> java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could
> not instantiate relation: java.lang.reflect.InvocationTargetException
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743)
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606)
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542)
> >        at java.util.concurrent.FutureTask.run(Unknown Source)
> >        ... 3 more
> > Caused by: java.util.concurrent.ExecutionException:
> java.lang.RuntimeException: Could not instantiate relation:
> java.lang.reflect.InvocationTargetException
> >        at java.util.concurrent.FutureTask.report(Unknown Source)
> >        at java.util.concurrent.FutureTask.get(Unknown Source)
> >        at
> com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329)
> >        at
> com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236)
> >        at
> com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604)
> >        at
> com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391)
> >        at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240)
> >        at
> com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837)
> >        at
> com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414)
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756)
> >        at
> com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697)
> >        ... 6 more
> > Caused by: java.lang.RuntimeException: Could not instantiate relation:
> java.lang.reflect.InvocationTargetException
> >        at
> com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982)
> >        at
> com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464)
> >        at
> com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333)
> >        at
> com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301)
> >        at
> com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272)
> >        at
> com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687)
> >        at
> com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744)
> >        at
> com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700)
> >        ... 4 more
> > Caused by: java.lang.reflect.InvocationTargetException
> >        at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown
> Source)
> >        at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
> >        at java.lang.reflect.Constructor.newInstance(Unknown Source)
> >        at
> com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963)
> >        ... 11 more
> > Caused by: java.lang.ClassCastException:
> com.bigdata.journal.TemporaryStore cannot be cast to
> com.bigdata.journal.Journal
> >        at
> com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
> >        ... 15 more
> >
> >
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > Bigdata-developers mailing list
> > Big...@li...
> > https://lists.sourceforge.net/lists/listinfo/bigdata-developers
> >
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > Bigdata-developers mailing list
> > Big...@li...
> > https://lists.sourceforge.net/lists/listinfo/bigdata-developers
> >
> >
> ------------------------------------------------------------------------------
> > _______________________________________________
> > Bigdata-developers mailing list
> > Big...@li...
> > https://lists.sourceforge.net/lists/listinfo/bigdata-developers
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Bigdata-developers mailing list
> Big...@li...
> https://lists.sourceforge.net/lists/listinfo/bigdata-developers
>

Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Bryan T. <br...@sy...>]

The RWStore.properties is used by the war under a variety of deployment models. The GraphStore,properties is used by a single ant target and could probably be replaced by the use of the RWStore.properties file. 

Are you configuring the kb instance with full read/write transaction support or incremental truth maintenance? Both of those use a temporary store and might account for the exception. Try using unisolated indices (do not specify the bigdata sail option ISOLATABLE_INDICES) and try turning off incremental truth maintenance.  Let us know which one is responsible for the issue and then we can file a ticket for this.

Bryan

> On Aug 18, 2014, at 7:25 AM, Antoni Mylka <ant...@qu...> wrote:
> 
> Hi,
> 
> Yet another update. I still get the exceptions. It doesn't seem to depend on the JVM.
> 
> The query works, but only if I load data, restart the server and then do the query. Then, after the first update, I start getting the exceptions. That's why it started working with curl after a restart of Tomcat with a different JVM. The moment I fired up my app, which started writing stuff to the store and doing queries - the exceptions reappeared.
> 
> Is it a bug? Do I need to do anything between loading data and doing GAS queries?
> 
> Best regards,
> 
> -- 
> Antoni Myłka
> Software Engineer
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
> 
> ----- Ursprüngliche Mail -----
> Von: "Antoni Myłka" <ant...@qu...>
> An: big...@li...
> Gesendet: Montag, 18. August 2014 11:34:46
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources
> 
> Hi,
> 
> The exception doesn't appear when I switch from JRE 8 to JRE 7. The query seems to work.
> 
> Best Regards,
> 
> -- 
> Antoni Myłka
> Software Engineer
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
> 
> ----- Ursprüngliche Mail -----
> Von: "Antoni Myłka" <ant...@qu...>
> An: big...@li...
> Gesendet: Montag, 18. August 2014 10:37:17
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources
> 
> Hi
> 
> I'm trying to experiment with the BFS program. The example "BFS with extracted subgraph" seems most interesting to me. I do this:
> 
> curl -X POST 'http://localhost:28080/bigdata/namespace/our.namespace/sparql' -o out.xml \
> --data-urlencode 'query=PREFIX gas: <http://www.bigdata.com/rdf/gas#>
> SELECT ?depth ?out ?p ?o 
> WHERE {
>    SERVICE gas:service {
>     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
>     gas:program gas:in <my-starting-point> . 
>     gas:program gas:out ?out . 
>     gas:program gas:out1 ?depth . 
>     gas:program gas:maxIterations 1 . 
>  }
>  ?out ?p ?o .
> }'    
> 
> 
> But the out.xml file contains an exception where the root cause is (Full stack trace below):
> 
> Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
>        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
>        ... 15 more
> 
> It seems like some configuration issue. Is there anything I must or can't put in the configuration files before I can use GAS? I also don't quite understand why there are two configuration files: RWStore.properties and GraphStore.properties. What is the relation between them? Is a "graph store" something separate from a normal RDF store? 
> 
> -- 
> Antoni Myłka
> Software Engineer
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
> 
> 
> PREFIX gas: <http://www.bigdata.com/rdf/gas#>
> SELECT ?depth ?out ?p ?o
> WHERE {
>    SERVICE gas:service {
>     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
>     gas:program gas:in <my-starting-point> .
>     gas:program gas:out ?out . 
>     gas:program gas:out1 ?depth . 
>     gas:program gas:out2 ?predecessor . 
>     gas:program gas:maxIterations 1 . 
>  }
>  ?out ?p ?o . 
> }
> java.util.concurrent.ExecutionException: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625)
>        at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182)
>        at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237)
>        at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
>        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
>        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
>        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
>        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
>        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
>        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
>        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
>        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
>        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
>        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>        at java.lang.Thread.run(Unknown Source)
> Caused by: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191)
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
>        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
>        ... 1 more
> Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
>        at org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90)
>        at org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52)
>        at org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63)
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310)
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164)
>        ... 5 more
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
>        at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
>        at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
>        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
>        ... 10 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
>        ... 15 more
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82)
>        at com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197)
>        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222)
>        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
>        ... 4 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
>        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477)
>        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
>        ... 9 more
> Caused by: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894)
>        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789)
>        ... 3 more
> Caused by: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315)
>        ... 8 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314)
>        ... 8 more
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        ... 3 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329)
>        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236)
>        at com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604)
>        at com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391)
>        at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240)
>        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837)
>        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697)
>        ... 6 more
> Caused by: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982)
>        at com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464)
>        at com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333)
>        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301)
>        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272)
>        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687)
>        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744)
>        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700)
>        ... 4 more
> Caused by: java.lang.reflect.InvocationTargetException
>        at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
>        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
>        at java.lang.reflect.Constructor.newInstance(Unknown Source)
>        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963)
>        ... 11 more
> Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
>        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
>        ... 15 more
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Bigdata-developers mailing list
> Big...@li...
> https://lists.sourceforge.net/lists/listinfo/bigdata-developers
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Bigdata-developers mailing list
> Big...@li...
> https://lists.sourceforge.net/lists/listinfo/bigdata-developers
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> Bigdata-developers mailing list
> Big...@li...
> https://lists.sourceforge.net/lists/listinfo/bigdata-developers

Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Antoni M. <ant...@qu...>]

Hi,

Thanks for your answer.

Our RWStore.properties file doesn't contain any entries for com.bigdata.rdf.sail.truthMaintenance nor com.bigdata.rdf.sail.isolatableIndices. AFAIU this means that the default values are used, which is true for truth maintenance and false for isolatable indices. 

I'll try to do another attempt without truth maintenance. AFAIU the inference closure is always computed when transaction is committed. If I need to write and then read within the same transaction - I need to call BigdataSailConnection.computeClosure. I don't, so in my case this change won't have any influence on the application code. I can just flip the switch in the configuration and the app won't notice.

You seem to say, that "full read/write transaction support" is only available with the "isolatableIndices" configuration property. We don't use it, but we thought that calling setAutoCommit(false) and then commit() on the RepositoryConnection gives us transaction isolation "out of the box". Doesn't it?

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business

----- Ursprüngliche Mail -----
Von: "Bryan Thompson" <br...@sy...>
An: "Antoni Mylka" <ant...@qu...>
CC: big...@li...
Gesendet: Montag, 18. August 2014 13:45:41
Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

The RWStore.properties is used by the war under a variety of deployment models. The GraphStore,properties is used by a single ant target and could probably be replaced by the use of the RWStore.properties file. 

Are you configuring the kb instance with full read/write transaction support or incremental truth maintenance? Both of those use a temporary store and might account for the exception. Try using unisolated indices (do not specify the bigdata sail option ISOLATABLE_INDICES) and try turning off incremental truth maintenance.  Let us know which one is responsible for the issue and then we can file a ticket for this.

Bryan

> On Aug 18, 2014, at 7:25 AM, Antoni Mylka <ant...@qu...> wrote:
> 
> Hi,
> 
> Yet another update. I still get the exceptions. It doesn't seem to depend on the JVM.
> 
> The query works, but only if I load data, restart the server and then do the query. Then, after the first update, I start getting the exceptions. That's why it started working with curl after a restart of Tomcat with a different JVM. The moment I fired up my app, which started writing stuff to the store and doing queries - the exceptions reappeared.
> 
> Is it a bug? Do I need to do anything between loading data and doing GAS queries?
> 
> Best regards,
> 
> -- 
> Antoni Myłka
> Software Engineer
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
> 
> ----- Ursprüngliche Mail -----
> Von: "Antoni Myłka" <ant...@qu...>
> An: big...@li...
> Gesendet: Montag, 18. August 2014 11:34:46
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources
> 
> Hi,
> 
> The exception doesn't appear when I switch from JRE 8 to JRE 7. The query seems to work.
> 
> Best Regards,
> 
> -- 
> Antoni Myłka
> Software Engineer
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
> 
> ----- Ursprüngliche Mail -----
> Von: "Antoni Myłka" <ant...@qu...>
> An: big...@li...
> Gesendet: Montag, 18. August 2014 10:37:17
> Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources
> 
> Hi
> 
> I'm trying to experiment with the BFS program. The example "BFS with extracted subgraph" seems most interesting to me. I do this:
> 
> curl -X POST 'http://localhost:28080/bigdata/namespace/our.namespace/sparql' -o out.xml \
> --data-urlencode 'query=PREFIX gas: <http://www.bigdata.com/rdf/gas#>
> SELECT ?depth ?out ?p ?o 
> WHERE {
>    SERVICE gas:service {
>     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
>     gas:program gas:in <my-starting-point> . 
>     gas:program gas:out ?out . 
>     gas:program gas:out1 ?depth . 
>     gas:program gas:maxIterations 1 . 
>  }
>  ?out ?p ?o .
> }'    
> 
> 
> But the out.xml file contains an exception where the root cause is (Full stack trace below):
> 
> Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
>        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
>        ... 15 more
> 
> It seems like some configuration issue. Is there anything I must or can't put in the configuration files before I can use GAS? I also don't quite understand why there are two configuration files: RWStore.properties and GraphStore.properties. What is the relation between them? Is a "graph store" something separate from a normal RDF store? 
> 
> -- 
> Antoni Myłka
> Software Engineer
> 
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
> 
> 
> PREFIX gas: <http://www.bigdata.com/rdf/gas#>
> SELECT ?depth ?out ?p ?o
> WHERE {
>    SERVICE gas:service {
>     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
>     gas:program gas:in <my-starting-point> .
>     gas:program gas:out ?out . 
>     gas:program gas:out1 ?depth . 
>     gas:program gas:out2 ?predecessor . 
>     gas:program gas:maxIterations 1 . 
>  }
>  ?out ?p ?o . 
> }
> java.util.concurrent.ExecutionException: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625)
>        at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182)
>        at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237)
>        at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
>        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
>        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
>        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
>        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
>        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
>        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
>        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
>        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
>        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
>        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
>        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
>        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>        at java.lang.Thread.run(Unknown Source)
> Caused by: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191)
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
>        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
>        ... 1 more
> Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
>        at org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90)
>        at org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52)
>        at org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63)
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310)
>        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164)
>        ... 5 more
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
>        at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
>        at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
>        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
>        ... 10 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
>        ... 15 more
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82)
>        at com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197)
>        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222)
>        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
>        ... 4 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
>        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477)
>        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
>        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
>        ... 9 more
> Caused by: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894)
>        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789)
>        ... 3 more
> Caused by: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315)
>        ... 8 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314)
>        ... 8 more
> Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542)
>        at java.util.concurrent.FutureTask.run(Unknown Source)
>        ... 3 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at java.util.concurrent.FutureTask.report(Unknown Source)
>        at java.util.concurrent.FutureTask.get(Unknown Source)
>        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329)
>        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236)
>        at com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604)
>        at com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391)
>        at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240)
>        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837)
>        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756)
>        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697)
>        ... 6 more
> Caused by: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
>        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982)
>        at com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464)
>        at com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333)
>        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301)
>        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272)
>        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687)
>        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744)
>        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700)
>        ... 4 more
> Caused by: java.lang.reflect.InvocationTargetException
>        at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
>        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
>        at java.lang.reflect.Constructor.newInstance(Unknown Source)
>        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963)
>        ... 11 more
> Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
>        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
>        ... 15 more
> 
> 
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> 
> ------------------------------------------------------------------------------
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> 
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Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Antoni M. <ant...@qu...>]

Hi,

Yet another update. I still get the exceptions. It doesn't seem to depend on the JVM.

The query works, but only if I load data, restart the server and then do the query. Then, after the first update, I start getting the exceptions. That's why it started working with curl after a restart of Tomcat with a different JVM. The moment I fired up my app, which started writing stuff to the store and doing queries - the exceptions reappeared.

Is it a bug? Do I need to do anything between loading data and doing GAS queries?

Best regards,

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business

----- Ursprüngliche Mail -----
Von: "Antoni Myłka" <ant...@qu...>
An: big...@li...
Gesendet: Montag, 18. August 2014 11:34:46
Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

Hi,

The exception doesn't appear when I switch from JRE 8 to JRE 7. The query seems to work.

Best Regards,

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business

----- Ursprüngliche Mail -----
Von: "Antoni Myłka" <ant...@qu...>
An: big...@li...
Gesendet: Montag, 18. August 2014 10:37:17
Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

Hi

I'm trying to experiment with the BFS program. The example "BFS with extracted subgraph" seems most interesting to me. I do this:

curl -X POST 'http://localhost:28080/bigdata/namespace/our.namespace/sparql' -o out.xml \
--data-urlencode 'query=PREFIX gas: <http://www.bigdata.com/rdf/gas#>
SELECT ?depth ?out ?p ?o 
WHERE {
    SERVICE gas:service {
     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
     gas:program gas:in <my-starting-point> . 
     gas:program gas:out ?out . 
     gas:program gas:out1 ?depth . 
     gas:program gas:maxIterations 1 . 
  }
  ?out ?p ?o .
}'    


But the out.xml file contains an exception where the root cause is (Full stack trace below):

Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
        ... 15 more

It seems like some configuration issue. Is there anything I must or can't put in the configuration files before I can use GAS? I also don't quite understand why there are two configuration files: RWStore.properties and GraphStore.properties. What is the relation between them? Is a "graph store" something separate from a normal RDF store? 

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business


PREFIX gas: <http://www.bigdata.com/rdf/gas#>
SELECT ?depth ?out ?p ?o
WHERE {
    SERVICE gas:service {
     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
     gas:program gas:in <my-starting-point> .
     gas:program gas:out ?out . 
     gas:program gas:out1 ?depth . 
     gas:program gas:out2 ?predecessor . 
     gas:program gas:maxIterations 1 . 
  }
  ?out ?p ?o . 
}
java.util.concurrent.ExecutionException: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625)
        at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182)
        at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237)
        at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        ... 1 more
Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
        at org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90)
        at org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52)
        at org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164)
        ... 5 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
        at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
        at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
        ... 10 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
        ... 15 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82)
        at com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197)
        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222)
        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
        ... 4 more
Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477)
        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
        ... 9 more
Caused by: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789)
        ... 3 more
Caused by: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315)
        ... 8 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314)
        ... 8 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        ... 3 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329)
        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236)
        at com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604)
        at com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391)
        at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240)
        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837)
        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697)
        ... 6 more
Caused by: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982)
        at com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464)
        at com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687)
        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744)
        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700)
        ... 4 more
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963)
        ... 11 more
Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
        ... 15 more


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Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Antoni M. <ant...@qu...>]

Hi,

The exception doesn't appear when I switch from JRE 8 to JRE 7. The query seems to work.

Best Regards,

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business

----- Ursprüngliche Mail -----
Von: "Antoni Myłka" <ant...@qu...>
An: big...@li...
Gesendet: Montag, 18. August 2014 10:37:17
Betreff: Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

Hi

I'm trying to experiment with the BFS program. The example "BFS with extracted subgraph" seems most interesting to me. I do this:

curl -X POST 'http://localhost:28080/bigdata/namespace/our.namespace/sparql' -o out.xml \
--data-urlencode 'query=PREFIX gas: <http://www.bigdata.com/rdf/gas#>
SELECT ?depth ?out ?p ?o 
WHERE {
    SERVICE gas:service {
     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
     gas:program gas:in <my-starting-point> . 
     gas:program gas:out ?out . 
     gas:program gas:out1 ?depth . 
     gas:program gas:maxIterations 1 . 
  }
  ?out ?p ?o .
}'    


But the out.xml file contains an exception where the root cause is (Full stack trace below):

Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
        ... 15 more

It seems like some configuration issue. Is there anything I must or can't put in the configuration files before I can use GAS? I also don't quite understand why there are two configuration files: RWStore.properties and GraphStore.properties. What is the relation between them? Is a "graph store" something separate from a normal RDF store? 

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business


PREFIX gas: <http://www.bigdata.com/rdf/gas#>
SELECT ?depth ?out ?p ?o
WHERE {
    SERVICE gas:service {
     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
     gas:program gas:in <my-starting-point> .
     gas:program gas:out ?out . 
     gas:program gas:out1 ?depth . 
     gas:program gas:out2 ?predecessor . 
     gas:program gas:maxIterations 1 . 
  }
  ?out ?p ?o . 
}
java.util.concurrent.ExecutionException: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625)
        at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182)
        at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237)
        at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        ... 1 more
Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
        at org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90)
        at org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52)
        at org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164)
        ... 5 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
        at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
        at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
        ... 10 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
        ... 15 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82)
        at com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197)
        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222)
        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
        ... 4 more
Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477)
        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
        ... 9 more
Caused by: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789)
        ... 3 more
Caused by: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315)
        ... 8 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314)
        ... 8 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        ... 3 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329)
        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236)
        at com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604)
        at com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391)
        at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240)
        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837)
        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697)
        ... 6 more
Caused by: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982)
        at com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464)
        at com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687)
        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744)
        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700)
        ... 4 more
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963)
        ... 11 more
Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
        ... 15 more


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Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Antoni M. <ant...@qu...>]

Hi

I'm trying to experiment with the BFS program. The example "BFS with extracted subgraph" seems most interesting to me. I do this:

curl -X POST 'http://localhost:28080/bigdata/namespace/our.namespace/sparql' -o out.xml \
--data-urlencode 'query=PREFIX gas: <http://www.bigdata.com/rdf/gas#>
SELECT ?depth ?out ?p ?o 
WHERE {
    SERVICE gas:service {
     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
     gas:program gas:in <my-starting-point> . 
     gas:program gas:out ?out . 
     gas:program gas:out1 ?depth . 
     gas:program gas:maxIterations 1 . 
  }
  ?out ?p ?o .
}'    


But the out.xml file contains an exception where the root cause is (Full stack trace below):

Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
        ... 15 more

It seems like some configuration issue. Is there anything I must or can't put in the configuration files before I can use GAS? I also don't quite understand why there are two configuration files: RWStore.properties and GraphStore.properties. What is the relation between them? Is a "graph store" something separate from a normal RDF store? 

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business


PREFIX gas: <http://www.bigdata.com/rdf/gas#>
SELECT ?depth ?out ?p ?o
WHERE {
    SERVICE gas:service {
     gas:program gas:gasClass "com.bigdata.rdf.graph.analytics.BFS" .
     gas:program gas:in <my-starting-point> .
     gas:program gas:out ?out . 
     gas:program gas:out1 ?depth . 
     gas:program gas:out2 ?predecessor . 
     gas:program gas:maxIterations 1 . 
  }
  ?out ?p ?o . 
}
java.util.concurrent.ExecutionException: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.rdf.sail.webapp.QueryServlet.doQuery(QueryServlet.java:625)
        at com.bigdata.rdf.sail.webapp.QueryServlet.doPost(QueryServlet.java:182)
        at com.bigdata.rdf.sail.webapp.RESTServlet.doPost(RESTServlet.java:237)
        at com.bigdata.rdf.sail.webapp.MultiTenancyServlet.doPost(MultiTenancyServlet.java:135)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
        at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.Exception: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1191)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:500)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        ... 1 more
Caused by: org.openrdf.query.QueryEvaluationException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:188)
        at org.openrdf.query.impl.TupleQueryResultImpl.hasNext(TupleQueryResultImpl.java:90)
        at org.openrdf.query.QueryResultUtil.report(QueryResultUtil.java:52)
        at org.openrdf.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:63)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$TupleQueryTask.doQuery(BigdataRDFContext.java:1310)
        at com.bigdata.rdf.sail.webapp.BigdataRDFContext$AbstractQueryTask.call(BigdataRDFContext.java:1164)
        ... 5 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1523)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator._hasNext(BlockingBuffer.java:1710)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.hasNext(BlockingBuffer.java:1563)
        at com.bigdata.striterator.AbstractChunkedResolverator._hasNext(AbstractChunkedResolverator.java:365)
        at com.bigdata.striterator.AbstractChunkedResolverator.hasNext(AbstractChunkedResolverator.java:341)
        at com.bigdata.rdf.sail.Bigdata2Sesame2BindingSetIterator.hasNext(Bigdata2Sesame2BindingSetIterator.java:134)
        ... 10 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.relation.accesspath.BlockingBuffer$BlockingIterator.checkFuture(BlockingBuffer.java:1454)
        ... 15 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:59)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.close(RunningQueryCloseableIterator.java:73)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.hasNext(RunningQueryCloseableIterator.java:82)
        at com.bigdata.striterator.ChunkedWrappedIterator.hasNext(ChunkedWrappedIterator.java:197)
        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:222)
        at com.bigdata.striterator.AbstractChunkedResolverator$ChunkConsumerTask.call(AbstractChunkedResolverator.java:197)
        ... 4 more
Caused by: java.util.concurrent.ExecutionException: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.util.concurrent.Haltable.get(Haltable.java:273)
        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:1477)
        at com.bigdata.bop.engine.AbstractRunningQuery.get(AbstractRunningQuery.java:104)
        at com.bigdata.rdf.sail.RunningQueryCloseableIterator.checkFuture(RunningQueryCloseableIterator.java:46)
        ... 9 more
Caused by: java.lang.Exception: task=ChunkTask{query=d4747392-722c-46ab-80e2-e9fb27dddd7c,bopId=1,partitionId=-1,sinkId=3,altSinkId=null}, cause=java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1335)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTaskWrapper.run(ChunkedRunningQuery.java:894)
        at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at com.bigdata.concurrent.FutureTaskMon.run(FutureTaskMon.java:63)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkFutureTask.run(ChunkedRunningQuery.java:789)
        ... 3 more
Caused by: java.util.concurrent.ExecutionException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1315)
        ... 8 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.doServiceCallWithConstant(ServiceCallJoin.java:341)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:293)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask.call(ServiceCallJoin.java:205)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        at com.bigdata.bop.engine.ChunkedRunningQuery$ChunkTask.call(ChunkedRunningQuery.java:1314)
        ... 8 more
Caused by: java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:743)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:606)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.call(ServiceCallJoin.java:542)
        at java.util.concurrent.FutureTask.run(Unknown Source)
        ... 3 more
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at java.util.concurrent.FutureTask.report(Unknown Source)
        at java.util.concurrent.FutureTask.get(Unknown Source)
        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:329)
        at com.bigdata.rdf.graph.impl.GASEngine$ParallelFrontierStrategy.call(GASEngine.java:236)
        at com.bigdata.rdf.graph.impl.GASContext.scatterEdges(GASContext.java:604)
        at com.bigdata.rdf.graph.impl.GASContext.doRound(GASContext.java:391)
        at com.bigdata.rdf.graph.impl.GASContext.call(GASContext.java:240)
        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:837)
        at com.bigdata.rdf.graph.impl.bd.GASService$GASServiceCall.call(GASService.java:414)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doBigdataServiceCall(ServiceCallJoin.java:756)
        at com.bigdata.bop.controller.ServiceCallJoin$ChunkTask$ServiceCallTask.doServiceCall(ServiceCallJoin.java:697)
        ... 6 more
Caused by: java.lang.RuntimeException: Could not instantiate relation: java.lang.reflect.InvocationTargetException
        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:982)
        at com.bigdata.relation.locator.DefaultResourceLocator.cacheMiss(DefaultResourceLocator.java:464)
        at com.bigdata.relation.locator.DefaultResourceLocator.locate(DefaultResourceLocator.java:333)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.resolveKB(BigdataGASEngine.java:301)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getKB(BigdataGASEngine.java:272)
        at com.bigdata.rdf.graph.impl.bd.BigdataGASEngine$BigdataGraphAccessor.getEdges(BigdataGASEngine.java:687)
        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:744)
        at com.bigdata.rdf.graph.impl.GASContext$ScatterTask.call(GASContext.java:700)
        ... 4 more
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.GeneratedConstructorAccessor27.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at com.bigdata.relation.locator.DefaultResourceLocator.newInstance(DefaultResourceLocator.java:963)
        ... 11 more
Caused by: java.lang.ClassCastException: com.bigdata.journal.TemporaryStore cannot be cast to com.bigdata.journal.Journal
        at com.bigdata.rdf.store.LocalTripleStore.<init>(LocalTripleStore.java:163)
        ... 15 more

Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Mike P. <mi...@sy...>]

Sounds like a perfect job for the GAS engine.

http://wiki.bigdata.com/wiki/index.php/RDF_GAS_API


---
Mike Personick
Managing Partner
Systap, LLC
www.systap.com
801-243-3678
skype: mike.personick


On Fri, Aug 15, 2014 at 10:17 AM, Antoni Myłka <ant...@qu...>
wrote:

> Hi,
>
> I have a list of URIs. I want to get all triples whose subjects are the
> given URIs. To do that I use:
>
> CONSTRUCT { ?s ?p ?o . } WHERE { ?s ?p ?o. FILTER (?s in ($MY_LIST)) }
>
> I iterate over the result triples. For each triple, if the object is an
> URI I add it to a set. Then I use that set to generate a similar query to
> get triples on the second hop from the input uris. Then another query to
> get triples on the third hop. In my application code I remember all URIs to
> make sure I never request information about a resource more than once. I
> can also filter out predicates that I don't want to follow (like rdf:type).
>
> This seems to work with three queries. The problem is that those lists can
> get pretty large (thousands) and the SPARQL query that I push over the
> network gets large as well. My question is: how to do it faster? How to get
> triples up to n hops from the given set of starting points.
>
> I've tried the following:
>
> CONSTRUCT { ?s ?p ?o . } WHERE {
>  { ?s ?p ?o . FILTER (?s in ($MY_LIST)) }
>  UNION
>  { ?start ?p1 ?s . ?s ?p ?o. FILTER (?start in ($MY_LIST)) }
>  UNION
>  { ?start ?p1 ?o1 . ?o1 ?p2 ?s . ?s ?p ?o . FILTER (?start in ($MY_LIST)) }
> }
>
> CONSTRUCT { ?s ?p1 ?o1 . ?o1 ?p2 ?o2 . ?o2 ?p3 ?o3 . }
> WHERE {
>     ?s ?p1 ?o1 .
>     OPTIONAL {
>         ?o1 ?p2 ?o2 .
>         OPTIONAL {
>              ?o2 ?p3 ?o3 .
>         }
>     }
>     FILTER (?s in ($MY_LIST))
> }
>
> Both are MUCH too slow. Only the iterative version stays within seconds on
> my dataset. The simple unions and optionals like the ones above go well
> beyond minutes, variants that filter out certain predicates, or those that
> try to avoid returning the same triples more than once seem even slower.
>
> What is the fastest way to do that in Bigdata?
>
> I use bigdata 1.2.3, deployed as a .war on Tomcat.
>
> Cheers,
>
> --
> Antoni Myłka
> Software Engineer
>
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Bigdata-developers mailing list
> Big...@li...
> https://lists.sourceforge.net/lists/listinfo/bigdata-developers
>

Re: [Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Bryan T. <br...@sy...>]

If you use the 1.3.1 release, you have access to the vertex-centric
API of the GASService.[1]. This is designed to support a wide variety
of graph traversal patterns and can be used transparently from SPARQL.
See the examples on that wiki page.

Thanks,
Bryan

[1] http://wiki.bigdata.com/wiki/index.php/RDF_GAS_API
----
Bryan Thompson
Chief Scientist & Founder
SYSTAP, LLC
4501 Tower Road
Greensboro, NC 27410
br...@sy...
http://bigdata.com
http://mapgraph.io

CONFIDENTIALITY NOTICE:  This email and its contents and attachments
are for the sole use of the intended recipient(s) and are confidential
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is prohibited. If you have received this communication in error,
please notify the sender by reply email and permanently delete all
copies of the email and its contents and attachments.


On Fri, Aug 15, 2014 at 10:17 AM, Antoni Myłka
<ant...@qu...> wrote:
> Hi,
>
> I have a list of URIs. I want to get all triples whose subjects are the given URIs. To do that I use:
>
> CONSTRUCT { ?s ?p ?o . } WHERE { ?s ?p ?o. FILTER (?s in ($MY_LIST)) }
>
> I iterate over the result triples. For each triple, if the object is an URI I add it to a set. Then I use that set to generate a similar query to get triples on the second hop from the input uris. Then another query to get triples on the third hop. In my application code I remember all URIs to make sure I never request information about a resource more than once. I can also filter out predicates that I don't want to follow (like rdf:type).
>
> This seems to work with three queries. The problem is that those lists can get pretty large (thousands) and the SPARQL query that I push over the network gets large as well. My question is: how to do it faster? How to get triples up to n hops from the given set of starting points.
>
> I've tried the following:
>
> CONSTRUCT { ?s ?p ?o . } WHERE {
>  { ?s ?p ?o . FILTER (?s in ($MY_LIST)) }
>  UNION
>  { ?start ?p1 ?s . ?s ?p ?o. FILTER (?start in ($MY_LIST)) }
>  UNION
>  { ?start ?p1 ?o1 . ?o1 ?p2 ?s . ?s ?p ?o . FILTER (?start in ($MY_LIST)) }
> }
>
> CONSTRUCT { ?s ?p1 ?o1 . ?o1 ?p2 ?o2 . ?o2 ?p3 ?o3 . }
> WHERE {
>     ?s ?p1 ?o1 .
>     OPTIONAL {
>         ?o1 ?p2 ?o2 .
>         OPTIONAL {
>              ?o2 ?p3 ?o3 .
>         }
>     }
>     FILTER (?s in ($MY_LIST))
> }
>
> Both are MUCH too slow. Only the iterative version stays within seconds on my dataset. The simple unions and optionals like the ones above go well beyond minutes, variants that filter out certain predicates, or those that try to avoid returning the same triples more than once seem even slower.
>
> What is the fastest way to do that in Bigdata?
>
> I use bigdata 1.2.3, deployed as a .war on Tomcat.
>
> Cheers,
>
> --
> Antoni Myłka
> Software Engineer
>
> Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
> http://www.quantinum.com - Bee for Business
>
> ------------------------------------------------------------------------------
> _______________________________________________
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[Bigdata-developers] Getting triples up to 3 hops from a given set of resources

[Antoni M. <ant...@qu...>]

Hi,

I have a list of URIs. I want to get all triples whose subjects are the given URIs. To do that I use:

CONSTRUCT { ?s ?p ?o . } WHERE { ?s ?p ?o. FILTER (?s in ($MY_LIST)) }

I iterate over the result triples. For each triple, if the object is an URI I add it to a set. Then I use that set to generate a similar query to get triples on the second hop from the input uris. Then another query to get triples on the third hop. In my application code I remember all URIs to make sure I never request information about a resource more than once. I can also filter out predicates that I don't want to follow (like rdf:type).

This seems to work with three queries. The problem is that those lists can get pretty large (thousands) and the SPARQL query that I push over the network gets large as well. My question is: how to do it faster? How to get triples up to n hops from the given set of starting points.

I've tried the following:

CONSTRUCT { ?s ?p ?o . } WHERE {
 { ?s ?p ?o . FILTER (?s in ($MY_LIST)) }
 UNION
 { ?start ?p1 ?s . ?s ?p ?o. FILTER (?start in ($MY_LIST)) }
 UNION
 { ?start ?p1 ?o1 . ?o1 ?p2 ?s . ?s ?p ?o . FILTER (?start in ($MY_LIST)) }
}

CONSTRUCT { ?s ?p1 ?o1 . ?o1 ?p2 ?o2 . ?o2 ?p3 ?o3 . }
WHERE {
    ?s ?p1 ?o1 .
    OPTIONAL {
        ?o1 ?p2 ?o2 .
        OPTIONAL {
             ?o2 ?p3 ?o3 .
        }
    }
    FILTER (?s in ($MY_LIST))
}

Both are MUCH too slow. Only the iterative version stays within seconds on my dataset. The simple unions and optionals like the ones above go well beyond minutes, variants that filter out certain predicates, or those that try to avoid returning the same triples more than once seem even slower. 

What is the fastest way to do that in Bigdata?

I use bigdata 1.2.3, deployed as a .war on Tomcat.

Cheers,

-- 
Antoni Myłka
Software Engineer

Quantinum AG, Birkenweg 61, CH-3013 Bern - Fon +41 31 388 20 40
http://www.quantinum.com - Bee for Business